Freesurfer December 2020

freesurfer@nmr.mgh.harvard.edu

97 participants
131 discussions

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

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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

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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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segmentHA_T1.sh Error
by Zachary Miller 21 Dec '20

21 Dec '20

External Email - Use Caution Hello, I am having trouble running segmentHA_T1.sh and I hope that someone will know the solution. Per a similar thread on this mail archive, I have verified that I have writing permissions in the subject directory. My command line and FS output are below. Thank you, Zach Command: segmentHA_T1.sh CDN0001_MSB_10_7.1.1 FStests/CDN0001_MSB Output: #@# Hippocampal Subfields processing (T1) left Fri Dec 18 14:14:40 CST 2020 ------------------------------------------ Setting up environment variables --- LD_LIBRARY_PATH is .:/panfs/roc/msisoft/freesurfer/7.1.1/MCRv84//runtime/glnxa64:/panfs/roc/msisoft/freesurfer/7.1.1/MCRv84//bin/glnxa64:/panfs/roc/msisoft/freesurfer/7.1.1/MCRv84//sys/os/glnxa64:/panfs/roc/msisoft/freesurfer/7.1.1/MCRv84//sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/panfs/roc/msisoft/freesurfer/7.1.1/MCRv84//sys/java/jre/glnxa64/jre/lib/amd64/server:/panfs/roc/msisoft/freesurfer/7.1.1/MCRv84//sys/java/jre/glnxa64/jre/lib/amd64/client:/panfs/roc/msisoft/freesurfer/7.1.1/MCRv84//sys/java/jre/glnxa64/jre/lib/amd64:/panfs/roc/msisoft/netcdf/4.6.2-gcc8.2.0-serial/lib:/panfs/roc/msisoft/hdf5/hdf5-1.10.4-gcc8.2.0-ompi-4.0.0/lib:/panfs/roc/msisoft/openmpi/el6/4.0.0/gnu-8.2.0.CentOS7/lib:/panfs/roc/msisoft/java/openjdk-11.0.2/lib:/panfs/roc/msisoft/java/openjdk-11.0.2/lib/jli:/panfs/roc/msisoft/java/openjdk-11.0.2/lib/server:/panfs/roc/msisoft/gcc/8.2.0/lib64:/panfs/roc/msisoft/isl/0.19_gcc8.1.0/lib:/panfs/roc/msisoft/mpc/1.1.0_gcc8.1.0/lib:/panfs/roc/msisoft/mpfr/4.0.1_gcc8.1.0/lib:/panfs/roc/msisoft/gmp/6.1.2_gcc8.1.0/lib:/panfs/roc/msisoft/fsl/6.0.1/lib:/panfs/roc/msisoft/matlab/R2014b/runtime/glnxa64:/panfs/roc/msisoft/gcc/8.1.0/lib64 Registering imageDump.mgz to hippocampal mask from ASEG Error using myMRIread (line 16) Error in myMRIread: temporary directory does not exist Error in segmentSubjectT1_autoEstimateAlveusML (line 157) @#@FSTIME 2020:12:18:14:14:40 run_segmentSubjectT1_autoEstimateAlveusML.sh N 14 e 26.52 S 1.16 U 7.38 P 32% M 268532 F 598 R 75671 W 0 c 1553 w 10745 I 492960 O 0 L 2.09 8.46 13.64 @#@FSLOADPOST 2020:12:18:14:15:06 run_segmentSubjectT1_autoEstimateAlveusML.sh N 14 2.32 8.00 13.35 Linux cn0224 3.10.0-1160.6.1.el7.x86_64 #1 SMP Tue Nov 17 13:59:11 UTC 2020 x86_64 x86_64 x86_64 GNU/Linux T1 hippocampal subfields exited with ERRORS at Fri Dec 18 14:15:06 CST 2020 -- Zachary Miller Researcher | Institute of Child Development | College of Education and Human Development | cehd.umn.edu University of Minnesota | umn.edu mill5076(a)umn.edu

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Freesurfer December 2020