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[0] Elble RJ, Central mechanisms of tremor.J Clin Neurophysiol 13:2, 133-44 (1996 Mar)

[0] Carmena JM, Lebedev MA, Crist RE, O'Doherty JE, Santucci DM, Dimitrov DF, Patil PG, Henriquez CS, Nicolelis MA, Learning to control a brain-machine interface for reaching and grasping by primates.PLoS Biol 1:2, E42 (2003 Nov)

[0] Taylor DM, Tillery SI, Schwartz AB, Direct cortical control of 3D neuroprosthetic devices.Science 296:5574, 1829-32 (2002 Jun 7)

[0] Rektor I, Kaiiovský P, Bares M, Brázdil M, Streitová H, Klajblová H, Kuba R, Daniel P, A SEEG study of ERP in motor and premotor cortices and in the basal ganglia.Clin Neurophysiol 114:3, 463-71 (2003 Mar)

[0] Caminiti R, Johnson PB, Galli C, Ferraina S, Burnod Y, Making arm movements within different parts of space: the premotor and motor cortical representation of a coordinate system for reaching to visual targets.J Neurosci 11:5, 1182-97 (1991 May)

[0] Caminiti R, Johnson PB, Urbano A, Making arm movements within different parts of space: dynamic aspects in the primate motor cortex.J Neurosci 10:7, 2039-58 (1990 Jul)[1] Caminiti R, Johnson PB, Galli C, Ferraina S, Burnod Y, Making arm movements within different parts of space: the premotor and motor cortical representation of a coordinate system for reaching to visual targets.J Neurosci 11:5, 1182-97 (1991 May)

[0] Taira M, Boline J, Smyrnis N, Georgopoulos AP, Ashe J, On the relations between single cell activity in the motor cortex and the direction and magnitude of three-dimensional static isometric force.Exp Brain Res 109:3, 367-76 (1996 Jun)

[0] Wahnoun R, Helms Tillery S, He J, Neuron selection and visual training for population vector based cortical control.Conf Proc IEEE Eng Med Biol Soc 6no Issue 4607-10 (2004)[1] Wahnoun R, He J, Helms Tillery SI, Selection and parameterization of cortical neurons for neuroprosthetic control.J Neural Eng 3:2, 162-71 (2006 Jun)[2] Fetz EE, Operant conditioning of cortical unit activity.Science 163:870, 955-8 (1969 Feb 28)[3] Fetz EE, Finocchio DV, Operant conditioning of specific patterns of neural and muscular activity.Science 174:7, 431-5 (1971 Oct 22)[4] Fetz EE, Finocchio DV, Operant conditioning of isolated activity in specific muscles and precentral cells.Brain Res 40:1, 19-23 (1972 May 12)[5] Fetz EE, Baker MA, Operantly conditioned patterns on precentral unit activity and correlated responses in adjacent cells and contralateral muscles.J Neurophysiol 36:2, 179-204 (1973 Mar)[6] Humphrey DR, Schmidt EM, Thompson WD, Predicting measures of motor performance from multiple cortical spike trains.Science 170:959, 758-62 (1970 Nov 13)

[0] Kettner RE, Schwartz AB, Georgopoulos AP, Primate motor cortex and free arm movements to visual targets in three-dimensional space. III. Positional gradients and population coding of movement direction from various movement origins.J Neurosci 8:8, 2938-47 (1988 Aug)[1] Georgopoulos AP, Kettner RE, Schwartz AB, Primate motor cortex and free arm movements to visual targets in three-dimensional space. II. Coding of the direction of movement by a neuronal population.J Neurosci 8:8, 2928-37 (1988 Aug)[2] Schwartz AB, Kettner RE, Georgopoulos AP, Primate motor cortex and free arm movements to visual targets in three-dimensional space. I. Relations between single cell discharge and direction of movement.J Neurosci 8:8, 2913-27 (1988 Aug)[3] Georgopoulos AP, Kalaska JF, Caminiti R, Massey JT, On the relations between the direction of two-dimensional arm movements and cell discharge in primate motor cortex.J Neurosci 2:11, 1527-37 (1982 Nov)

[0] Pollak P, Benabid AL, Gross C, Gao DM, Laurent A, Benazzouz A, Hoffmann D, Gentil M, Perret J, [Effects of the stimulation of the subthalamic nucleus in Parkinson disease]Rev Neurol (Paris) 149:3, 175-6 (1993)

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ref: -0 tags: gtk.css scrollbar resize linux qt5 gtk-3 gtk-4 date: 08-22-2023 20:23 gmt revision:4 [3] [2] [1] [0] [head]

Put this in ~/.config/gtk-3.0/gtk.css and ~/.config/gtk-4.0/gtk.css to make scrollbars larger & permanently visible on high-DPI screens. ref

.scrollbar {
  -GtkScrollbar-has-backward-stepper: 1;
  -GtkScrollbar-has-forward-stepper: 1;
  -GtkRange-slider-width: 16;
  -GtkRange-stepper-size: 16;
}
scrollbar slider {
    /* Size of the slider */
    min-width: 16px;
    min-height: 16px;
    border-radius: 16px;

    /* Padding around the slider */
    border: 2px solid transparent;
}

.scrollbar.vertical slider,
scrollbar.vertical slider {
    min-height: 16px;
    min-width: 16px;
}

.scrollbar.horizontal.slider,
scrollbar.horizontal slider {
min-width: 16px;
min-height: 16px;
}

/* Scrollbar trough squeezes when cursor hovers over it. Disabling that
 */

.scrollbar.vertical:hover:dir(ltr),
.scrollbar.vertical.dragging:dir(ltr) {
    margin-left: 0px;
}

.scrollbar.vertical:hover:dir(rtl),
.scrollbar.vertical.dragging:dir(rtl) {
    margin-right: 0px;
}

.scrollbar.horizontal:hover,
.scrollbar.horizontal.dragging,
.scrollbar.horizontal.slider:hover,
.scrollbar.horizontal.slider.dragging {
    margin-top: 0px;
}
undershoot.top, undershoot.right, undershoot.bottom, undershoot.left { background-image: none; }
undershoot.top, undershoot.right, undershoot.bottom, undershoot.left { background-image: none; }

Also add:

export GTK_OVERLAY_SCROLLING=0 
to your ~/.bashrc

This does not work with GTK4, though -- to do that, put the following in ~/.config/gtk-4.0/settings.ini:

[Settings]
gtk-overlay-scrolling = false

To make the scrollbars a bit easier to see in QT5 applications, run qt5ct (after apt-getting it), and add in a new style sheet, /usr/share/qt5ct/qss/scrollbar-simple-backup.qss

/* SCROLLBARS (NOTE: Changing 1 subcontrol means you have to change all of them)*/
QScrollBar{
  background: palette(alternate-base);
}
QScrollBar:horizontal{
  margin: 0px 0px 0px 0px;
}
QScrollBar:vertical{
  margin: 0px 0px 0px 0px;
}
QScrollBar::handle{
  background: #816891;
  border: 1px solid transparent;
  border-radius: 1px;
}
QScrollBar::handle:hover, QScrollBar::add-line:hover, QScrollBar::sub-line:hover{
  background: palette(highlight);
}
QScrollBar::add-line{
subcontrol-origin: none;
}
QScrollBar::add-line:vertical, QScrollBar::sub-line:vertical{
height: 0px;
}
QScrollBar::add-line:horizontal, QScrollBar::sub-line:horizontal{
width: 0px;
}
QScrollBar::sub-line{
subcontrol-origin: none;
}

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ref: -0 tags: 3D SHOT Alan Hillel Waller 2p photon holography date: 05-31-2019 22:19 gmt revision:4 [3] [2] [1] [0] [head]

PMID-29089483 Three-dimensional scanless holographic optogenetics with temporal focusing (3D-SHOT).

  • Pégard NC1,2, Mardinly AR1, Oldenburg IA1, Sridharan S1, Waller L2, Adesnik H3,4
  • Combines computer-generated holography and temporal focusing for single-shot (no scanning) two-photon photo-activation of opsins.
  • The beam intensity profile determines the dimensions of the custom temporal focusing pattern (CTFP), while phase, a previously unused degree of freedom, is engineered to make 3D holograph and temporal focusing compatible.
  • "To ensure good diffraction efficiency of all spectral components by the SLM, we used a lens Lc to apply a small spherical phase pattern. The focal length was adjusted so that each spectral component of the pulse spans across the short axis of the SLM in the Fourier domain".
    • That is, they spatially and temporally defocus the pulse to better fill the SLM. The short axis of the SLM in this case is Y, per supplementary figure 2.
  • The image of the diffraction grating determines the plane of temporal focusing (with lenses L1 and L2); there is a secondary geometric focus due to Lc behind the temporal plane, which serves as an aberration.
  • The diffraction grating causes the temporal pattern to scan to produce a semi-spherical stimulated area ('disc').
  • Rather than creating a custom 3D holographic shape for each neuron, the SLM is after the diffraction grating -- it imposes phase and space modulation to the CTFP, effectively convolving it with a holograph of a cloud of points & hence replicating at each point.

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ref: -0 tags: diffraction terahertz 3d print ucla deep learning optical neural networks date: 02-13-2019 23:16 gmt revision:1 [0] [head]

All-optical machine learning using diffractive deep neural networks

  • Pretty clever: use 3D printed plastic as diffractive media in a 0.4 THz all-optical all-interference (some attenuation) linear convolutional multi-layer 'neural network'.
  • In the arxive publication there are few details on how they calculated or optimized given diffractive layers.
  • Absence of nonlinearity will limit things greatly.
  • Actual observed performance (where thy had to print out the handwritten digits) rather poor, ~ 60%.

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ref: -0 tags: bone regrowth hyperelastic 3d print implant hydroxyapatite polycaptolactone date: 09-30-2016 18:27 gmt revision:0 [head]

Hyperelastic “bone”: A highly versatile, growth factor–free, osteoregenerative, scalable, and surgically friendly biomaterial

  • (From the abstract): hyperelastic “bone” is composed of 90 weight % (wt %) hydroxyapatite and 10 wt % polycaprolactone or poly(lactic-co-glycolic acid),
  • Can be rapidly three-dimensionally (3D) printed (up to 275 cm3/hour) from room temperature extruded liquid inks.
  • Mechanical properties: ~32 to 67% strain to failure, ~4 to 11 MPa elastic modulus & was highly absorbent (50% material porosity)
  • Supported cell viability and proliferation, and induced osteogenic differentiation of bone marrow–derived human mesenchymal stem cells cultured in vitro over 4 weeks without any osteo-inducing factors in the medium.
  • HB did not elicit a negative immune response, became vascularized, quickly integrated with surrounding tissues, and rapidly ossified and supported new bone growth without the need for added biological factors.

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ref: -0 tags: ACF chip bonding parylene field's metal polyimide date: 07-10-2013 18:34 gmt revision:10 [9] [8] [7] [6] [5] [4] [head]

We're making parylene electrodes for neural recording, and one critical step is connecting them to recording electronics.

Currently Berkeley uses ACF (anisotropic conductive film) for connection, which is widely used for connecting flex tape to LCD panels, or for connecting driver chips to LCD glass. According to the internet, pitches can be as low as 20um, with pad areas as low as 800um^2. source

However, this does not seem to be a very reliable nor compact process with platinum films on parylene, possibly because ACF bonding relies on raised areas between mated conductors (current design has the Pt recessed into the parylene), and on rigid substrates. ACF consists of springy polymer balls coated in Ni and Au and embedded in a thermoset epoxy resin. The ACF film is put under moderate temperature (180C) and pressure (3mpa, 430psi), which causes the epoxy to cure in a state that leaves the gold/nickel/polymer balls to be compressed between the two conductors. Hence, even if the conductors move slightly due to thermal cycling, the small balls maintain good mechanical and electrical contact. The balls are dispersed sufficiently in the epoxy matrix that there is little to no chance of conduction between adjacent pads.

(Or so I have learned from the internet.) Now, as mentioned, this is an imperfect method for joining Pt on parylene films, possibly because the parylene is so flexible, and the platinum foil is very thin (200-300 nm). Indeed, platinum does not bond very strongly to parylene, hence care must be taken to allow sufficient overlap to prevent water ingress. My proposed solution -- to be tested shortly -- is to use a low-melting temperature metal with strong wetting ability -- such as Field's metal (bismuth, tin, indium, melting point 149F, see http://www.gizmology.net/fusiblemetals.htm) to low-temperature solder the platinum to a carrier board (initially) or to a custom amplifier ASIC (later!). Parylene is stable to 200C (392F), so this should be safe. One worry is that the indium/bismuth will wet the parylene or polyimide, too; however I consider this unlikely due to the difficulty in attaching parylene to any metal.

That said, there must be good reason why ACF is so popular, so perhaps a better ultimate solution is to stiffen the parylene (or ultimately polyimide) substrate so that it can support both the temperature/pressure of ACF bonding and the stress of a continued electrical/mechanical bond to polyimide fan-out board or ASIC. It may also be possible to gold or nickel electroplate the connector pads to be slightly raised instead of recessed.


Update: ACF bond to rigid 1/2 oz copper, 4mil trace / space connector (3mil trace/space board):

Note that the copper traces are raised, and the parylene is stretched over the uneven surface (this is much easier to see with the stereo microscope). To the left of the image, the ACF paste has been sqeezed out from between the FR4 and parylene. Also note that the platinum can make potential contact with vias in the PCB.


Update 7/2: Fields metal (mentioned above) does stick to platinum reasonably well, but it also sticks to parylene (somewhat), and glass (exceptionally well!). In fact, I had a difficult time removing traces of field's metal from the Pyrex beakers that I was melting the metal with. These beakers were filled with boiling water, which may have been the problem.

When I added flux (Kester flux-pen 951 No-clean MSDS), the metal became noticeably more shiny, and the contact angle increased on the borosilicate glass (e.g. looked more like mercury); this leads me to believe that it is not the metal itself that attaches to glass, but rather oxides of indium and bismuth. Kester 951 flux consists of:

  • 2-propanol 15% (as a denaturing agent) boiling point 82.6C
  • Ethanol 73% (solvent) boiling point 78.3C
  • Butyl Acetate 7% boiling point 127C, flash point 27C
  • Methanol <3% b.p. 64.7C
  • Carboxylic acids < 3% -- proton donors? formic or oxalic acid?
  • Surfacants < 1% -- ?
Total boiling point is 173F.

After coating the parylene/platinum sample with flux, I raised the field's metal to the flux activation point, which released some smoke and left brown organic residues on the bottom of the glass dish. Then I dipped the parylene probe into the molten metal, causing the flux again to be activated, and partially wetting the platinum contacts. The figure below shows the result:

Note the incomplete wetting, all the white solids left from the process, and how the field's metal caused the platinum to delaminate from the parylene when the cable was (accidentally) flexed. Tests with platinum foil revealed that the metal bond was not actually that strong, significantly weaker than that made with a flux-core SnPb solder. also, I'm not sure of the activation temperature of this flux, and think I may have overheated the parylene.


Update 7/10:

Am considering electrodeless Ni / Pt / Au deposition, which occurs in aqueous solution, hence at much lower temperatures than e-beam evaporation Electrodeless Ni ref. On polyimide substrates, there is extensive literature describing how to activate the surface for plating: Polyimides and Other High Temperature Polymers: Synthesis ..., Volume 4. Parylene would likely need a different possibly more aggressive treatment, as it does not have imide bonds to open.

Furthermore, if the parylene / polyimide surface is *not* activated, the electrodeless plating could be specific to the exposed electrode and contact sites, which could help to solve the connector issue by strengthening & thickening the contact areas. The second fairly obvious solution is to planarize the contact site on the PCB, too, as seen above. ACF bonds can be quite reliable; last night I took apart (and successfully re-assembled) my 32" Samsung LCD monitor, and none of the flex-on-glass or chip-on-flex binds failed (despite my clumsy hands!).

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ref: -0 tags: implicit motor sequence learning basal ganglia parkinson's disease date: 03-06-2012 22:47 gmt revision:2 [1] [0] [head]

PMID-19744484 What can man do without basal ganglia motor output? The effect of combined unilateral subthalamotomy and pallidotomy in a patient with Parkinson's disease.

  • Unilateral lesion of both STN and GPi in one patient. Hence, the patient was his own control.
    • DRastically reduced the need for medication, indicating that it had a profound effect on BG output.
  • Arm contralateral lesion showed faster reaction times and normal movement speeds; ipsilateral arm parkinsonian.
  • Implicit sequence learning in a task was absent.
  • In a go / no-go task when the percent of no-go trials increased, the RT speriority of contralateral hand was lost.
  • " THe risk of persistent dyskinesias need not be viewed as a contraindication to subthalamotomy in PD patients since they can be eliminated if necessary by a subsequent pallidotomy without producting deficits that impair daily life.
  • Subthalamotomy incurs persistent hemiballismus / chorea in 8% of patients; in many others chorea spontaneously disappears.
    • This can be treated by a subsequent pallidotomy.
  • Patient had Parkinsonian symptoms largely restricted to right side.
  • Measured TMS ability to stimulate motor cortex -- which appears to be a common treatment. STN / GPi lesion appears to have limited effect on motor cortex exitability 9other things redulate it?).
  • conclusion: interrupting BG output removes such abnormal signaling and allows the motor system to operate more normally.
    • Bath DA presumably calms hyperactive SNr neurons.
    • Yuo cannot distrupt output of the BG with compete imuntiy; the associated abnormalities may be too subtle to be detected in normal behaviors, explaniing the overall clinical improbement seen in PD patients after surgery and the scarcity fo clinical manifestations in people with focal BG lesions (Bhatia and Marsden, 1994; Marsden and Obeso 1994).
      • Our results support the prediction that surgical lesions of the BG in PD would be associated with inflexibility or reduced capability for motor learning. (Marsden and Obeso, 1994).
  • It is better to dispense with faulty BG output than to have a faulty one.

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ref: Foffani-2004.07 tags: STN motor preparation human 2003 basal_ganglia DBS SMA date: 01-26-2012 17:23 gmt revision:3 [2] [1] [0] [head]

PMID-15249649 Involvement of the human subthalamic nucleus in movement preparation

  • STN receives large afferent from SMA, so it should be involved in movement planning.
  • the STN and nearby structures are active before self-paced movements in humans.
  • normal patients show a negative EEG movement-related potential (MRP) starting 1-2 seconds before the onset of self-paced movements.
  • STN also shows premovement negative MRP.
    • REquire very sensitive methods to record this MRP -- it's on the order of 1 uv.
  • the amplitude of the scalp MRP is reduced in parkinson's patients.
    • impairment of movement preparation in PD may be related to deficits in the SMA and M1, e.g. underactivity.
    • the MRP is normalized with the administration of levodopa.
  • MPTP monkeys have increased activity in the STN
  • examined the role of the STN in movement preparation and inhibition via MRP recorded from DBS electrodes in the STN + simultaneously recorded scalp electrodes.
  • their procedure has the leads externalized during the first week after surgery.

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ref: Elble-1996.03 tags: tremor STN VIM thalamus basal_ganglia Elble Parkinson's ET dyskinesia thalamus VIM DBS date: 01-24-2012 21:19 gmt revision:7 [6] [5] [4] [3] [2] [1] [head]

PMID-8849968[] Central Mechanisms of Tremor -- available through Duke's Ovid system. also in email.

  • focuses at first on the nonlinear aspect of all control: the systems are hard to understand because of the complexities of their interactions.
    • nonlinear systems are capable of complex interactions that are not predicted by the sum of their individual behaviors.
  • in general, there are two different types of tremor:
    • mechanical reflex oscillations (depend on sensorimotor loops), permit damped oscillations in response to pulsate perturbations.
      • is effected by the stifness and inertia of the segment involved.
    • central oscillations
      • frequencies independent of limb mechanics/segment length.
      • still subject to modulation by sensorimotor feedback.
      • if the tremor is at the same frequency as the mechanical resonance, the tremor will be worse!
  • physiologic tremor has both components of mechanical oscillations (3-5Hz) and central oscillations (8-12hz), which are usually attenuated by the low-pass property of the musculoskeletal system.
    • associated spindle and tendon organ discharge are not sufficient to produce 8 - 12 Hz oscillation - hence, this is most likely from a central source, eg. the cortex, inferior olive, and thalamus.
  • Essential tremor is also centrally generated, though it appears to be affected by somatosensory driving.
    • essential tremor frequency is strongly correlated with patient age (where the frequency decreases with increasing age).
    • the origin of ET is unknown: postmortem examinations reveal no deficits in M1/S1, thalamus, inferior olive, raphe nucleus, and reticular nuclei, globus pallidus, and spinal cord...
    • but, the inferior olive seems to be the most likely culprit:
      • tremor induced by harmaline increased inhibition-rebound properties of neurons, and this induces intention-related tremor in monkeys
      • harmaline induced olivary oscillation is similar to ET in terms of frequency, EMG, and drug-response.
      • olivary hypothesis is supported by PET scans, which show increased glucose consumption there in ET patients.
      • the ventrolateral (VL) thalamus and Ventralis intermedius (VIM) receives input from the contralateral cerebellar nuclei.
        • this is why VIM is such a good target for treatment of ET.
  • parkinsons tremor:
    • VOP is a better target for treating bradykinesia and other symptoms of PD, while VIM is the best for treating tremor
    • neurons in the globus pallidus and STN become entrained to tremor. STN lesion / HFS is effective in treating dyskinesia and other PD symptoms.
    • in MPTP monkeys, STN/ GPi neurons are also entrained to the tremor frequency.
  • other tremor:
    • neuropathic/tumorogenic tremor usually takes weeks to appear, suggesting that CNS reorganization is a cause of tremor, not intrinsic sensorimotor deafferentation
      • local lesions in the striatum, thalamus, & globus pallidus often cause dystonias, not tremor.
  • Cerebellar tremor
    • seems to be caused by an inability to properly compensate/ brake with antagonist muscles during voluntary and postural movements. movement control becomes heavily dependent on sensory feedback, which is often too slow for adequate compensation.
  • neuroleptic drugs can often cause tremor (or tardive dyskinesia). Neurolepric - calming, tranquilizer, antipsychotic.
    • lithium can cause permanent tremor due to cerebellar gliosis!
  • VOP projects to the supplementary motor area (SMA) and dorsolateral prefrontal cortex (DLPFC) PMID-21629131 ; VIM projects to M1 & contralateral cerebellum, as mentioned above.

____References____

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ref: Hoogerwerf-1994.12 tags: Wise Michigan array MEA recording 3D date: 01-15-2012 07:12 gmt revision:4 [3] [2] [1] [0] [head]

IEEE-335862 (pdf) A three-dimensional microelectrode array for chronic neural recording.

  • see {995} for reasonable photos (they don't show up in the black and white IEEE scan).
  • 16-channel, 4 shanks.
  • 3D : 16 shanks, 64 channels, includes a 16:1 MNOS mux on the attached micromachined silicon platform.
  • Nickel plated lead stransfers (90 deg) see figure 6 electroplating current.
    • This was a point of difficulty, it seems.

____References____

Hoogerwerf, A.C. and Wise, K.D. A three-dimensional microelectrode array for chronic neural recording Biomedical Engineering, IEEE Transactions on 41 12 1136 -1146 (1994)

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ref: Carmena-2003.11 tags: Carmena nicolelis BMI learning 2003 date: 01-08-2012 18:53 gmt revision:5 [4] [3] [2] [1] [0] [head]

PMID-14624244[0] Learning to control a brain-machine interface for reaching and grasping by primates.

  • strong focus on learning & reorganization.
  • Jose's first main paper.
  • focuses on two engineering / scientific questions: what signal to use, and how much of it, and from where.
    • As for where, of course we suggest that the representation is distributed.
  • Quality of predictions: gripping force > hand velocity > hand position.
  • Showed silent EMGs during BMI control.
  • Put a robot in the feedback path; this ammounted for some nonlinearities + 60-90ms delay.
  • Predictions follow anatomical expectation:
    • M1 (33-56 cells) predicts 73% variance for hand pos, 66% velocity, 83% for gripping force .
    • SMA (16-19 cells) 51% position, 51% velocity, 19% gripping force.
    • They need a table for this shiz.
  • Relatively high-quality predictions. (When I initially looked at the data, I was frustrated with the noise!)
  • Learning was associated with increased contribution of single units.
    • appeared to be more 'learning' in SMA.
    • Training on a position model seemed to increase the ctx representation of hand position.
  • changes between pole control and brain control:
    • 68% of of sampled neurons showed reduced tuning in BCWOH
    • 14% no change
    • 18% enhanced tuning.
  • Directional tuning curves clustered in a band during brain control -- neurons clustering around the first PC?
    • All cortical areas tested showed increases in correlated firing -- arousal?
    • this puts some movements into the nullspace of the Wiener matrix. Or does it? should have had the monkey make stereotyped movements to dissociate movement directions.
  • Knocks {334} in that:
    • preferred directions were derived not from actual movements, but from firing rates during target appearance time windows.
    • tuning strength could have increased simple because the movements became straighter with practice.
  • From Fetz, {329}: Interestingly, the conversion parameters obtained for one set of trials provided increasingly poor predictions of future responses, indicating a source of drift over tens of minutes in the open-loop condition. This problem was alleviated when the monkeys observed the consequences of their neural activity in ‘real time’ and could optimize cell activity to achieve the desired goal under ‘closed-loop’ conditions.

____References____

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ref: Taylor-2002.06 tags: Taylor Schwartz 3D BMI coadaptive date: 01-08-2012 04:29 gmt revision:7 [6] [5] [4] [3] [2] [1] [head]

PMID-12052948[0] Direct Cortical Control of 3D Neuroprosthetic Devices

  • actually not a bad paper... reasonable and short. they adapted the target size to maintain a 70% hit rate, and one monkey was able to floor this (reach and stay at the minimum)
  • coadaptive algorithm removed noise units based on (effectively) cross-validation.
    • both arms were restrained during performance & co-adaptation. Monkeys initially strained to move the cursor, but eventually relaxed.
  • Changes from hand control to brain control random but apparently somewhat consistent between days.
  • continually increasing performance in brain-control for both monkeys, arguably due to the presence of feedback and learning. They emphasize the difference between open-loop (Wessberg) and closed-loop control. (42 ± 5% versus 12 ± 5% of targets hit)
    • still, the percentage of correct trials is low - ~50% for the 8 target 3D task.
    • monkeys improved target hit rate by 7% from the first to the third block of 8 closed-loop movements each day.
  • claim that they were able to record some units for up to 2 months ?? ! In their other monkey, with teflon/polymide coated stainless electrodes, the neural recordings changed nearly every day, and eventually went away.
  • quote: Cell-tuning functions obtained during normal arm movements were not good predictors of intended movement once both arms were restrained. interesting.
  • coadaptive algorithm:
    • Raw PV yielded poor predictions.
    • first, effectively z-score the firing rate of each neuron.
    • junk / hash neurons were not removed.
    • Two different weights per neuron per axis (hence 6 weights altogether), one if firing rate was above the mean value, another if it was below. corrected for resulting drift. Sum (neuronal firing rates * weights) controlled velocity on each of the axes. (Hence, it is not surprising that the brain-control tuning was significantly different from the hand control - the output model is vastly different).
    • restarted the coadaptive algorithm every day?
    • coadaptive algorithm appears to be something like stochastic gradient descent with a step-size that decreases with increasing performance.
      • From her Case-western website, Dawn Taylor still seems to be on the coadaptive kick. Seems like it's bad to get stuck on one idea all your life ... though perhaps that is the best way to complete something.
    • Their movies in supplementary materials look rather good, better than most of the stuff that we have done. She did not quantify SNR or correlation coefficient.

____References____

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ref: notes-2007 tags: clementine BMI robot kinarm timarm 032807 date: 01-06-2012 00:07 gmt revision:14 [13] [12] [11] [10] [9] [8] [head]

  1. http://m8ta.com/tim/clementine.MOV -- opens with totem, MJPG compressor.
  2. http://m8ta.com/tim/timarm_servocontroller.JPG
  3. http://m8ta.com/tim/images/spikeInformation_shuffled.jpg
    1. shuffled information distribution -- high significance level ;)
  4. kinarm.
    1. http://www.hardcarve.com/tim/kinarm.JPG
    2. http://www.hardcarve.com/tim/kinarm2.JPG
    3. http://www.hardcarve.com/tim/kinarm3.JPG
  5. robot svg or timarm png
    1. http://www.hardcarve.com/tim/timarm/timarm_side.jpg
    2. http://m8ta.com/tim/robotPulleyDetail.png
  6. bmi predictions clem 032807
      1. x & y predictions
      1. x & y predictions
      1. z velocity predictions - pretty darn good, snr 2
    1. Movie of the day: http://m8ta.com/tim/clem032807_3dBMI.MPG
      1. cells for that day - 40 in all

{941}
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ref: Penfield-1937 tags: Penfield 1937 motor cortex stimulation ICMS human neurosurgery electrodes date: 01-03-2012 22:08 gmt revision:3 [2] [1] [0] [head]

No PMID / bibtex penfield-1937. Somatic motor and sensory representation in the cerebral cortex of man as studied by electrical stimulation

  • Fritsch and Hitzig (1870) [0] cited as the first paper in electrical excitation of the CNS.
  • Good review of the scientific experiments thereafter, including stimulation to S1 by Ferrier, work with apes etc.
  • Central sulcus called the 'Rolandic fissure'.
  • Interesting! quote:

The account of Bartholow (1874) is interesting to say the least and may be cited. His patient was a 30-year old-domestic. As an infant this unfortunate had chanced to fall into the fire, burning her scalp so badly that " hair was never reproduced." A piece of whale bone in the wig she was forced to wear irritated the scarred scalp and, by her statement, three months before she was admitted, an ulcer appeared. When she presented herself for relief, this had eroded the skull over a space 2 in. in diameter " where the pulsations of the brain are plainly seen." Although " rather feeble-minded " Bartholow observed that Mary returned replies to all questions and no sensory or motor loss could be made out in spite of the fact that brain substance apparently had been injured in the process of evacuation of pus from the infected area. The doctor believed, therefore, that fine insulated needles could be introduced without further damage.

While the electrodes were in the right side Bartholow decided to try the effect of more current. ' Her countenance exhibited great distress and she began to cry. Very soon the left hand was extended as if in the act of taking hold of some object in front of her; the arm presently was agitated with clonic spasms ; her eyes became fixed with pupils widely dilated ; the lips were blue and she frothed at the mouth ; her breathing became stertorous, she lost conscious-ness and was violently convulsed on the left side. This convulsion lasted for five minutes and was succeeded by coma. She returned to consciousness in twenty minutes from the beginning of the attack and complained of some weakness and vertigo." Three days after this stimulation, following a series of right-sided seizures, the patient died.

  • Relatively modern neurosurgical procedures.
  • They observe changes to blood circulation prior epileptic procedures. wow!
  • Very careful hand-drawn maps of what they have observed. Important, as you'll probably never get this trough an IRB. It pays to be meticulous.

____References____

[0] Fritsch G, Hitzig E, Electric excitability of the cerebrum (Uber die elektrische Erregbarkeit des Grosshirns).Epilepsy Behav 15:2, 123-30 (2009 Jun)

{994}
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ref: Wilson-1993.08 tags: Wilson McNaughton 1993 sleep hippocampus array recording date: 01-03-2012 00:57 gmt revision:2 [1] [0] [head]

PMID-8351520[0] Dynamics of the hippocampal ensemble code for space.

  • 73-148 neurons.
  • Could accurately decode the rat's movement through space.
  • "The parallel recording methods outlined here make possible the study of the dynamics of neuronal interactions during unique behavioral events."

PMID-8036517[1] Reactivation of hippocampal ensemble memories during sleep.

  • "Information acquired during active behavior is thus re-expressed in hippocampal circuits during sleep, as postulated by some theories of memory consolidation."

____References____

[0] Wilson MA, McNaughton BL, Dynamics of the hippocampal ensemble code for space.Science 261:5124, 1055-8 (1993 Aug 20)
[1] Wilson MA, McNaughton BL, Reactivation of hippocampal ensemble memories during sleep.Science 265:5172, 676-9 (1994 Jul 29)

{926}
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ref: Nicolelis-1998.11 tags: spatiotemporal spiking nicolelis somatosensory tactile S1 3b microwire array rate temporal coding code date: 12-28-2011 20:42 gmt revision:3 [2] [1] [0] [head]

PMID-10196571[0] Simultaneous encoding of tactile information by three primate cortical areas

  • owl monkeys.
  • used microwires arrays to decode the location of tactile stimuli; location was encoded through te population, not within single units.
  • areas 3b, S1 & S2.
  • used LVQ (learning vector quantization) backprop, LDA to predict/ classify touch trials; all yielded about the same ~60% accuracy. Chance level 33%.
  • Interesting: "the spatiotemporal character of neuronal responses in the SII cortex was shown to contain the requisite information for the encoding of stimulus location using temporally patterned spike sequences, whereas the simultaneously recorded neuronal responses in areas 3b and 2 contained the requisite information for rate coding."
    • They support this result by varying bin widths and looking at the % of correctly classivied trials. in SII, increasing bin width decreases (slightly but significantly) the prediction accuracy.

____References____

[0] Nicolelis MA, Ghazanfar AA, Stambaugh CR, Oliveira LM, Laubach M, Chapin JK, Nelson RJ, Kaas JH, Simultaneous encoding of tactile information by three primate cortical areas.Nat Neurosci 1:7, 621-30 (1998 Nov)

{938}
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ref: -0 tags: Georgopoulos 1988 M1 population vector tuning 3D single unit date: 12-20-2011 00:58 gmt revision:2 [1] [0] [head]

PMID-3411363[0] Primate motor cortex and free arm movements to visual targets in three-dimensional space. III. Positional gradients and population coding of movement direction from various movement origins.

  • In comparison to the first experiment, where they showed that movement direction was encoded by single units within M1, here they varied the starting position of the movements.
  • tonic discharge of many cells varied in and orderly fashion with the position at which the hand was actively maintained in space.
  • however, cell activity changes were the same independent of movement onset and dependent on movement direction.
    • similar but not that similar -- vary based on tonic firing rate. See figure 9.

____References____

[0] Kettner RE, Schwartz AB, Georgopoulos AP, Primate motor cortex and free arm movements to visual targets in three-dimensional space. III. Positional gradients and population coding of movement direction from various movement origins.J Neurosci 8:8, 2938-47 (1988 Aug)

{900}
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ref: Helms-2003.01 tags: Schwartz BMI adaptive control Taylor Tillery 2003 date: 11-26-2011 00:58 gmt revision:1 [0] [head]

PMID-12929922 Training in cortical control of neuroprosthetic devices improves signal extraction from small neuronal ensembles.

  • Lays out the coadaprive algorithm.
  • with supervised / adaptive training, ML estimator is able to get 80% of the targets correct.
  • Reviews in the Neurosciences (conference) Workshop on Neural and Artificial Computation.

{785}
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ref: -0 tags: convert m4b to mp3 linux date: 09-11-2009 17:16 gmt revision:0 [head]

Recently I got an audiobook in m4b format, but I wanted to play it on my mp3 (only!) device. So, had to convert it. To do this, on my Debian Lenny box I first:

 apt-get install ffmpeg libmp3lame30 libfaad0 libavcodec51 

The last one seems to be the most important, nothing works even though libavcodec51 wold seem to have nothing to do with mp3 encoding... Then used a bash script:

#!/bin/bash
for i in *.m4b; do
        ffmpeg -i "$i" -acodec libmp3lame "${i%m4b}mp3";
done

to convert all the m4b files in a directory. Later, I used easytag to add tags to the mp3s so they would show up properly on the device {770}. Simplest way to get this to work was to just change the name of the containing folder to Artist - Title; didn't want to manually change the tags on all the mp3's, and I didn't find a 'apply all' button.

{770}
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ref: life-0 tags: RCA Thompson lyra mp3 player ARM teardown date: 09-11-2009 17:15 gmt revision:4 [3] [2] [1] [0] [head]

During the GOSH! summit there was an intensive talk about making a open-hardware USBkey-to-television converter/computer/mp4 player, an idea (patented!) by Joshua Kauffman and Gwendolyn Floyd. Since this was a very hands-on workshop, I decided to get an mp4 player in downtown Banff and take it apart to see how it works. The selected device, a RCA Lyra MC4202-A portable media player, is, in accordance with its low price, electrically simple on the inside. What follows is a rough teardown of the internals.

-- View of the Lya with the back plastic panel removed.

  • A - STMP3710 SOC & ARM9 processor @ 206Mhz, 100 pin TQFP package, Freescale logo. comparison table. Device does not have enough processing power to support full mp4 playback; you have to use a special CODEC to put video files on the device.
  • B - Hynix HY27UU08AG5A 2GB Nand flash. Probably the first few blocks are reserved for booting; these blocks must be accessible through USB, as RCA/Thompson offers firmware updates. Were I motivated, I could packet sniff the USB update procedure to allow flashing with any firmware. (I would have to be very motivated!)
  • C Mini-USB type B connector. The STMP supports both full speed and high speed USB transfers.
  • D Audio out jack. Doubles as a FM antenna.
  • E Microphone. Not really sure where the amplification / digitization for this is - it may be an all digital mic, e.g. LMV1024 and sit on the I2C bus.
  • F Inductor for the external supply - 3V.
  • G Inductor for processor core supply - 1.2V (? - Freescale documentation is less than freely available on the internet)
  • H 24 Mhz crystal (large) + 32kHz real-time-clock crystal (small). The yellow tape covers a bunch of 0402 capacitors and resistors.
  • I Keypad lock switch. This makes the device a bit (but not very) tricky to re-assemble. Yes, my player continues to work after re-assembly.
  • J Lithium-ion battery. Due to the sticky tape on it's back, I bent the battery while taking the player apart. Fortunately, it did not explode! This battery is slightly thinner than that in my LG cell phone, yet its capacity is 1/3 as much - this is a cut-rate battery.
  • K Flexible kapton lead to the sub-QVGA LCD, behind the battery.

-- View underneath the main PCB, showing the keypad PCB.

  • A STFM1000 FM demodulator & clock generator chip.
  • The main PCB is 4 layers, with about 0.005" trace / 0.007" (?) space clearance. Keypad PCB slightly rougher and only 2 payers. Capacitors and transistors on this are used to drive the backlighting LEDS on the other side.
  • If you assemble these together with the screws in the wrong holes, the keypad will only partially work, probably due to connector spacing / shorting issues. I discovered this the hard way :-)

{664}
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ref: Darmanjian-2006.01 tags: wireless neural recording university Florida Principe telemetry msp430 dsp nordic date: 04-15-2009 20:56 gmt revision:1 [0] [head]

PMID-17946962[0] A reconfigurable neural signal processor (NSP) for brain machine interfaces.

  • use a Texas instruments TMS320VC33 200MFLOPS (yes floating point) DSP,
  • a nordic NRF24L01,
  • a MSP430F1611x as a co-processor / wireless protocol manager / bootloader,
  • an Altera EPM3128ATC100 CPLD for expansion / connection.
  • uses 450 - 600mW in use (running an LMS algorithm).

____References____

[0] Darmanjian S, Cieslewski G, Morrison S, Dang B, Gugel K, Principe J, A reconfigurable neural signal processor (NSP) for brain machine interfaces.Conf Proc IEEE Eng Med Biol Soc 1no Issue 2502-5 (2006)

{610}
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ref: Rektor-2003.03 tags: ERP basal ganglia P300 EEG date: 09-25-2008 02:35 gmt revision:2 [1] [0] [head]

PMID-12705427[0] A SEEG study of ERP in motor and premotor cortices and in the basal ganglia.

  • SEEG = stereo (algorithmically (not electrically) differential) EEG.
  • Used depth electrodes in epilepsy patients.
  • targeted M1, SMA & premotor cortices as well as the basal ganglia.
  • ERP larger and more frequent in the basal ganglia, with no difference in the latency between the ERP in the cortex and in the basal ganglia.
  • ERP were in response to visual and auditory 'oddball' tasks
    • Patients had to detect the less usual tone or visual object & count it; sometimes detection involved pressing a button.

____References____

{520}
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ref: bookmark-0 tags: DSP Benford's law Fourier transform book date: 12-07-2007 06:14 gmt revision:1 [0] [head]

http://www.dspguide.com/ch34.htm -- awesome!!

{504}
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ref: bookmark-0 tags: blackfin BF537 uClinux webserver USB2 vmware date: 11-21-2007 22:32 gmt revision:0 [head]

http://www.camsig.co.uk/ -- blackfin is hot like chernobyl. 1" sq 600mhz webserver etc.

  • uses NET2272 high-speed USB-2.0 peripheral from PLX technology.
  • has a 10/100 ethernet mac w/o magnetics
  • 99 GBP
  • specsheet - no power consumption figures
  • attaches with a rubberized compression connector - no solder required!
  • Develop programs with a VMware virtual appliance (openSuSE 10.2) - brilliant! (though the download is HUGE ... and hosted by amazon)

{404}
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ref: -0 tags: blackfin BF532 memory map date: 11-21-2007 21:18 gmt revision:1 [0] [head]

page 6 on the spec sheet. 55

{394}
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ref: notes-0 tags: blackfin LED kernel module linux BF537 STAMP tftp BF537 bridge date: 11-13-2007 17:59 gmt revision:4 [3] [2] [1] [0] [head]

so, you want to control the LEDs on a BF537-STAMP board? You'll need a linux box with a serial port, then will need to do a few things:

  1. get the blackfin build tools:
    1. download the RPM file from blackfin.uclinux.org and use alien (if you are on debian, like me) to install it.
    2. installation instructions
  2. get uClinux distribution and compile it. http://blackfin.uclinux.org/gf/project/uclinux-dist/frs/
    1. unpack it to a local directory
    2. 'make menuconfig'
    3. select your vendor & device
    4. make sure runtime module loading is enabled.
    5. 'make' (it takes much less time than the full linux kernel)
    6. this will result in a linux.bin image, which uBoot can use.
  3. you need to set up a tftp server for uboot, see http://linuxgazette.net/125/pramode.html
  4. attach the blackfin stamp to the serial port on your computer. configure kermit with:
    set line /dev/ttyS1
    set speed 57600
    set carrier-watch off
    set prefixing all
    set parity none
    set stop-bits 1
    set modem none
    set file type bin
    set file name lit
    set flow-control none
    set prompt "Linux Kermit> " 
    (this is assuming that your serial port is /dev/ttyS1)
  5. power on the stamp, at the uBoot prompt press space.
  6. issue the following commands:
    set serverip 192.168.1.149
    set ipaddr 192.168.1.200
    tftpboot 0x1000000  linux
    bootelf 0x1000000 
    to get the device to boot your new uClinux image from SDRAM. your IP addresses will vary.
    1. note: you can boot any ELF image at this point; for example, the 'blink' example in the blackfin tool trunk SVN, 'make' produces a ELF file, which can be loaded into SDRAM via tftp and executed. I'm not sure what part of L1 uboot uses for its instruction, but conceivably you could load into L1 / data ram and execute from there. see also {403} you would do something like:
set serverip 192.168.1.149
set ipaddr 192.168.1.200
tftpboot 0x1000000  blink
bootelf 0x1000000 
  1. at the uCLinux prompt : ifconfig eth0 192.168.1.200
  2. write a simple kernel module, for example:
    #include <linux/module.h>
    //#include <linux/config.h>
    #include <linux/init.h>
    #include <linux/fs.h>
    
    #include <asm/uaccess.h>
    #include <asm/blackfin.h>
    #include <asm/io.h>
    #include <asm/irq.h>
    #include <asm/dma.h>
    #include <asm/cacheflush.h>
    
    MODULE_LICENSE("GPL");
    
    int major;
    char *name = "led";
    int count = 0;
    
    ssize_t led_write(struct file* filp, const char *buf, size_t size, loff_t *offp)
    {
    	printk("LED write called "); 
    	if (size < 2) return -EMSGSIZE;
    	if (!buf) return -EFAULT;
    	printk("led_write called with: %s ", buf); 
    	if(buf[0] == '0') {bfin_write_PORTFIO_CLEAR(1<< 6); }
    	else{ bfin_write_PORTFIO_SET(1<<6); }
    	return size;
    }
    int led_open(struct inode *inode, struct file *file){
    	printk("led opened"); 
    	return 0; 
    }
    int led_release(struct inode *inode, struct file *file){
    	printk("led released"); 
    	return 0; 
    }
    struct file_operations fops = {
    	 .owner = THIS_MODULE,
    	.read = NULL,
    	.write = led_write,
    	.open = led_open,
    	.release = led_release
    	};
    int __init init_module(void)
    {
    	// Set PF2 as output -- clear the FER bit.
    	bfin_write_PORTF_FER(bfin_read_PORTF_FER() & (~(1 << 6))); 
    	bfin_write_PORTFIO_SET(1<< 6);
    	bfin_write_PORTFIO_DIR(bfin_read_PORTFIO_DIR() | (1<<6)); 
    	major = register_chrdev(0, name, &fops);//hope it succeeds!
    	printk("registered, major = %d ", major); 
    	printk("portF = %d", bfin_read_PORTFIO()); 
    	printk("portF_FER = %d", bfin_read_PORTF_FER()); 
    	printk("portF_DIR = %d", bfin_read_PORTFIO_DIR()); 
    	return 0;
    }
    
    void __exit cleanup_module(void)
    {
    	unregister_chrdev(major, name);
    	printk("led: cleanup "); 
    }
  3. write a makefile for this module, for example:
    obj-m:=led.o
    default:
            make -C /uClinux-dist/linux-2.6.x/ M=`pwd`
    
  4. setup apache on your computer, e.g. 'apt-get install apache2'
  5. 'ln -s' your build directory to /var/www/, so that you can wget the resulting kernel module
  6. rm led.ko
    wget http://192.168.1.149/blackfin/led.ko (for example)
    insmod led.ko
    rm /dev/led
    mknod /dev/led c 253 0
    chmod 0644 /dev/led
    echo 1 >> /dev/led 

{465}
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ref: notes-0 tags: CRC32 ethernet blackfin date: 10-10-2007 03:57 gmt revision:1 [0] [head]

good explanation of 32-bit CRC (from the blackfin BF537 hardware ref):

{428}
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ref: notes-0 tags: activewire ez-usb an2131 cypress date: 08-16-2007 00:33 gmt revision:1 [0] [head]

to get the activewire board working under linux (debian):

  1. I had to install fxload (in the apt repository).
  2. install hex (1) , which is a simple LED blink routine from http://ezusb2131.sourceforge.net/ via:
    1. sudo fxload -I led2.hex -D /proc/bus/usb/006/118 where 118 is the address from dmesg | tail and led2.hex is hex(1)
  3. install hex (2), which is from http://activewire-osx.cvs.sourceforge.net/ -- it is the most recent i could find. translated via {427}
    1. sudo fxload -I awfirm2.hex -D /proc/bus/usb/006/118 awfirm2.hex is, of course, hex(2)
  4. check dmesg | tail - the EZ-USB chip should disconnect and reconnect with a new address. I don't know why the first ex is required - perhaps it resets the processor?
  5. run the awusb-linux program, for example, and do what you like.

I have no idea why this is required. perhaps my board is broken abit?

hex (1):

:03000000020100FA
:10010000907F947400F0907F9D7410F0907F9774AE
:1001100010F012012D12012D12012D907F97740005
:10012000F012012D12012D12012D02010C786490A4
:0C013000FB50A3E582458370F9D8F4224F
:00000001FF

hex(2):

:1007B600D204C203C200C202C201120653D2E843E7
:1007C600D820907FAB74FFF0907FA9F0907FAAF0BD
:1007D6005391EF907FAFE04401F0907FAEE0440D7F
:1007E600F0D2AF20014C750C00750B00750A007530
:1007F60009007F487E927D007C00AB0CAA0BA90AFB
:10080600A809C31207A5502020011D7A0079007897
:1008160000E50C2401F50CEA350BF50BE9350AF574
:100826000AE83509F50980CA2001B8D205120D7B00
:0F08360080B1300105120100C20112045180F39C
:010845002290
:10010000907FE9E070030201DF14700302025B24B8
:10011000FE70030202CF24FB70030201D9147003A6
:100120000201D31470030201C71470030201CD242D
:10013000056003020323120E33400302032F907F56
:10014000EBE024FE6016146040240270707403908B
:100150007FD4F07437907FD5F002032F907FEAE0D0
:10016000FF120A2D8B0D8A0E890FEA496011AE022B
:10017000EE907FD4F0AF01EF907FD5F002032F9087
:100180007FB4E04401F002032F907FEAE0FF120AFF
:100190007C8B0D8A0E890FEA496018AE02EE907FC3
:1001A000D4F0AF01EF907FD5F0120705907FB5F046
:1001B00002032F907FB4E04401F002032F907FB43C
:1001C000E04401F002032F120DFD02032F120E1F57
:1001D00002032F120E1702032F120DEF02032F122C
:1001E0000E35400302032F907FE8E0247F60241443
:1001F00060312402705BA200E433FF25E0FFA2021D
:10020000E4334F907F00F0E4A3F0907FB57402F0E8
:1002100002032FE4907F00F0A3F0907FB57402F00A
:1002200002032F907FECE0F45480FFC4540FFFE0F2
:1002300054072F25E024B4F582E4347FF583E0549D
:10024000FD907F00F0E4A3F0907FB57402F002030C
:100250002F907FB4E04401F002032F120E374003C9
:1002600002032F907FE8E024FE601D240260030259
:10027000032F907FEAE0B40105C20002032F907FB4
:10028000B4E04401F002032F907FEAE07038907FE1
:10029000ECE0F45480FFC4540FFFE054072F25E036
:1002A00024B4F582E4347FF583E4F0907FECE054ED
:1002B00080FF131313541FFFE054072F907FD7F0D4
:1002C000E04420F08069907FB4E04401F080601247
:1002D0000E39505B907FE8E024FE60182402704FD6
:1002E000907FEAE0B40104D2008044907FB4E044FF
:1002F00001F0803B907FEAE07020907FECE0F454C6
:1003000080FFC4540FFFE054072F25E024B4F5828A
:10031000E4347FF5837401F08015907FB4E04401EC
:10032000F0800C120C035007907FB4E04401F09071
:060330007FB4E04402F07E
:0103360022A4
:03003300020E2F8B
:040E2F0053D8EF3273
:100337001201000100000040540801010000010201
:1003470000010902C00001010080960904000004B1
:10035700FFFFFF00070581020200000705010240B9
:1003670000000705820202000007050202400000A4
:100377000904000100FFFFFF000904000200FFFF5E
:10038700FF000904000300FFFFFF00090400040049
:10039700FFFFFF000904000500FFFFFF000904003D
:1003A7000600FFFFFF000904000700FFFFFF000929
:1003B70004000800FFFFFF000904000900FFFFFF1A
:1003C700000904000A08FFFFFF0007058102020079
:1003D700000705010240000007058202020000072E
:1003E700050202400000070583020100000705031C
:1003F700020300000705040240000007050502404C
:10040700000004030904220341006300740069002B
:100417007600650057006900720065002C00200017
:1004270049006E0063002E001E0341006300740044
:1004370069007600650057006900720065002000BA
:0A04470055005300420000000000C1
:10065300907FDE740FF0907FACF0907FDF743FF0FB
:10066300907FADF0907FAE741FF0E4FF74802FF5A0
:1006730082E4347DF583E4F074002FF582E4347E64
:10068300F583E4F074802FF582E4347EF583E4F09F
:1006930074C02FF582E4347CF583E4F074402FF5C5
:1006A30082E4347DF583E4F074C02FF582E4347D75
:1006B300F583E4F074402FF582E4347EF583E4F0AF
:1006C3000FBF40A8E4907F9CF0907F9DF0907F9EA9
:1006D300F0907F93F0907F94F0907F95F0907F96C9
:1006E300F0907F97F0907F98F0751D01D200F51977
:1006F300F51AF518F51BF51CC206F516F517120EBB
:020703002722AB
:10045100907F9AE0907E80F0907F9BE0907E81F08B
:10046100907FB77402F0907F9DE0907E00F0907FC6
:100471009EE0907E01F0907FB97402F0907FCCE015
:1004810030E103020507907FBAE030E108E51C1571
:100491001C7002151B300669E4F50D907FCDE0FF5D
:1004A100E50DC39F5051E51AB40108E51C900FF00A
:1004B100F0800AE51B900FF0F0E51CA3F0051CE5A8
:1004C1001C7002051B74C0250DF582E4347CF58394
:1004D100E0FF74F0251AF582E4340FF583EFF0AFF5
:1004E10019E51A04FD7A0F7BF0120DBC7F0A7E001C
:1004F100120DD8050D80A4E4907FBBF0F516751799
:1005010008E4907FCDF0907FBAE030E10CA3E06089
:1005110008E51764084516704B30063DE51AB4012D
:1005210008E51C900FF0F0800AE51B900FF0F0E554
:100531001CA3F0051CE51C7002051BAF19AD1A7A4E
:100541000F7BF0120DBCAF197D027A0F7BF0120DFB
:10055100A0900FF0E0907D80F0907FBB7401F0E4FB
:05056100F516F517225C
:100BDA00907F9E74FFF0907F9DF0907F9CF0E49050
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ref: notes-0 tags: blackfin BF537 memory map date: 08-01-2007 19:23 gmt revision:0 [head]

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ref: thesis-0 tags: clementine 042307 operant conditioning date: 04-24-2007 01:37 gmt revision:2 [1] [0] [head]

Today, once again, I tried BMI both via pole control and with operant conditioning. The latter worked the best; because the fit/predictions were so shitty i didn't even try brain control with the wiener filter or kalman filter. Here is the output of BMIsql on ~6500 data slices, 18 neurons, 5 taps:

here is the prediction summary... note that target x position is doing rather well (probably because we are training units to respond to this)

output of BMIsql:

order of columns: unit,channel, lag, snr, variable

    2.0000   29.0000         0    1.0872    6.0000
    1.0000   53.0000    3.0000    1.0870    3.0000
    1.0000   53.0000    2.0000    1.0820    3.0000
    1.0000   82.0000    1.0000    1.0801    7.0000
    1.0000   82.0000    5.0000    1.0678    1.0000
    1.0000   82.0000    4.0000    1.0625    1.0000
    1.0000   82.0000    2.0000    1.0563    7.0000
    1.0000   53.0000    1.0000    1.0558    6.0000
    1.0000    8.0000         0    1.0550    8.0000
    1.0000   70.0000    3.0000    1.0549    2.0000
    1.0000   70.0000    2.0000    1.0536    2.0000
    2.0000   82.0000    4.0000    1.0524    1.0000
    2.0000   82.0000    5.0000    1.0516    1.0000
    1.0000   53.0000    4.0000    1.0506    3.0000
    1.0000   70.0000    4.0000    1.0503    2.0000
    2.0000   29.0000    1.0000    1.0497    5.0000
    2.0000   82.0000    3.0000    1.0494    1.0000
    1.0000   82.0000    3.0000    1.0464    7.0000
    1.0000    8.0000    1.0000    1.0454    8.0000
    1.0000   24.0000    1.0000    1.0450    8.0000
    1.0000   24.0000         0    1.0442    8.0000
    1.0000    8.0000    2.0000    1.0415    8.0000
    1.0000   70.0000    5.0000    1.0396    2.0000
    2.0000   82.0000    1.0000    1.0395    7.0000
    1.0000   24.0000    2.0000    1.0392    8.0000
    1.0000   70.0000    1.0000    1.0389    2.0000
    1.0000   81.0000    1.0000    1.0356    8.0000
    1.0000    8.0000    3.0000    1.0355    8.0000
    2.0000   29.0000    2.0000    1.0334    8.0000
    1.0000   81.0000    2.0000    1.0326    8.0000
    1.0000   24.0000    4.0000    1.0318    8.0000
    1.0000    8.0000    4.0000    1.0298    8.0000
    1.0000   24.0000    3.0000    1.0297    8.0000
    1.0000   28.0000    3.0000    1.0293   11.0000
    2.0000   82.0000    2.0000    1.0292    4.0000
    1.0000   28.0000    1.0000    1.0286   11.0000
    1.0000   28.0000    4.0000    1.0262   11.0000
    1.0000   28.0000    2.0000    1.0243   11.0000
    1.0000   28.0000         0    1.0238   11.0000
    2.0000   29.0000    3.0000    1.0221    8.0000
    1.0000   53.0000         0    1.0215    9.0000
    1.0000   81.0000    3.0000    1.0207    8.0000

Operant conditioning worked exceptionally well for the X axis (channel 29, yellow unit 1 - adding both unit's activity together did not work, the monkey would not play). see http://m8ta.com/tim/clem042307_trainX.MPG For a while he tried controlling the cursor position with the joystick, then after a while he realized this was unnecessary and just modulated unit 29.

Initially I tried operant conditioning of channel 82 for the Y axis, but it quickly appeared that he did not care and that it would not work. Hence I switched to channel 71, which was tried on Saturday the 20th. As before, this unit was tonically active while he was asleep, and almost silent while he was paying attention. an attention neuron? possibly. It also showed high firing rate changes when he struggled, suggesting volitional control. He was somewhat able to control it today... see http://m8ta.com/tim/clem042307_trainY.MPG

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ref: Caminiti-1991.05 tags: transform motor control M1 3D population_vector premotor Caminiti date: 04-09-2007 20:10 gmt revision:2 [1] [0] [head]

PMID-2027042[0] Making arm movements within different parts of space: the premotor and motor cortical representation of a coordinate system for reaching to visual targets.

  • trained monkeys to make similar movements in different parts of external/extrinsic 3D space.
  • change of preferred direction was graded in an orderly manner across extrinsic space.
  • virtually no correlations found to endpoint static position: "virtually all cells were related to the direction and not to the end point of movement" - compare to Graziano!
  • yet the population vector remained an accurate predictor of movement: "Unlike the individual cell preferred directions upon which they are based, movement population vectors did not change their spatial orientation across the work space, suggesting that they remain good predictors of movement direction regardless of the region of space in which movements are made"

____References____

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ref: Caminiti-1990.07 tags: transform motor control M1 3D population_vector premotor Caminiti date: 04-09-2007 20:07 gmt revision:4 [3] [2] [1] [0] [head]

PMID-2376768[0] Making arm movements within different parts of space: dynamic aspects in the primate motor cortex

  • monkeys made similar movements in different parts of external/extrinsic 3D space.
  • change of preferred direction was graded in an orderly manner across extrinsic space.
    • this change closely followed the changes in muscle activation required to effect the observed movements.
  • motor cortical cells can code direction of movement in a way which is dependent on the position of the arm in space
  • implies existence of mechanisms which facilitate the transformation between extrinsic (visual targets) and intrinsic coordinates
  • also see [1]

____References____

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ref: Taira-1996.06 tags: 3D Georgopoulos SUA M1 force motor control direction tuning date: 04-09-2007 15:16 gmt revision:1 [0] [head]

PMID-8817266[0] On the relations between single cell activity in the motor cortex and the direction and magnitude of three-dimensional static isometric force.

  • 3D isometric joystick.
  • stepwise multiple linear regression.
  • direction of force is a signal especially prominent in the motor cortex.
    • the pure directional effect was 1.8 times more prevalent in the cells than in the muscles studied (!)

____References____

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ref: Wahnoun-2004.01 tags: BMI population_vector neural selection Brown 3D arizona ASU date: 04-06-2007 23:28 gmt revision:3 [2] [1] [0] [head]

PMID-17271333[0] Neuron selection and visual training for population vector based cortical control.

  • M1 and Pmd (not visual areas), bilateral.
  • a series of experiments designed to parameterize a cortical control algorithm without an animal having to move its arm.
  • a highly motivated animal observes as the computer drives a cursor move towards a set of targets once each in a center-out task.
    • how motivated? how did they do this? (primate working for its daily water rations)
  • I do not think this is the way to go. it is better to stimulate in the proper afferents and let the brain learn the control algorithm, the same as when a baby learns to crawl.
    • however, the method described here may be a good way to bootstrap., definitely.
  • want to generate an algorithm that 'tunes-up' control with a few tens of neurons, not hundreds as Miguel estimates.
  • estimate the tuning from 12 seconds of visual following (1.5 seconds per each of the 8 corners of a cube)
  • optimize over the subset of neurons (by dropping them) & computing the individual residual error.
  • their paper seems to be more of an analysis of this neuron-removal method.
  • neurons seem to maintain their tuning between visual following and brain-control.
  • they never actually did brain control

PMID-16705272[1] Selection and parameterization of cortical neurons for neuroprosthetic control

  • here they actually did neuroprosthetic control.
  • most units add noise to the control signal, a few actually improve it -> they emphasize cautious unit selection leaning to simpler computational/electrical systems.
  • point out that the idea of using chronically recorded neural signals has a very long history.. [2,3,4,5] [6] etc.
  • look like it took the monkeys about 1.6-1.8 seconds to reach the target.
    • minimum summed path length / distance to target = 3.5. is that good?

____References____

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ref: Kettner-1988.08 tags: 3D motor control population_vector Schwartz Georgopoulos date: 04-05-2007 17:09 gmt revision:1 [0] [head]

A triptych of papers (good job increasing your publication count, guys!):

  • PMID-3411363[0] Primate motor cortex and free arm movements to visual targets in three-dimensional space. III. Positional gradients and population coding of movement direction from various movement origins.
    • propose multilinear model to predict firing rate of nneuron (a regression that is the same direction as the kalman filter)
    • i don't see how this is that much different from below (?)
  • PMID-3411362[1] Primate motor cortex and free arm movements to visual targets in three-dimensional space. II. Coding of the direction of movement by a neuronal population.
    • they show, basically, that they can predict movement direction (note this is different from actual movement!) using the poulation vector scheme.
  • PMID-3411361[2] Primate motor cortex and free arm movements to visual targets in three-dimensional space. I. Relations between single cell discharge and direction of movement.
    • 568 cells!!
    • 8 directional targets, again -- not sure how they were aranged; they say 'in approximately equal angular intervals'
    • these findings generalize the previous 2D results [3] (tuning to external space) to 3D

____References____

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ref: Pollak-1993.01 tags: DBS STN subthalamic nucleus original 1993 Benabid date: 03-12-2007 04:58 gmt revision:2 [1] [0] [head]

PMID-8235208[] Effects of the stimulation of the subthalamic nucleus in Parkinson disease

  • the original study! (in french:)
  • even back then, they used a quadripolar medtronic stimulating electrode w/ stimulation frequency of 130Hz.
  • how far have we come? not too far.

____References____

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ref: Barik-1996.1 tags: parkinsons dopamine cerebellum D3 essential tremor ET date: 0-0-2007 0:0 revision:0 [head]

  • PMID-8930390
    • There is a high concentration of dopamine in the 9 and 10 lobule of the cerebellum. quote: similar but weaker than the D3 response in the nucelus accumbens.
    • lobules 9 and 10 are involved in vestibular control of posture (?)
  • D3 is metabotropic inhibitory (sorta): molecular biology of the dopamine receptor subtypes
  • D3 is an autoreceptor; antagonism probably increases DA synaptic transmission.
    • Amisulpride is a D3 antagonist of the autoreceptor, and is used to treat the depressive elements at low doses(where it blocks autoreceptor) of schizophrenia at high doses (blocks postsynaptic recepor).
  • PMID-14622169 dopamine receptor expression is repressed in parkinsonian patients.
  • PMID-16809426 French patients with familial essential tremor are associated with polymorphisms in the D3 receptor gene.
    • a mutation which increases the affinity for dopamine causes an increase in the cAMP and MAPK response.
    • this mutation is harder to treat with parkinson's drugs - they suggest D3 antagonists for these patients of essential tremor.