Freesurfer October 2017

freesurfer@nmr.mgh.harvard.edu

119 participants
179 discussions

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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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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Re: [Freesurfer] segmentHA znzread failed error
by Maksimovskiy, Arkadiy 27 Oct '17

27 Oct '17

Thank you so much for your help with this. Much appreciated, * Arkadiy

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hippocampal subfields downsampling question
by NIELS JANSSEN . 26 Oct '17

26 Oct '17

In the mri output folder, I noticed that both the 0.33 mm and 1 mm (voxelspace) maps have subfields that do not overlap in space, meaning that each subfield occupies a unique location in space that does not overlap with other subfields (i.e., 12 subfields and 12 unique voxel intensities). I am wondering how this is achieved for both resolutions simultaneously. Do you 'fit' the subfields first to the 0.33 mm data and then transform the data to the 1mm space, or do you fit to both spaces separately? I would like to transform the subfields to 1.5 mm data and are able to do so accurately, but I run into problems with subfield overlap because of the down sampling. I am wondering how to best deal with this issue, and from seeing non-overlapping subfields at both 0.33 and 1 mm I am thinking there must be someway to deal with this issue. -- Niels Janssen Brain Imaging Laboratory Institute of Biomedical Technologies Center for Biomedical Research of the Canary Islands University of La Laguna Tenerife, Spain https://sites.google.com/view/nielsjanssen/

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Preproc-sess Error
by Hsu, Eugene 26 Oct '17

26 Oct '17

Hi FreeSurfer Experts, We're trying to run preproc-sess on FreeSurfer 6, but we're encountering an error when motion correcting: ERROR: cannot find AFNI command 3dvolreg.afni When we tried Freesurfer 5.3 the preproc-sess ran to completion. Thanks for your help! --Eugene

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freesurfer errors-windows bash
by Alexandre Obert 26 Oct '17

26 Oct '17

Dear all, I'm would like to run a hippocampal segmentation on my data. However, I'm a beginner with freesurfer thus, I juste try to run the commands with subject training data. I first try to run commands following the recent development ( https://surfer.nmr.mgh.harvard.edu/fswiki/HippocampalSubfieldsAndNucleiOfAm…) However, terminal says that the command segmentHA.sh doesn't exist. I guess that it could be linked to the fact that I used bash in Windows but I can't find a way to check this..; Any idea ? Regards, Alexandre

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Freesurfer October 2017