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30132 discussions

GLM
by 郑凤莲 23 Sep '18

23 Sep '18

External Email - Use Caution Dear experts, I am using FS 6.0 for some studies. I want to calculate the thickness difference between males and females in two group, Young group and Old group. In DODS model: The first step: creat a FSDG file: GroupDescriptorFile 2 Title Tutorial Class Young, Female Class Old, Male Variables education Input P01 Young Female 11 Input P02 Old Male 9 Input P03 Young Male 10 The second step: creat contrast matrix 1 -1 -1 1 0 0 0 0 Is it right? I am not sure if the FSDG file and contrast file are right. Waiting for you to solve my problem. Thanks for your attention and help. Sincerely, Zheng

2 1

mri_glmfit-sim error
by C.P.E. Rollins 23 Sep '18

23 Sep '18

External Email - Use Caution Hello Freesurfer Developpers, I'm trying to use mri_glmfit-sim to make clusterwise corrections but am running into the following error: ------------- XFM matrix (RAS2RAS) --------------- /lustre/group/p00355/REST_Beijing_SCZ/Freesurfer/fsaverage/mri/transforms/talairach.xfm 1.00000 0.00000 0.00000 0.00000; 0.00000 1.00000 0.00000 0.00000; 0.00000 0.00000 1.00000 0.00000; 0.00000 0.00000 0.00000 1.00000; MRISread('\ufffd\ufffd): could not open file No such file or directory ---------------------------------------------------- Reading source surface /lustre/group/p00355/REST_Beijing_SCZ/Freesurfer/fsaverage/surf/rh.white mri_surfcluster.bin: could not read surface /lustre/group/p00355/REST_Beijing_SCZ/Freesurfer/fsaverage/surf/rh.white No such file or directory I've attached here the log file. I was wondering if you had any insights into the error? Thanks a lot for your help. Colleen

2 1

Blood vessels FreeSurfer
by Žaneta Železnikova 23 Sep '18

23 Sep '18

External Email - Use Caution Hello, I couldn't find a clear answer online but it's possible to visualize only blood vessels of the brain? Thank you

2 1

Problems with thalami nuclei segmentation
by stdp82＠virgilio.it 22 Sep '18

22 Sep '18

External Email - Use Caution Hi list, 1- I have run the segmentThalamicNuclei.sh but .stats file has been not produced in any subjects. I have also try to re-run recon-all with dev version but fulling. 2 - Moreover, when I use the thalami segmentation as seed in FS-FAST I obtain the error listed below 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 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 Please could you give me can help? Stefano

1 0

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>

3 5

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

1 0

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

2 1

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

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