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Hi Yujing,
I think you are not understanding the question/issue I'm asking. I am aware
that they are not creating links of those files and that it will be generated
when it reaches these steps.
My folders are located on an exFAT drive. The symbolic link cannot be created
due to exFAT format. Hence, my question isn't about whether lh.white.K is
created or not or if it was missing from directory that causes it to be missing.
The question that I'm asking is if there's a solution to workaround external
drives that are formatted as exFAT? As symbolic links can't be generated on
exFAT formatted drives. Hope that clarifies.
Cheers,
Mervin
________________________________
From: freesurfer-boun...@nmr.mgh.harvard.edu
<freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Huang, Yujing
<yhuan...@mgh.harvard.edu>
Sent: 25 September 2023 22:17
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] Unable to complete all the steps of recon-all
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lh.white.K and lh.white.H normally created as links to lh.white.preaparc.K and
lh.white.preaparc.H
I don’t see ‘lh.white.K’ in your surf/ directory either as a file or a symbolic
link.
Yujing
From: freesurfer-boun...@nmr.mgh.harvard.edu
<freesurfer-boun...@nmr.mgh.harvard.edu> On Behalf Of Mervin Tee
Sent: Monday, September 25, 2023 10:03 AM
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] Unable to complete all the steps of recon-all
External Email - Use Caution
Hi Yujing,
You can find the directory listed before, however, before you start heading
down the wrong path of this error. I have and am able to complete recon-all
with no issue on my internal ssd that is formatted to work with symlink.
ls
/media/mt/Expansion/Disk9/EDIS_751_alreadytrftoFS/ED751_SAG_MPRAGE_p2_NON-SSc.nii/surf/
autodet.gw.stats.lh.dat lh.volume
autodet.gw.stats.rh.dat lh.volume.fsaverage.mgh
lh.area lh.volume.fsaverage.mris_preproc.log
lh.area.fsaverage.mgh lh.w-g.pct.mgh
lh.area.fsaverage.mris_preproc.log lh.white
lh.area.mid lh.white.preaparc
lh.area.pial lh.white.preaparc.H
lh.area.pial.fsaverage.mgh lh.white.preaparc.K
lh.area.pial.fsaverage.mris_preproc.log rh.area
lh.avg_curv rh.area.mid
lh.curv rh.area.pial
lh.curv.fsaverage.mgh rh.avg_curv
lh.curv.fsaverage.mris_preproc.log rh.curv
lh.curv.pial rh.curv.pial
lh.defect_borders rh.defect_borders
lh.defect_chull rh.defect_chull
lh.defect_labels rh.defect_labels
lh.defects.pointset rh.defects.pointset
lh.fsaverage.sphere.reg rh.fsaverage.sphere.reg
lh.inflated rh.inflated
lh.inflated.nofix rh.inflated.nofix
lh.jacobian_white rh.jacobian_white
lh.orig rh.orig
lh.orig.nofix rh.orig.nofix
lh.orig.premesh rh.orig.premesh
lh.pial rh.pial
lh.pial.T1 rh.pial.T1
lh.qsphere.nofix rh.qsphere.nofix
lh.smoothwm rh.smoothwm
lh.smoothwm.BE.crv rh.smoothwm.BE.crv
lh.smoothwm.C.crv rh.smoothwm.C.crv
lh.smoothwm.FI.crv rh.smoothwm.FI.crv
lh.smoothwm.H.crv rh.smoothwm.H.crv
lh.smoothwm.K1.crv rh.smoothwm.K1.crv
lh.smoothwm.K2.crv rh.smoothwm.K2.crv
lh.smoothwm.K.crv rh.smoothwm.K.crv
lh.smoothwm.nofix rh.smoothwm.nofix
lh.smoothwm.S.crv rh.smoothwm.S.crv
lh.sphere rh.sphere
lh.sphere.reg rh.sphere.reg
lh.sulc rh.sulc
lh.sulc.fsaverage.mgh rh.thickness
lh.sulc.fsaverage.mris_preproc.log rh.volume
lh.thickness rh.w-g.pct.mgh
lh.thickness.fsaverage.mgh rh.white
lh.thickness.fsaverage.mris_preproc.log rh.white.preaparc
Cheers,
Mervin
________________________________
From:
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
<freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
on behalf of Huang, Yujing
<yhuan...@mgh.harvard.edu<mailto:yhuan...@mgh.harvard.edu>>
Sent: 25 September 2023 21:43
To: Freesurfer support list
<freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] Unable to complete all the steps of recon-all
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The error says “ERROR: cannot find
/media/mt/Expansion/Disk9/EDIS_751/ED751_SAG_MPRAGE_p2_NON-SSc.nii/surf/lh.white.K”.
Can you send what your subject surf/ directory looks like - ‘ls -lt
/media/mt/Expansion/Disk9/EDIS_751/ED751_SAG_MPRAGE_p2_NON-SSc.nii/surf/’?
Yujing
From:
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
<freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
On Behalf Of Mervin Tee
Sent: Monday, September 25, 2023 9:39 AM
To: Freesurfer support list
<freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] Unable to complete all the steps of recon-all
External Email - Use Caution
HI Yujing,
Here's the log file you have requested. Do take note that I have followed a
post to modify my recon-all from ln to cp. so, the commands might look
different.
Cheers,
Mervin
________________________________
From:
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
<freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
on behalf of Huang, Yujing
<yhuan...@mgh.harvard.edu<mailto:yhuan...@mgh.harvard.edu>>
Sent: 25 September 2023 20:49
To: Freesurfer support list
<freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] Unable to complete all the steps of recon-all
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Can you send the recon-all.log?
Yujing
From:
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
<freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
On Behalf Of Mervin Tee
Sent: Monday, September 25, 2023 2:53 AM
To: freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] Unable to complete all the steps of recon-all
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<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
<freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
on behalf of fsbuild <fsbu...@contbay.com<mailto:fsbu...@contbay.com>>
Sent: 25 September 2023 10:10
To: freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>
<freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>>
Cc: Mervin Tee <mervin...@nus.edu.sg<mailto: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<mailto: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 2023
The 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.mgh
What should I do to resolve this issue?
Cheers,
Mervin
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