Freesurfer

freesurfer@nmr.mgh.harvard.edu

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30076 discussions

Re: [Freesurfer] mghread : cannot open the file
by fsbuild 13 Oct '22

13 Oct '22

External Email - Use Caution Looks like your setting for SUBJECTS_DIR together with the last 2 command line arguments, tester  /mri/norm.mgz - is causing it to look for the path $SUBJECTS_DIR/tester/mri/aseg.mgz - which does not exist.   Or I don’t see a directory $SUBJECTS_DIR/tester in the 7.3.2 release to read from and you cannot by default write to or create a new subdirectory ./tester under $SUBJECTS_DIR Did you mean to set  SUBJECTS_DIR to something different where $SUBEJCTS_DIR/tester/mri/aseg.mgz already exists?  Maybe you need to change your command line arguments to be different. - R. On Oct 12, 2022, at 22:25, priya padma <priya(a)phenomx.ai> wrote:        External Email - Use Caution        Hello Team, I am trying to find the volume of WM, GM, CSF separately and I came across this command namely"mri_compute_volume_fractions"Looking through all the email archives I gave the following line as the command after setting the paths$ mri_compute_volume_fractions --o test --regheader tester /mri/norm.mgzbut I get the following erroruser-MacBook-Pro:sub-AD003S1059S61129 user$ mri_compute_volume_fractions --o test --regheader tester /mri/norm.mgz supposed to be reproducible but seed not set7.3.2sysname  Darwinhostname user-MacBook-Pro.localmachine  x86_64user     <username>setenv SUBJECTS_DIR /Applications/freesurfer/7.3.2/subjectscd /Applications/freesurfer/7.3.2/subjects/sub-AD003S1059S61129mri_compute_volume_fractions --o test --regheader tester /mri/norm.mgz outstem testregfile (null)regtype 0segfile aseg.mgzwsurf whitepsurf pialTempVolFile /mri/norm.mgzUSF 2Reading in aseg and surfs from /Applications/freesurfer/7.3.2/subjects/testerLoading /Applications/freesurfer/7.3.2/subjects/tester/mri/aseg.mgzerror: mghRead(/Applications/freesurfer/7.3.2/subjects/tester/mri/aseg.mgz, -1): could not open fileI set all the paths so why am I not able to read the mgz file?Could anyone help me with this ?Thank you -- Best RegardsPadma PriyaAI Developer PhenoMx, Inc.priya(a)phenomx.ai | (+82)10-5405-2685_______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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version upgrade/migration
by Victor Montal Blancafort 13 Oct '22

13 Oct '22

External Email - Use Caution Dear Fs experts, We have multiple subjects with strong/focal atrophy processed with Freesurfer5.1 We want to re-process them to the newest version in order to have all the capabilities/segmentations/outputs from the newest recon-all, but we do NOT want to loose the huge amount of ours of manual correction (control points + wm + pial). I made some tests, and from the logs its clear that the brainmask is NOT updates (thus, the pial edits will be incoportated). Its not that clear if the wm.mgz and the control points are used for the new/updated segmentation? Is re-running recon-all enough and will incorporate all the manual edits? Which is the best approach to migrate/update? Thank you in advance for your help, Victor Montal

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Running recon-all in parallel
by priya padma 12 Oct '22

12 Oct '22

External Email - Use Caution Hello team, As freesurfer takes lot of time for processing one subject, I was searching on how to run recon-all for multiple subjects in parallel and I found the following in Andy's brain book doc https://secure-web.cisco.com/1MEMXaE4I_nNiI-Rew0Vd8aEQB5KqBzrJ54sB6YQjjf_p8… and ran $ ls *.nii | parallel --jobs 8 recon-all -s {.} -i {} -all -qcache and I get the error "/usr/bin/bash: /home/***/***/freesurfer/bin/recon-all: /bin/tcsh: bad interpreter: No such file or directory " I believe that this is not the right command for linux, ubuntu 20 OS but I am not sure. Could anyone help me with this? Thank you -- Best Regards Padma Priya *AI Developer * *PhenoMx, Inc.* *priya(a)phenomx.ai <priya(a)phenomx.ai> | (+82)10-5405-2685*

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Issue with rotation during longitudinal base creation
by Nathan Kindred (PGR) 12 Oct '22

12 Oct '22

External Email - Use Caution Hi, I have been processing longitudinal data using the longitudinal processing stream but for some subjects I am having getting this error when creating the base: Input rotation's max deviation from rotation is: 0.000258493 MyMatrix::RotationMean input(s) not rotation What would be the best way to fix this? Best, Nathan

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Re: [Freesurfer] Entering MRISpositionSurface error
by fsbuild 12 Oct '22

12 Oct '22

External Email - Use Caution Not sure what your container is running for Freesurfer.   I would check you are running the latest version = 7.3.2 compiled for Ubuntu 20 from, https://secure-web.cisco.com/1HfVaiagqDrkuTglakaaQb9f9tkuN3NAisGLhceeHTxDiD… Looks like recon-all crashed with a core dump while running MRISpositionSurface()Segmentation fault (core dumped)Linux 2824b6974774 5.15.0-48-generic #54~20.04.1-Ubuntu SMP Thu Sep 1 16:17:26 UTC 2022 x86_64 x86_64 x86_64 GNU/LinuxCould be the docker container does not have adequate run time resources, e.g., RAM.  Maybe you could send along the core dump file. - R. On Oct 12, 2022, at 02:46, 梁群君 <liangqunjun(a)foxmail.com> wrote:<recon-all-rh.log>

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Virtual Machine Passcode
by marie 11 Oct '22

11 Oct '22

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password
by Agustina Fragueiro 11 Oct '22

11 Oct '22

External Email - Use Caution Hello, I am installing FreeSurfer 7.2.0 on a virtual box in Windows. How could I get the password to unzip the file? Thank you, Agustina -- Agustina Fragueiro, Ph.D. Postdoctoral researcher EMPENN research unit INRIA - National Institute for Research in Digital Science and Technology Rennes, France

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Virtual machine password
by Daphné Rimsky-Robert 10 Oct '22

10 Oct '22

External Email - Use Caution Hello, I understand I need a password to be able to use the freesurfer virtual machine. I hope this is the correct place to request it ? Best regards, Daphné Rimsky-Robert

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Thalamic nucleus segmentation 3D export
by Paulk, Angelique C.,PHD 10 Oct '22

10 Oct '22

Hello, I apologize if this has been answered before though I could not find this specific information in the archives. We are hoping to export the Thalamic nuclei segmentations to 3D volumes outside of Freeview/Freesurfer (e.g. .stl or other options) to perform a number of calculations in python or Matlab or visualize in Blender. I have been able to use 3DSlicer and get segmentation and 3D renders by importing the "aparc.DKTatlas+aseg.mgz" file and export .stl files in 3DSlicer, but, when I import the "ThalamicNuclei.v12.T1.FSvoxelSpace.mgz" file, it is only showing the entire thalamus as a mask in 3DSlicer though the nuclei are segmented in Freeview. Is there another type of export from FreeSurfer that would allow this type of saved volume/surface export? Thank you for all your help, Angelique

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Hemisphere in Yellow
by Jun Yeon Won 10 Oct '22

10 Oct '22

External Email - Use Caution Dear Freesurfer experts, I am running a linear regression analysis and found a significant result showing below (cache.th20.abs.sig.cluster.summary file). [image: image.png] I ran the below script to get this result. Right hemisphere was focused for this analysis. mri_glmfit-sim --glmdir rh.thickness.10.glmdir \ --cache 2 abs \ --cwp 0.05 But, when visualizing the cache.th20.abs.sig.cluster.mgh file, it shows below - the hemisphere is in yellow. [image: image.png] The below is a visualization of sig.mgh. The underlay should be gray but I am not sure why the underlay looks yellow when overlaying the thresholded result. [image: image.png] I saw somebody posted the same issue here ( https://secure-web.cisco.com/1OHcN_bRSEDk0roNAjIAfufCwrh4xf7rzgQtoclY3flDVp…) but I was not able to find the solution from here. Could you please let me know what is an issue and how to resolve this? Best, Jun

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