Freesurfer May 2012

freesurfer@nmr.mgh.harvard.edu

137 participants
209 discussions

OBJ conversion
by Darshan P 03 May '12

03 May '12

Hello all, I was wondering if I can convert the surface outputs to an OBJ mesh file format . Since most of the applications are in windows I was hoping if there is conversion tool to do this . Regards Darshan

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Question about version upgrade
by Efrat Kliper 02 May '12

02 May '12

Dear FreeSurfer expert, I am currently working on FreeSurfer Version 4.5.0 and already performed an analysis for approximately 200 subjects. Is there a way to change the version that I am working on (4.5.0) to 5.0.1 without the need to run recon-all again in the new version? Thanks in advanced, efrat

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correlation coefficient
by Tetiana Dadakova 02 May '12

02 May '12

Dear FS experts, I try to look at correlation between thickness and performance. I run mri_glmfit (using performance as covariate) and mri_glmfit-sim. After this I get some significant clusters. I would like to ask if I could get a correlation coefficient for these clusters, or/and a regression plot? Thank you, Tanja.

2 1

How to obtain cortical thickness in fsaverage space
by ZhiLiangLong 02 May '12

02 May '12

Hi all: After finishing group analysis, how can i obtain the thickness value of each ROIs showing significant group-difference in fsaverage space? That is to say, how i get the value of each ROIs which have been normalized to the fsaverage template. The method suggested in tutorials page(http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/QdecGroupAnalysis) just tells the way to get the thickness values in individual space.

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Re: [Freesurfer] Freeview chrash
by Focke, Niels 02 May '12

02 May '12

Dear Ruopeng, this happens with any surface, for example "bert" lh/rh.pial (that comes with Freesurfer). I have attached a locally generated surface as well, but I would guess that the problem is not the surface (files) but rather freeview itself or an incompatibility maybe with the Centos 5 libraries (btw. I have the same problem on Centos 5.2 on another machine). I have just noted, that another user has reported the same (or similar) problem recently (https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2012-April/023361.htm l) in ubuntu. Although this thread seems to have ended without resolution. Cheers, Niels __________________________________________________________________________ Dr. Niels Focke Klinische Neurophysiologie UMG - Universitätsmedizin Göttingen

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mri_path2label segmentation fault, with recon-all -localGI
by veronica misc 01 May '12

01 May '12

Hi all, I've been getting a segmentation fault and was hoping someone could help/advise. I have been running recon-all -s [subject] -localGI, and eventually I get an segmentation fault (log below). The error occurs with all subjects, running on numerous machines. I remember I was able to run the same command a few months ago with success. The seg fault seems to happen during mri_path2label, and it doesn't crash right away but gets pretty far along first. I am running Freesurfer 'stable5' on Martinos. I tried with 'stable' and got the same error. Thanks! Veronica Filling 1176 nlabel 10560 Saving label file /autofs/cluster/purdonlab/users/vsw/archive/intracranial-induction/freesurfer-output/mg43/surf/tmp-mris_compute_lgi-rh.pial/rh.pial.001301.label LabelWrite: saving to /autofs/cluster/purdonlab/users/vsw/archive/intracranial-induction/freesurfer-output/mg43/surf/tmp-mris_compute_lgi-rh.pial/rh.pial.001301.label Connecting and filling vertices in path at fillseed 160894 Finding path.................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................... done Segmentation fault (core dumped) ERROR: mri_path2label --confillxfn rh.pial /autofs/cluster/purdonlab/users/vsw/archive/intracranial-induction/freesurfer-output/mg43/surf/tmp-mris_compute_lgi-rh.pial/mri_path2label.input failed!

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How to fix pial surface looping errors
by Laura M. Tully 01 May '12

01 May '12

Hi Freesurfer Experts, I am finding strange loops in the pial surface of my subjects and I'm not sure how to fix them. They do not seem to be caused by problems in the brainmask.mgz - the wm surface looks fine - and they do no seem to be caused by problems in the wm.mgz. What is the best way to deal with them? I have attached a few tiff examples of these loops as visualized in the brainmask.mgz and accomanying saved points in the inflated surfaces so that you can see what I am referencing. Any advice you have would be most appreciated! Best, Laura. -- Laura Tully Social Neuroscience & Psychopathology Harvard University 840 William James Hall 33 Kirkland St Cambridge, MA 02138 ltully(a)fas.harvard.edu -- My musings as a young clinical scientist: http://theclinicalbrain.blogspot.com/

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WM-hypointensities
by Steven Korycinski 01 May '12

01 May '12

To all, I've been using aseg.stats to gather volumetric data about size of the left caudate for a group of subjects. For one subject in particular, there's a large purple-colored area labeled "WM-hypointensities" near the left caudate in aseg.mgz (see attached image) that looks to me like it should be labeled caudate instead (though I'll admit, I'm not an expert in neuroanatomy). I know that aseg.mgz is used in generating the statistics in aseg.stats, so I'm concerned that if I am correct the statistics I've been using are not accurate. Can anyone help me understand what these "WM-hypointensities" are and why there seems to be a large area labeled as such for this particular subject? Am I correct in assuming that an error of some kind may have occurred, and that this area should actually be labeled as caudate? Thanks, -Steve

2 1

mutualinfo in flirt T1->MNI registration
by Andi Heckel 01 May '12

01 May '12

Dear Tracula Team, i noticed that TRACULA uses fsl's flirt with "mutualinfo" as cost function to register the anatomical individual T1 brain (brain_anat.nii.gz) to the MNI152 space T1 template (MNI152_T1_1mm_brain.nii.gz), i.e. for an intramodal registration. I was wondering why "mutualinfo" (which is often used for intermodal registrations) is also used for a an intramodal registration in TRACULA'S implementation rather than e.g. least squares or correlation ratio, the latter being the fsl default. Is "mutualinfo" preferable not only for intermodal (e.g., b0 -> t1) but also for intramodal t1->t1 registrations for your purpose ? - I am just curious to know :) kind regards, andi

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Freesurfer May 2012