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-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@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-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Huang, Yujing <YHUANG43@MGH.HARVARD.EDU>
Sent: 25 September 2023 21:43
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] Unable to complete all the steps of recon-all

- External Email -

External Email - Use Caution

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-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@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>
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-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Huang, Yujing <YHUANG43@MGH.HARVARD.EDU>
Sent: 25 September 2023 20:49
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] Unable to complete all the steps of recon-all

- External Email -

External Email - Use Caution

Can you send the recon-all.log?

Yujing

From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> On Behalf Of Mervin Tee
Sent: Monday, September 25, 2023 2:53 AM
To: 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-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of fsbuild <fsbuild@contbay.com>
Sent: 25 September 2023 10:10
To: freesurfer@nmr.mgh.harvard.edu <freesurfer@nmr.mgh.harvard.edu>
Cc: Mervin Tee <mervintee@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 <mervintee@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

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 list
Freesurfer@nmr.mgh.harvard.edu
MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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.