http://gru.stanford.edu/ 2026-05-15T00:00:45-0700 http://gru.stanford.edu/ http://gru.stanford.edu/lib/tpl/gru/images/favicon.ico text/html 2022-08-30T13:40:22-0700 Anonymous (anonymous@undisclosed.example.com) http://gru.stanford.edu/doku.php/grupub/anatomy?rev=1661892022&do=diff GRU Anatomy Retinotopy Categotopy database Download the database from svn checkout http://gru.brain.riken.jp/svnpub/ganatret ganatret Subject ID Anatomy Surfaces Retinotopy ROIs unclear ROIs Comments Category localizer* Category ROIs Category comments text/html 2022-08-30T13:40:22-0700 Anonymous (anonymous@undisclosed.example.com) http://gru.stanford.edu/doku.php/grupub/categorylocalizerdetails?rev=1661892022&do=diff IT category localizer parameters Scanned 2013 or later Scan Coil: LifeServices (16 channel receive, 4 channel transmit) seqfil: epi_riken_ptx petable: epi76lin4k Matrix size: 64×64 FOV 19.2 x 19.2 cm2 Slice thickness: 3 mm, no gap Voxel size 3 x 3 x 3 mm3 text/html 2022-08-30T13:40:22-0700 Anonymous (anonymous@undisclosed.example.com) http://gru.stanford.edu/doku.php/grupub/crfaa_manuscript?rev=1661892022&do=diff Resubmission * [Rebuttal] * [Manuscript] * [Figures] * [Supp info] text/html 2022-08-30T13:40:22-0700 Anonymous (anonymous@undisclosed.example.com) http://gru.stanford.edu/doku.php/grupub/cuecon_s001?rev=1661892022&do=diff right loc4_rV1_1(14): nice curve, tiered. loc4_rV1_2(12): more patchy, but more or less the same response as the first roi... loc4_rV1(18): combination of loc1_rV1_1 and rV1_2. loc4_rV2d(17): ped1>ped2, but ped3>>ped12. loc4_rV3d(6): split. ped3 text/html 2022-08-30T13:40:22-0700 Anonymous (anonymous@undisclosed.example.com) http://gru.stanford.edu/doku.php/grupub/cuecon_s005?rev=1661892022&do=diff s005 Negative Responses area loc1 loc2 loc3 loc4 notes V1 in loc1_rV1_neg_in(11) V1 out V2 in loc1_rV2v_neg_in(26) loc2_lV2v_neg_in(23) loc3_lV2d_neg_in(11) hole cued>>>uncued V2 out loc1_rV2v_neg_out(21) loc2_lV2v_neg_out(25) text/html 2022-08-30T13:40:22-0700 Anonymous (anonymous@undisclosed.example.com) http://gru.stanford.edu/doku.php/grupub/cuecon_s006?rev=1661892022&do=diff s006 negs loc1 loc2 loc3 loc4 V1 loc1_rV1_NEG loc4_rV1_NEG V2 loc1_rV2v_NEG loc2_lV2v_NEG loc4_rV2d_NEG V3 V4 text/html 2022-08-30T13:40:22-0700 Anonymous (anonymous@undisclosed.example.com) http://gru.stanford.edu/doku.php/grupub/cuecon_s007?rev=1661892022&do=diff right hemisphere loc1_rV1(22): good loc1_rV2v(12): loc1_rV3v(37): loc1_rhV4(13): great! loc1_rV3A(10): pl. but ped2>ped3 loc4_rV1(22): same vox size as loc1, but checked that they were different rois!! loc4_rV2d(24): loc4_rV3d(7): loc4_rhV4(9): great! text/html 2022-08-30T13:40:22-0700 Anonymous (anonymous@undisclosed.example.com) http://gru.stanford.edu/doku.php/grupub/cuecon_s012?rev=1661892022&do=diff s012 Negative ROIs loc1 loc2 loc3 loc4 V1 loc1_rV1_NEG( ) loc2_lV1_NEG( ) loc3_lV1_NEG( ) loc4_rV1_NEG( ) split up text/html 2022-08-30T13:40:22-0700 Anonymous (anonymous@undisclosed.example.com) http://gru.stanford.edu/doku.php/grupub/cuecon_s016?rev=1661892022&do=diff s016 each roi right side left side concats [] pedOnly(1) V1: {15,1}[ok ? ? ok].rOK.l?.all? V2: {15,1}[ok ? ? ok].rOK.l?.all? V3: {15,1}[ok ? ? ok].rOK.l?.all? V3A: {15,1}[noTier ? ? noTier].rOK,noTier.l?.all? hV4: {15,1}[tiers ? ? ok...].rOK, but tiering flipped.l?.all? text/html 2022-08-30T13:40:22-0700 Anonymous (anonymous@undisclosed.example.com) http://gru.stanford.edu/doku.php/grupub/cueconanalysisnotes?rev=1661892022&do=diff Psychophysical task The task should be run outside and inside the scanner. A complete staircase ~30 trials for the twoCues trials and ~90 trials for the oneCue and fourCues conditions. Outside the scanner, this is about 90 minutes per staircase. Inside the scanner, it will be about two days of data (15-20runs) per staircase. text/html 2022-08-30T13:40:22-0700 Anonymous (anonymous@undisclosed.example.com) http://gru.stanford.edu/doku.php/grupub/dofmrigru?rev=1661892022&do=diff Overview The whole pipeline from fid to MLR is done mostly automatically with a matlab script. There are the steps you need to do: * Run dofmrigru to create directories and move files This part creates a few directories: Etc, Pre, Pre/Aux, Pre/Mask. Fid files/directories are placed in text/html 2022-08-30T13:40:22-0700 Anonymous (anonymous@undisclosed.example.com) http://gru.stanford.edu/doku.php/grupub/dofmrigrutsense?rev=1661892022&do=diff Overview The whole pipeline from fid to MLR is done mostly automatically with a matlab script. There are the steps you need to do: * Run dofmrigru to create directories and move files This part creates a few directories: Etc, Pre, Pre/Aux, Pre/Mask. Fid files/directories are placed in text/html 2025-08-28T11:00:32-0700 Anonymous (anonymous@undisclosed.example.com) http://gru.stanford.edu/doku.php/grupub/eyelink?rev=1756404032&do=diff Eyelink libraries You can download eyelink libraries from SR-Research. You will need to register for a free account with them before being able to access the support pages. The manual is here. Follow the download instructions here. The following worked for me: python3 -m pip install --index-url=https://pypi.sr-support.com sr-research-pylink text/html 2022-08-30T13:40:22-0700 Anonymous (anonymous@undisclosed.example.com) http://gru.stanford.edu/doku.php/grupub/eyelinkmri?rev=1661892022&do=diff Eyelink camera mount Some pictures of the mount for the Eyelink camera in the MRI suite at RIKEN Brain Science Institute. [Complete design drawings] Mirror mount Some pictures of the mirror setup for the Eyelink eyetracker system in the MRI suite at RIKEN Brain Science Institute. text/html 2022-08-30T13:40:22-0700 Anonymous (anonymous@undisclosed.example.com) http://gru.stanford.edu/doku.php/grupub/gruanatnotes?rev=1661892022&do=diff s006 110524: Found that retinotopy's session anatomy had not been scaled (even though there was a file called anat_preGradCoil inside the Anatomy dir). This probably explains why rois looked jagged on the flatmap. In Feb '11, s006's anatomy was updated to have a better segmentation: hum3d_freesurfer, hum3d_freesurfer/surfRelax. However, since the old anatomy (s006_mprage_pp.hdr, no hum3d in the title) may still be used by others, the links were left intact. The new anatomies were just added … text/html 2022-08-30T13:40:22-0700 Anonymous (anonymous@undisclosed.example.com) http://gru.stanford.edu/doku.php/grupub/grubin?rev=1661892022&do=diff Accessing GRU from home grubin shell scripts You can download some shell scripts that make it easy to do things like screen share and copy files from gru computers from home: svn checkout http://gru.stanford.edu/svn/grubin grubin Add the following to your shell path (e.g. in your .cshrc or .cshrc.mine file): text/html 2022-08-30T13:40:22-0700 Anonymous (anonymous@undisclosed.example.com) http://gru.stanford.edu/doku.php/grupub/informed_consent?rev=1661892022&do=diff Informed consent For all experiments, fMRI and psychophysics, you need to have the informed consent from subject. First, you need to explain about subject rights and possible matters described in the experiment explanation. NOTE THAT EVERYTHING WRITTEN IN THE FORM SHOULD BE FULLY UNDERSTOOD BY SUBJECT. text/html 2022-08-30T13:40:22-0700 Anonymous (anonymous@undisclosed.example.com) http://gru.stanford.edu/doku.php/grupub/lcd?rev=1661892022&do=diff SONY PVM-L2300 Tested on 5/15/2012. Screen size changes by the resolutions. Timing test looks problematic. PC:DVI-D -> DVI-D Spectrum of RGB KW CMY Gamma for each color channel measured separately: }} Associated xy values: Gray levels calibration: text/html 2022-08-30T13:40:22-0700 Anonymous (anonymous@undisclosed.example.com) http://gru.stanford.edu/doku.php/grupub/lectures?rev=1661892022&do=diff Lectures Note that if you want to access these slides from outside of RIKEN you will be prompted to login: Name: gru Password: gru Lecture topic Who Date Slides Series Faces Topi March 19, 2013 Slides Informal lecture Informal lecture on decoding text/html 2022-08-30T13:40:22-0700 Anonymous (anonymous@undisclosed.example.com) http://gru.stanford.edu/doku.php/grupub/mpts?rev=1661892022&do=diff We have a tactile stimulator from Dancer Design. note that we needed to have a powered USB extension (not only bass power cable) for RIKEN's setup. It may be because of about 20 meters extension we needed. Below is warning to use the equipment. mPTS / Plectrum instructions text/html 2022-08-30T13:40:22-0700 Anonymous (anonymous@undisclosed.example.com) http://gru.stanford.edu/doku.php/grupub/postgradcoilscalingfactor?rev=1661892022&do=diff Scaling your pre-grad coil replacement images Images taken since the gradient coil replacement, November 2009 are slightly larger than images taken before the gradient coil replacement. Based on measurements taken on a phantom, post-grad coil replacement images were determined to be closer to actual scale - so we recommend you scale our pre-grad coil replacement images to fit the new calibration. text/html 2022-08-30T13:40:22-0700 Anonymous (anonymous@undisclosed.example.com) http://gru.stanford.edu/doku.php/grupub/projectors?rev=1661892022&do=diff Projectors Conclusion was that JVC and Panasonic had similar TF response and 10-bit luminance steps, but that the Panasonic had slightly better color gamut and color linearity as well as more input types and probably higher overall luminance output. Sanyo had poor TF response. Sony does not have 10 bit luminance. text/html 2022-08-30T13:40:22-0700 Anonymous (anonymous@undisclosed.example.com) http://gru.stanford.edu/doku.php/grupub/retinotopytutorial?rev=1661892022&do=diff Retinotopy tutorial Place: BSI East Building 1F Seminar Room Time: June 8th and 9th, 4:00-5:00 PM The purpose of this tutorial is to teach you how to identify visual areas in your subjects using a standard traveling-wave retinotopic mapping experiment. The tutorial will focus on the use of text/html 2022-08-30T13:40:22-0700 Anonymous (anonymous@undisclosed.example.com) http://gru.stanford.edu/doku.php/grupub/samscanhistory?rev=1661892022&do=diff Sam Super Scan History Scan ID Scan Type Notes s00620100113 Venogram Pilot Various voxel sizes (1,.75,.5) - 1 is suitable s00620100203 VTDots First run of VTdots - localizer and analysis poor - needs further improvement s00720100208 Retinotopy text/html 2022-08-30T13:40:22-0700 Anonymous (anonymous@undisclosed.example.com) http://gru.stanford.edu/doku.php/grupub/samscribbles?rev=1661892022&do=diff Sam's Scribbles At some point I would like to streamline all commands into one comprehensive script. Analysis Commands Generating ahl gmpva and pva classification performance by voxel number: samnewclassdefault (samneclassdefault9 for s007) Batch resampling and analyzing data can be run from: samBatchResAnal (look inside this script for subscripts used). text/html 2022-08-30T13:40:22-0700 Anonymous (anonymous@undisclosed.example.com) http://gru.stanford.edu/doku.php/grupub/scanhistory?rev=1661892022&do=diff Yuko Fabulicious Scan History Scan ID Scan Type Notes Scaled? s00120090618 3D Anatomy HiRes 20jan10 s00220090622 3D Anatomy HiRes s00120090622 Pilot Retinotopy tested different tr, different te times s00120090706 Full Retinotopy used optimal te = t2* text/html 2022-08-30T13:40:22-0700 Anonymous (anonymous@undisclosed.example.com) http://gru.stanford.edu/doku.php/grupub/shareddrive?rev=1661892022&do=diff Shared Directory, GRU We decided to have a Freesurfer shared directory on our server. To connect it from your MAC, open “Finder” and select “Go” from the top menu then, select “connect to server”. You will see following window. type text/html 2022-08-30T13:40:22-0700 Anonymous (anonymous@undisclosed.example.com) http://gru.stanford.edu/doku.php/grupub/svn?rev=1661892022&do=diff SVN getting started The complete reference for SVN is the svn red book. Basics SVN is used from a terminal program and allows you to checkout a repository of code for use and editing locally on your machine. If you prefer a GUI you might try Cornerstone. If you are simply using a repository without making any changes, you should at least be familiar with using the commands: checkout and update. text/html 2022-08-30T13:40:22-0700 Anonymous (anonymous@undisclosed.example.com) http://gru.stanford.edu/doku.php/grupub/yukocv?rev=1661892022&do=diff Yuko Hara Technical Staff, Gardner Research Unit Tel: (048) 462-1111 x7069 Email: yuko_hara (at) brain.riken.jp Languages: English, Japanese, French (conversational) text/html 2022-08-30T13:40:22-0700 Anonymous (anonymous@undisclosed.example.com) http://gru.stanford.edu/doku.php/grupub/yukoscribbles?rev=1661892022&do=diff Yuko's Scribbles Computational Neuroscience Seminars: <http://pdl.brain.riken.jp/staff/dalex/computational_neuroscience_seminar/> Yuko Hara Toshima-ku Kanamecho 1-15-3 Frais Kanamecho #402, Tokyo, JAPAN 171-0043 c/o RIKEN Brain Science Institute 2-1 Hirosawa, Wako-shi, Saitama JAPAN 351-0198 Tel: +81 (048) 462-1111 x7069 tel: +81 (90) 6106-1358, yuko.hara@brain.riken.jp