Freesurfer September 2018

freesurfer@nmr.mgh.harvard.edu

109 participants
160 discussions

Visualization fo brain vessels
by Patrik Krumpolec 24 Sep '18

24 Sep '18

External Email - Use Caution Good morning! I want to ask if it is possible to visualize compartment of brain vessels in freesurfer through freeview. Thank You very much and have a nice day! patrik krumpolec

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calculated cortical thickness from segmented binary gray matter and white matter images from other software
by yuanchao.zhang8＠gmail.com 23 Sep '18

23 Sep '18

External Email - Use Caution Dear experts, Is there any way I can calculate the cortical thickness based on gray matter and white matter binary images from other software. I mean I have a image in native space with white matter voxels labelled as 10 and gray matter voxels labelled as 5. Is there any way I can manage to calculate the cortical maps from this image using freesurfer? Thanks a lot! Best, Yuanchao Zhang yuanchao.zhang8(a)gmail.com

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make_average_subject error
by C.P.E. Rollins 23 Sep '18

23 Sep '18

External Email - Use Caution Hello Freesurfer Developpers, I'm attempting to make a study specific template using all of my subjects as input using the make_average_subject command, but am receiving the following error: Building hash of lh white Building hash of lh pial Building hash of rh white Building hash of rh pial Loading aseg from /lustre/group/p00355/REST_Beijing_SCZ/Freesurfer/average_v2/mri/aseg.presurf.hypos.mgz ASeg Vox2RAS: ----------- -1.00000 0.00000 0.00000 128.00000; 0.00000 0.00000 1.00000 -128.00000; 0.00000 -1.00000 0.00000 128.00000; 0.00000 0.00000 0.00000 1.00000; mghRead(mri/norm.mgz, -1): could not open file ------------------------- Labeling Slice relabeling unlikely voxels in interior of white matter Segmentation fault (core dumped) Linux wbic-cs-5 3.16.0-6-amd64 #1 SMP Debian 3.16.57-2 (2018-07-14) x86_64 GNU/Linux recon-all -s average_v2 exited with ERRORS at Fri Sep 21 11:11:25 BST 2018 I've attached here the full log file. I read in this forum: https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg57030.html to try installing the following patch: https://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/6.0.0-patch/ and had asked our computing support team to install it before the current run of make_average_subject, so the error seems to be happening despite the patch. I would greatly appreciate your suggestions for resolving the error. Thanks very much, Colleen

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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

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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

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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

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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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Freesurfer September 2018