Freesurfer

freesurfer@nmr.mgh.harvard.edu

30132 discussions

mris_make_face_parcellation
by Franz Liem 13 Feb '12

13 Feb '12

Dear Freesurfers, I have some questions regarding mris_make_face_parcellation (and possibly found one error in the .tri file). (I am working with freesurfer-Darwin-leopard-i686-stable-pub-v5.1.0). I would like to make a high res parcellation of several subjects and used ic3.tri. Parcels should correspond across subjects. I computed mris_make_face_parcellation ../surf/lh.sphere $FREESURFER_HOME/lib/bem/ic3.tri ./lh.ic3.annot 1. It seems not to make a difference whether I choose .sphere or .sphere.reg as input, the resulting parcellations are identical (i checked by comparing vertex label values in matlab; .inflated deviates a bit, but not substantially). According to Bruce (http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg18509.html) "You want to use either ?h.sphere if you want it to be uniform in subject space or ?h.sphere.reg if you want the parcels to correspond across subjects" Could anybody tell me how the parcellation is performed exactly? I thought it was performed on the input surf (the input surf is parcellated into (e.g.) 642 equally sized parcels), which should lead to different results at .sphere and .sphere.reg, shouldn't it? Alternatively, would it be better to mris_make_face_parcellation the fsaverage and mri_surf2surf the high res parcellation onto each subject to get cross-subject correspondency (I tried this. It didn't look that great with this command: mri_surf2surf --srcsubject fsaverage --sval-annot ic3.annot --trgsubject subject1 --tval ic3s03.annot --hemi lh )? To recap, what is the best strategy to arrive with cross-subject-corresponing parcellations? Performing mris_make_face_parcellation with ?h.sphere.reg for each subject individually? 2. There seems to be duplicate structNames/annotationValues when applying mris_make_face_parcellation with ic3.tri In fsaverage at least the following labelnames are given to two spatially separated labels. ic3.tri_vertex_25 (cluster 1 around vertex 41132, cluster 2 around vertex 157199) ic3.tri_vertex_42 (cluster 1 around vertex 137845, cluster 2 around vertex 155417) How come? Thanks for you help, Franz

2 2

make_average_volume error
by Martina Ly 13 Feb '12

13 Feb '12

Dear freesurfers, I am coming across an error in the beginning of make_average_volume of make_average_subject where mri_convert fails. make_average_surface finished without a problem so hopefully that part will not need to be re-run. I've check permissions, cpu space, paths but couldn't find anything... Any help/suggestions would greatly appreciated. Below is the error message: INFO: Applying transformation from file /study/NCCAM/Data/MRI/processed/structural/freesurfer//WB101_1//mri/transforms/talairach.xfm... --------------------------------- INFO: Transform Matrix (linear_ras_to_ras) 1.156 0.062 0.028 -2.110; -0.102 1.113 0.318 -31.524; -0.029 -0.322 1.218 4.598; 0.000 0.000 0.000 1.000; INFO: Transform dst volume info is not used (valid flag = 0). INFO: assumes that the dst volume given is the same as the dst for the transform mghWrite(/study/NCCAM/Data/MRI/processed/structural/freesurfer//average/tmp/make_average_vol-tmp-2117/orig-WB101_1/.mgh, -1): could not open file --------------------------------- Applying LTAtransformInterp (resample_type 1) writing to /study/NCCAM/Data/MRI/processed/structural/freesurfer//average/tmp/make_average_vol-tmp-2117/orig-WB101_1/.mgh... ERROR: failure writing /study/NCCAM/Data/MRI/processed/structural/freesurfer//average/tmp/make_average_vol-tmp-2117/orig-WB101_1/.mgh /study2/NCCAM/Data/MRI/processed/structural/freesurfer ERROR: mri_convert failed. Many thanks in advance, Martina

2 3

Hippocampal subfield: average standard T1 ore use higher resolution
by Grimm, Oliver 12 Feb '12

12 Feb '12

Dear FreeSurfer-User, some of my questions are mentioned in some older postings, but I still struggle with some basic questions. We are planning to use the new hippocampal subfield segmentation of FS 5.1 with 3 T Siemens TRIO with 32 channel head coil. Still, I do not fully understand how to optimize our image processeing pipeline: 1. Freesurfer works internally with 1x1x1 mm3 but the hippocampal segmenat uses a higher res. of 0.5 x 0.5 x 0.5 mm3. So should we instead use a higher resolution for the hippocampal subfield seg.? 2. I understand that the recent FS version is not working well with high resolution images, e.g. the atlases are not provided in a higher res, however the hippocampal subfield segmentation seems to make use of aseg.stats. So is is possible at all to use the FS-pipleine in this case (hippocampal subfields)? 3. Instead of using a high resolution image, we could average over several pictures. When I tried this, I had the visual impression, that there was almost no gain in this, the volume estimates were bouncing within a range of 10% but did not converge when averaging from scan 1-5 to a specific value. So is it necessary for a good quality to average images when using hippocampal subfield segmentation ? Thanks for your efforts! Best, Dr. med. Oliver Grimm Zentralinstitut für Seelische Gesundheit www.zi-mannheim.de SNiP | Systems Neuroscience in Psychiatry 68159 Mannheim Germany Tel: +49-621-1703-6341 Fax: +49-621-1703-6305 email oliver.grimm(a)zi-mannheim.de <mailto:oliver.grimm@zi-mannheim.de>

3 2

Hippocampal-subfields to ROI
by Joshua Lee 12 Feb '12

12 Feb '12

Hi All, I am wanting to run a functional analysis in spm using the hippo-subfields as individual roi's. Thus I need to convert into a binary mask that is in SPM space. Knowing that the sub-field segmentations are probabilities [0..255] I chose a threshold (i.e. ~95% certainty, corresponding to a value of ~240) and ran mri_binarize with a min set at 240. However, the resultant image doesn't retain the same dimensions as say brain.mgz, and appears as a black square when overlayed. I suspect this will not work as a mask for roi analysis. Any suggestions? Thanks Josh

1 0

Re: [Freesurfer] Interactions for continuous variables
by Katherine Reiter 11 Feb '12

11 Feb '12

Hi Doug and FreeSurferers, I came across this email chain and am having a similar problem. I am working on an interaction between a categorical and continuous variable, covarying for a categorical variable. (E.g. the interaction between group membership and age, covarying for gender). I know this is not possible with the QDEC GUI and there seems to be more options in performing group analysis using the command line, however is this comparison possible in the command line with mris_preproc, mri_surf2surf and mri_glmfit? Thanks, Katie

1 0

Configuring TKMEDIT 4-panel Display
by Vy Dinh 10 Feb '12

10 Feb '12

Dear Experts, Is it possible to link the four panel display so that as we are scrolling through each slice in one view, the other three views will automatically scroll to the next slice (without having the user click the cursor on a new point)? This was possible in SPM Display tool, so I wonder if it has been built into TKMEDIT yet. Thanks, Vy

3 2

selxavg3-sess error
by Daniel Cole 10 Feb '12

10 Feb '12

Hello Freesurfers, I think my last email failed to send so here it is again - I'm running into problems using fs-fast for a polar only, retinotopic analysis. The error message I get is: ********************* Retinotopy dcole$ selxavg3-sess -analysis rtopy.self.lh -sf sessid Surface data self lh -------------------------------------------------------------- selxavg3-sess logfile is /rcbiUsers/dcole/Retinotopy/log/selxavg3-sess-bold-rtopy.self.lh-120209144554.log -------------------------------------------------------------- preproc-sess -s SUB01 -d /rcbiUsers/dcole/Retinotopy -a rtopy.self.lh -nolog -------------------------------------------------------------- preproc-sess logfile is /dev/null -------------------------------------------------------------- $Id: preproc-sess,v 1.45.2.1 2011/03/22 17:16:19 greve Exp $ dcole setenv FREESURFER_HOME /Volumes/RCBI/freesurfer setenv SUBJECTS_DIR /Volumes/rcbiUsers/dcole/Retinotopy/Subjects/test Darwin commissure.local 11.2.0 Darwin Kernel Version 11.2.0: Tue Aug 9 20:54:00 PDT 2011; root:xnu-1699.24.8~1/RELEASE_X86_64 x86_64 /rcbiUsers/dcole/Retinotopy /Volumes/RCBI/freesurfer/fsfast/bin/preproc-sess -s SUB01 -d /rcbiUsers/dcole/Retinotopy -a rtopy.self.lh -nolog Thu Feb 9 14:45:54 EST 2012 instem f mc 1 f fmcpr stc 0 fmcpr sm 0 mask 1 brain SUB01 Template ----------------------------- mktemplate-sess -s SUB01 -d /rcbiUsers/dcole/Retinotopy -fsd bold -nolog -update Session: /rcbiUsers/dcole/Retinotopy/SUB01 ---------------- Thu Feb 9 14:45:54 EST 2012 Detected input format at nii SUB01 Update not needed Run: 001 ---------------- Thu Feb 9 14:45:54 EST 2012 SUB01 001 Update not needed Run: 002 ---------------- Thu Feb 9 14:45:54 EST 2012 SUB01 002 Update not needed Run: 003 ---------------- Thu Feb 9 14:45:55 EST 2012 SUB01 003 Update not needed Run: 004 ---------------- Thu Feb 9 14:45:55 EST 2012 SUB01 004 Update not needed Run: 005 ---------------- Thu Feb 9 14:45:55 EST 2012 SUB01 005 Update not needed Thu Feb 9 14:45:55 EST 2012 mktemplate-sess completed SUB01 Mask ------------------------ mkbrainmask-sess -maskstem brain -fsd bold -s SUB01 -d /rcbiUsers/dcole/Retinotopy -nolog -update ------------------------------------------------ /rcbiUsers/dcole/Retinotopy/SUB01 Thu Feb 9 14:45:55 EST 2012 SUB01 Update not needed for session-level mask SUB01 Update not needed for run 001 mask SUB01 Update not needed for run 001 meanval SUB01 Update not needed for run 002 mask SUB01 Update not needed for run 002 meanval SUB01 Update not needed for run 003 mask SUB01 Update not needed for run 003 meanval SUB01 Update not needed for run 004 mask SUB01 Update not needed for run 004 meanval SUB01 Update not needed for run 005 mask SUB01 Update not needed for run 005 meanval Thu Feb 9 14:45:55 EST 2012 mkbrainmask-sess done SUB01 Registration ----------------------------- register-sess -s SUB01 -d /rcbiUsers/dcole/Retinotopy -fsd bold -dof 6 -per-run -nolog -update -------------------------------------------------------------- register-sess logfile is /dev/null -------------------------------------------------------------- Thu Feb 9 14:45:55 EST 2012 setenv SUBJECTS_DIR /Volumes/rcbiUsers/dcole/Retinotopy/Subjects/test cd /rcbiUsers/dcole/Retinotopy /Volumes/RCBI/freesurfer/fsfast/bin/register-sess -s SUB01 -d /rcbiUsers/dcole/Retinotopy -fsd bold -dof 6 -per-run -nolog -update freesurfer-Darwin-leopard-i686-stable-pub-v5.1.0 Darwin commissure.local 11.2.0 Darwin Kernel Version 11.2.0: Tue Aug 9 20:54:00 PDT 2011; root:xnu-1699.24.8~1/RELEASE_X86_64 x86_64 Session: /rcbiUsers/dcole/Retinotopy/SUB01 ---------------- Thu Feb 9 14:45:55 EST 2012 Run: 001 ---------------- Thu Feb 9 14:45:55 EST 2012 Update not needed Run: 002 ---------------- Thu Feb 9 14:45:55 EST 2012 Update not needed Run: 003 ---------------- Thu Feb 9 14:45:55 EST 2012 Update not needed Run: 004 ---------------- Thu Feb 9 14:45:55 EST 2012 Update not needed Run: 005 ---------------- Thu Feb 9 14:45:55 EST 2012 Update not needed Thu Feb 9 14:45:55 EST 2012 register-sess completed SUB01 MC ----------------------------- mc-sess -fstem f -fmcstem fmcpr -s SUB01 -d /rcbiUsers/dcole/Retinotopy -fsd bold -per-run -nolog -update Logfile is /dev/null ------------------------------------------- /rcbiUsers/dcole/Retinotopy/SUB01 RunList: 001 002 003 004 005 SUB01 001 Update not needed SUB01 002 Update not needed SUB01 003 Update not needed SUB01 004 Update not needed SUB01 005 Update not needed Thu Feb 9 14:45:55 EST 2012 mc-sess completed SUCCESSFULLY SUB01 To Surface ----------------------------- rawfunc2surf-sess -fwhm 5 -s SUB01 -d /rcbiUsers/dcole/Retinotopy -fsd bold -hemi lh -self -nolog -update instem fmcpr outstem fmcpr.sm5.self.hemi ------------------------------ 1/1 SUB01 1/1 SUB01 001 lh --------- Thu Feb 9 14:45:55 EST 2012 SUB01 001 Update not needed 1/1 SUB01 002 lh --------- Thu Feb 9 14:45:55 EST 2012 SUB01 002 Update not needed 1/1 SUB01 003 lh --------- Thu Feb 9 14:45:56 EST 2012 SUB01 003 Update not needed 1/1 SUB01 004 lh --------- Thu Feb 9 14:45:56 EST 2012 SUB01 004 Update not needed 1/1 SUB01 005 lh --------- Thu Feb 9 14:45:56 EST 2012 SUB01 005 Update not needed Thu Feb 9 14:45:56 EST 2012 rawfunc2surf-sess completed ---------------------------------------- Started at Thu Feb 9 14:45:54 EST 2012 Ended at Thu Feb 9 14:45:56 EST 2012 preproc-sess done ------------------------------------------- /rcbiUsers/dcole/Retinotopy/SUB01 Thu Feb 9 14:45:56 EST 2012 anadir = /rcbiUsers/dcole/Retinotopy/SUB01/bold/rtopy.self.lh DoGLMFit = 1 DoContrasts = 1 UpdateNeeded = 1 ------------------------------------------ ------- matlab output -------------------- Warning: Unable to open display 'iconic'. You will not be able to display graphics on the screen. 2012-02-09 14:45:56.773 MATLAB[17738:7103] This process is attempting to exclude an item from Time Machine by path without administrator privileges. This is not supported. 2012-02-09 14:45:56.775 MATLAB[17738:7103] This process is attempting to exclude an item from Time Machine by path without administrator privileges. This is not supported. 2012-02-09 14:45:56.776 MATLAB[17738:7103] This process is attempting to exclude an item from Time Machine by path without administrator privileges. This is not supported. 2012-02-09 14:45:56.777 MATLAB[17738:7103] This process is attempting to exclude an item from Time Machine by path without administrator privileges. This is not supported. 2012-02-09 14:45:56.778 MATLAB[17738:7103] This process is attempting to exclude an item from Time Machine by path without administrator privileges. This is not supported. 2012-02-09 14:45:56.779 MATLAB[17738:7103] This process is attempting to exclude an item from Time Machine by path without administrator privileges. This is not supported. 2012-02-09 14:45:56.780 MATLAB[17738:7103] This process is attempting to exclude an item from Time Machine by path without administrator privileges. This is not supported. 2012-02-09 14:45:56.781 MATLAB[17738:7103] This process is attempting to exclude an item from Time Machine by path without administrator privileges. This is not supported. 2012-02-09 14:45:56.783 MATLAB[17738:7103] This process is attempting to exclude an item from Time Machine by path without administrator privileges. This is not supported. 2012-02-09 14:45:56.796 MATLAB[17738:7103] This process is attempting to exclude an item from Time Machine by path without administrator privileges. This is not supported. 2012-02-09 14:45:56.797 MATLAB[17738:7103] This process is attempting to exclude an item from Time Machine by path without administrator privileges. This is not supported. 2012-02-09 14:45:56.798 MATLAB[17738:7103] This process is attempting to exclude an item from Time Machine by path without administrator privileges. This is not supported. 2012-02-09 14:45:56.812 MATLAB[17738:7103] This process is attempting to exclude an item from Time Machine by path without administrator privileges. This is not supported. 2012-02-09 14:45:56.813 MATLAB[17738:7103] This process is attempting to exclude an item from Time Machine by path without administrator privileges. This is not supported. 2012-02-09 14:45:56.815 MATLAB[17738:7103] This process is attempting to exclude an item from Time Machine by path without administrator privileges. This is not supported. < M A T L A B (R) > Copyright 1984-2010 The MathWorks, Inc. Version 7.10.0.499 (R2010a) 64-bit (maci64) February 5, 2010 2012-02-09 14:45:57.634 MATLAB[17738:7103] This process is attempting to exclude an item from Time Machine by path without administrator privileges. This is not supported. 2012-02-09 14:45:57.636 MATLAB[17738:7103] This process is attempting to exclude an item from Time Machine by path without administrator privileges. This is not supported. 2012-02-09 14:45:57.636 MATLAB[17738:7103] This process is attempting to exclude an item from Time Machine by path without administrator privileges. This is not supported. 2012-02-09 14:45:57.637 MATLAB[17738:7103] This process is attempting to exclude an item from Time Machine by path without administrator privileges. This is not supported. 2012-02-09 14:45:57.638 MATLAB[17738:7103] This process is attempting to exclude an item from Time Machine by path without administrator privileges. This is not supported. 2012-02-09 14:45:57.639 MATLAB[17738:7103] This process is attempting to exclude an item from Time Machine by path without administrator privileges. This is not supported. 2012-02-09 14:45:57.639 MATLAB[17738:7103] This process is attempting to exclude an item from Time Machine by path without administrator privileges. This is not supported. 2012-02-09 14:45:57.640 MATLAB[17738:7103] This process is attempting to exclude an item from Time Machine by path without administrator privileges. This is not supported. 2012-02-09 14:45:57.641 MATLAB[17738:7103] This process is attempting to exclude an item from Time Machine by path without administrator privileges. This is not supported. 2012-02-09 14:45:57.642 MATLAB[17738:7103] This process is attempting to exclude an item from Time Machine by path without administrator privileges. This is not supported. 2012-02-09 14:45:57.643 MATLAB[17738:7103] This process is attempting to exclude an item from Time Machine by path without administrator privileges. This is not supported. 2012-02-09 14:45:57.643 MATLAB[17738:7103] This process is attempting to exclude an item from Time Machine by path without administrator privileges. This is not supported. 2012-02-09 14:45:57.644 MATLAB[17738:7103] This process is attempting to exclude an item from Time Machine by path without administrator privileges. This is not supported. 2012-02-09 14:45:57.645 MATLAB[17738:7103] This process is attempting to exclude an item from Time Machine by path without administrator privileges. This is not supported. 2012-02-09 14:45:57.646 MATLAB[17738:7103] This process is attempting to exclude an item from Time Machine by path without administrator privileges. This is not supported. 2012-02-09 14:45:57.646 MATLAB[17738:7103] This process is attempting to exclude an item from Time Machine by path without administrator privileges. This is not supported. 2012-02-09 14:45:57.647 MATLAB[17738:7103] This process is attempting to exclude an item from Time Machine by path without administrator privileges. This is not supported. 2012-02-09 14:45:57.648 MATLAB[17738:7103] This process is attempting to exclude an item from Time Machine by path without administrator privileges. This is not supported. 2012-02-09 14:45:57.649 MATLAB[17738:7103] This process is attempting to exclude an item from Time Machine by path without administrator privileges. This is not supported. 2012-02-09 14:45:57.649 MATLAB[17738:7103] This process is attempting to exclude an item from Time Machine by path without administrator privileges. This is not supported. 2012-02-09 14:45:57.650 MATLAB[17738:7103] This process is attempting to exclude an item from Time Machine by path without administrator privileges. This is not supported. 2012-02-09 14:45:57.651 MATLAB[17738:7103] This process is attempting to exclude an item from Time Machine by path without administrator privileges. This is not supported. 2012-02-09 14:45:57.651 MATLAB[17738:7103] This process is attempting to exclude an item from Time Machine by path without administrator privileges. This is not supported. 2012-02-09 14:45:57.652 MATLAB[17738:7103] This process is attempting to exclude an item from Time Machine by path without administrator privileges. This is not supported. 2012-02-09 14:45:57.653 MATLAB[17738:7103] This process is attempting to exclude an item from Time Machine by path without administrator privileges. This is not supported. 2012-02-09 14:45:57.654 MATLAB[17738:7103] This process is attempting to exclude an item from Time Machine by path without administrator privileges. This is not supported. 2012-02-09 14:45:57.654 MATLAB[17738:7103] This process is attempting to exclude an item from Time Machine by path without administrator privileges. This is not supported. 2012-02-09 14:45:57.655 MATLAB[17738:7103] This process is attempting to exclude an item from Time Machine by path without administrator privileges. This is not supported. 2012-02-09 14:45:57.656 MATLAB[17738:7103] This process is attempting to exclude an item from Time Machine by path without administrator privileges. This is not supported. 2012-02-09 14:45:57.657 MATLAB[17738:7103] This process is attempting to exclude an item from Time Machine by path without administrator privileges. This is not supported. 2012-02-09 14:45:57.657 MATLAB[17738:7103] This process is attempting to exclude an item from Time Machine by path without administrator privileges. This is not supported. 2012-02-09 14:45:57.658 MATLAB[17738:7103] This process is attempting to exclude an item from Time Machine by path without administrator privileges. This is not supported. 2012-02-09 14:45:57.659 MATLAB[17738:7103] This process is attempting to exclude an item from Time Machine by path without administrator privileges. This is not supported. 2012-02-09 14:45:57.660 MATLAB[17738:7103] This process is attempting to exclude an item from Time Machine by path without administrator privileges. This is not supported. 2012-02-09 14:45:57.660 MATLAB[17738:7103] This process is attempting to exclude an item from Time Machine by path without administrator privileges. This is not supported. 2012-02-09 14:45:57.661 MATLAB[17738:7103] This process is attempting to exclude an item from Time Machine by path without administrator privileges. This is not supported. 2012-02-09 14:45:57.662 MATLAB[17738:7103] This process is attempting to exclude an item from Time Machine by path without administrator privileges. This is not supported. 2012-02-09 14:45:57.663 MATLAB[17738:7103] This process is attempting to exclude an item from Time Machine by path without administrator privileges. This is not supported. 2012-02-09 14:45:57.663 MATLAB[17738:7103] This process is attempting to exclude an item from Time Machine by path without administrator privileges. This is not supported. 2012-02-09 14:45:57.664 MATLAB[17738:7103] This process is attempting to exclude an item from Time Machine by path without administrator privileges. This is not supported. 2012-02-09 14:45:57.665 MATLAB[17738:7103] This process is attempting to exclude an item from Time Machine by path without administrator privileges. This is not supported. 2012-02-09 14:45:57.666 MATLAB[17738:7103] This process is attempting to exclude an item from Time Machine by path without administrator privileges. This is not supported. 2012-02-09 14:45:57.666 MATLAB[17738:7103] This process is attempting to exclude an item from Time Machine by path without administrator privileges. This is not supported. 2012-02-09 14:45:57.667 MATLAB[17738:7103] This process is attempting to exclude an item from Time Machine by path without administrator privileges. This is not supported. 2012-02-09 14:45:57.668 MATLAB[17738:7103] This process is attempting to exclude an item from Time Machine by path without administrator privileges. This is not supported. 2012-02-09 14:45:57.669 MATLAB[17738:7103] This process is attempting to exclude an item from Time Machine by path without administrator privileges. This is not supported. 2012-02-09 14:45:57.669 MATLAB[17738:7103] This process is attempting to exclude an item from Time Machine by path without administrator privileges. This is not supported. 2012-02-09 14:45:57.670 MATLAB[17738:7103] This process is attempting to exclude an item from Time Machine by path without administrator privileges. This is not supported. To get started, type one of these: helpwin, helpdesk, or demo. For product information, visit www.mathworks.com. >> >> >> >> >> >> >> /Volumes/RCBI/freesurfer/fsfast/toolbox/fast_selxavg3.m >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> #@# SUB01 ############################### /rcbiUsers/dcole/Retinotopy/SUB01 ------------------------- $Id: fast_selxavg3.m,v 1.100 2011/03/02 16:14:38 greve Exp $ /Volumes/RCBI/freesurfer/fsfast/toolbox/fast_selxavg3.m /Volumes/RCBI/freesurfer/fsfast/toolbox/fast_ldanaflac.m /Volumes/RCBI/freesurfer/matlab/MRIread.m ------------------------- outtop = /rcbiUsers/dcole/Retinotopy Extension format = nii.gz nruns = 5 autostimdur = outanadir = /rcbiUsers/dcole/Retinotopy/SUB01/bold/rtopy.self.lh Found 15746/149363 (10.5) voxels in mask Creating Design Matrix ... creation time = 0.011 sec DoMCFit = 1 ntptot = 1305, nX = 39, DOF = 1266 Saving X matrix to /rcbiUsers/dcole/Retinotopy/SUB01/bold/rtopy.self.lh/Xtmp.mat ??? Error using ==> svd Input to SVD must not contain NaN or Inf. Error in ==> cond at 40 s = svd(A); Error in ==> fast_selxavg3 at 254 XCond = cond(XtX); >> ------------------------------------------ ERROR: fast_selxavg3() failed\n ********************* I think the problem is with the "??? Error using ==> svd... " error, not the matlab errors. I've found that many people were reporting this matlab error but it's presumably more of an annoyance than a technical issue. I'm following the tutorial at http://surfer.nmr.mgh.harvard.edu/fswiki/FsFastIndividualRetinotopyAnalysis. I'm pretty sure I have my directories set up properly and I've used Mricron's dcm2nii tool on my raw functionals/structurals. I've also already successfully preprocessed my data and made the rtopy.par files (preproc-sess & mkanalysis-sess). I haven't been able to find a response that fixed the problem and was hoping for some suggestions. Thanks so much, Daniel -- Daniel Cole University of Rochester Brain and Cognitive Sciences dcole10(a)u.rochester.edu

2 1

Tracula - bedpost failure
by Kiely Donnelly 10 Feb '12

10 Feb '12

Hi Everyone -- I've been having difficulty getting Tracula to run smoothly on our cluster. Similar to others on the listserv, the bedpost step was not creating the necessary files causing an error during the -path step. Based on previous posts, I ran bedpostx on the dmri directory. This initially seemed to work (I no longer received the message "1 slice processed" over and over), but for some reason the merged_ph1samples.nii.gz file is still not being created and I continue to run into an error when I run -path. It does create a merged_ph2samples.nii.gz output file. Any help would be greatly appreciated. Thanks, Kiely

3 5

Cortical thickness nearly zero
by Gabriele Corbetta 10 Feb '12

10 Feb '12

Dear all, I'm not familiar with Freesurfer and I have a very naive question... I'm reading with Matlab the .thickness files of a few subjects and I see that there are some nearly zero / zero values.. how do I interpret them? Maybe they correspond to regions which are not considered as cortex? Had I to compute the mean cortical thickness of the whole brain, would I have to discard them? Thanks in advance. Gabriele

2 1

Flattened data
by Tuomas Tolvanen 10 Feb '12

10 Feb '12

Dear surfers, Using [faces verts] = freesurfer_read_surf(surface) gives me the face list and vertices coordinates. I assume that using different surface (e.g. lh.white and lh.sphere) changes only the coordinates and the face list remains the same (?). What about with flattened patch? I converted the flattened patch to ascii and read it to Matlab. This is what I got: First ten rows: '#!ascii version of patch ./lh.orig. The 1st index is not a vertex number' '25720 50563' '1 vno=0' '6.217312 34.772942 0.000000' '2 vno=1' '6.013689 34.451294 0.000000' '3 vno=2' '5.807863 33.961815 0.000000' '4 vno=3' '6.546745 34.426727 0.000000' ... At somepoint the rows changes to this: '0' '0 1 3 ' '1' '4 3 1 ' '2' '0 75 1 ' '3' '76 1 75 ' '4' '0 3 83 ' '5' It's obvious that every second row, starting from the 4th row, is the xyz-coordinates of the vertex on the flatmap. Is the latter part of the ascii data the face list? And if it is, are those indices referring to the original vertice indices? Long story short: does the ascii data (of the flat patch) consist of the vertice coordinates and the face list in the same way as lh.white (with the exception that indices are reduced by one [1=0, 2=1...])? -Tuomas

2 5

Jump to page:

2026

2025

2024

2023

2022

2021

2020

2019

2018

2017

2016

2015

2014

2013

2012

2011

2010

2009

2008

2007

2006

2005

2004

Freesurfer