External Email - Use Caution If the files can be read from inside the VM from the external drive, then I'd think you could copy them into the Linux file system. You would have to run the “mount” or some other command in the Linux terminal window to determine the path on the exFAT drive to what SUBEJCTS_DIR is there. But usually things are mounted under /media $ mount | grep media… check output ...
Let’s say your path to SUBJECTS_DIR on the exFAT drive as visible in the Linux file system is /media/exfat/data/subj034 You need to find a location in Linux where you have enough space to copy the data. I will assume using your home directory in the Linux VM below. So in the Linux terminal window to use your home directory you could try the commands below. NOTE - that if you have spaces in a path or directory name on the exFAT drive, then quote them below, e.g., subj 034 ==> "subj 034" $ cd… or ...$ cd $HOME$ pwd/home/developer <— your result will differ… see how much disk space you have …$ df -h .… check output … and if you have enough space to copy data, if so, make a subdirectory for the copy …$ mkdir data_copy$ cd data_copy… try using the tar utility to copy all data from the drive …$ (cd /media/exfat/data; tar cpf - subj034) | tar xpf -… may take a while depending on speed of drive and size of data … $ cd subj034… check all the data is there $ ls -lRt * | more… hit q to stop output from more command ... $ pwd/home/developer/data_copy/subj034 … then set SUBJECTS_DIR in the environment or in script, etc. that runs the recon-all $ export SUBJECTS_DIR=/home/developer/data_copy/subj034 - R. On Sep 25, 2023, at 02:52, Mervin Tee <mervin...@nus.edu.sg> wrote: External Email - Use Caution Hi R,Thanks for getting back, indeed a copy of those files doesn't help because just like what you have mentioned at some point a check failed and I could not proceed with the remaining steps of recon-all. The command I pasted was obtain from the last line of the error log text file where it indicates where the step of which the error occurred. But the main error is mostly due to symlink on exFAT storage on linux. Hence, the question here is if there is any solution that allows me to still work on external exFAT storage. As symlink doesn't seems to work on exFAT storage. As my data are bitlocked on an external storage, which doesn't allow me to change the format for the storage drive. So, I was hoping to look for a workaround that allows me to continue working on exFAT storage. Cheers,Mervin From: freesurfer-boun...@nmr.mgh.harvard.edu <freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of fsbuild <fsbu...@contbay.com>Sent: 25 September 2023 10:10To: freesurfer@nmr.mgh.harvard.edu <freesurfer@nmr.mgh.harvard.edu>Cc: Mervin Tee <mervin...@nus.edu.sg>Subject: Re: [Freesurfer] Unable to complete all the steps of recon-all - External Email - External Email - Use Caution I don’t see an error message in what you posted below.I would not assume changing soft links to actual copies of the same file (by a different name) will work, i.e., anything that makes a soft link may subsequently test for a soft link using the link name. That test will fail if the soft link has been replaced by an actual (duplicate) copy of the file. The expectation is when writing output e.g., during recon-all, that SUBJECTS_DIR points to a linux compatible file system that supports creating all the Linux file system file types (including soft links) and support all Linux file privileges.-R.On Sep 24, 2023, at 01:58, Mervin Tee <mervin...@nus.edu..sg> wrote: External Email - Use Caution Hi, I'm trying to complete my recon-all command. I'm currently working on Ubuntu 22 and processing the images from an exFAT drive.After digging a bit, I realised that symbolic links cannot be created on exFAT drives. I then came across another post that suggest to change all 'ln' to cp instead. While that works for the remaining steps. It started exiting with errors at this stage..The stage where it stops#@# Qdec Cache preproc lh white.K fsaverage Wed Sep 13 15:40:33 +08 2023The error that was in the error log.CMD mris_preproc --s ED751_SAG_MPRAGE_p2_NON-SSc.nii --hemi lh --meas white.K --target fsaverage --out lh.white.K.fsaverage.mghWhat should I do to resolve this issue? Cheers,Mervin Important: This email is confidential and may be privileged. If you are not the intended recipient, please delete it and notify us immediately; you should not copy or use it for any purpose, nor disclose its contents to any other person. Thank you._______________________________________________Freesurfer mailing listfreesur...@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/freesurferImportant: This email is confidential and may be privileged. If you are not the intended recipient, please delete it and notify us immediately; you should not copy or use it for any purpose, nor disclose its contents to any other person. Thank you._______________________________________________Freesurfer mailing listfreesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard..edu/mailman/listinfo/freesurfer
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