Freesurfer

freesurfer@nmr.mgh.harvard.edu

18 participants
30131 discussions

cluster spanning multiple labels
by Siddharth Srivastava 14 May '09

14 May '09

Hi everyone, For a cluster spanning multiple labels based on a specific annotation, is it possible to automatically generate a list of labels (text) of the regions it overlaps with? What command/process should do this? mri_surfcluster is just providing me with the parcellation where the maxima is located. thanks, sid.

2 1

FSL --> FreeSurfer
by Vina Goghari 14 May '09

14 May '09

Hello all, I have group contrast fMRI activations analzyed by FSL Flame 1 that I want to extract individual thickness data for each subject from data processed by FreeSurfer? Is that possible and if so, how? Thanks! Vina

2 4

[Fwd: mri_convert batch converting]
by ozgun ozalay 14 May '09

14 May '09

also i've tried ; //mri_convert -it dicom -ot nii /home/ozgun/AnV/dti samples/KARABAY_NURI_.MR.EGE_HEAD.4.1.2008.07.21.21.20.51.578125.24527595.IMA /home/ozgun/AnV/ok.nii / output was; / $Id: mri_convert.c,v 1.146.2.4 2009/01/30 02:30:42 nicks Exp $ reading from /home/ozgun/AnV/dti samples/KARABAY_NURI_.MR.EGE_HEAD.4.1.2008.07.21.21.20.51.578125.24527595.IMA... Starting DICOMRead2() dcmfile = /home/ozgun/AnV/dti samples/KARABAY_NURI_.MR.EGE_HEAD.4.1.2008.07.21.21.20.51.578125.24527595.IMA dcmdir = /home/ozgun/AnV/dti samples Ref Series No = 4 Found 73 files, checking for dicoms Found 70 dicom files in series. First Sorting Computing Slice Direction Vs: 0 0 0 Vs: nan nan nan Second Sorting Counting frames nframes = 70 nslices = 1 ndcmfiles = 70 PE Dir = COL (dicom read) TransferSyntaxUID: --1.2.840.10008.1.2.1-- jpegUID: --1.2.840.10008.1.2.4-- Loading pixel data TR=10700.00, TE=103.00, TI=0.00, flip angle=90.00 i_ras = (-1, -0, 0) j_ras = (-0, -1, 0) k_ras = (nan, nan, nan) Reslicing using trilinear interpolation *MRIresample(): error inverting matrix; determinant is nan, matrix is:* -2.000 -0.000 nan nan; -0.000 -2.000 nan nan; 0.000 0.000 nan nan; 0.000 0.000 0.000 1.000; /i think problem occurs because of the bold line. Does anyone have any idea to correct this ? Thanks anyway Yours Ozgun

1 0

mri_convert batch converting
by ozgun ozalay 14 May '09

14 May '09

Hi; i have 70 Siemens .ima files in a single directory. Does anyone know how to convert ALL files in a folder into another format using mri_convert ? Do i have to convert them one by one? Does "--sdcmlist" option does this? Simple usage; /mri_convert <input file> <outputfile>/ ie: mri_convert /home/ozgun/AnV/aman.ima /home/ozgun/AnV/aman.nii Thanks anyway Ozgun

3 2

RE: GLUT Error
by Andrew Jahn 14 May '09

14 May '09

Hi again, I have been encountering an error when attempting to use either tksurfer or tkmedit via VNC on a local server. Here is the output whenever I type tkmedit or tksurfer: GLUT: Fatal Error in tkmedit.bin: OpenGL GLX extension not supported by display: 1.0 I looked through the threads regarding this problem, but still have been unable to find a solution. The output of 'cat /etc/redhat-release' is Red Hat Enterprise Linux WS release r (Nahant Update 7) and here is the output from the command ldd `which tkmedit.bin`: libtix8.1.8.4.so => not found libtk8.4.so => /usr/lib64/libtk8.4.so (0x0000003d43d00000) libtcl8.4.so => /usr/lib64/libtcl8.4.so (0x0000003d43b00000) libGLU.so.1 => /usr/X11R6/lib64/libGLU.so.1 (0x0000003d48300000) libGL.so.1 => /usr/lib64/libGL.so.1 (0x0000003d48500000) libXext.so.6 => /usr/X11R6/lib64/libXext.so.6 (0x0000003d44f00000) libX11.so.6 => /usr/X11R6/lib64/libX11.so.6 (0x0000003d44d00000) libXmu.so.6 => /usr/X11R6/lib64/libXmu.so.6 (0x0000003d47900000) libjpeg.so.62 => /usr/lib64/libjpeg.so.62 (0x0000003d47100000) libtiff.so.3 => /usr/lib64/libtiff.so.3 (0x0000003d4c000000) libz.so.1 => /usr/lib64/libz.so.1 (0x0000003d45100000) libcrypt.so.1 => /lib64/libcrypt.so.1 (0x0000003d48a00000) libdl.so.2 => /lib64/libdl.so.2 (0x0000003d44b00000) libpthread.so.0 => /lib64/tls/libpthread.so.0 (0x0000003d45300000) libstdc++.so.6 => /usr/lib64/libstdc++.so.6 (0x0000003d47500000) libm.so.6 => /lib64/tls/libm.so.6 (0x0000003d44900000) libgcc_s.so.1 => /lib64/libgcc_s.so.1 (0x0000003d47300000) libc.so.6 => /lib64/tls/libc.so.6 (0x0000003d44600000) libGLcore.so.1 => /usr/lib64/libGLcore.so.1 (0x0000002a95586000) libnvidia-tls.so.1 => /usr/lib64/tls/libnvidia-tls.so.1 (0x0000003d44400000) libXt.so.6 => /usr/X11R6/lib64/libXt.so.6 (0x0000003d4a100000) libSM.so.6 => /usr/X11R6/lib64/libSM.so.6 (0x0000003d45700000) libICE.so.6 => /usr/X11R6/lib64/libICE.so.6 (0x0000003d45500000) /lib64/ld-linux-x86-64.so.2 (0x0000003d43900000) Also, here is the content of the .xdebug_tkmedit file following an unsuccessful tkmedit command: tkmedit started: Thu May 14 14:55:44 2009 tkmedit.bin $Id: tkmedit.c,v 1.320.2.9 2009/01/27 20:41:02 greve Exp $ $Name: stable4 $ Any help or advice is greatly appreciated in advance. Thanks! -Andrew

1 0

License Key issue (not recognized)
by ozgun ozalay 14 May '09

14 May '09

Hi; I'm Ozgun Ozalay, researcher at Ege University/Turkey. One of my friends recommended FreeSurfer's "mri_convert" program to convert my Siemens .IMA files to a more common format .nii. i've downloaded freesurfer from your wiki pages and made my registration too. i've recieved an e-mail with details of my license. Upon installing "freesurfer" to /home/ozgun/AnV/freesurfer i configured enviroment too as described in wiki with bash shell; /export FREESURFER_HOME=/home/ozgun/freesurfer/ /source $FREESURFER_HOME/SetUpFreeSurfer.sh/ I recieved no errors during this process. /source /home/ozgun/AnV/freesurfer/SetUpFreeSurfer.sh/ /-------- freesurfer-Linux-centos4_x86_64-stable-pub-v4.3.0 --------/ /Setting up environment for FreeSurfer/FS-FAST (and FSL)/ /FREESURFER_HOME /home/ozgun/AnV/freesurfer// /FSFAST_HOME /home/ozgun/AnV/freesurfer//fsfast/ /FSF_OUTPUT_FORMAT nii/ /SUBJECTS_DIR /home/ozgun/AnV/freesurfer//subjects/ /MNI_DIR /home/ozgun/AnV/freesurfer//mni/ /FSL_DIR /home/ozgun/AnV/FSL/fsl/ But when i try to execute "mri_convert" it says my license isn't ok. /ozgun@linux-dkvs:~/AnV/freesurfer/bin> ./mri_convert /home/ozgun/AnV/orn.IMA/ //home/ozgun/orn.nii/ /./mri_convert /home/ozgun/AnV/orn.IMA /home/ozgun/orn.nii/ /$Id: mri_convert.c,v 1.146.2.4 2009/01/30 02:30:42 nicks Exp $/ /reading from /home/ozgun/AnV/orn.IMA.../ /--------------------------------------------------------------------------/ /ERROR: Invalid FreeSurfer license key found in license file/ //home/ozgun/AnV/freesurfer/.license/ /If you are outside the NMR-Martinos Center,/ /go to http://surfer.nmr.mgh.harvard.edu to/ /get a valid license file (it's free)./ /If you are inside the NMR-Martinos Center,/ /make sure to source the standard environment./ /--------------------------------------------------------------------------/ / / I created ".license" file in my freesurfer home directory (/home/ozgun/AnV/freesurfer) and pasted 3 lines from your e-mail to this empty document and saved. Also attaching the .license file i've created. Did i do something wrong? By the way, i'm using OpenSuse 11.1 with kernel 2.6.27.21-0.1-default, KDE 4.1 as desktop enviroment. Thanks anyway ;) #---------------CUT HERE--------------- ozgun.ozalay(a)gmail.com 7235 *CZag.N9G9Ekc #---------------CUT HERE---------------

2 1

smoothing with mri_surf2surf
by Gregory Dierksen 14 May '09

14 May '09

Hi, I want to smooth a cortical thickness map using values only in a specific area. Basically I want to mask out all other segmentations, for example smooth with fwhm of 20 only in the postcentral region. I've used quite a few combinations of the -label-src and -label-trg flags and noticed a slight problem: Using the command line (which seems to give the "best" results): mri_surf2surf --hemi rh --s fsaverage --sval ./rh.Input.mgh --fwhm 20 --label-trg ./postcentral.label --tval rh.Output.mgz When the rh.Input.mgh has been masked before running surf2surf using postcentral.label (so only the postcentral region is non-zero), I get DIFFERENT values than if rh.Input.mgh is NOT previously masked by postcentral.label (ie ALL verticies have non-zero values inside and outside postcentral region). How can I get mri_surf2surf (or perhaps some other command) to smooth only within a specified region without taking values from outside this region? Thanks for the help, Greg

2 4

From MNI152 to Subject's space
by Campanella Martina 14 May '09

14 May '09

Hi "Freesurfer", We need to remap a volume in MNI152 to a subject space in order to find the correspondent label... Any suggestion? Cheers, Martina Campanella

2 1

Can fieldsigns be added across sessions?
by Jeff Phillips 14 May '09

14 May '09

Hi all, I would like to add fieldsigns across multiple retinotopy sessions in the same subject, in order to get a metric of the reliability of the mapping. However, when I tried to do this in one subject, I found that fieldsigns from two sessions largely canceled one another out. This led to a discussion in our lab of whether the fieldsign 1) has a consistent meaning across sessions and subjects, or 2) whether the fieldsign in a given region, say V1, may switch from positive to negative due to noise or between-subject differences. For example, a colleague speculated that paint-sess could start with +1 at an arbitrary starting point on the edge of an occipital patch, then flip the sign whenever the polar angle/eccentricity gradients reversed themselves. Thus, V5 might be +1, V4 = -1, V3 = +1, V2 = -1, and V1 would be +1. However, if noise in a given session resulted in a failure to detect V4, then V1 would end up being the opposite fieldsign, -1. Is this correct? If so, then I might be shooting myself in the foot by adding fieldsign maps from different sessions. I would really appreciate any insight about how the fieldsign is assigned, and whether circumstances like the ones I describe could cause it to flip for a given functional region. Thanks, Jeff Phillips

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Re: [Freesurfer] Literature values for cortical thickness
by Bruce Fischl 14 May '09

14 May '09

Hi Falk, we published some values in our Cerebral Cortex paper , but I suspect the effective thickness will vary a bit as a function of pulse sequence, and certainly it will vary with things like age. Rahul has probably tabulated by parcellation unit if that helps. cheers Bruce On Wed, 13 May 2009, Falk Lüsebrink wrote: > Hi everyone, > > > > As I dont do a study in which I compare a group of subjects with some kind > of abnormality with a control group I was looking for literature values for > cortical thickness. The only paper I found which was written by von Economo > et al. in 1925 doing a post-mortem analysis. > > > > Are there any more recent sources available which maybe even cover in-vivo > values for regional cortical thickness? Actually Im looking for average > values across the whole lobes. > > > > Thanks in advance, > > Falk > >

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