Freesurfer

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30076 discussions

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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Re: [Freesurfer] Passcode VM
by fsbuild 05 May '22

05 May '22

External Email - Use Caution Sending the info to your email shortly. - R. On May 5, 2022, at 16:36, Marius Zeinhofer <mariusz(a)simula.no> wrote:        External Email - Use Caution        Hi,I am interested in the passcode for the VM as explained on the Freesurfer website.Thank you very much.Best,Marius_______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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Re: [Freesurfer] Library Error
by fsbuild 05 May '22

05 May '22

External Email - Use Caution Hello Jabeur, Please check your setup.  When the VM is first setup and run, there should be no library errors from freeview.  You can test this with the following commands. developer@developer-VirtualBox:~$ cd $HOMEdeveloper@developer-VirtualBox:~$ pwd/home/developerdeveloper@developer-VirtualBox:~$ which freeview/usr/local/freesurfer/7.2.0/bin/freeviewdeveloper@developer-VirtualBox:~$ ldd `which freeview` | grep "not found"developer@developer-VirtualBox:~$ If you still see a library reported as not found then something happened with your environment and/or how freesurfer is now setup to cause the error.  In that case, I recommend you delete the current FS_7_2_0_ubuntu_18_04_06 virtual machine from the VirtualBox client (choose to delete the files), setup the VM again, and when you first login check freeview again with the above commands. When you want to process your own subject data we recommend you create a new directory in your home directory and set the environment variable SUBJECTS_DIR to point to it.  The install of freesurfer including the provided subject data is meant for reference and the files are in a protected system directory.  So it’s preferable to not modify and/or write files to where SUBJECTS_DIR points to out of the box.  Instead, just create a new directory for processing subjects with, e.g., developer@developer-VirtualBox:~$ cd $HOMEdeveloper@developer-VirtualBox:~$ mkdir my_subjectsdeveloper@developer-VirtualBox:~$ export SUBJECTS_DIR=$HOME/my_subjects - and put your subject data to process in $HOME/my_subjects - R. On May 5, 2022, at 19:14, Jabeur Mouna <jabeurmouna(a)gmail.com> wrote:        External Email - Use Caution        <image.png>_______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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Library Error
by Jabeur Mouna 05 May '22

05 May '22

External Email - Use Caution [image: image.png]

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Curvature data question
by Samuel Paré 05 May '22

05 May '22

External Email - Use Caution Hello, We are looking at some of our data acquired on a 7T magnet. We ran recon-all with the “highres” flag. The obtained results for cortical thickness and cortical volume are very comparable to data that we obtain when using 3 T brain images. However, the results for cortical curvature are significantly different from what we get by our 3 T data. I attach the output of mean cortical curvature values using the Destrieux atlas for a 3T and 7T dataset on healthy controls. As you can notice, they differ roughly by a factor of 2. Any explanation for what may cause this large difference? Thanks, Samuel [image: image.png] -- *Samuel Paré, MSc* Laboratoire du développement et plasticité du système visuel École d'optométrie Université de Montréal

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