https://crcns.org These are the search results for the query, showing results 541 to 555. https://crcns.org/forum/using-datasets/883011296/329540345 I am going through the data from HC-1 and they are really nice. In particular, I would be interested in spontaneous activity data. Is there any session in HC-1 during which the intracellular signals have been recorded without any type of input current and for which the firing rate is still good?   Many thanks in advance! Cesare No publisher cesaremagri 2015-02-10T11:32:32Z Comment https://crcns.org/forum/using-datasets/941521493/973448517 Hi,  I would like to use the EstimatedResponses.mat for analysis. Variable dataTrn is 1,750 x ~25,000 matrix, where 25,000 is the number of voxels. I would like to know the space location of these voxels. How to do it? For example, I use following code to read a nii file in Python: import nibabel as nib img = nib . load ( 'data/Sub1_Ses1_Run1_Trn.nii.gz' ) img_np = img . get_data () print img_np . shape   (64, 64, 18, 672)   In above array img_np(64,64,18), what are the index of 25,000 voxels in dataTrn? I need these space information in my current work.   Thanks Jiancheng No publisher JianchengSun 2014-09-21T22:07:03Z Comment https://crcns.org/forum/using-datasets/601153057/237931630 Hello, In the description of the hc-2 data it states that it contains "The coordinate and direction of the rats head during the experiment".  I looked at the data and it contained (x,y) values for the two LEDS. However, I don't understand how this can give me head direction relative to the body without having a third LED. Am I missing something? Thank you, Dan Howarth No publisher dhowarth 2011-10-14T22:37:34Z Comment https://crcns.org/forum/using-datasets/601153056/413298727 Hello, There doesn't seem to be the necessary data for generating the orientation and spatial frequency tuning plots for the cells recorded with the 2D stimuli. Based on Jon Touryan's paper it seems these tuning curves were measured, so I was hoping to get that data for comparison purposes. Thanks! Michael Oliver No publisher mdoliver 2011-09-26T17:39:11Z Comment https://crcns.org/forum/using-datasets/62983963/629109012 Hi Johannes, Normal 0 false false false EN-US JA X-NONE /* Style Definitions */ table.MsoNormalTable {mso-style-name:"Table Normal"; mso-tstyle-rowband-size:0; mso-tstyle-colband-size:0; mso-style-noshow:yes; mso-style-priority:99; mso-style-parent:""; mso-padding-alt:0cm 5.4pt 0cm 5.4pt; mso-para-margin-top:0cm; mso-para-margin-right:0cm; mso-para-margin-bottom:10.0pt; mso-para-margin-left:0cm; line-height:115%; mso-pagination:widow-orphan; font-size:11.0pt; font-family:"Calibri","sans-serif"; mso-ascii-font-family:Calibri; mso-ascii-theme-font:minor-latin; mso-hansi-font-family:Calibri; mso-hansi-theme-font:minor-latin;} Thanks a lot for your interest in our data sets. The sampling rate of the digital video camera was 30Hz. We extracted the positions of LEDs from the video movie, synchronized the video movie and electrophysiological data (.eeg file), and generated .whl files by interpolate the LEDs positions at 1/32 of the sampling rate of the .eeg file. In most cases, the sampling rate of .eeg files was 1250Hz, therefore the sampling rate of the .whl files was 1250/32 = 39.625 Hz. Thanks. Kenji Mizuseki   Previously Johannes Zirkelbach wrote: Hi everyone! I have a question regarding the rate at which the two LED positions of the hc-2 data set (in the *.whl files) are sampled: - In the data description it says: 39.06 Hz - In the supplementary material of the related publication ( http://www.cell.com/cms/attachment/602520/4755694/mmc1.pdf ) it says: "For tracking the position of the animal,two small light-emitting diodes (10-15 cm separation) mounted above the headstage were recorded by a digital video camera and sampled at 30 Hz" Does anybody know, what the actual rate is? Thanks! Johannes   No publisher kmizuseki 2016-01-20T00:22:44Z Comment https://crcns.org/forum/using-datasets/871652035/709371151 Dear Contributor, I have been analyzing dataset v2-1 and found incompleteness in the dataset.   1) Loading data for r0336 fails. 2) For many cells, data for grating stimuli are missing. 3) For many cells, data for stimulus presentations with 10 or more repetitions are missing.   It would help me if you could make data as complete as possible.   Best regards,   Haruo No publisher hahosoya 2013-09-19T02:35:38Z Comment https://crcns.org/forum/using-datasets/826607086/181758359 Three questions: 1. How can I project the fMRI data to surface as shown in the paper: Reconstructing Visual Experiences from Brain Activity Evoked by Natural Movies? 2. Some regions of inter, ex: FFA, were not provided in the indexing file. Is it because these areas were not included? 3. Are the three subjects' dataset in the MNI space? Because when I check the files, it seems like they were not aligned consistently.   Thank you very much!   Junxing Shi No publisher jshi 2015-05-24T17:08:35Z Comment https://crcns.org/forum/using-datasets/826607085/671085125 1) Are the spike times in filename.res.N expressed as multiples of the 20kHz sampling rate, so that time in seconds = (spike time in file) / (20e3)? Yes 2) Do the cluster indices in the various cluster files for a given session refer to the same clusters? So for example would cluster 2 in Mouse12-120806.clu.1 refer to the same cell as cluster 2 in Mouse12-120806.clu.2? No. Mouse12-120806.clu.1 refers to the identity of cells recorded on the first shank of the silicon probe, for the entire session. Mouse12-120806.clu.2 refers to shank #2. The number of lines in the the clu files is the same as in the res files plus on (the first value is the total number of clusters). 3) In the states files (e.g., Mouse12-120806.states.REM, Mouse12-120806.states.SWS, Mouse12-120806.Wake) are the numbers also times expressed in terms of the 20 kHz sampling rate? No, sorry, it's a tiny difference with the hc-3 datasets. It's in seconds! 4) Finally, I gather the .whl file contains the LED coordinates in the format (x1, y1, x2, y2):  a. Is this still at a sample rate of 39.06 Hz, so that the nth sample is at time n/39.06? b. Is it synced with the spike times in any other way? The Methods mention that there's a random misalignment to start with. Would this affect matching spikes to head position? c. Do you calculate the head direction as the angle of the vector pointing from the 2nd to the 1st LED? To address this question, the following two archive files are added to the data set: PosFiles.tar AngFiles.tar The "pos" files are smoothed (i.e. interpolated) positions of the animals in centimeters (the way we used the positions for analysis), still sampled at 39.062 Hz (which is not just a magic number btw: it's EEG sampling rate – 1250 Hz - divided by 32 so that the sampling of the position is an integer number of LFP samples). The absolute time is the same as for spikes, no need to realign anything. HOWEVER, as you said, there is a tiny jitter (up to, maybe sometimes, 100 msec) between spikes and video. This jitter is constant across an entire session (it was a problem with the trigger starting data recording that we discovered once all the data were recorded...). This jitter seems to be always positive (the spike times always lag behind the video). So there is one analysis that can't be done: it's the anticipatory properties of HD cells in the thalamus that was reported by Blair and others. The second tar file (AngFiles.tar) contains "ang" files: these are the orientation of the head in radians (between 0 and 2 pi), in the same reference frame as the (X,Y) positions given by pos files (i.e. at 0 rad, the animal points right). In both files (pos and ang), -1 values mean that the detection failed.   No publisher apeyrache 2015-05-13T14:45:20Z Comment https://crcns.org/forum/using-datasets/708216874/897932104 Thanks Jeff and Anton! I was able to convert the data, but I wanted to just add a few follow up notes here for other forum readers. Regarding the LoadBinary call you suggested: data = LoadBinary('./buzsaki_data/d5331/d533101.dat', 6, 6); The third argument is the total number of channels, nChannels, which is not 6 - I get an error if I add in that third argument.  The second argument is the specific channel I want, #6, so only calling the function with 2 arguments works just fine and is quick. I tried the LoadPar function to check on the par values as you suggested. Regarding the par file comments: sampling rate should be indicated in par file Indeed, it was and it matched the value in the README.txt, 10000.  However, not all the values in the .xml Par file made sense: SampleTime is listed as 100, but the data vector covers 240 s.  Voltage Range is listed as 20 and Amplification as 1000, but in the dataset description file the "voltage amplication" is listed as 50. That makes sense if the voltage amplification is defined as amplification/voltage range, but I don't know the relation between the terms in the Par file "Voltage Range", "Amplification" and the terms in your post "voltage amplification", "gain." The par file also gives nBits = 16.  However, when I used the conversion listed above for nBits = 16: Vm = data./2^15*200; I get a voltage trace that is not realistic.  I used the conversion for nBits = 12: Vm = (data-Par.Offset)./2^11*200; and got a realistic trace (meaning AP threshold, AP amplitude, and resting membrane potential are realistic/within usual physiological range). No publisher majacase 2012-04-19T23:05:47Z Comment https://crcns.org/forum/using-datasets/708216874/158243658 Hello, I am using the MATLAB scripts to view the hc-1 dataset and want to understand the output units of the LoadBinary function.  I downloaded the data for d533101 and called the loadBinary function to read it into MATLAB: function [data OrigIndex]= LoadBinary(FileName, Channels, varargin) I only wanted the intracellular trace which the README.txt says is the 6th channel, so my call looked like: [data OrigIndex]= LoadBinary('./buzsaki_data/d5331/d533101.dat', 6); I received an error because the function 'datatypesize' was undefined; I created one myself that returns the size in bytes of the data type passed in as a string. The resulting output resembles an intracellular trace, but I'm unsure of the units. For the x-axis, I assume it is just sample number; the README.txt gives the sampling rate (10 kHz) so I can get the time easily.  For the y-axis, the y values range from 1114 to 2193. I don't know what those values mean nor how to convert them into mV? No publisher majacase 2012-04-17T18:11:08Z Comment https://crcns.org/forum/using-datasets/931502129/965799389 The spike timestamps are in microseconds, data format is binary 64-bit unsigned integers, as described on pg.9 of the user guide. You can read them in Matlab with the following two lines: fid = fopen(filename.spk) a = fread(fid, 'uint64') good luck! Tim. No publisher blanche 2011-06-01T17:11:58Z Comment https://crcns.org/forum/using-datasets/440665814/751828530 Hello, I have downloaded the ac-1 data set and opened it in Matlab, but am unsure what the various numbers refer to.  I assume the "trace" matrix in "response" is where the principal data is, but I don't know what the numbers in "trace" mean or why they are all negative. Any clarification would be greatly appreciated. Thank you very much. No publisher ndepw 2012-06-29T19:42:30Z Comment https://crcns.org/forum/using-datasets/996335119/552945187 Hi community :) My name is Ilya, I am a PhD student at the Computational Neuroscience lab in University of Tartu and I have a few questions about the PVC-2 dataset. I am interested in the part of the dataset related to the natural images (<pre>crcns-pvc2/2D_noise_natural</pre>) and I have a trouble understanding the structure of the data​: 1) In the articles it is mentioned that "three distinct natural ensembles were used in this study", but there are 8 <pre>Equalpower*</pre> files inside the <pre>Stimulus_Files</pre>. Why is that? What letters A,B,C and numbers 1,2,3 mean? Are these different sequences of images or same images but in different order? 2) Inside the <pre>Spike_and_Log_Files</pre> folder we have folders with names like <pre>030605.A.b02</pre>. What does the <pre>b02</pre> part mean? Is it the code for the test subject (cat)? Or it is an ID of a neuron? 3) Inside the folder <pre>030605.A.b02</pre> there are files with names <pre>030605.A.b02cequalpower_B3.sa0</pre>, <pre>030605.A.b02dequalpower_B3.sa0</pre>, <pre>030605.A.b02eequalpower_B3.sa0</pre>. What those letters <b>c, d, e</b> indicate? 4) The description of the data says that the data was recorded from 60 channels. But for every <pre>.sa0</pre> file when I load it using <pre>fget_hdr</pre> the <pre>hdr.DataInfo.Channel</pre> is always 0. What is the correct way to interpret this number?   No publisher IlyaKuzovkin 2014-11-10T13:32:52Z Comment https://crcns.org/marketplace/data-sets-wanted/395699066/978472307 I think the pvc-2 data set has spiking responses in pvc to oriented moving stimuli.  It includes software that allows plotting responses vs. orientation (tuning curves).   No publisher jteeters 2015-03-19T17:02:55Z Comment https://crcns.org/forum/using-datasets/115877553/941335025 Hi Bryan, You are right.  Sessions in directory "gor01", "vvp01", "i01_maze15", "j01_maze04" and "j01_maze05" are missing the "whl" files.  Most of these missing files have been located and have now been added to the data set in file "additional_whl_files.tar.gz" which is in the "docs" directory of the data set.   The following sessions are still missing whl files:   directory         session                         behavior ec014.n329    2007-3-29_16-06-46  ZigZag i01_maze15    i01_maze15_MS.001   bigSquare j01_maze04    j01_maze04_M.001    bigSquare j01_maze04    j01_maze04_M.003    bigSquare j01_maze04    j01_maze04_M.004    bigSquare j01_maze05    j01_maze05_M.001    bigSquare   If additional whl files are located, they will be added to the "docs/additional_whl_files.tar.gz" file.   Thanks for pointing out this omission.  And thanks to Kenji Mizuseki for locating the files that have been added.   Best regards, Jeff       No publisher admin 2015-03-04T02:11:31Z Comment