Freesurfer

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30132 discussions

trac all - cant allocate memory
by Michael Scheel 17 Jul '12

17 Jul '12

Dear FS experts, when running tracula I get the following error (see below and trac-all.log attached to this mail). It seems that memory cannot be allocated but I have a PowerMac with 12 GB RAM and I suppose this should be enough. Any ideas how I can solve this problem? Thanks, Michael dmri_train(50487) malloc: *** mmap(size=159744) failed (error code=12) *** error: can't allocate region *** set a breakpoint in malloc_error_break to debug MRIalloc(218, 182, 182): could not allocate 158704 bytes for 14th slice Cannot allocate memory Darwin fslmachine.charite.de 10.8.0 Darwin Kernel Version 10.8.0: Tue Jun 7 16:33:36 PDT 2011; root:xnu-1504.15.3~1/RELEASE_I386 i386 trac-preproc exited with ERRORS at Tue Jun 26 15:12:03 CEST 2012

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"Splotchy" labels after transformation from fsaverage to native
by Michael Waskom 16 Jul '12

16 Jul '12

Hi, I'm using mri_label2label to reverse normalize labels from fsaverage space to the native surface. I'm ending up with some splotchy-looking labels, for lack of a better word. See what I mean here: http://web.mit.edu/mwaskom/www/splotchy.png I'm doing this normalization in a script with the following relevant line, which seems to be what happens inthe BAlabes step of recon-all mri_label2label --srclabel ../fsaverage/label/${hemi}.${roi}.label \ --srcsubject fsaverage --trgsubject ${subj} \ --trglabel label/$hemi.${roi}.label \ --regmethod surface --hemi $hemi Any idea how I can avoid this splotchiness or, failing that, do a closing on the label to clean up some of the noise? Cheers, Michael

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recon-all for non-human primates failed and what to do next?
by Leon 16 Jul '12

16 Jul '12

Hi, FreeSurfer experts. I have successfully used FreeSurfer to reconstruct monkey brains, but when I used the same scripts on chimpanzees, it failed miserably (see the attached figure). I tried several strategies, such as normalizing the wm.mgz to 110, but the scripts still did not work. Could someone tell me what other strategies I could use to make it work? Many thanks in advance! Leon

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Restart from somewhere in the middle of mri_ca_register
by Joshua Lee 16 Jul '12

16 Jul '12

Is it possible/pracitcal? This is a long step, and unfortunately my analysis computer was rebooted in the middle of this step, and I was hoping to present the volumes tomorrow.. ouch. - Josh

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ROI functional & anatomical cross
by Huiting Liu 16 Jul '12

16 Jul '12

Hello, I'm trying to do an ROI analysis that crosses the group-level functional activation with specific anatomical structures. Currently the clusters found for our group-level functional activation are too large and need to be separated into many structures. Is there a command I could use that would cross the group level map with each cortical structure generated by freesurfer's recon-all? Thanks.

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plotting cortical parcellation surfaces using 2009 atlas
by Maria Kharitonova 16 Jul '12

16 Jul '12

Hello, I apologize if my question is too basic, but I am trying to pull up cortical parcellation surfaces for my data, like shown here: http://surfer.nmr.mgh.harvard.edu/fswiki/CorticalParcellation I tried typing in "tksurfer subjec_number lh inflated -aparc", but that produces the lateral surface using the 2005 atlas. Can you help me by suggesting which command can pull up parcellated surfaces using the 2009 atlas? Putting in "-aparc.a2009s" does not seem to work (no parcellation is shown). I would like to see both lateral and medial surfaces, if possible. Thank you in advance! Sincerely, Maria **************************************** Maria Kharitonova, Ph.D. Laboratory of Cognitive Neuroscience Children's Hospital Boston

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parcellations to fmri space
by Christopher Bell 16 Jul '12

16 Jul '12

Hello Freesurfers, I have developed a pipeline that uses mri_label2vol to take freesurfer parcellations to native fmri space, and uses dilation (within mri_label2vol) to make the ROIs larger since our resolution is only 3.5x3.5x4 we would end up with only a few voxels for some ROIs due to large voxel size and partial voluming wihout the dilation. However, since the lh and rh are done separately by mri_label2vol, I now have overlap on the midline and have to go through a bunch of masking steps to eliminate it. My question is; is there a tool that will take both lh/rh parcellations to a new coordinate system, do dilation, and most importantly control for lh/rh overlap? Or any other similar suggestions. Thanks! Basically I am looking to rework my pipeline, and it seems I should be able to find a more parsimonious solution, than my "Rube Goldberg" approach. Chris

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the make_average_subject without aparc.annot
by Leon 16 Jul '12

16 Jul '12

Hi, Doug I found from the archive that you made a version of make_average_surface without the need for aparc.annot. I tried to download it but the link is not valid anymore. Could you please send me a copy of the file? I need to generate an averaged surface for a group of non-human primates and I was asked to input these annotation files that do not exist for non-human primate data. Many thanks! Leon Re: [Freesurfer] how to generate aparc.annotion files? Douglas N Greve Mon, 08 Nov 2010 09:55:49 -0800 It is needed in make_average_surface. I've created a new version that does not use the aparc (thought I have not tested it). You can get it from here: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/make_average_… Make a backup of your current version of make_average_surface and then copy this one over it douig

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Clusterwise correction for multiple comparisons
by Ed Gronenschild 16 Jul '12

16 Jul '12

Hi, I'm performing a clusterwise correction for multiple comparisons with the command mri_glmfit-sim --glmdir my_glmdir --sim mc-z 5000 1.3 basename \ --sim-sign abs For version v4.5.0 this took about 40 hours to complete. However, for v5.1.0 it is now running for more than 6 days and from the csd file I can read that it still has more than 1000 steps to go. Is it possible that it takes that much time? Cheers, Ed

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annot 2 label file conversion
by Arnaud Messé 16 Jul '12

16 Jul '12

Hi there, I've some troubles with parcellisation schemes. I've used mri_annotation2label to extract labels within annot file. When I read the annot file within matlab (read_annotation.m), I found 869 entries, everything looks good so far. However, when I look at the output directory of labels, I only found 770 label file. For another parcellisation scheme, I found 325 entries in annot file and 496 label files... These findings are consistent across several subjects. So my question is how mri_annotation2label processes annot file? and how to find correspondence between annot and label files? Any advice would be greatly appreciate, -- Arnaud Messé, PhD Laboratoire d'imagerie fonctionnelle (LIF) UMRS 678 Inserm/UPMC CHU Pitié-Salpêtrière 91 boulevard de l'Hôpital F-75634 Paris Cedex 13 +33(0)1538284 03 (fax: 48) Arnaud.Messe(a)imed.jussieu.fr http://www.imed.jussieu.fr

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