So the problem is that there are spaces in the path? That will probably
cause a lot of FS to fail
On 4/2/2021 11:30 PM, zalewk wrote:
External Email - Use Caution
Hi freesurfer team,
I've tried running recon-all as mentioned before with the -xf flag
under different conditions.
As far as I can tell, any line using the UpdateNeeded function. e.g.:
"set ud = `UpdateNeeded $thickness $pial $white`" fails with the
following if statement because the variable $ud includes paths as
strings in it instead of a 0/1 integer. Setting it to a 1 or 0
beforehand also seems to solve the problem. The function UpdateNeeded
only seems to return an integer as an exit status, so I'm not sure why
there are path strings in it causing it to fail.
If I print out the $ud variable before it fails and the result is:
"/subjectDirectory/subjectID_FREESURFER/mri mri mri_FREESURFER
/subjectDirectory/subjectID_FREESURFER/mri/mri_FREESURFER/stats 1"
It returns the exit status of 1 preceded by the path of the subject's
mri directory, just "mri", "mri_FREESURFER" and the subject's stats
directory (all subjects in this particular study have the suffix
"_FREESURFER"). It prints this out these strings no matter the
variables as .mgz file names, or number of variables passed to the
UpdateNeeded function. I still don't have a clue what would cause this
behavior. The UpdateNeeded function seems to work fine and as intended
as far as I can tell, so I still don't know why these paths/strings
are being added and causing it to crash.
Best,
Kody Zalewski
Message: 3
Date: Fri, 02 Apr 2021 03:49:02 +0200
From: fsbuild <fsbu...@contbay.com>
Subject: Re: [Freesurfer] recon-all bug
To: freesurfer@nmr.mgh.harvard.edu
Cc: cm...@neurosurgery.washington.edu
Message-ID: <1617328142.6066780ef2...@trashmail.com>
Content-Type: text/plain; charset="utf-8"
External Email - Use Caution
Hello Kody,
One thing you could try to get more information printed about what
is going on is to edit the very first line in the recon-all script
to be:
#! /bin/tcsh -xf
? instead of
#! /bin/tcsh -f
Adding the x option will echo each line in the script as it?s run
with the variable values expanded, and seeing that output could
help with debugging.
- R.
On Apr 1, 2021, at 20:29, zalewk <zal...@uw.edu>
wrote: External
Email - Use
Caution Hi
Freesurfer team, My lab recently switched over from FS6 to
FS7 and I think I've encountered a bug with recon-all.. I'm
running subjects stepwise and editing them, running recon-all with
the -autorecon2 and -autorecon3 flags initially are no problem,
they run fine. Trying to re-run them or use the
-autorecon2-wm, -autorecon-pial etc. flags lead to crashing at
certain parts of the program. The error message I get is "if:
expression syntax". Digging into the code, it seems to crash when
it hits a line of code "if($ud || $ForceUpdate)". The syntax
superficially looks right (I don't know tcsh), checking the
variables it seems like $ForceUpdate is never set, but removing it
from recon-all doesn't fix the problem. It seems the
$ud variable is for checking if updates are !
needed fo
r a set of volumes passed to the program. I don't know why that
would be a problematic argument, removing that part seems to fix
it, but this also seems like an important variable and I don't
know enough about tcsh to understand why it works after removing
it. Can one of the folks who wrote the recon-all script help me
out? I'm running the commands step-wise as a work-around, but that
is much less convenient. Best, Kody
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