Freesurfer

freesurfer@nmr.mgh.harvard.edu

14 participants
30063 discussions

Qdec for Brodmann Areas
by Mohamed Ali Bahri 30 Oct '17

30 Oct '17

Dear Freesurfer experts, I would like to use "Qdec" tool to study the volume/cortical thickness of one region (Perirhinal) belonging to the Brodmann areas. As I understand Qdec load only the aparc and aseg stat lists. I am wondering if we could realty to do that with "Qdec"? Any suggestion/advice will be very welcome. Many thanks in advance, Best regards, Mohamed -- Dr. Mohamed Ali Bahri, 1er Logisticien de Recherche, Cyclotron Research Centre, University of Liège, Belgium m.bahri(a)uliege.be

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Recons for Allen Brain Institute T1 images with v5.3 online
by Melanie Ganz 30 Oct '17

30 Oct '17

Hi, So here’s the Wiki page for the human Allen brain data recons: https://surfer.nmr.mgh.harvard.edu/fswiki/AllenBrainAtlas Right now there’s only the v5.3 recons, but the v6 recons are coming asap. Cheers, Melanie

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dmrirc_v1
by 郑凤莲 30 Oct '17

30 Oct '17

Hi Professor， Thank you for publishing Freesurfer software. Now I am studying DTI using Freesurfer. And I am interested in the technology of TRACULA. But when I run it, I encountered an error about valid frame numbers, as shown in the picture. And there is my dmrirc file. Do you know which part is wrong? Have you met this error? My DTI data has 63 directions. I don't know how to correct it. I really appreciate your help. I am looking forward your reply. Thank you very much.

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cortical/subcortical volume based analysis
by miracle ozzoude 30 Oct '17

30 Oct '17

Hello FreeSurfer experts, I want to perform a whole brain volume based group analysis for cortical and subcortical regions. That's something very similar to surface based group analysis for cortical thickness however, for volume. Is there a tutorial on how to do it? if yes, please can i get the link. If not, please can someone direct me how to go about doing it? My goal is to perform a group comparison between control and PD patients based on volume. Thank you very much. Best, Paul

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dmrirc_v1
by 郑凤莲 30 Oct '17

30 Oct '17

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Dimensions change using mris_fill
by Fereshte 28 Oct '17

28 Oct '17

Dear Experts When I use " mris_fill" to fill inside a surface; the output volume dimension increases from 256 to such a huge number ( 700 or so). I'm not sure what the case is. I'd appreciate your help with it. Regards

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Recon-all error message
by Lee, Seonjoo 27 Oct '17

27 Oct '17

Dear Freesurfers, I had the following error message while I was running recon-all: Reading curvature file /Data/MRI/002_S_1155-S178671/surf/lh./Data/MRI/002_S_1155-S178671/surf/lh.white.K MRISreadCurvature: could not open Data/MRI/002_S_1155-S178671/surf/lh./Data/MRI/ 002_S_1155-S178671/surf/lh.white.K No such file or directory ERROR: reading curvature file I set the SUBJECTS_DIR=/Data/MRI and it seems something to do with this error, but not sure how to fix it. Any thought? Thank you so much. -Seonjoo

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Re: [Freesurfer] lGI mris_fill Error
by Maksimovskiy, Arkadiy 27 Oct '17

27 Oct '17

Thank you so much for this suggestion. It worked perfectly. I really appreciate all of your help- with this and the previous question. Best, Arkadiy -- Arkadiy L. Maksimovskiy, Ph.D. Postdoctoral Research Fellow McLean Imaging Center, McLean Hospital Department of Psychiatry, Harvard Medical School

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lGI mris_fill Error
by Maksimovskiy, Arkadiy 27 Oct '17

27 Oct '17

Dear LGI Experts, I am attempting to run LGI using the freesurfer Dev Version (2017), and am getting the following error: [arkadiysimac:Freesurfer/Freesurfer_Files_with_Freesurfer_Masks/Post_Manual_Edits] amaksimovskiy% recon-all -s SUBJ002 -localGI INFO: FreeSurfer build stamps do not match Subject Stamp: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c Current Stamp: freesurfer-Darwin-OSX-dev-20171020-5567595 INFO: SUBJECTS_DIR is /Volumeslab/Arkadiy/Freesurfer/Freesurfer_Files_with_Freesurfer_Masks/Post_Manual_Edits Actual FREESURFER_HOME /Applications/freesurfer -rwx------ 1 amaksimovskiy staff 2449841 Oct 27 13:40 /Volumeslab/Arkadiy/Freesurfer/Freesurfer_Files_with_Freesurfer_Masks/Post_Manual_Edits/SUBJ002/scripts/recon-all.log Darwin arkadiysimac.mclean.harvard.edu 16.7.0 Darwin Kernel Version 16.7.0: Thu Jun 15 17:36:27 PDT 2017; root:xnu-3789.70.16~2/RELEASE_X86_64 x86_64 INFO: current FREESURFER_HOME does not match that of previous processing. Current: /Applications/freesurfer Previous: /cm/shared/freesurfer /Volumeslab/Arkadiy/Freesurfer/Freesurfer_Files_with_Freesurfer_Masks/Post_Manual_Edits/SUBJ002/surf #-------------------------------------------- #@# Local Gyrification Index lh Fri Oct 27 13:52:07 EDT 2017 \n mris_compute_lgi --i lh.pial \n ================= rm -Rf /Volumeslab/Arkadiy/Freesurfer/Freesurfer_Files_with_Freesurfer_Masks/Post_Manual_Edits/SUBJ002/surf/tmp-mris_compute_lgi-lh.pial ================= ================= mkdir -p /Volumeslab/Arkadiy/Freesurfer/Freesurfer_Files_with_Freesurfer_Masks/Post_Manual_Edits/SUBJ002/surf/tmp-mris_compute_lgi-lh.pial ================= ================= mris_fill -c -r 1 lh.pial /Volumeslab/Arkadiy/Freesurfer/Freesurfer_Files_with_Freesurfer_Masks/Post_Manual_Edits/SUBJ002/surf/tmp-mris_compute_lgi-lh.pial/lh.pial.filled.mgz ================= reading surface from lh.pial... freadInt: fread failed conforming output volume setting resolution for intermediate calculations to 1.0000 No such file or directory dyld: lazy symbol binding failed: Symbol not found: ___emutls_get_address Referenced from: /Applications/freesurfer/bin/../lib/gcc/lib/libgomp.1.dylib Expected in: /usr/lib/libSystem.B.dylib dyld: Symbol not found: ___emutls_get_address Referenced from: /Applications/freesurfer/bin/../lib/gcc/lib/libgomp.1.dylib Expected in: /usr/lib/libSystem.B.dylib Abort ERROR: mris_fill -c -r 1 lh.pial /Volumeslab/Arkadiy/Freesurfer/Freesurfer_Files_with_Freesurfer_Masks/Post_Manual_Edits/SUBJ002/surf/tmp-mris_compute_lgi-lh.pial/lh.pial.filled.mgz failed! Darwin arkadiysimac.mclean.harvard.edu 16.7.0 Darwin Kernel Version 16.7.0: Thu Jun 15 17:36:27 PDT 2017; root:xnu-3789.70.16~2/RELEASE_X86_64 x86_64 recon-all -s SUBJ002 exited with ERRORS at Fri Oct 27 13:52:08 EDT 2017 For more details, see the log file /Volumeslab/Arkadiy/Freesurfer/Freesurfer_Files_with_Freesurfer_Masks/Post_Manual_Edits/SUBJ002/scripts/recon-all.log To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting I have not found anything similar to this issue in the archives, and wondering if anyone might have suggestions. Much appreciated, Arkadiy -- Arkadiy L. Maksimovskiy, Ph.D. Postdoctoral Research Fellow McLean Imaging Center, McLean Hospital Department of Psychiatry, Harvard Medical School

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XL Defect Correction
by Arsenije Subotic 27 Oct '17

27 Oct '17

Dear Freesurfer experts, During my recon-all I encountered a problem for one of my subjects, where the process got stalled at "CORRECTING DEFECT 12 (vertices=21293, convex hull=1791) XL defect detected...". I've checked the output and it seems that skull-stripping hasn't been performed properly, but I do not know exactly if there are any other underlying issues. I've attached some screenshots for your consideration. I know that some defects can be fixed using manual correction or using control points, but I'm unsure exactly of what steps to take going forward. I appreciate your help and any input. Best regards, Arsenije

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