Freesurfer May 2022

freesurfer@nmr.mgh.harvard.edu

86 participants
124 discussions

mri_surf2surf error: could not read surface
by Margot Wagner 12 May '22

12 May '22

External Email - Use Caution Hello FreeSurfer Developers, I am attempting to run the HCPPipeline <https://secure-web.cisco.com/1PrAyMCdNwWvmMb6-wd3cHZJPug7g4q9HEG-M9vN9SZYsj…> using their provided example data according to their Installation and Usage Intructions <https://secure-web.cisco.com/1Y9my6pk8D5YRbrVEZ1pMFY43_her0g021-eYiIxAcX3X1…> . Currently, I am trying to run FreeSurferPipelineBatch.sh and got an error message in FreeSurferPipeline.sh when it tries to run mri_surf2surf: Reading source surface reg /nadata/cnl/home/mwagner/projects/hcp/Pipelines_ExampleData/100307/T1w/100307/surf/lh.white.preaparc No such file or directory mri_surf2surf: could not read surface /nadata/cnl/home/mwagner/projects/hcp/Pipelines_ExampleData/100307/T1w/100307/surf/lh.white.preaparc No such file or directory ERROR: This occurs immediately after attempting to run mri_surf2surf --s 100307 --hemi lh --sval-xyz white.preaparc --surfreg white.preaparc --reg transforms/rawavg2conf.dat rawavg.cmdc.mgz --tval-xyz rawavg.cmdc.mgz --tval white.preaparc.rawavg It appears no file lh.white.preaparc is made, nor any file matching "white" or "preaparc". I have been unable to find similar errors. Attached is the output from the FreeSurferPipeline run as well as recon-all.log. 1) FreeSurfer version: freesurfer-x86_64-unknown-linux-gnu-stable6-20170118 2) Platform: Debian GNU/Linux 10 (buster) 3) uname -a: Linux porter 4.19.0-20-amd64 #1 SMP Debian 4.19.235-1 (2022-03-17) x86_64 GNU/Linux 4) recon-all.log: see attached Thank you for your assistance. -- Best Regards, Margot Wagner Graduate Student Researcher UCSD Bioengineering

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Reversing mri_convert
by Zeng, Victor (BIDMC - Keshavan - Psychiatry) 12 May '22

12 May '22

External Email - Use Caution Hi, I convert orig.mgz -> T1.nii using mri_convert orig.mgz T1.nii I now have something registered to the T1.nii and would like to move it back to Freesurfer space. How would you go about doing that? I am assuming I would do the inverse of the mri_convert, but I can't seem to find the option to write the matrix. Victor Zeng Beth Israel Deaconess Medical Center Keshavan Lab --

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Recon-all
by krystaly 12 May '22

12 May '22

External Email - Use Caution Dear Freesurfer experts, I am new to FS 7.2.0 (Window 10), and trying to run the Recon-all command as demonstrated on the website (https://secure-web.cisco.com/1UHVC1FSZYmyuNB9-Imz9busENdngVDz-sSAkkWD-mKGV9…) Before running the command, I have converted DICOM files into NIFTI files. I, then, moved the nii files to Desktop at FS. They are in the folder named “Sub-132”. However, I got the following errors: developer@developer-VirtualBox:~/Desktop/Sub-132$ recon-all -s Sub-132 -i Sub-132_SAG_T1_MPRAGE_(INC_UPPER_CX_AS_MUCH)__2.nii -all bash: syntax error near unexpected token `(' To make another attempt, I tried to process with another T1 image, and I got the following error: developer@developer-VirtualBox:~/Desktop/Sub-132$ recon-all -s Sub-132 -i Sub-132_T1_COR_5_0.5__250_i00002.nii -all mkdir: cannot create directory '/usr/local/freesurfer/7.2.0/subjects/Sub-132': Permission denied mkdir: cannot create directory '/usr/local/freesurfer/7.2.0/subjects/Sub-132': Permission denied mkdir: cannot create directory '/usr/local/freesurfer/7.2.0/subjects/Sub-132': Permission denied cp: cannot create regular file '/usr/local/freesurfer/7.2.0/subjects/Sub-132/scripts/build-stamp.txt': No such file or directory cat: /usr/local/freesurfer/7.2.0/subjects/Sub-132/scripts/build-stamp.txt: No such file or directory INFO: FreeSurfer build stamps do not match Subject Stamp: Current Stamp: freesurfer-linux-ubuntu18_x86_64-7.2.0-20210721-aa8f76b /usr/local/freesurfer/7.2.0/subjects/Sub-132/scripts/patchdir.txt: No such file or directory. I reckoned that the T1 images could not be processed with only 1 plane. Would you please kindly advise on merging 3-plane T1 images into one comprehensive T1-weighter image for further processing? Or would you please let me know what went wrong in this case? Thanks. Best regards, Krystal

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error estimates in FS total brain volumes
by Alexopoulos, Dimitrios 12 May '22

12 May '22

External Email - Use Caution Hi all, What is a reasonable estimate of the error margin in the total brain volume estimates of Freesurfer? Is there a reference that discusses this? Jim ________________________________ 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.

2 1

Request VM passcode
by Santiago Fernández 12 May '22

12 May '22

External Email - Use Caution Hi, I would like to use the VM with FreeSurfer. Could you send me the passcode? Thanks! Regards, Santi.

1 0

DT_recon error
by m-maiworm＠web.de 11 May '22

11 May '22

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VirtualBox Installation Password
by Viktor Pavliska 11 May '22

11 May '22

External Email - Use Caution Hello, please, where can I find the password of the VB image? I am following the instructions from the page: https://secure-web.cisco.com/1GwKqSd9gI16dUp0cqEmM-2_qILdbuXCQ2bXYCAxSOJGjE… Freesurfer 7.2.0 release in Ubuntu 18.04.06: FS_7_2_0_Ubuntu_18_04_06.ova.7z Best Regards -- RNDr. Viktor PAVLISKA, Ph. D. University of Ostrava Institute for Research and Applications of Fuzzy Modeling National Supercomputing Centre IT4Innovations 30. dubna 22 701 00 Ostrava 1 Czech Republic https://secure-web.cisco.com/1ERmDiIP2bUfj8wdW6dR7287YkQCoypPA35riqYyQKtdWM…

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Compiling thalamic nuclei segmentation volumes
by O'Dor, Sarah Louise 11 May '22

11 May '22

Good morning, I apologize in advance that my background is not in coding. I have run the freesurfer thalamic segmentation tool on over 100 subjects. I am now trying to compile the data. I know that the instructions for this command are: quantifyThalamicNuclei.sh <output_file> <analysisID> <OPTIONAL_SUBJECTS_DIR> For <output_file>, I have specified the name and location for the text file it will generate. For <analysisID>, I’m using the T1 that was processed through freesurfer, so I simply put T1. For <OPTIONAL_SUBJECTS_DIR>, I specify the subject directory. When I run the script above as: quantifyThalamicNuclei.sh [complete path]/ThalamicSegSheet.txt T1 [complete path]/Subjects/ The response is: Gathering results from subjects in: [complete path]/Subjects And writing them to: [complete path]/ThalamicSegSheet.txt …but nothing is generated. Any advice? I’d hate to compile the date individually for over 100 subjects. Many thanks, Sarah

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Re: [Freesurfer] VM Passcode
by fsbuild 10 May '22

10 May '22

External Email - Use Caution Sending the info to your email shortly. - R. On May 10, 2022, at 09:29, D R <deinrasenmaeher(a)gmx.de> wrote:       External Email - Use Caution        hello,I would like to get a passcode for the .7z file for the VM.Thank you in advance_______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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Recon-all Freezes on Parallel
by Joanna L Eckhardt 10 May '22

10 May '22

External Email - Use Caution Dear FreeSurfer Team, I have been trying to use the parallel command (following FreeSurfer tutorial) to run multiple subjects (Windows os running Ubuntu VM). I only have 2 cores, so I have it set to 2 jobs instead of 8 as in the tutorial. When I use the code from the tutorial, there is an error with the .nii, and I assume it is because my files are .nii.gz. developer@developer-VirtualBox:~/FreeSurfer/Cannabis_Reduced$ ls *.nii | parallel --jobs 3 recon-all -s {.} -i {} -all -qcache ls: cannot access '*.nii': No such file or directory So I changed the code to .gz with everything else the same, and FreeSurfer does nothing (it stalls/freezes). Is this just because my computer cannot handle the job? Is there anything else I can do to run parallel? If not, I can always just run 1 subject at a time, but I want to check and see if there is another way to get this to work. Thank you for your time! Joanna

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Freesurfer May 2022