Freesurfer

freesurfer@nmr.mgh.harvard.edu

4 participants
30076 discussions

Gcut error: gcutted brain is much smaller than the mask
by Begüm Cerrahoğlu 21 Mar '22

21 Mar '22

External Email - Use Caution Dear developers, I am trying to clean up the extra dura left after skullstripping. Watershed parameter does not prove to be much helpful and when I try gcut I get the error below. I checked the release notes of freesurfer 5.1 and mri_gcut is not run by default. In the archives I came across this exact problem before, under this message: msg18797 <https://secure-web.cisco.com/1Gix4yHAghaLSVAVD-cOy4QmehGJB3UyVkUd5GwVNmFNq_…> However, there was not an end solution available in the archived email exchange. I am not interested in cerebellum and am okay with cutting the cerebellum out of the brain mask as long as it does not interfere with being able to distinctly separate cortex from cerebellum in the following steps. From skullstripping tutorials,I have read that one should not start erasing cerebellum from the brainmask directly and was wondering if you could let me know why? In sum, are there important reasons to keep the cerebellum despite only being interested in analyzing the cortex? If not, could you please let me know what could be the reason for gcut's failure and if there is anyway to disable failure detection so I can see if the gcutted brain is usable? >> " rm -f brainmask.gcuts.mgz >> mri_gcut -110 -mult brainmask.auto.mgz T1.mgz brainmask.auto.mgz >> brainmask.gcuts.mgz >> >> INFO: Care must be taken to thoroughly inspect your data >> when using mri_gcut. In particular, inspect the edges of >> gm and cerebellum for over-aggressive cutting. >> Add -segmentation brainmask.gcuts.mgz to the tkmedit >> command string to view the voxels which gcut has removed. >> >> reading mask... >> white mean: 107.529232 >> threshold set to: 107.529232*0.400000=43.011693 >> calculating weights... >> doing mincut... >> now doing maxflow, be patient... >> g-cut done! >> post-processing... >> post-processing done! >> masking... >> ** Gcutted brain is much smaller than the mask! >> ** Using the mask as the output instead! >> >> cp brainmask.auto.mgz brainmask.mgz " 1) FreeSurfer version: freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0. 2) Platform: Linux Mint 20.2 Thank you greatly for your time and efforts. Kindest regards, Begum Cerrahoglu

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Trouble with fs_install_mcr script
by Andrei Bieger 19 Mar '22

19 Mar '22

External Email - Use Caution Hello, everyone, I`m having trouble installing the MatLab Runtime 2014b as required for running the new hippocampal subfields pipeline. The "fs_install_mcr 2014b" command returns me the message below: *andrei@andrei-VirtualBox:~/Programs/freesurfer/7.2.0/bin$ fs_install_mcr 2014b % Total % Received % Xferd Average Speed Time Time Time Current Dload Upload Total Spent Left Speed100 10 100 10 0 0 2 0 0:00:05 0:00:04 0:00:01 2Archive: installer.zip End-of-central-directory signature not found. Either this file is not a zipfile, or it constitutes one disk of a multi-part archive. In the latter case the central directory and zipfile comment will be found on the last disk(s) of this archive.unzip: cannot find zipfile directory in one of installer.zip or installer.zip.zip, and cannot find installer.zip.ZIP, period.* Then I tried running the specific line of the script to download the file so I could take a look at it: *andrei@andrei-VirtualBox:~/Programs/freesurfer/7.2.0/bin$ curl --location https://secure-web.cisco.com/1EdMsU-hQ3VZ1K97z-aS22OCA3G_bwtGWsa4wkPQY7WCPE… <https://secure-web.cisco.com/1EdMsU-hQ3VZ1K97z-aS22OCA3G_bwtGWsa4wkPQY7WCPE…> -o installer.zip % Total % Received % Xferd Average Speed Time Time Time Current Dload Upload Total Spent Left Speed100 10 100 10 0 0 161 0 --:--:-- --:--:-- --:--:-- 161andrei@andrei-VirtualBox:~/Programs/freesurfer/7.2.0/bin$ file installer.zipinstaller.zip: ASCII text* *andrei@andrei-VirtualBox:~/Programs/freesurfer/7.2.0/bin$ unzip installer.zipArchive: installer.zip End-of-central-directory signature not found. Either this file is not a zipfile, or it constitutes one disk of a multi-part archive. In the latter case the central directory and zipfile comment will be found on the last disk(s) of this archive.unzip: cannot find zipfile directory in one of installer.zip or installer.zip.zip, and cannot find installer.zip.ZIP, period.* It does not recognize it as a .zip file, and the Ubuntu Archive Manager won`t recognize it either: *"An error occurred while loading the archive."* I know this is more of a Linux/Matlab issue than a freesurfer one. But I wonder if anyone else is facing this issue? Might that be a problem with the curl package, Matlab support to older Runtime versions or my Linux distro? Also, could you please give me instructions on where to install the file manually from https://secure-web.cisco.com/1f47DuzXT9iWt3QZ-FmPoYU6PuX8nCvVAsdXGDH3F_QY6C… ? Thank you! -- Andrei Bieger

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Tracula 6.0 or 7.2 - sub in alternative metric maps
by Thorn, Kathryn 18 Mar '22

18 Mar '22

External Email - Use Caution Hi Freesurfer/Tracula experts, I would like to use my own diffusivity and anisotropy maps (FA, MD, etc) with Tracula as opposed to the maps generated by dtifit during the course of trac-all -prep. I see that there is a -notensor option to stop dtifit from producing metric maps; however I am wondering if there's any way to get Tracula to recognize alternative metric maps that I supply to it. My main goal is to sub in my own metric maps for the purposes of having Tracula generate tract profiles (pathstats.byvoxel.txt) with metric maps I generated via an alternative fitting method to dtifit. Is there any way to do this? Additionally, is there any way to have Tracula perform these same types of analyses with kurtosis maps or other types of dMRI data? I've been working mainly with Tracula 6.0 as I have received an as yet unresolved mri_binarize error with Tracula 7.2. However, I am curious if the above is possible with either or both versions. Thank you! Kayti Thorn (she/her) Database Specialist Medical University of South Carolina Department of Neurology Center for Biomedical Imaging 135 Cannon St. CS101 Charleston, SC 29425

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Re: [Freesurfer] Hippocampal segmentation Matlab crash
by Caitlin R Bowman 18 Mar '22

18 Mar '22

External Email - Use Caution Tried it, but I still get the same error. -- Caitlin Bowman, Ph.D. Assistant Professor of Psychology University of Wisconsin-Milwaukee From: <freesurfer-bounces(a)nmr.mgh.harvard.edu> on behalf of "Hoopes, Andrew" <AHOOPES(a)mgh.harvard.edu> Reply-To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> Date: Tuesday, March 8, 2022 at 3:18 PM To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] Hippocampal segmentation Matlab crash Hi Cait, Before running the command, can you try unsetting the LD_LIBRARY_PATH variable? You can do this in bash with: unset LD_LIBRARY_PATH or in cshell with: unsetenv LD_LIBRARY_PATH best, Andrew From: freesurfer-bounces(a)nmr.mgh.harvard.edu <freesurfer-bounces(a)nmr.mgh.harvard.edu> on behalf of Caitlin R Bowman <bowman2(a)uwm.edu> Date: Tuesday, March 8, 2022 at 3:14 PM To: freesurfer(a)nmr.mgh.harvard.edu <freesurfer(a)nmr.mgh.harvard.edu> Subject: [Freesurfer] Hippocampal segmentation Matlab crash External Email - Use Caution Hello, I am trying to run the hippocampal segmentation used in freesurfer 7. I have tried with both 7.1.1 and 7.2 and have run into an issue at the same spot. I am running on a computing cluster, not locally. The same code works fine on my local computer. The managers of the computing cluster have tried to help but are stuck themselves. Find the command that I run below followed by the full error log. Best, Cait Command: segmentHA_T2.sh sub-110033 $ANATDIR/sub-110033_T2w.nii.gz T2 0 Error log: ------------------------------ USER bowman2 HOST compute-081.mortimer PROCESSID 11325 PROCESSOR x86_64 OS Linux Linux compute-081.mortimer 3.10.0-1160.49.1.el7.x86_64 #1 SMP Tue Nov 30 15:51:32 UTC 2021 x86_64 x86_64 x86_64 GNU/Linux ------------------------------ #-------------------------------------------- #@# Hippocampal Subfields processing (T2) left Thu Feb 24 14:14:35 CST 2022 ------------------------------------------ Setting up environment variables --- LD_LIBRARY_PATH is .:/sharedapps/LS/psych_imaging/freesurfer/7.2.0/freesurfer/MCRv84//runtime/glnxa64:/sharedapps/LS/psych_imaging/freesurfer/7.2.0/freesurfer/MCRv84//bin/glnxa64:/sharedapps/LS/psych_imaging/freesurfer/7.2.0/freesurfer/MCRv84//sys/os/glnxa64:/sharedapps/LS/psych_imaging/freesurfer/7.2.0/freesurfer/MCRv84//sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/sharedapps/LS/psych_imaging/freesurfer/7.2.0/freesurfer/MCRv84//sys/java/jre/glnxa64/jre/lib/amd64/server:/sharedapps/LS/psych_imaging/freesurfer/7.2.0/freesurfer/MCRv84//sys/java/jre/glnxa64/jre/lib/amd64/client:/sharedapps/LS/psych_imaging/freesurfer/7.2.0/freesurfer/MCRv84//sys/java/jre/glnxa64/jre/lib/amd64:/sharedapps/LS/psych_imaging/fsl/6.0.4/lib:/sharedapps/LS/psych_imaging/freesurfer/7.2.0/freesurfer/MCRv84/sys/os/glnxa64::/sharedapps/LS/psych_imaging/freesurfer/7.2.0/freesurfer/MCRv84/bin/glnxa64:/sharedapps/LS/psych_imaging/freesurfer/7.2.0/freesurfer/MCRv84/runtime/glnxa64:/sharedapps/LS/psych_imaging/freesurfer/7.2.0/freesurfer/lib/vtk/lib/vtk-5.6/:/sharedapps/LS/psych_imaging/freesurfer/7.2.0/freesurfer/lib/tcltktixblt/lib/:/sharedapps/LS/psych_imaging/freesurfer/7.2.0/freesurfer/lib/KWWidgets/lib/KWWidgets:/sharedapps/LS/psych_imaging/freesurfer/7.2.0/freesurfer/mni/lib:/sharedapps/LS/psych_imaging/freesurfer/7.2.0/freesurfer/lib ------------------------------------------------------------------------ std::terminate() detected at Thu Feb 24 14:14:37 2022 ------------------------------------------------------------------------ Configuration: Crash Decoding : Disabled Default Encoding : UTF-8 GNU C Library : 2.17 stable MATLAB Architecture: glnxa64 MATLAB Root : /raid-07/sharedapps/LS/psych_imaging/freesurfer/7.2.0/freesurfer/MCRv84 MATLAB Version : 8.4.0.150421 (R2014b) Operating System : Linux 3.10.0-1160.49.1.el7.x86_64 #1 SMP Tue Nov 30 15:51:32 UTC 2021 x86_64 Processor ID : x86 Family 6 Model 63 Stepping 2, GenuineIntel Fault Count: 1 Abnormal termination: std::terminate() Register State (captured): RAX = 0000000000000000 RBX = 00002baa657204e8 RCX = 0000000000000000 RDX = 00002baa6570f758 RSP = 00002baa93ffb0b0 RBP = 00002baa93ffb470 RSI = 00002baa654c3fb3 RDI = 00002baa93ffb0c0 R8 = 0000000000000000 R9 = 00002baa60271f90 R10 = 0000000000000000 R11 = 0000000000000000 R12 = 00002baa65730520 R13 = 00002baa93ffc0b0 R14 = 00002baa93ffc090 R15 = 00002baa93ffc470 RIP = 00002baa65422f4e EFL = 0000000000000000 CS = 0000 FS = 0000 GS = 0000 Stack Trace (captured): [ 0] 0x00002baa65422f4e /sharedapps/LS/psych_imaging/freesurfer/7.2.0/freesurfer/MCRv84//bin/glnxa64/libmwfl.so+00966478 _ZN2fl4diag5linux12context_base12capture_dataEv+00000030 [ 1] 0x00002baa65420424 /sharedapps/LS/psych_imaging/freesurfer/7.2.0/freesurfer/MCRv84//bin/glnxa64/libmwfl.so+00955428 [ 2] 0x00002baa740ef0f5 /raid-07/sharedapps/LS/psych_imaging/freesurfer/7.2.0/freesurfer/MCRv84/bin/glnxa64/libmwmcr.so+00868597 [ 3] 0x00002baa740f12ca /raid-07/sharedapps/LS/psych_imaging/freesurfer/7.2.0/freesurfer/MCRv84/bin/glnxa64/libmwmcr.so+00877258 [ 4] 0x00002baa740f13c1 /raid-07/sharedapps/LS/psych_imaging/freesurfer/7.2.0/freesurfer/MCRv84/bin/glnxa64/libmwmcr.so+00877505 [ 5] 0x00002baa740f1743 /raid-07/sharedapps/LS/psych_imaging/freesurfer/7.2.0/freesurfer/MCRv84/bin/glnxa64/libmwmcr.so+00878403 [ 6] 0x00002baa740f17b3 /raid-07/sharedapps/LS/psych_imaging/freesurfer/7.2.0/freesurfer/MCRv84/bin/glnxa64/libmwmcr.so+00878515 [ 7] 0x00002baa5ffe4a06 /lib64/libstdc++.so.6+00387590 [ 8] 0x00002baa5ffe4a33 /lib64/libstdc++.so.6+00387635 [ 9] 0x00002baa5ffe4c53 /lib64/libstdc++.so.6+00388179 [ 10] 0x00002baa60fe3822 /sharedapps/LS/psych_imaging/freesurfer/7.2.0/freesurfer/MCRv84//bin/glnxa64/libmwi18n.so+00325666 _ZN2fl4i18n14MessageCatalog17GetMessageCatalogERKNS0_9CatalogIDERKNS0_8MwLocaleE+00001186 [ 11] 0x00002baa60fe4113 /sharedapps/LS/psych_imaging/freesurfer/7.2.0/freesurfer/MCRv84//bin/glnxa64/libmwi18n.so+00327955 _ZN2fl4i18n14MessageCatalog11get_messageERKN13resource_core9BaseMsgIDERKNS0_8MwLocaleE+00000051 [ 12] 0x00002baa6589bf57 /sharedapps/LS/psych_imaging/freesurfer/7.2.0/freesurfer/MCRv84//bin/glnxa64/libmx.so+01482583 [ 13] 0x00002baa6589ae6f /sharedapps/LS/psych_imaging/freesurfer/7.2.0/freesurfer/MCRv84//bin/glnxa64/libmx.so+01478255 [ 14] 0x00002baa65832a44 /sharedapps/LS/psych_imaging/freesurfer/7.2.0/freesurfer/MCRv84//bin/glnxa64/libmx.so+01051204 _Z14mxWarningMsgIdRKN13resource_core9BaseMsgIDE+00000052 [ 15] 0x00002baa74443a95 /raid-07/sharedapps/LS/psych_imaging/freesurfer/7.2.0/freesurfer/MCRv84/bin/glnxa64/libmwjmi.so+01100437 [ 16] 0x00002baa74443d2f /raid-07/sharedapps/LS/psych_imaging/freesurfer/7.2.0/freesurfer/MCRv84/bin/glnxa64/libmwjmi.so+01101103 _Z50mljInitFirstCrackSignalHandlerIfJavaAlreadyStartedv+00000015 [ 17] 0x00002baa740c5855 /raid-07/sharedapps/LS/psych_imaging/freesurfer/7.2.0/freesurfer/MCRv84/bin/glnxa64/libmwmcr.so+00698453 [ 18] 0x00002baa740b64ec /raid-07/sharedapps/LS/psych_imaging/freesurfer/7.2.0/freesurfer/MCRv84/bin/glnxa64/libmwmcr.so+00636140 [ 19] 0x00002baa740a2cdd /raid-07/sharedapps/LS/psych_imaging/freesurfer/7.2.0/freesurfer/MCRv84/bin/glnxa64/libmwmcr.so+00556253 [ 20] 0x00002baa607adea5 /lib64/libpthread.so.0+00032421 [ 21] 0x00002baa60ac0b0d /lib64/libc.so.6+01043213 clone+00000109 If this problem is reproducible, please submit a Service Request via: MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be http://secure-web.cisco.com/118J8xb20RT93i80kANwrgAlajqHThJt-SNhm0DJUsUTVUk…<https://secure-web.cisco.com/1sWwW4ZPn37eyMEn2XV0J_7cDBgIf6OqYIkEUaQB3x0FDi…> A technical support engineer might contact you with further information. Thank you for your help.** This crash report has been saved to disk as /home/bowman2/matlab_crash_dump.11396-1 ** MATLAB is exiting because of fatal error /sharedapps/LS/psych_imaging/freesurfer/7.2.0/freesurfer/bin/run_segmentSubjectT2_autoEstimateAlveusML.sh: line 40: 11396 Killed /sharedapps/LS/psych_imaging/freesurfer/7.2.0/freesurfer/bin/segmentSubjectT2_autoEstimateAlveusML sub-CC110037 /home/bowman2/Data/camcan/fs_camcan/ /raid-18/LS/bowman2/camcan/imaging/anat/sub-CC110037/sub-CC110037_T2w.nii.gz 0.333333333333333333333333333333333333 /sharedapps/LS/psych_imaging/freesurfer/7.2.0/freesurfer/average/HippoSF/atlas/AtlasMesh.gz /sharedapps/LS/psych_imaging/freesurfer/7.2.0/freesurfer/average/HippoSF/atlas/AtlasDump.mgz /sharedapps/LS/psych_imaging/freesurfer/7.2.0/freesurfer/average/HippoSF/atlas/compressionLookupTable.txt 0.05 left L-BFGS v21 T2 '/sharedapps/LS/psych_imaging/freesurfer/7.2.0/freesurfer/bin/fs_run_from_mcr /sharedapps/LS/psych_imaging/freesurfer/7.2.0/freesurfer/bin/' 0 1 0 @#@FSTIME 2022:02:24:14:14:35 run_segmentSubjectT2_autoEstimateAlveusML.sh N 18 e 1.65 S 0.13 U 1.19 P 80% M 67608 F 0 R 19447 W 0 c 32 w 559 I 0 O 84720 L 5.00 5.06 4.81 @#@FSLOADPOST 2022:02:24:14:14:37 run_segmentSubjectT2_autoEstimateAlveusML.sh N 18 5.00 5.06 4.81 Linux compute-081.mortimer 3.10.0-1160.49.1.el7.x86_64 #1 SMP Tue Nov 30 15:51:32 UTC 2021 x86_64 x86_64 x86_64 GNU/Linux T2 hippocampal subfields exited with ERRORS at Thu Feb 24 14:14:37 CST 2022 -- Caitlin Bowman, Ph.D. Assistant Professor of Psychology University of Wisconsin-Milwaukee

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run_samseg output folder permissions error
by daedalus39＠aol.com 18 Mar '22

18 Mar '22

External Email - Use Caution Dear experts, Having installed Freesurfer on WSL2, I was able to get the basic FS segmentation to run without error. However, when I tried to run_samseg on a single T1 image, I received the following error message (permissions denied creating the "output folder") Is there anything in the trace (below) that provides a clue? daedalus@DESKTOP-TILLA3B:/usr/local/freesurfer/7-dev/subjects$ run_samseg --input o_ADNI_002_S_4654__MRI-m072.nii --output /T1-only -samsegOutput/ Traceback (most recent call last): File "/usr/local/freesurfer/7-dev/python/scripts/run_samseg", line 67, in <module> os.makedirs(args.outputDirectory, exist_ok=True) File "/usr/local/freesurfer/7-dev/python/lib/python3.6/os.py", line 220, in makedirs mkdir(name, mode) PermissionError: [Errno 13] Permission denied: '/T1-only-samsegOutput/'

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Extraction of CC Labels and Conversion to FSL MNI Space
by Hua, Jessica 17 Mar '22

17 Mar '22

External Email - Use Caution Hi FreeSurfer, I am trying to extract CC subregion labels from aparc+aseg.mgz (ids: 251-255) into a format that is compatible with MNI space in FSL. I was planning on extracting CC labels and then converting the labels from fsaverage space to MNI space. I first tried to extract the 5 separate CC labels using the command: mri_vol2label --c aparc+aseg.mgz --id 255 --l 255.label. When viewed in FreeView, the labels were spotty looking. Did I do this mgz to label extraction correctly? [cid:7dee544f-74a8-43d0-be89-9af1a0c74e2f] And also do you have a recommended code to convert FreeSurfer CC subregions into MNI space ROIs for FSL? Best, Jessica

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recon-all errors after mri_pretess
by Alexopoulos, Dimitrios 17 Mar '22

17 Mar '22

External Email - Use Caution Hi, we're running FS 7.2 'recon-all -all' on a subject and are getting errors on our cluster (CentOS 8) The attached recon-all.log file is attached for details. The last several lines of the file are below. Any comments as to why its failing? Jim. pass 1 (--): 0 found - 0 modified | TOTAL: 0 pass 1 (-+): 0 found - 0 modified | TOTAL: 0 Total Number of Modified Voxels = 631 (out of 421942: 0.149547) binarizing input wm segmentation... Ambiguous edge configurations... mri_pretess done @#@FSTIME 2022:03:03:12:51:58 mri_pretess N 4 e 3.84 S 0.01 U 3.70 P 96% M 56636 F 1 R 2214 W 0 c 330 w 325 I 8801 O 646 L 3.37 3.47 3.45 @#@FSLOADPOST 2022:03:03:12:52:02 mri_pretess N 4 3.37 3.47 3.45 #-------------------------------------------- #@# Fill Thu Mar 3 12:52:02 CST 2022 ________________________________ The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail.

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Using vol2surf to fsaverage.
by Jacoby, John 17 Mar '22

17 Mar '22

Hi all, Usually when I want to map volume data to the fsaverage surface, I use mri_vol2surf with a registration that transforms the volume into the space of the subject's orig.mgz and with --trgsubject set to 'fsaverage'. Currently, I have some volumes that have already been transformed to the subjects' orig.mgz space that I want to bring to the fsaverage surface. Can I still just give mri_vol2surf the same registration that I used to transform this volume in the first place, or will this try to re-apply that registration and end up in the wrong space? If that's incorrect, what's the best way to go about doing this? Thank you! Best, John

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FWHM errors for mri_glmfit-sim for lgi?
by Zeng, Victor (BIDMC - Keshavan - Psychiatry) 17 Mar '22

17 Mar '22

External Email - Use Caution I receive FWHM values much larger than what average/mult-comp-cor/fsaverage/rh/cortex has (around ~50) w/ LGI, but normal when looking at GM thickness. Is this expected? Victor Zeng Beth Israel Deaconess Medical Center Keshavan Lab --

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Re: [Freesurfer] Freesurfer Digest, Vol 217, Issue 29
by Goeckner, Bryna 17 Mar '22

17 Mar '22

External Email - Use Caution Anastasia, Thanks for your help on this! I looked through the subjects for which the corticospinal tract failed, and the scans didn’t seem truncated compared to the ones that ran successfully. But since we are not particularly concerned with the cst, I thought I’d try to run all other pathways. Based on info for setting up the config file, I thought adding this line to the config file would work: set pathlist = ( acomm cc.bodyc cc.bodypf cc.bodypm cc.bodyp cc.bodyt cc.genu cc.rostrum cc.splenium mcp lh.af lh.ar lh.atr lh.cbd lh.cbv lh.emc lh.fat lh.fx lh.ilf lh.mlf lf.or lh.slf1 lh.sl2 lh.slf3 lh.uf rh.af rh.ar rh.atr rh.cbd rh.cbv rh.emc rh.fat rh.fx rh.ilf rh.mlf rh.or rh.slf1 rh.slf2 rh.slf3 rh.uf ) But I got this error message: ERROR: length of pathway list (acomm cc.bodyc cc.bodypf cc.bodypm cc.bodyp cc.bodyt cc.genu cc.rostrum cc.splenium mcp lh.af lh.ar lh.atr lh.cbd lh.cbv lh.emc lh.fat lh.fx lh.ilf lh.mlf lf.or lh.slf1 lh.sl2 lh.slf3 lh.uf rh.af rh.ar rh.atr rh.cbd rh.cbv rh.emc rh.fat rh.fx rh.ilf rh.mlf rh.or rh.slf1 rh.slf2 rh.slf3 rh.uf) and endpoint label ID list ERROR: (0 0 0 0 0 0 0 0 0 0 0 10 10 0 0 0 0 28 0 0 0 0 0 0 49 49 0 0 0 0 60 0 0 49 0 0 0 0) do not match Looks like I need to change the endpoint label ID list? How would I do that? Bryna Goeckner (she/her) Graduate Student Medical College of Wisconsin Neuroscience Doctoral Program Date: Thu, 17 Mar 2022 18:18:26 +0000 From: "Yendiki, Anastasia" <AYENDIKI(a)mgh.harvard.edu> Subject: Re: [Freesurfer] Reposting TRACULA trac-all -prep finishes with errors To: "freesurfer(a)nmr.mgh.harvard.edu" <freesurfer(a)nmr.mgh.harvard.edu> Message-ID: <MN2PR04MB681631333C83A03772141E4B8A129(a)MN2PR04MB6816.namprd04.prod.outlook.com> Content-Type: text/plain; charset="windows-1252" Hi Bryna - I see that the error occurs in the corticospinal tract. Any change the top or bottom of the brain is truncated in this subject's scan? Anastasia. ________________________________ From: freesurfer-bounces(a)nmr.mgh.harvard.edu <freesurfer-bounces(a)nmr.mgh.harvard.edu> on behalf of Goeckner, Bryna <bgoeckner(a)mcw.edu> Sent: Thursday, March 17, 2022 11:53 AM To: freesurfer(a)nmr.mgh.harvard.edu <freesurfer(a)nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] Reposting TRACULA trac-all -prep finishes with errors External Email - Use Caution Attaching config file & link to trac-all.log (trac-all/log is kind of big ? so freesurfer listserv blocked email). Hopefully you are able to access them this way. MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://secure-web.cisco.com/1pFVh-66Hoz8ai7X8JA6lojOQYdcauq9l7ExKYgOe8pXrh…<https://secure-web.cisco.com/1NOZCdcgx_oUa395czxw_g_-1lzisZMf2N17J7ReicSYgO…> <https://secure-web.cisco.com/1TJ2tok7mbzdMdCHQyHMjDCCmd4IqA_r-HGdAkeg6_NrmO… > From: Goeckner, Bryna <bgoeckner(a)mcw.edu> Date: Monday, February 14, 2022 at 4:42 PM To: freesurfer(a)nmr.mgh.harvard.edu <freesurfer(a)nmr.mgh.harvard.edu> Subject: TRACULA trac-all -prep finishes with errors Hi FreeSurfer Developers, I am attempting to run data for several subjects through TRACULA using trac-all -prep, but some of them have finished with errors. I have checked registration for all of them and it looks ok. I am including a link to my confi

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