Freesurfer October 2022

freesurfer@nmr.mgh.harvard.edu

89 participants
132 discussions

Quality control of longitudinal recon-all output for >500 participants
by Blujus, Jenna 16 Oct '22

16 Oct '22

External Email - Use Caution Hi all, I am processing a large longitudinal dataset of T1-weighted anatomical images through the recon-all pipeline (N=680). I know that the gold standard for quality control following recon-all is visual inspection of the output surfaces and parcellations. However, given the large sample size, I was writing to see if the community has any recommendations for automatic QC pipelines. I read a few papers discussing the use of Euler numbers to detect outlier datasets for exclusion (see citations below). Does anyone have any other recommendations? Thank you in advance! Best, Jenna References: 1. Rosen, A. F., Roalf, D. R., Ruparel, K., Blake, J., Seelaus, K., Villa, L. P., ... & Satterthwaite, T. D. (2018). Quantitative assessment of structural image quality. *Neuroimage*, *169*, 407-418. 2. de Lange, A. M. G., Kaufmann, T., Quintana, D. S., Winterton, A., Andreassen, O. A., Westlye, L. T., & Ebmeier, K. P. (2021). Prominent health problems, socioeconomic deprivation, and higher brain age in lonely and isolated individuals: A population-based study. *Behavioural Brain Research*, *414*, 113510.

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mris_make_average_surface, flirt transformations question
by Chris Adamson 14 Oct '22

14 Oct '22

External Email - Use Caution Freesurfer experts, I'm trying to make average surfaces for a collection of subjects into a template space. I have performed the following flirt registration per subject: flirt -in $SUBJECTS_DIR/$CURSUBJECT/mri/T2.nii.gz -ref template0.nii.gz -omat $SUBJECTS_DIR/$CURSUBJECT/mri/transforms/talairach.fslmat -out $SUBJECTS_DIR/$CURSUBJECT/mri/transforms/talairach.nii.gz -dof 12 -searchrx -$D $D -searchry -$D $D -searchrz -$D $D Then make the talairach.xfm files for each subject lta_convert --infsl $SUBJECTS_DIR/$CURSUBJECT/mri/transforms/talairach.fslmat --outmni $SUBJECTS_DIR/$CURSUBJECT/mri/transforms/talairach.xfm --src $SUBJECTS_DIR/$CURSUBJECT/mri/T2.mgz -trg template0.nii.gz Then run mris_make_average_surface mris_make_average_surface -i 7 -s $CURSURFTYPE $CURHEMI $CURSURFTYPE.flirt sphere.reg2 fsaverage The resulting average surface does not overlay onto template0.nii.gz correctly, it is in the wrong orientation. It isn't in TKR space, so I convert it to TKR space. mris_convert --vol-geom template0.nii.gz $SUBJECTS_DIR/fsaverage/surf/$CURHEMI.$CURSURFTYPE.flirt $SUBJECTS_DIR/fsaverage/surf/$CURHEMI.$CURSURFTYPE.flirt.volgeom mris_convert --vol-geom template0.nii.gz --to-tkr $SUBJECTS_DIR/fsaverage/surf/$CURHEMI.$CURSURFTYPE.flirt.volgeom $SUBJECTS_DIR/fsaverage/surf/$CURHEMI.$CURSURFTYPE The resulting surface $SUBJECTS_DIR/fsaverage/surf/$CURHEMI.$CURSURFTYPE overlays onto the template template0.nii.gz but it is offset slightly and not overlaid correctly. Am I doing something wrong? Thanks in advance, Chris. Dr Chris Adamson Senior Research Officer, Developmental Imaging, Clinical Sciences (0.3 EFT) Software Engineer, Cardiovascular Research (0.7 EFT) Murdoch Childrens Research Institute The Royal Children's Hospital Flemington Road, Parkville, VIC 3052 Australia E chris.adamson(a)mcri.edu.au<mailto:chris.adamson@mcri.edu.au> http://secure-web.cisco.com/1xDAoEUxMPPuCsJFESgxVj8G_Fqd-g7vRsh53KrQ6HSMvkl…<http://secure-web.cisco.com/17tnfb4NVhmhEj8eHc-vz41g2VE4LFjxQeJHBYmM2X28Zoj…> Disclaimer This e-mail and any attachments to it (the "Communication") are, unless otherwise stated, confidential, may contain copyright material and is for the use only of the intended recipient. If you receive the Communication in error, please notify the sender immediately by return e-mail, delete the Communication and the return e-mail, and do not read, copy, retransmit or otherwise deal with it. Any views expressed in the Communication are those of the individual sender only, unless expressly stated to be those of Murdoch Children’s Research Institute (MCRI) ABN 21 006 566 972 or any of its related entities. MCRI does not accept liability in connection with the integrity of or errors in the Communication, computer virus, data corruption, interference or delay arising from or in respect of the Communication.

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Password for unzipping of VM
by Malina Jop 14 Oct '22

14 Oct '22

External Email - Use Caution Dear FreeSurfer experts, I would like to unzipp the VM in order to run FreeSurfer on windows. Could you provide me the password for unzipping? Thank you very much in advance, best regards, Malina

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FreeSurfer Password
by José Carlos López Mata 14 Oct '22

14 Oct '22

External Email - Use Caution Hi, my name us José Carlos López Mata. I'm a biomedical engineering at Universidad Autonoma Metropolitana in Mexico City. I'm working with fMRi images and i need to use Freesurfer for my project so, i request de activation password, please.

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Password to unzip freesurfer 7.2.0
by Chien Nguyenle 13 Oct '22

13 Oct '22

External Email - Use Caution Dear freesurfer, I am a researcher at vietnam medical university.I have just downloaded FS_7_2_0_ubuntu_18_04_06.ova.7z from your website and intend to run on linux/ubuntu.May I know the password for unzip and whether this version of freesurfer requires license file?Best regardsChien Nguyen

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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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Freesurfer October 2022