Freesurfer September 2018

freesurfer@nmr.mgh.harvard.edu

109 participants
160 discussions

matlab MEXFile error in thalamic nuclei segmentation script
by Carme Uribe Codesal 21 Sep '18

21 Sep '18

External Email - Use Caution Dear FreeSurfer users, I am trying to run the Thalamic nuclei and the hippocampal/amygdala segmentation scripts but there is an error with the matlab license. The error message is: LD_LIBRARY_PATH is .:/nas01/users/carme/freesurfer/MCRv84//runtime/glnxa64:/nas01/users/carme/freesurfer/MCRv84//bin/glnxa64:/nas01/users/carme/freesurfer/MCRv84//sys/os/glnxa64:/nas01/users/carme/freesurfer/MCRv84//sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/nas01/users/carme/freesurfer/MCRv84//sys/java/jre/glnxa64/jre/lib/amd64/server:/nas01/users/carme/freesurfer/MCRv84//sys/java/jre/glnxa64/jre/lib/amd64/client:/nas01/users/carme/freesurfer/MCRv84//sys/java/jre/glnxa64/jre/lib/amd64:/usr/libexec/NX3/lib64/Xinerama:/usr/lib/nx/X11 Invalid MEX-file '/tmp/MCR_714808722/.mcrCache8.4/Segmen0/autofs/space/panamint_005/users/iglesias/software/freesurfer.GEMS2/bin/kvlGEMSMatlab.mexa64': /lib64/libc.so.6: version `GLIBC_2.14' not found (required by /tmp/MCR_714808722/.mcrCache8.4/Segmen0/autofs/space/panamint_005/users/iglesias/software/freesurfer.GEMS2/bin/kvlGEMSMatlab.mexa64) Error in kvlClear (line 11) Error in SegmentThalamicNuclei (line 203) MATLAB:invalidMEXFile Thanks! Carme Uribe

3 2

trac-all using nifti
by Heidi Emmanuel Foo 21 Sep '18

21 Sep '18

External Email - Use Caution Hi Anastasia, I am currently trying to run trac-all with my DWI data. I do not have the DICOM but only the Nifti files and I would like to use the same bval and bvec template for every subject. I created a configiration file as attached. However, I have the following error message: : Command not found. : Command not found. set: Variable name must begin with a letter. does not exist.DIR /data_int/heidi/forHeidi/Preprocessed It would be great if you could advise me on what to do. Thank you! Best Regards, Heidi Foo

2 8

segmentThalamicNuclei.sh do not produce .stats
by stdp82＠virgilio.it 20 Sep '18

20 Sep '18

External Email - Use Caution Hi list, the segmentThalamicNuclei.sh do not produce thalamic-nuclei.lh.v10.T1.stats. All the other files are produced (ThalamicNuclei.v10.T1.volumes.txt/mgz). The segmentation viewed by freeview is fine. Thanks. Stefano

1 0

ERROR: no voxels found in segmentation- Outputs of segmentThalamicNuclei.sh in FS-FAST
by stdp82＠virgilio.it 20 Sep '18

20 Sep '18

External Email - Use Caution Hi I'm using as seed in FS-FAST the outputs of segmentThalamicNuclei.sh. However when I run fcseed-config -segid 8103 -fcname L_AV.dat -fsd rest -mean -cfg mean.L_AV.config fcseed-sess -sf sessid -cfg mean.L_AV.config this error occurs: Voxel Volume is 36.3469 mm^3 Generating list of segmentation ids Found 1 segmentations Computing statistics for each segmentation Reporting on 0 segmentations Using PrintSegStat Computing spatial average of each frame ERROR: no voxels found in segmentation

1 0

asegstats2table - env: python2: No such file or directory
by stdp82＠virgilio.it 20 Sep '18

20 Sep '18

External Email - Use Caution I'm using last version dev with MacOS High Sierra 10.13.6. I have run, for each subject: segmentThalamicNuclei.sh but when I run the command line "asegstats2table", I obtain: env: python2: No such file or directory Thanks Stefano

2 1

Re: [Freesurfer] Reporting Cohen's D for a significant cluster
by Maksimovskiy, Arkadiy 20 Sep '18

20 Sep '18

Hi Bruce, Thank you so much for the tip and the quick response. For some reason, the position and Cohen’s D value do not change when I input the vertex and I think this might be due to an outdated Freeview version (2.0) that I am using. I attempted to load the new one from this link: https://surfer.nmr.mgh.harvard.edu/fswiki/UpdateFreeview But I am getting an error: The requested URL /pub/dist/freesurfer/freeview/freeview_osx.tar.gz was not found on this server. I was wondering if you have this file available at another location? Thanks again, arkadiy -- Arkadiy L. Maksimovskiy, Ph.D. Postdoctoral Research Fellow McLean Imaging Center, McLean Hospital Department of Psychiatry, Harvard Medical School -- Arkadiy L. Maksimovskiy, Ph.D. Postdoctoral Research Fellow McLean Imaging Center, McLean Hospital Department of Psychiatry, Harvard Medical School

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Reporting Cohen's D for a significant cluster
by Maksimovskiy, Arkadiy 20 Sep '18

20 Sep '18

Dear Experts, I was requested to report the Cohen’s D value for a significant cluster, which resulted from a cortical thickness analysis. I was able to calculate it and open the resulting Cohen’s D mgh file in Freeview, together with the file, indicating a significant cluster. As expected, when I move the cursor within the significant cluster, Cohen’s D value changes with every vertex. I was wondering if you might have any recommendations for which of the Cohen’s D values to report, and how best to obtain that value? Thank you for your help, arkadiy -- Arkadiy L. Maksimovskiy, Ph.D. Postdoctoral Research Fellow McLean Imaging Center, McLean Hospital Department of Psychiatry, Harvard Medical School

2 2

Troubles to determine the type of recon editing needed
by Diamond, Bram Ryder 20 Sep '18

20 Sep '18

Hi Matthieu, I've taken a look through the files you shared with us and I see the poor surfaces in the posterior right hemisphere you were referring to in your message. It looks like your subject has a combination of abnormally large ventricles and significant wm abnormalities, so I'm surprised FreeSurfer did as well as it did. As for the recon editing - I would recommend editing the wm.mgz to more accurately represent the wm from slice 84 to 39. You can take a look at the white matter edits tutorial<https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/WhiteMatterEditsV6.0> for details on how to do that. Then run the following command (substituting <subj_id> for your subject's id): recon-all -autorecon2-wm -autorecon3 -subjid <subj_id> The surface reconstruction may also benefit from labeling the right lateral ventricle in the wm.mgz (as an intensity of 250) - but I'm not certain since you didn't send us the surfaces for the left hemisphere. Before you do that, edit the wm.mgz as explained in the tutorial and tell us how that goes. All the best, Bram Bram R. Diamond, BSc Research Technician II Laboratory for Computational Neuroimaging Martinos Center for Biomedical Imaging Massachusetts General Hospital 149 13th Street Charlestown, MA 02129 (p): 617-726-6598

3 12

Error running recon-all
by Mark Wagshul 20 Sep '18

20 Sep '18

External Email - Use Caution Hi. I am getting the following error trying to run recon-all (with Version 6.0), it is failing while running the routine mri_nu_correct.mni: Can't locate MNI/Startup.pm in @INC (@INC contains: /usr/local/lib64/perl5 /usr/local/share/perl5 /usr/lib64/perl5/vendor_perl /usr/share/perl5/vendor_perl /usr/lib64/perl5 /usr/share/perl5 .) at /public/apps/freesurfer/6.0.0/mni/bin/nu_correct line 37. I am guessing that this has to do with the setup of the environment variables, but not sure what needs fixing. Any advice would be much appreciated, thanks. Mark ____________________ Mark Wagshul, PhD Associate Professor Gruss Magnetic Resonance Research Center Albert Einstein College of Medicine Bronx, NY 10461 Ph: 718-430-4011 FAX: 718-430-3399 Email: mark.wagshul(a)einstein.yu.edu<mailto:mark.wagshul@einstein.yu.edu> [einstein-logo-rgb] This email message and any accompanying attachments may contain privileged information intended only for the named recipient(s). If you are not the intended recipient(s), you are hereby notified that the dissemination, distribution, and or copying of this message is strictly prohibited. If you receive this message in error, or are not the named recipient(s), please notify the sender at the email address above, delete this email from your computer, and destroy any copies in any form immediately.

1 0

freeview automated screenshots using color wheel scale & qt library issues
by Emil H.J. Nijhuis 20 Sep '18

20 Sep '18

External Email - Use Caution Hi, I am attempting to generate automated screenshots with freeview version 3.July 2018 and I noticed that when applying the color wheel option for a surface overlay the coloring would be wrongly applied and I would need to enter the configuration window to fix/refresh the overlay coloring. Is there any way to enforce a refresh for overlays using the command line? Also is there a way to save/load custom color scales with the command line? I tried to use the latest developmental freeview.bin, however it gives me the error: version 'qt_5' not found; for 4 existing qt libraries which are softlinked to a newer versions (qt 5.5) in my system. Do you have any advice to achieve automated screenshots with freeview? With kind regards, Emil Nijhuis

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Freesurfer September 2018