https://crcns.org These are the search results for the query, showing results 601 to 615. https://crcns.org/forum/using-datasets/626349982/484520664 Hi  Pranav, Thanks for your questions.  Kenji and I went over this more.  The explanation follows: To be included in the sess-cells.csv, the cell had to generate at least 50 spikes in the session.  (This is described in file "00_README.txt" which is included with the sess-cells.csv).  Session ec016.234 has 98 cells that were considered "good quality" with at least one spike but only 61 cells with at least 50 spikes.  The queries that show this are included later in this post. As you determined, there are actually 100 cells (not 98).  The reason is that two of the cells (with id's 4732 and 4736) are not included in the SQLite table proving cell information (e.g. table"cell") because they are flagged as bad cells in the MatLab "Clean" array.  The query I used to find that is also shown below. There were eleven recording sessions associated with topdir "ec016.17".  The reason that only two of these (ec016.233 and ec016.234) were made available for download is that during the other 9 sessions, the animal was sleeping, and the decision was made, for this data set, to prioritize making available data during which the animal was awake and behaving.  Otherwise the dataset would be much larger (there are 1095 sleep sessions, total duration 347 hours; vs. 'only' 443 sessions with an awake behavior, total duration 200 hours).  Note:  The "hc-4" data set at CRCNS.org is a supplement to the hc-3 data set.  It contains a complete set of sessions (including raw data files) for topdir "'ec014.39'".   There are plans to add more topdir's along with all data recorded from them to the hc-4 data set.   Below are the SQLite queries used to determine the information given above.   Thanks again for your questions.  Don't hesitate to ask more if something is still not clear. Jeff & Kenji     cd hc3-metadata-tables $ ls 00-README.txt        hc3-file.csv        hc3-spike_count.csv    hc3-tables.xlsx hc3-cell.csv        hc3-session.csv        hc3-tables.db        old hc3-epos.csv        hc3-session_a.csv    hc3-tables.sql        whl-list.txt $ sqlite3 hc3-tables.db SQLite version 3.8.0.2 2013-09-03 17:11:13 Enter ".help" for instructions Enter SQL statements terminated with a ";" sqlite> .tables cell         file         session_a    whl_file   epos         session      spike_count --Number of cells with 50 or more spikes (what is in hc3-cells.csv): sqlite> select count(*)    from session s, spike_count k, cell c    where c.id = k.cellId and s.id = k.sessId and k.nSpikes > 49    and s.session = 'ec016.234'; 61 (Matches what is in sess-cells.csv). -- Number of cells with one or more spikes: sqlite> select count(*)    from session s, spike_count k, cell c    where c.id = k.cellId and s.id = k.sessId and k.nSpikes > 0    and s.session = 'ec016.234'; 98 (Close to 100 but still does not match number of clusters which is 100).   -- Go to SQLite table (hc3.db) which is a direct copy of original MatLab structures:   cd ./hc3-original-docs $ ls DecidePyrIntRegion.m    KenjiData.mat        hc3.db ElePosition.txt        README.txt        tables.sql $ sqlite3 hc3.db sqlite> .schema clean CREATE TABLE clean ( -- from MatLab Clean matrix.   id integer,  -- row in Beh  -- SHOULD BE ROW in pmMap (see below)   good integer -- ==0 if bad cell ); sqlite> select count(*) from clean; 8569 sqlite> select count(*) from pmMap; 8569 sqlite> select id, good from clean where id in (4732, 4736); id    good 4732    0   -- (value zero indicates these cells are bad) 4736    0   -- Back to using the main SQLite database for the data set   $ sqlite3 hc3-tables.db  sqlite> select s.session, s.behavior from session_a s where topdir='ec016.17';  -- Note: "session_a" not "session". session behavior ec016.228 sleep ec016.229 sleep ec016.230 sleep ec016.231 sleep ec016.233 linear ec016.234 linear ec016.236 sleep ec016.237 sleep ec016.238 sleep ec016.239 sleep ec016.240 sleep   -- Shows that ec016.233 and ec016.234 have behavior "linear".  All others in 'ec016.17' have behavior sleep.   -- Get count and total duration of sleep sessions: sqlite> select count(*), round(sum(s.duration)/3600.0, 1) hours from session_a s where s.behavior = 'sleep' group by s.behavior; count(*) hours 1095    347.3   -- Get count and total duration of non-sleep sessions: select count(*), round(sum(s.duration)/3600.0, 1) hours from session_a s where s.behavior != 'sleep' group by '*'; count(*) hours 443  199.8     No publisher jteeters 2015-04-21T05:33:10Z Comment https://crcns.org/forum/using-datasets/6343405/382286266 Hello Dai (and anyone else with the same question), We will not be providing the code for the basis-restricted separable model.  However, you may find the MATLAB code in GLMdenoise ( http://kendrickkay.net/GLMdenoise/ ) useful, specifically, the GLMestimatemodel.m function.  This function implements a separable model with a FIR basis, and could be relatively easily tweaked to use a different basis (e.g. sines and cosines).  (GLMdenoise itself provides denoising benefits, but that was not used on the 2008 data.)   No publisher mlescroart 2013-12-11T01:48:18Z Comment https://crcns.org/forum/using-datasets/552430301/259739148 hi in the readme.pdf file, it is said that "To get the spike train data, use fget_spk.m to load the *.sa0 files".  but, I cannot use them, please tell me how to read the Spike Times whit *.sa0 format in matlab.  Thanks! No publisher meysam13659 2013-02-06T23:39:22Z Comment https://crcns.org/forum/using-datasets/552430300/278363842 I am trying to implement encoding model described in Kay et al. Identifying natural images from fMRI scan, Nature 2008. To validate the GWP (Gabor wavelet pyramid) model, the authors compared the retinotopic maps for both GWP model and Multifocal retinotopic model in supplementary figure 10. Which surface were voxel data assigned to? Was it the surface between grey-white matter?  If high resolution anatomical scan was needed to get this surface, would you shared the data in the webpage.    regards, dai. No publisher todaizhang 2013-01-07T18:11:34Z Comment https://crcns.org/forum/using-datasets/869956214/517784263 Hi, We are analysing data in the hc-3 dataset recorded during linear track behavioral task. Since spike sorting was performed across sessions of the same day, we thought about pooling sessions of the same day for our analysis. However, the position data does not directly match between sessions of the same day. For example, see the attached figure for position data from ec013.37 linear track sessions. Is there some rule by which to merge position data from different sessions on the same day? Thank you. No publisher stanni 2015-07-01T12:49:46Z Comment https://crcns.org/forum/using-datasets/869956213/920094792 Hi,   Could someone tell me how to extract the .whl file (hc-3 data set) into matlab?  It is not entirely apparent to me; I've been able to extract the .eeg binary file but not the .whl file. If you could tell me the call to do this, it would save me quite a bit of time.     S No publisher svijayan 2015-06-14T19:58:48Z Comment https://crcns.org/marketplace/data-sets-wanted/843629651/200461018 Dear all, I am looking for action potentials recorded intracellularly (when possible also simultaneously extracellularly) from a neuron in a sensory area while parametric or naturalistic sensory stimuli are presented. Current injections and electrical stimulation won't work for this analysis. Ideallz each stimulus should be presented several time. Does anyone have this kind of data and would be interested in sharing it? Best Regards, Cesare No publisher cesaremagri 2015-06-10T15:16:06Z Comment https://crcns.org/forum/using-datasets/37426736/152288364 Hi Mike, do you also have data including whole spikes? If yes would you be willing to share them in the database? Thanks a lot for sharing your beautiful data. Best Regards, Cesare   Previously Mike DeWeese wrote: Hi Cesare, Thanks for your interest in these data.  As described in the Methods section of DeWeese & Zador, J Neurophy 2004, I included QX-314, an intracellular sodium channel blocker, in the internal solution of my patch electrode for all recordings that didn't involve TTX application to the surface of the cortex (TTX, or tetrodotoxin, is an extracellular sodium channel blocker).  So one way or the other, I was pharmacologically preventing spiking in these neurons, though you might find a few spikes across the data set.  I hope this is helpful! Mike deweese@berkeley.edu   No publisher cesaremagri 2015-06-10T10:47:30Z Comment https://crcns.org/forum/using-datasets/285568554/345598693 Thank the lab of Loren Frank at UCSF for sharing the data hc-6.  Paper: Mattias P. Karlsson and Loren M. Frank, 2009, "Awake replay of remote experiences in the hippocampus". According the paper (Figure 1a), the shape of the W-shaped track has three arms of equal width. But the animal’s trajectory at the ends of three arms in W-shaped track seems to being broader. I am a bit confused whether the real track does have broader width at the end of the track or the animal prefer to walk in a broader area at the end of the track arm. Looking forward to replies. Best, John   No publisher xuzhiqin1990 2016-07-18T03:19:20Z Comment https://crcns.org/forum/using-datasets/794112990/208885184 Previously Jeremy Dobrzanski wrote: Update for others with similar issues: Moving forward under these assumptions: 1) Initial row (including '-1' no-data rows) of .whl file corresponds to timestamp zero for the spike times.  This assumption seems reasonable since enough of the directories have .whl files with time lengths that are longer then the last spike timestamp time and often the last spike timestamp is close-ish to the last position time.   Yes, you are right. please see my previous comment.   2) Green led is the head/body, while red led is the nose.  In reviewing the video files, the green led's position is more stable, while the red led leads movement. Yes, red led is anterior (nose) and green is posterior.     3) Confirming how the four float values correspond to the leds will require mapping various combinations of values to position in the video file.  Have not done this step yet but will post my results.  Guessing that it is GreenX GreenY RedX RedY.   .whl = (Anterior_X, Anterior_Y, Posterior_X, Posterior_Y). You can confirm this by plotting both Anterior and Posterior positions as a function of time. Animal usually walk forward (to anterior direction).     My final project is due Friday, hence using assumptions since there isn't a requirement for perfectly accurate results.  Imagine that real researchers would like confirmation of these questions, however.   Again, CRCNS is an excellent endeavor, cheers.   No publisher kmizuseki 2015-02-12T06:32:27Z Comment https://crcns.org/forum/using-datasets/794112990/208885183 Previously Jeremy Dobrzanski wrote: Looking at ec013.553 1) The description states that the sampling rate is 30 hertz but I can not find nor figure out how the positions register to the spike times.  Help here is much appreciated.   The original video is 30 Hz, but .whl file is re-sampled at 39.0625 Hz (1250 Hz/32 = 39.0625 Hz). The start and end of .whl  file are in register with the start and end of .eeg, .dat, and .res files.   2) The .whl file contains 4 floats.  I assume its x1 y1 x2 y2 where one of them is the red led and the other is the green led.  In any case, what is the format?  What is red/green and what is head/body? Yes, the 4 columns are (x1, y1, x2, y2). 1 = anterior (usually red LED), 2 = posterior (green LED).     Many thanks to this website and to the researchers who have the vision to share neural data.   No publisher kmizuseki 2015-02-12T06:31:12Z Comment https://crcns.org/forum/using-datasets/901659658/573346192 Hello, I just wanted to mention that we added raw data for this dataset (available for download via NERSC) in case it might be useful. We apologize for the delay. Best regards, Natalia Bilenko, Gallant Lab No publisher nbilenko 2015-09-29T21:08:37Z Comment https://crcns.org/forum/general/709838404/331683422 Not sure if this is the right place to ask this but is there any software that can automatically convert ephys data in other formats (blackrock, plexon, etc.) to nwb? My lab is interested in converting all of our data to nwb but would prefer not to write out own code to do so if we don't have to. No publisher gcwarner1 2016-02-22T16:11:47Z Comment https://crcns.org/forum/using-datasets/62983966/704785793 In log files in the 1D_white_noise folder, what are the parameters under the section "[TunningCurve]" describing? Why are there different directions given? Aren't the bars presented only in the preferred direction of each complex cell? Were the used to determine the tuning curves of the cells? Can they be ignored if we are just interested in the spike triggered averages? Also, for the purposes of data analysis, can each of the different files in 1D_white_noise be treated as a different "cell" since they provide information about the response of a cell to different stimuli? No publisher viveks 2016-02-15T18:50:51Z Comment https://crcns.org/forum/using-datasets/904521541/811984173 Hi Erick, The BOLD responses have not been deconvolved. In Nishimoto et al. 2011, the stimuli were convolved with hemodynamic response filters after the motion energy filters to incorporate the hemodynamic response function in model fitting. I would not suggest simply time shifting the stimuli, since the hemodynamic response function spans multiple TRs. You can find the details of the convolution of the stimuli with the hemodynamic response filters in the Supplemental Experimental Procedures section of Nishimoto et al, 2011 under the headings "Motion-Energy Encoding Model" and "Model Fitting". Hope this helps! Best, Natalia  No publisher nbilenko 2016-08-11T16:17:48Z Comment