Freesurfer

freesurfer@nmr.mgh.harvard.edu

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30080 discussions

Re: [Freesurfer] Recon-all Freezes on Parallel
by fsbuild 09 May '22

09 May '22

External Email - Use Caution The VirtualBox settings indicate you host machine has 4 real and 4 virtual cores with 16G of RAM. You could try shutting down the VM, and then change the VirtualBox settings to give the VM 4 cores (instead of 2) and 12G of RAM (instead of 8G).  Then start the VM and try running your command again to see if performance improves maybe first with 2 jobs and then 4.   I would try not to run other applications on your host machine at this time. - R. On May 9, 2022, at 17:47, Joanna L Eckhardt <jeckhardt(a)health.ucsd.edu> wrote:        External Email - Use Caution        Oops, I meant to reply all: Hi R ,See below, I gave 8 GB and 2 CPU in settings.<image.png><image.png>--Joanna EckhardtNeurosciences Graduate ProgramUniversity of California, San DiegoSent: Monday, May 9, 2022 2:41 PMTo: freesurfer@nmr.mgh.harvard.edu <freesurfer@nmr.mgh.harvard.edu>Cc: Joanna L Eckhardt <jeckhardt@health.ucsd.edu>Subject: Re: [Freesurfer] Recon-all Freezes on Parallel In the VirtualBox settings, did you give the VM both cores to use?It would also be good to know much memory your machine has, and how much of that you gave to the VM in the VirtualBox settings.- R.On May 9, 2022, at 17:27, Joanna L Eckhardt <jeckhardt(a)health.ucsd.edu> wrote:        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_______________________________________________Freesurfer mailing listFreesurfer(a)nmr.mgh.harvard.eduMailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to behttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer_____________… mailing listFreesurfer@nmr.mgh..harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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Re: [Freesurfer] Recon-all Error
by fsbuild 09 May '22

09 May '22

External Email - Use Caution Hello Mouna, You should not need to set FREESURFER_HOME in the terminal window or source the setup script as that is already set in the environment to the pre-installed 7.2.0 release of freesurfer.  if the setup information listing FREESURFER_HOME etc. is not automatically displayed when you open a new terminal window, then something is not right with your current VM setup. Please see the online documentation https://secure-web.cisco.com/1gznVcTKDzEuwdybT3u9uoWvv2v… contains a link to the document Vbox_load_image showing how to setup the VM, i.e., page 12 says you can go to http://secure-web.cisco.com/1q0X87yBimuGRycgbM3K-M42AWFTRmdTzLmdSTP… obtain a license and how to use it in the terminal window. - R. On May 9, 2022, at 10:01, Mouna JABEUR <mouna.jabeur(a)enetcom.u-sfax.tn> wrote:        External Email - Use Caution        Hi,how can i solve this please ?<Capture d’écran 2022-05-09 145325.png><Capture d’écran 2022-05-09 145137.png><Capture d’écran 2022-05-09 145019.png>_______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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Re: [Freesurfer] Recon-all Freezes on Parallel
by Joanna L Eckhardt 09 May '22

09 May '22

External Email - Use Caution Oops, I meant to reply all: Hi R , See below, I gave 8 GB and 2 CPU in settings. [cid:f2395341-7e91-40b6-bc1c-d89bca3e4876] [cid:32cfdb7f-40af-4c07-babd-c07a17f81269] -- Joanna Eckhardt Neurosciences Graduate Program University of California, San Diego ________________________________ From: fsbuild(a)convergenceservice.com <fsbuild(a)convergenceservice.com> Sent: Monday, May 9, 2022 2:41 PM To: freesurfer(a)nmr.mgh.harvard.edu <freesurfer(a)nmr.mgh.harvard.edu> Cc: Joanna L Eckhardt <jeckhardt(a)health.ucsd.edu> Subject: Re: [Freesurfer] Recon-all Freezes on Parallel In the VirtualBox settings, did you give the VM both cores to use? It would also be good to know much memory your machine has, and how much of that you gave to the VM in the VirtualBox settings. - R. On May 9, 2022, at 17:27, Joanna L Eckhardt <jeckhardt(a)health.ucsd.edu> wrote: 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 _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu> https://secure-web.cisco.com/1D16OXl4F3D7EzPXJHwCPdzg7739Ei-nFn--qsir3PrQym…<https://secure-web.cisco.com/1gcVuUnsNGIajmH36BBP5ji4ZbVCz3onJbt4vYs8FHb4t2…>

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Recon-all Error
by Mouna JABEUR 09 May '22

09 May '22

External Email - Use Caution Hi, how can i solve this please ? [cid:f249d482-90f9-43e9-a1f3-dc5a2f46ab7a] [cid:60b6d04d-5312-4ec4-a039-a79871a083a3][cid:6d8eb673-c4d0-472a-afa3-0e61e3bc4826]

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Recon-all Error: "ln: failed to create symbolic link 'lh.white.H': Operation not permitted"
by Joanna L Eckhardt 07 May '22

07 May '22

External Email - Use Caution Dear FreeSurfer Team, I am attempting to run Recon-all on practice cannabis data on the tutorial, using Ubuntu18 VM for Windows os (also I completely new to coding and Ubuntu). On my first attempt to run Recon-all, I got the error shown below: "ln: failed to create symbolic link 'lh.white.H': Operation not permitted." mris_curvature -w -seed 1234 lh.white.preaparc setting seed for random number generator to 1234 total integrated curvature = 25.993*4pi (326.639) --> -25 handles ICI = 146.8, FI = 1524.9, variation=23628.367 writing Gaussian curvature to ./lh.white.preaparc.K...done. writing mean curvature to ./lh.white.preaparc.H...done. @#@FSTIME 2022:05:05:23:34:15 mris_curvature N 4 e 1.66 S 0.10 U 1.30 P 84% M 144988 F 3 R 39631 W 0 c 13 w 718 I 616 O 0 L 1.08 1.11 1.08 @#@FSLOADPOST 2022:05:05:23:34:17 mris_curvature N 4 1.08 1.11 1.08 rm -f lh.white.H ln -s lh.white.preaparc.H lh.white.H ln: failed to create symbolic link 'lh.white.H': Operation not permitted Linux developer-VirtualBox 5.4.0-109-generic #123~18.04.1-Ubuntu SMP Fri Apr 8 09:48:52 UTC 2022 x86_64 x86_64 x86_64 GNU/Linux recon-all -s sub101-sesBL exited with ERRORS at Thu May 5 23:34:17 EDT 2022 For more details, see the log file /home/developer/guest_shared/fs-subjects/sub101-sesBL/scripts/recon-all.log To report a problem, see http://secure-web.cisco.com/1qOeaquoMOTkikWpYGZ4Zmm7T4aU7IdoLWz_R7WjwgxWoQG… After searching through the archives, I see that other people have had the same problem in that their os is not able to create a symbolic link. I tried following one of the archives and did: developer@developer-VirtualBox:~/guest_shared/mv-ds000174-1.0.1-Cannabis/sub-101/ses-BL/anat$ cd /home/developer/guest_shared/fs-subjects developer@developer-VirtualBox:~/guest_shared/fs-subjects$ ln -s /home/developer/guest_shared/fs-subjects/fsaverage ln: failed to create symbolic link './fsaverage': Operation not permitted But I again received the "failed to create symbolic link. How can I allow symbolic links? Also, I was generally wondering how do you rerun recon-all starting from a specific step once I get this working? Does one have to rerun all of recon-all each time there is an error or can I start from where I left off? Thank you so much for your help! Best wishes, Joanna

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Passcode Request
by Eric Mokri 06 May '22

06 May '22

External Email - Use Caution Hello, Can I please have the passcode to open the following file for MRI processing: FS_7_2_0_Ubuntu_18_04_06.ova.7z Regards, Eric Mokri

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An estimated date for FreeSurfer 7.3 release
by King-Wai Chu 06 May '22

06 May '22

External Email - Use Caution Hello, I saw in https://secure-web.cisco.com/15xzpk6DF2_1DXEdVnlyo_B20R76xyd06ashqKEsp8aYWp… that TRACULA in FreeSurfer 7.3 is upcoming. Do you have an estimated date of when that will happen? We want to update our version 7.1.1 to the latest release. If 7.3 is coming out in a couple of months, we can wait for it. Or should we install 7.2 instead? Thanks, King-Wai

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Recon-All Error: "Command exited with non-zero status"
by Joanna L Eckhardt 06 May '22

06 May '22

External Email - Use Caution Hi FreeSurfer Team, I am trying to run Recon-all on the cannabis test data on the freesurfer tutorial (I am running Ubuntu 18 VM on Windows os). When I try to use the Recon-all command, I get the error "Command exited with non-zero status" and "recon-all -s sub101 exited with ERRORS." Can you help me solve this? I am completely new to coding/Ubuntu so I am also confused about the SUBJECTS_DIR. Where can I find that folder? I do not see /usr/local/freesurfer/7.2.0/subjects anywhere in the VM. Also, if there is a better way to export and present my code to you other than copy-pasting it as I have done below, please let me know so I can do that with future emails. developer@developer-VirtualBox:~/guest_shared/mv ds000174-1.0.1 Cannabis/sub-101/ses-BL/anat$ recon-all -s sub101 -i sub-101_ses-BL_T1w.nii.gz -all Subject Stamp: freesurfer-linux-ubuntu18_x86_64-7.2.0-20210721-aa8f76b Current Stamp: freesurfer-linux-ubuntu18_x86_64-7.2.0-20210721-aa8f76b INFO: SUBJECTS_DIR is /usr/local/freesurfer/7.2.0/subjects Actual FREESURFER_HOME /usr/local/freesurfer/7.2.0 Linux developer-VirtualBox 5.4.0-109-generic #123~18.04.1-Ubuntu SMP Fri Apr 8 09:48:52 UTC 2022 x86_64 x86_64 x86_64 GNU/Linux /usr/local/freesurfer/7.2.0/subjects/sub101 mri_convert /home/developer/guest_shared/mv ds000174-1.0.1 Cannabis/sub-101/ses-BL/anat/sub-101_ses-BL_T1w.nii.gz /usr/local/freesurfer/7.2.0/subjects/sub101/mri/orig/001.mgz mri_convert /home/developer/guest_shared/mv ds000174-1.0.1 Cannabis/sub-101/ses-BL/anat/sub-101_ses-BL_T1w.nii.gz /usr/local/freesurfer/7.2.0/subjects/sub101/mri/orig/001.mgz mri_convert: extra arguments ("Cannabis/sub-101/ses-BL/anat/sub-101_ses-BL_T1w.nii.gz" and following) type mri_convert -u for usage Command exited with non-zero status 1 @#@FSTIME 2022:05:05:15:24:40 mri_convert N 4 e 0.00 S 0.00 U 0.00 P 100% M 6204 F 0 R 242 W 0 c 0 w 1 I 0 O 0 L 0.19 0.11 0.04 @#@FSLOADPOST 2022:05:05:15:24:40 mri_convert N 4 0.19 0.11 0.04 Linux developer-VirtualBox 5.4.0-109-generic #123~18.04.1-Ubuntu SMP Fri Apr 8 09:48:52 UTC 2022 x86_64 x86_64 x86_64 GNU/Linux recon-all -s sub101 exited with ERRORS at Thu May 5 15:24:40 EDT 2022 For more details, see the log file /usr/local/freesurfer/7.2.0/subjects/sub101/scripts/recon-all.log To report a problem, see http://secure-web.cisco.com/1nsoXu7DCJVVepnD_TI4lsupkcqto3lUNXVTynw-dkWgX0j… Thank you! Joanna

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Re: [Freesurfer] Recon-all
by fsbuild 06 May '22

06 May '22

External Email - Use Caution Sorry if I did not see it before, but parentheses are one of several special characters in the linux/unix shell.  So either don’t use them in file names, or you can try escaping them by preceeding each instance with a backslash so they are interpreted literally, Sub-132_SAG_T1_MPRAGE_$INC_UPPER_CX_AS_MUCH$__2.nii -all- or you could try putting the entire file name in quotes, "Sub-132_SAG_T1_MPRAGE_(INC_UPPER_CX_AS_MUCH)__2.nii -all” - R. On May 6, 2022, at 04:17, krystaly <krystaly(a)hku.hk> wrote:        External Email - Use Caution        Dear R., Thanks for your reply. My apologies if I did not totally get your point – I moved the Sub-132 folder to Home directory and typed in the command as you suggested.  However, I still got the error as follows: developer@developer-VirtualBox:~$ export SUBJECTS_DIR=/home/developerdeveloper@developer-VirtualBox:~$ recon-all -s Sub-132 -i Sub-132_SAG_T1_MPRAGE_(INC_UPPER_CX_AS_MUCH)__2.nii -allbash: syntax error near unexpected token `('developer@developer-VirtualBox:~$ lsDesktop    ExternalHD.txt  license.txt  Pictures  TemplatesDocuments  fsl_507         matlab       Public    VideosDownloads  guest_shared    Music        Sub-132developer@developer-VirtualBox:~$ cd Sub-132developer@developer-VirtualBox:~/Sub-132$ recon-all -s Sub-132 -i Sub-132_SAG_T1_MPRAGE_(INC_UPPER_CX_AS_MUCH)__2.nii -allbash: syntax error near unexpected token `('developer@developer-VirtualBox:~/Sub-132$ Would you please kindly advise? Thank you so much! Best regards, Krystal  From: fsbuildSent: Friday, May 6, 2022 11:31 AMTo: freesurfer@nmr.mgh.harvard.eduCc: krystalySubject: Re: [Freesurfer] Recon-all Hello Krystally,Try putting the directory Sub-132 under your userid’s home directory, i.e., /home/developer/Sub-132, and then set SUBJECTS_DIR in the environment to point to it.  With the directory Sub-132 specified on your command line, you could then try,$ export SUBJECTS_DIR=/home/developer- R.On May 5, 2022, at 21:53, krystaly <krystaly(a)hku.hk> wrote:        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 (MailScanner has detected a possible fraud attempt from "secure-web..cisco.com" claiming to behttps://andysbrainbook.readthedocs.io/en/latest/FreeSurfer/FS_ShortCourse/FS_03_ReconAll.html). 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 -allbash: 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 -allmkdir: cannot create directory '/usr/local/freesurfer/7.2.0/subjects/Sub-132': Permission deniedmkdir: cannot create directory '/usr/local/freesurfer/7.2.0/subjects/Sub-132': Permission deniedmkdir: cannot create directory '/usr/local/freesurfer/7.2.0/subjects/Sub-132': Permission deniedcp: cannot create regular file '/usr/local/freesurfer/7.2.0/subjects/Sub-132/scripts/build-stamp.txt': No such file or directorycat: /usr/local/freesurfer/7.2.0/subjects/Sub-132/scripts/build-stamp.txt: No such file or directoryINFO: FreeSurfer build stamps do not matchSubject 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  _______________________________________________Freesurfer mailing listFreesurfer(a)nmr.mgh.harvard.eduMailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to behttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer_____________… mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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Re: [Freesurfer] Recon-all
by fsbuild 06 May '22

06 May '22

External Email - Use Caution Hello Krystally, Try putting the directory Sub-132 under your userid’s home directory, i.e., /home/developer/Sub-132, and then set SUBJECTS_DIR in the environment to point to it.  With the directory Sub-132 specified on your command line, you could then try,$ export SUBJECTS_DIR=/home/developer - R. On May 5, 2022, at 21:53, krystaly <krystaly(a)hku.hk> wrote:        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 (MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to behttps://andysbrainbook.readthedocs.io/en/latest/FreeSurfer/FS_ShortCourse/FS_03_ReconAll.html). 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 -allbash: 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 -allmkdir: cannot create directory '/usr/local/freesurfer/7.2.0/subjects/Sub-132': Permission deniedmkdir: cannot create directory '/usr/local/freesurfer/7.2.0/subjects/Sub-132': Permission deniedmkdir: cannot create directory '/usr/local/freesurfer/7.2.0/subjects/Sub-132': Permission deniedcp: cannot create regular file '/usr/local/freesurfer/7.2.0/subjects/Sub-132/scripts/build-stamp.txt': No such file or directorycat: /usr/local/freesurfer/7.2.0/subjects/Sub-132/scripts/build-stamp.txt: No such file or directoryINFO: FreeSurfer build stamps do not matchSubject 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  _______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail..nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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