Freesurfer

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30089 discussions

Allen Brain Institute to Freesurfer Labels
by MCLAREN, Donald 20 Jun '12

20 Jun '12

Does anyone have a mapping of the Allen Brain Institute labels to the freesurfer parcellations? Just the labels would be sufficient for these purposes. Best Regards, Donald McLaren ================= D.G. McLaren, Ph.D. Postdoctoral Research Fellow, GRECC, Bedford VA Research Fellow, Department of Neurology, Massachusetts General Hospital and Harvard Medical School Website: http://www.martinos.org/~mclaren Office: (773) 406-2464 ===================== This e-mail contains CONFIDENTIAL INFORMATION which may contain PROTECTED HEALTHCARE INFORMATION and may also be LEGALLY PRIVILEGED and which is intended only for the use of the individual or entity named above. If the reader of the e-mail is not the intended recipient or the employee or agent responsible for delivering it to the intended recipient, you are hereby notified that you are in possession of confidential and privileged information. Any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited and may be unlawful. If you have received this e-mail unintentionally, please immediately notify the sender via telephone at (773) 406-2464 or email.

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Re: [Freesurfer] Recent paper on FreeSurfer reliability
by Peter J. Molfese 20 Jun '12

20 Jun '12

We run things on an Xgrid cluster that is now a mixture of Macs running Snow Leopard (10.6.8) and Lion (10.7.x). We found the results given from asegstats2table and aparcstats2table are identical after running 100 subjects on both Mac OS X 10.7.4 and 10.6.8 with Freesurfer 5.1. I also ran a few subjects on the cluster and on individual computers (not on the cluster so to speak) and the results are identical. Best, Peter > Hi, > > The paper entitled > > “The Effects of FreeSurfer Version, Workstation Type, > and Macintosh Operating System Version on Anatomical > Volume and Cortical Thickness Measurements”, > PLoSONE, Vol 7(6), e38234 (2012) > > may be of interest to all of you. It can be found at: > > http://dx.plos.org/10.1371/journal.pone.0038234 > > Cheers, > Ed

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Assigning cluster index
by John Richey 20 Jun '12

20 Jun '12

Dear Freesurfer experts, I have a fairly simple question, but it is not immediately clear to me how to solve it. I have a statistical parameter map representing the results of a group-level analysis. After thresholding the map (p<.05), several significant clusters remain, and I want to assign each cluster a unique index number (e.g. 1,2,3 etc). This unique index will be useful to me later, but it is not clear how I could do this using freesurfer tools. Thanks in advance, John

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MNI coordinates of all the vertices of fsaverage
by Yolanda Vives 20 Jun '12

20 Jun '12

Dear Freesurfer experts, How could I know the MNI coordinates of the 163.842 vertices of the left hemisphere of fsaverage? Best regards, Yolanda

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mris_label2annot mislabeling
by Arno Klein 20 Jun '12

20 Jun '12

hello! i have saved a couple of .label files and am trying to convert them to a .annot file with: mris_label2annot --h lh --s MMRR-21-1 --l lh.superiorfrontal.label --l lh.superiorparietal.label --ctab FreeSurferColorLUT.txt --a output the stdout is: ColorTable atlas_colortable.txt AnnotName output nlables 2 LabelThresh 0 0.000000 Loading /usr/local/freesurfer/subjects/MMRR-21-1/surf/lh.orig 1 11829830 Left-Cerebral-Exterior 2 16119285 Left-Cerebral-White-Matter Mapping unhit to unknown ... clearly the anatomical names assigned are incorrect, and when i view the output with tksurfer, the labeled patches are in the right places but are assigned these same incorrect anatomical names. i have tried renaming the .label files to no avail. what am i doing wrong? cheers, @rno

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Editing Putamen Segmentation
by Kristin Javaras 20 Jun '12

20 Jun '12

Dear all, For a number of my participants, Freesurfer's automated segmentation of the putamen appears to include brain matter that isn't putamen - this problem persists across 5-6 slices, on average. I was wondering what people would recommend - should I edit the aseg? Thank you in advance for any advice, Kristin Javaras _______________________________ Kristin N. Javaras, PhD Waisman Laboratory for Brain Imaging and Behavior University of Wisconsin - Madison 1500 Highland Avenue Madison, WI 53705 Telephone : +1 (608) 890-1407

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Re: [Freesurfer] -inter error
by Anastasia Yendiki 20 Jun '12

20 Jun '12

Oops, that's a typo, meant "is unavailable". In any case something like this should show up early in the logs. On Wed, 20 Jun 2012, Bruce Fischl wrote: > "not unavailable"???? > > On Wed, 20 Jun 2012, Anastasia Yendiki wrote: > >> >> Hi Maria - Do you at any point get the following warning? >> "WARN: CVS template is not unavailable in the current version" >> >> Thanks, >> a.y >> >> On Wed, 20 Jun 2012, Maria Gemzicka wrote: >> >> > Hi, >> > I run -corr and -intra with no errors. -inter finishes without errors if >> > does not use doregcvs. >> > When I want to use cvs for registration, I get error: >> > >> > iterating >> > >> > done with candidates >> > >> > Active BCs = 91494 >> > >> > Total BCs = 548640 >> > >> > no-eqs = 245610 >> > >> > surf2vol(26656) malloc: *** mmap(size=295714816) failed (error code=12) >> > >> > *** error: can't allocate region >> > >> > *** set a breakpoint in malloc_error_break to debug >> > >> > [0]PETSC ERROR: --------------------- Error Message >> > ------------------------------------ >> > >> > [0]PETSC ERROR: Out of memory. This could be due to allocating >> > >> > [0]PETSC ERROR: too large an object or bleeding by not properly >> > >> > [0]PETSC ERROR: destroying unneeded objects. >> > >> > [0]PETSC ERROR: Memory allocated 0 Memory used by process 0 >> > >> > [0]PETSC ERROR: Try running with -malloc_dump or -malloc_log for info. >> > >> > [0]PETSC ERROR: Memory requested 295714444! >> > >> > >> > >> > trac-all.error in scripts: >> > >> > >> > ...... >> > >> > PROCESSOR x86_64 >> > >> > OS Darwin >> > >> > Darwin shemp.mri.yorku.ca 11.4.0 Darwin Kernel Version 11.4.0: Mon Apr >> > 9 >> > 19:32:15 PDT 2012; root:xnu-1699.26.8~1/RELEASE_X86_64 x86_64 >> > >> > $Id: trac-preproc,v 1.17.2.5 2011/05/20 06:51:51 ayendiki Exp $ >> > >> > /Users/Maria/Applications/freesurfer/bin/trac-preproc >> > >> > PWD /Users/Maria >> > >> > CMD mri_cvs_register --mov mgFS6 --template cvs_avg35 --outdir >> > /Users/maria/Desktop/mgFS/mgFS6/dmri/xfms/cvs >> > >> > >> > Thank you. >> > >> > >> >

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-inter error
by Maria Gemzicka 20 Jun '12

20 Jun '12

Hi, I run -corr and -intra with no errors. -inter finishes without errors if does not use doregcvs. When I want to use cvs for registration, I get error: iterating done with candidates Active BCs = 91494 Total BCs = 548640 no-eqs = 245610 surf2vol(26656) malloc: *** mmap(size=295714816) failed (error code=12) *** error: can't allocate region *** set a breakpoint in malloc_error_break to debug [0]PETSC ERROR: --------------------- Error Message ------------------------------------ [0]PETSC ERROR: Out of memory. This could be due to allocating [0]PETSC ERROR: too large an object or bleeding by not properly [0]PETSC ERROR: destroying unneeded objects. [0]PETSC ERROR: Memory allocated 0 Memory used by process 0 [0]PETSC ERROR: Try running with -malloc_dump or -malloc_log for info. [0]PETSC ERROR: Memory requested 295714444! trac-all.error in scripts: ...... PROCESSOR x86_64 OS Darwin Darwin shemp.mri.yorku.ca 11.4.0 Darwin Kernel Version 11.4.0: Mon Apr 9 19:32:15 PDT 2012; root:xnu-1699.26.8~1/RELEASE_X86_64 x86_64 $Id: trac-preproc,v 1.17.2.5 2011/05/20 06:51:51 ayendiki Exp $ /Users/Maria/Applications/freesurfer/bin/trac-preproc PWD /Users/Maria CMD mri_cvs_register --mov mgFS6 --template cvs_avg35 --outdir /Users/maria/Desktop/mgFS/mgFS6/dmri/xfms/cvs Thank you.

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qdec
by Jenny Liu 20 Jun '12

20 Jun '12

Hello I am using the Qdec Analysis.The long and base directories are created already, and I am at the first stage of post-processing. For the long_mri_slopes command, there seems to be some difficulty for Qdec to find the appropriate folder. As background, in my qdec table, I have the fsid and the fsid-base (along with other variables) (see attached too) ie. fsid fsid-base group age painUnp tp WB101_1 WB101_template MNP 65.72 11.7 0 The first command that the instructions tell me to do is: long_mris_slopes --qdec ./qdec/long.qdec.table.dat --meas thickness --hemi lh --do-avg --do-rate --do-pc1 --do-spc --do-stack --do-label --time tp --qcache fsaverage However, the error comes up as: ERROR: /study/NCCAM/Data/MRI/processed/structural/freesurfer/WB101_1.long.WB101_template/label/lh.cortex.label does not exist! To check this error, I search the directory of freesurfer, and there are several folders for WB101. One is labeled "WB101_1.long.WB101_template"; another is labeled "WB101_template". The "WB101_1.long.WB101_template" directory does not contain the file "/label/lh.cortex.label" or the file "/surf/lh.thickness", but the "WB101_template" directory does. How do I change the commands of the long_mri_slopes so that it reads the "WB101_template" directory to find these two files, instead of the "WB101_1.long.WB101_template" directory? Or is the error due to another issue? Thanks, Jen

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ROI labels
by Cat Chong 19 Jun '12

19 Jun '12

Dear Freesurfers, I would like to show several ROI labels that we created on top of an an average brain which demonstrates the group results of cortical thinning with advancing age. In qdec, when I go into File>Load Label, I can only view one label at a time. Is there a way to show several labels together on an average brain, just for visualization purposes? cheers, Cat

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