From paul@corticometrics.com Thu Jul 15 09:01:59 2021
From: Paul Wighton <paul@corticometrics.com>
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] Missing freesurfer files after running recon-all
Date: Thu, 15 Jul 2021 09:01:44 -0400
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        External Email - Use Caution       =20

Hi Lisa,

I think is has something to do with these lines from the log:

```
INFO: fsaverage subject does not exist in SUBJECTS_DIR
INFO: Creating symlink to fsaverage subject...

 cd /dfs6/pub/ltaylor2/downs; ln -s
/data/opt/apps/freesurfer/6.0.1/subjects/fsaverage; cd -

ln: failed to create symbolic link './fsaverage': File exists
```

It can't find a copy of fsaverage in SUBJECTS_DIR, so recon-all tries to
link to one, but fails because it exists. (?)

I see the recon-all argument for subject (`-s imagedir/subid`) has a '/'
character in it. That might be the cause.  The 'imagedir' should be
specified by the environment variable SUBJECTS_DIR (which it looks like is
working fine in the log)

Can you try re-running it with just `-s subid` instead of `-s
imagedir/subid`?

If that's not it, is there anything else in common with the subject names
of the ones that fail? Another strange character perhaps?

For reference, the errors are starting around here in recon-all:
https://secure-web.cisco.com/1YE2a1xj00WKbbFVqM8gIEmudSBRD1jmHutdsxIQz2yLXszy=
aTJKc5y7AzGn6D8MM7REaznNm8YnkkVxeI-SrSWzpXfeZzgmDZgXtNcSKhnsinWRpK83BYLMIwATg=
iQHNx-nvEpB6fPZrRpbmGzQycSVbS0mixfs7eJDflUGxFEObZWrrLPT5s77RUL-XKuVqiTkMPDqd6=
HtGVmLTXoRo-FF1MJ9iFRx_7c6JtgkIvVy3aUoeav_LmNOxlL34gb97UT71LlQBAdPUyNBj040P4g=
/https%3A%2F%2Fgithub.com%2Ffreesurfer%2Ffreesurfer%2Fblob%2F5c50f486e478108e=
d8ce6800b50344d31af71ac3%2Fscripts%2Frecon-all%23L4913

-Paul


On Wed, Jul 14, 2021 at 5:44 PM Taylor, Lisa Marie <ltaylor2(a)hs.uci.edu>
wrote:

>         External Email - Use Caution
>
> Hi everyone,
>
> I could really use some help with figuring out an issue I've been
> struggling with the last few months. It seems that when I run recon-all on
> over 20 of my participants, not all freesurfer files are created. But I am
> not understanding why, and my technical capabilities are limited.
> Particularly, it seems there's an issue reading the lh.BA1_exvivo.label. I
> will attach a screenshot of a participant who has all the expected files
> vs. a participant who is missing important files. I will also attach the
> recon-all log file for any other information that it can provide.
>
> Also, I run a script for recon-all and these are the arguments: srun
> ${FREESURFER_HOME}/bin/recon-all -s imagedir/subid -no-isrunning -all
> -hippocampal-subfields-T1 -brainstem-structures -qcache
>
> Not sure if this is pertinent, but our HPC has been updated, but I am
> unaware if that can impact how freesurfer is run.
>
> Thank you for any insight you can provide!
>
> Lisa
>
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Ln_4MFjJ7zSwGhXkC2PxAgmiZOMvo_1SVrPwgLB4RGZKloNE7KDjod-TZgd_oe0vA-2w6sCwnMfqM=
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