Freesurfer

freesurfer@nmr.mgh.harvard.edu

30088 discussions

linux data and macbook
by emre 21 Sep '18

21 Sep '18

External Email - Use Caution hi freesurfer team, I analyzed the data at linux, this data i can use in macbook for segmantation? (linux only reconall -all, other analyze in macbook) Is it possible without problems? thanks, good luck Gönderen Outlook<http://aka.ms/weboutlook>

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Best way to update Freeview
by Maksimovskiy, Arkadiy 21 Sep '18

21 Sep '18

Dear Experts, Updating Freeview came up as a potential solution for a problem in a different thread, so I posting this as a separate issue, since the question stands on its own. I am currently using “Freeview Version 2.0” – Build Jan 19 2017. This version came with the Freesurfer 6.0 package, but from browsing the wiki, it seems that this version is out of date and requires a separate update. When I attempted to update Freeview, by clicking on “freeview_osx.tar.gz” using the link at Step 2 for Mac (located at this page: https://surfer.nmr.mgh.harvard.edu/fswiki/UpdateFreeview) I get the following error message: “The requested URL /pub/dist/freesurfer/freeview/freeview_osx.tar.gz was not found on this server.” I was wondering if there might a different way to obtain the latest Freeview version. Thank you for your help, arkadiy

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Dead Links to 3rd Party Libraries
by Moon, Joseph Young-Joon 21 Sep '18

21 Sep '18

External Email - Use Caution Hi, I’m trying to build Freesurfer according to the instructions athttp://surfer.nmr.mgh.harvard.edu/fswiki/freesurfer_linux_developers_page However, the FTP link to prebuilt 3rd party libraries seems to be down. The directory “ftp://surfer.nmr.mgh.harvard.edu/pub/dist/fs_supportlibs/prebuilt” is no longer being hosted. Please let me know if I misunderstood something! Thanks, Joseph Moon

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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

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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

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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

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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

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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

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