Freesurfer April 2008

freesurfer@nmr.mgh.harvard.edu

67 participants
102 discussions

mri_volcluster --ERROR: you must specify a pos or neg sign with --fwhm
by PKUNWAR＠nmr.mgh.harvard.edu 26 Aug '09

26 Aug '09

Hi all, I was going through the FSFAST TUTORIAL from wiki( https://surfer.nmr.mgh.harvard.edu/fswiki/FsFastTutorial?action=highlight&v…) I got the follwoing error during mri_volcluster, "NOT Adjusting threshold for 1-tailed test ERROR: you must specify a pos or neg sign with --fwhm" I have fwhm.dat file with 4. something vlaue. Command used, [galen:odd-v-0] (nmr-std-env) mri_volcluster --in tal.rfx.osgm/osgm/sig.nii --thmin 2 --fwhmdat tal.rfx.osgm/fwhm.dat --cwpvalthresh 0.1 --mask tal.rfx.osgm/mask.nii --fsaverage --sum tal.rfx.osgm/osgm/cluster.sum --cwsig tal.rfx.osgm/osgm/cwsig.cluster.nii --out tal.rfx.osgm/osgm/sig.cluster.nii --ocn tal.rfx.osgm/osgm/ocn.cluster.nii without --fwhmdat flag, it gave me another error "ERROR: need csd with --cwsig" will appreciate for help thanks pratap ----------------------------------- FREESURFER_HOME: /usr/local/freesurfer/stable4 Build stamp: freesurfer-Linux-centos4_x86_64-stable-v4.0.1-20070927 RedHat release: CentOS release 4.4 (Final) Kernel info: Linux 2.6.9-42.0.3.ELsmp x86_64 NMR Center info (/space/freesurfer exists): machine: galen SUBJECTS_DIR: /autofs/space/galen_003/users/carl/Tutorial/buckner_data/FsFastTutorialData/FSFTUTDIR/subjects PWD: /space/galen/3/users/carl/Tutorial/buckner_data/FsFastTutorialData/FSFTUTDIR/fb1-preproc-study/group-analysis-tut/sm-gamma-fwhm5/odd-v-0

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design matrix : inter-run effetcs
by Andersson Frederic 02 Dec '08

02 Dec '08

Hi, Computing individual fMRI analysis (several runs) and looking at the design matrix (X.mat), I saw that only one regressor represents each condition. I was expecting that the number of regressors concerning a condition would be the number of runs (as SPM). There are "inter-run effect" regressors but is this better if I affect a different value for each of run and each condition (see examples below). Other question concerning design matrix : only 3 movement parameters included in the design matrix. Why 3 rather than the 6 computed during movement correction? Concerning inter-run effects and movement parameters, is there any advantage of reducing the number of regressors but having a less ideal model? >>> 1 condition = 1regressor 0 = rest 1=conditionA 2=conditionB Pardagim files : RUN#1 RUN#2 RUN#3 0 0 0 0 0 0 3 0 3 0 3 0 6 0 6 0 6 0 9 0 9 0 9 0 12 0 12 0 12 0 15 1 15 1 15 1 18 1 18 1 18 1 21 1 21 1 21 1 24 1 24 1 24 1 27 1 27 1 27 1 30 0 30 0 30 0 33 0 33 0 33 0 36 0 36 0 36 0 39 0 39 0 39 0 42 2 42 2 42 2 45 2 45 2 45 2 48 2 48 2 48 2 51 2 51 2 51 2 54 2 54 2 54 2 57 0 57 0 57 0 >>> 1 condition = 1regressor / run 0=rest 1=conditionA run#1 2=conditionB run#1 3=conditionA run#2 4=conditionB run#2 5=conditionA run#3 6=conditionB run#3 Pardagim files : RUN#1 RUN#2 RUN#3 0 0 0 0 0 0 3 0 3 0 3 0 6 0 6 0 6 0 9 0 9 0 9 0 12 0 12 0 12 0 15 1 15 3 15 5 18 1 18 3 18 5 21 1 21 3 21 5 24 1 24 3 24 5 27 1 27 3 27 5 30 0 30 0 30 0 33 0 33 0 33 0 36 0 36 0 36 0 39 0 39 0 39 0 42 2 42 4 42 6 45 2 45 4 45 6 48 2 48 4 48 6 51 2 51 4 51 6 54 2 54 4 54 6 57 0 57 0 57 0 Frédéric ANDERSSON.

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Checking for spikes
by Brittany Cassidy 06 Aug '08

06 Aug '08

Hello all, I was looking for a general way to check for spiking from Freesurfer or the FSFast stream. Any ideas are appreciated. Thanks! -Brittany

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IO with freesurfer files (.mgh in particular) from Python
by Yaroslav Halchenko 21 Jul '08

21 Jul '08

Does anyone know any handy module to at least read in .mgh files from Python? Or should I simply try mri_convert them into .minc and use netcdf module within python? Thanks in advance for the ideas! -- Yaroslav Halchenko Research Assistant, Psychology Department, Rutgers-Newark Student Ph.D. @ CS Dept. NJIT Office: (973) 353-5440x263 | FWD: 82823 | Fax: (973) 353-1171 101 Warren Str, Smith Hall, Rm 4-105, Newark NJ 07102 WWW: http://www.linkedin.com/in/yarik

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documentation of the Freesurfer output and directory structure?
by Turner, Jessica 02 Jul '08

02 Jul '08

Hi experts-I have to document for some non-Freesurfer users what is in all the Freesurfer 3.05 subdirectories from an analysis. We have come up with a lot of it from the Wiki pages and tutorials, but there are some things that still aren't clear (what exactly is the bem directory for? What exactly is the mri_nu_correct.mni.log file? Etc.). Is it laid out clearly somewhere? I've seen the pages about which files are created by what process, etc. and it seems like it should say somewhere what these directories and files really are, I'm just missing it. Thanks, Jess ------------------------ Jessica Turner, Ph.D. Project Manager, FBIRN (www.nbirn.net) Department of Psychiatry and Human Behavior University of California, Irvine Phone: (949) 824-3331 Fax: (949) 824-3324

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cortical measures - normalised?
by Narly A Golestani 21 Jun '08

21 Jun '08

Dear all, Am I correct in thinking that the measures of cortical volume, area, and thickness, as well as subcortical volumes obtained after running the reconall pipeline (and found in the 'aparc' and 'aseg' files, respectively) are native ones? Or are they based on normalised brains, thus 'controlling' for overall brain volume differences? thanks, Narly.

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Question: can't display retinotopy fieldsign data
by Kai Hwang 13 May '08

13 May '08

Hello, I'm trying to use freesurfer to map the visual cortex and get region borders of V1, V2.. etc. We used a conventional rotating/expanding wedge paradigm, and I followed the steps described in FsFastIndividualRetinotopy Analysis (https://surfer.nmr.mgh.harvard.edu/fswiki/FsFastIndividualRetinotopyAnalysis) <https://surfer.nmr.mgh.harvard.edu/fswiki/FsFastIndividualRetinotopyAnalysis> Everything worked fine till the last step, I can't view the results with surf-sess. After I execute the command surf-sess, first a flatten cortex appeared, then the view screen turned black and nothing showed up. Here is what I have in the terminal window hwang@kaih:~/Subjects> surf-sess -s Pilot1 -a VM_retinotopy -retinotopy fieldsign -flat grep: /home/hwang/Subjects/Pilot1/session.info: No such file or directory ----------------------------------------------------------------- surf-sess logfile is /home/hwang/Subjects/log/surf-sess.VM_retinotopy.fs.log ----------------------------------------------------------------- ------------------------------------------------------ ------------------------------------------------------ Session: Pilot1 ---- ------ lh hemisphere ------ /home/hwang/Subjects/Pilot1/bold/VM_retinotopy ---------------------------------------------------------- /home/hwang/Subjects/Pilot1/bold/VM_retinotopy tksurfer -Pilot1 lh inflated -tcl /usr/local/freesurfer/lib/tcl/fs-flat.tcl ---------------------------------------------------------- Loading /usr/local/freesurfer/surface_labels.txt surfer: current subjects dir: /home/hwang/Subjects surfer: not in "scripts" dir ==> using cwd for session root surfer: session root data dir ($session) set to: surfer: /home/hwang/Subjects/Pilot1/bold/VM_retinotopy surfer: Reading header info from /home/hwang/Subjects/Pilot1/mri/T1.mgz surfer: vertices=149915, faces=299826 can't find talairach file '/home/hwang/Subjects/Pilot1/surf/../mri/orig/COR-.info/../transforms/talairach.xfm' surfer: ### redraw failed: no gl window open Reading /usr/local/freesurfer/lib/tcl/tkm_common.tcl Reading /usr/local/freesurfer/lib/tcl/tkm_wrappers.tcl Reading /usr/local/freesurfer/lib/tcl/fsgdfPlot.tcl Reading /usr/local/freesurfer/lib/tcl/tkUtils.tcl Successfully parsed tksurfer.tcl reading white matter vertex locations... tksurfer: fs-flat.tcl: set flags setdefpatchview: ### position.tcl for Pilot1 does not exist setdefpatchview: ### setting flatzrot to 90 (default) setdefpatchview: ### setting flatscale to 1.0 (default) setdefpatchview: ### setting flatxtrans to 0.0 (default) setdefpatchview: ### setting flatytrans to 0.0 (default) readenv.tcl: ==> read global setenv vars readenv: set invphaseflag 0 readenv: set fm fieldsign/fieldsignmask-lh readenv: set angle_offset 0 readenv: set dir /home/hwang/Subjects/Pilot1/bold/VM_retinotopy readenv: set truncphaseflag 0 readenv: set offset 0.4 readenv: set fmid 0.8 readenv: set fs fieldsign/fieldsign-lh readenv: set lat readenv: set fthresh 0.4 readenv: set complexname -imag readenv: set realname -real readenv: set eccendir eccen readenv: set floatstem map readenv: set hemi lh readenv: set rgbname map readenv: set use_vertex_arrays 0 readenv: set nosave 0 readenv: set polardir polar readenv: set noexit readenv: set curv lh.curv readenv: set patchname occip.patch.flat readenv: set fslope 1.3 readenv: set colscale 0 readenv: set mc () { . /usr/share/mc/bin/mc-wrapper.sh } readenv: set smoothsteps 2 readenv: set revpolarflag 0 readenv.tcl: ==> read rgbname-specific setenv vars % tksurfer: fs-flat.tcl: read curvature surfer: single buffered window surfer: using interface /usr/local/freesurfer/lib/tcl/tksurfer.tcl tksurfer: run tcl script: /usr/local/freesurfer/lib/tcl/fs-flat.tcl surfer: curvature read: min=-1.677210 max=1.267429 % tksurfer: fs-flat.tcl: read patch tksurfer: fs-flat.tcl: read fieldsign tksurfer: fs-flat.tcl: read fieldsign mask surfer: read_fieldsign(fieldsign/fieldsign-lh) surfer: mris->nvertices = 149915, vnum = 149915 surfer: read_fsmask(fieldsign/fieldsignmask-lh) % tksurfer: fs-flat.tcl: scale, position brain surfer: ### GL window already open: can't open second % tksurfer: fs-flat.tcl: save rgb's tksurfer: fs-flat.tcl: save rgb surfer: dipscale=0.000000 % tksurfer: fs-flat.tcl: nosave setenv'd => nothing will be saved invalid command name "dontsave_rgb_named"% surfer: dipscale=0.000000 % surfer: dipscale=0.000000 any suggestion how to make surf-sess work? Thanks! Kai

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--label2path option in mri_path2label
by Michael Harms 06 May '08

06 May '08

Hello, I'm trying to get the vertices of the border/edge/boundary (whatever you want to call it) of a contiguous, closed ROI/label on the surface. I've noticed an option "--label2path" in 'mri_path2label' (FS v4.0.2) that "will treat input as a label and output a path". When I tried this, I got the following output: ----------------- $ mri_path2label --label2path rh.middletemporal.label test.path INFO: Converting rh.middletemporal.label INFO: to test.path INFO: Label to path No encoded paths found in label file ------------------ So, my question is whether the "--label2path" option is supported, and if so, how is it intended to be used? (The output message implies that the path already has to be "encoded" somehow in the label file itself?) thanks, Mike H. -- Michael Harms, Ph.D. -------------------------------------------------------------------- Conte Center for the Neuroscience of Mental Disorders Washington University School of Medicine Department of Psychiatry, Box 8134 Renard Hospital, Room 6615 Tel: 314-747-6173 660 South Euclid Ave. Fax: 314-747-2182 St. Louis, MO 63110 Email: mharms(a)wustl.edu --------------------------------------------------------------------

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thickness file data structure
by Yaroslav Halchenko 03 May '08

03 May '08

Dear Freesurfers, First thanks everyone who helped me out with reading-in .mgh data from within Python (especial thanks to Krish). Now I wonder what actually I got ;-) and please pardon my ignorance When I read in thickness file in I get an array of (23406, 7, 58) dimensionality, where 58 makes sense to me since we have 58 subjects. P.S. I've got the same dimensions whenever I didn't use Krish's python binding but converted to minc and loaded using NetCDF module (in python though again, but python's numpy.ndarray dimensionality is not limited by short) What I wonder about is that why 23406 and 7? ok - the product is equal to the surface number of vertices:23406*7=163842, so it seems that I can simply collapse those two dimensions (which one goes first?) but why is that done so? according to http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/MghFormat and mri.h in particular I don't see any limit on width/hight to be of short (not int) type and int (4 bytes) should be good enough to store full index. Is that due to some historical perspective? or am I just completely missing smth? Thanks in advance for the hints! -- Yaroslav Halchenko Research Assistant, Psychology Department, Rutgers-Newark Student Ph.D. @ CS Dept. NJIT Office: (973) 353-5440x263 | FWD: 82823 | Fax: (973) 353-1171 101 Warren Str, Smith Hall, Rm 4-105, Newark NJ 07102 WWW: http://www.linkedin.com/in/yarik

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Problem with the volume brush
by Matt Colvin 30 Apr '08

30 Apr '08

Dear Free Surfers, Occasionally when using the "edit voxels" tool in Tkmedit, I have experienced a weird problem. The brush radius appears to spontaneously increase, usually to a radius of 2 but sometimes as high as 8 or 10. The results are easy enough to correct by undoing my last edit and changing the brush radius back, but it happens frequently enough that it has become quite annoying. Does anybody have a theory as to what may be causing it? Is it most likely a bug or could I be causing on my own without realizing? Thanks in advance if anybody can help. --Matthew Colvin

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Freesurfer April 2008