Freesurfer

freesurfer@nmr.mgh.harvard.edu

19 participants
30132 discussions

Recon-all error: MatrixMultiply: m1 is null!
by Boa Sorte Silva, Narlon 23 Dec '20

23 Dec '20

External Email - Use Caution Hi there, Hope this finds you well I have noticed the following error for some of my runs: @# Cortical ribbon mask Mon Dec 14 15:43:24 PST 2020 /Applications/freesurfer/7.1.1/subjects/BT_long/BT_055_base/mri \n mris_volmask --aseg_name aseg.presurf --label_left_white 2 --label_left_ribbon 3 --label_right_white 41 --label_right_ribbon 42 --save_ribbon --parallel BT_055_base \n SUBJECTS_DIR is /Applications/freesurfer/7.1.1/subjects/BT_long loading input data... Running hemis in parallel Processing left hemi Processing right hemi computing distance to right white surface computing distance to left white surface error: MatrixMultiply: m1 is null! Darwin PHTH-CDM-NBOASORT 18.5.0 Darwin Kernel Version 18.5.0: Mon Mar 11 20:40:32 PDT 2019; root:xnu-4903.251.3~3/RELEASE_X86_64 x86_64 recon-all -s BT_055_base exited with ERRORS at Mon Dec 14 15:43:27 PST 2020 Here are details of the computer and FS version I am using: * OS: macOS Mojave (10.14.4) * FS: 7.1.1 It seems to happen at random, whenever I run recon-all on the same subject again, the error doesn’t occur. This is true for cross-sectional, base, and long processing steps in my machine. I have seen an email relating to this issue before, but I wasn’t able to access the attachment file which would fix the problem. I was wondering if you guys would be able to help? Thank you Nárlon Cássio Nárlon Cássio Boa Sorte Silva, PhD CIHR/MSFHR Postdoctoral Research Fellow Aging, Mobility, and Cognitive Neuroscience Lab Djavad Mowafaghian Centre for Brain Health University of British Columbia Twitter: @BoaNarlon

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asegstats2table
by Alberto Del Cerro Leon 23 Dec '20

23 Dec '20

External Email - Use Caution Hello Freesurfers, I have a question about the command asegstats2table. I want to obtain the structural data of a group set based on labels created by myself. I see that this is possible with mris_anatomicalstats for 1 subject but can I obtain the data for all my subjects in some way like asegstats2table using my labels?

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group analyses
by Sara Lyn 23 Dec '20

23 Dec '20

External Email - Use Caution Hi FS developers, I ran mris_preproc, surf2 surf and glmfit and cluster analyses (monte carlo) for a surface based thickness group analysis. I am trying to extract volume measures from the same significant thickness ROIs. Is there any way to do this? Thank you! Sara

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linkedUbuntu 18 virtual disk image - Developer password {Disarmed}
by C. Teurlings 23 Dec '20

23 Dec '20

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Unable to unsubscribe {Disarmed}
by Snedden, Ali 23 Dec '20

23 Dec '20

External Email - Use Caution Hello, When I go to http://secure-web.cisco.com/1jgCpVnCnpYUf1STtrprTp2p1sr_-sFIyb-fzDa-XLhkXgR…, and go to “Freesurfer Subscribers” -> “Unsubscribe or edit options” and enter my email address and press the “Unsubscribe or edit options” button, I get a “The proxy server is refusing connections” Error. I see this (or similar message) in Firefox, Chrome and Safari. I’m on OSX 10.14.6. Ali

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Trouble with mris_divide_parcellation
by Hyon, Justin J. 23 Dec '20

23 Dec '20

External Email - Use Caution I am having some trouble with mris_divide_parcellation. When I follow the procedure in —help, my input and output annotations appear to be identical. The input annotation consists of 5 labels that I’m trying to divide into either 2 or 3 regions. The output contains the exact same 5 regions. I am running the command from the home directory. I’m on OS X Catalina and Freesurfer 7.1.0. The input and output are below: $ mris_divide_parcellation EM rh reg_to_subdivide.annot path/to/splittable/rh_splittable.txt subdivided_regs reading colortable from annotation file... colortable with 76 entries read (originally ./EM/label/custom/aparc.annot.a2009s.ctab) interpreting 4th command line arg as split file name dividing G_front_middle (15) into 3 parts dividing G_front_sup (16) into 3 parts dividing G_orbital (24) into 2 parts dividing G_rectus (31) into 2 parts dividing S_front_sup (55) into 3 parts dividing S_pericallosal (67) into 2 parts allocating new colortable with 5 additional units... supposed to be reproducible but seed not set saving annotation to subdivided_regs I was wondering what I was doing wrong, and how I can make the function output an annot with subdivided labels?

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convert .vtk to .annot
by 1248742467 23 Dec '20

23 Dec '20

External Email - Use Caution Hello, everyone I have lh.labels.DKT31.manual.vtk file, but I want to convert it to lh.labels.DKT31.manual.annot. Now, I use fs6 version, if you know please tell me! I also heard that convetr .vtk to .label then convert .label to .annot, just use mri_convert?

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Superficial white matter surface reconstruction
by Gugger, James J 22 Dec '20

22 Dec '20

External Email - Use Caution Good morning, I am interested in reconstructing the superficial white matter surface (i.e., the surface 1 or 2 mm below the white surface). Can you give me some guidance on how to do this or find it if it is part of recon-all? Thank you, Jim Gugger James Gugger, MD, PharmD Instructor of Neurology University of Pennsylvania

2 1

HCP_1200 parcellation problems
by najme soleimani 22 Dec '20

22 Dec '20

External Email - Use Caution Dear FreeSurfer Developers, I downloaded the HCP_1200 subjects' structural extended data. I am attempting to have equal sized parcellation on scale 100, so I used parcellation results of Desikan atlas and increased the parcels from 68 to 100. after obtaining split file, I run the following commands on FreeSurfer: mris_divide_parcellation subj lh aparc.annot splitfile Desikan100 mris_divide_parcellation subj rh aparc.annot splitfile Desikan100 mri_aparc2aseg --s subj --annot Desikan100 --old-ribbon --o $SUBJECTS_DIR/subj/mri/Desikan100.subj.mgz The interesting part is that after running this command some disconnectivity were seen in the parcels as it is shown in the picture. In 3D view, also, when the parcels were loaded on dsi studio, there were some holes on the parcels which caused disconnected parcels. I will appreciate if you help me to solve this problem. kind regards, Najme

2 2

ubuntu 20.4?
by Olga Kepinska 22 Dec '20

22 Dec '20

External Email - Use Caution Dear FS community, I’m following up on my previous communications about FS on Ubuntu (if interested see thread ‘FS on Ubuntu’). The advice (very useful, thank you!) given by the fsbuild team is to go with Ubuntu 18. If however, anyone out there has successfully used FS 7.1 (to run the structural pipeline) on Ubuntu 20.4, please reach out! Thank you, Olga -- Olga Kepinska, PhD  Postdoctoral Researcher Brain and Language Lab (http://secure-web.cisco.com/1RNPCPtqAShauqmWrgcwNoS3MJW1dY1znVsbd6I732e7CiD…) @olgakepinska

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