Dear All,
while being no exert, I assume the following:
in spatialsmooth-sess from freesurfer 4.0.5, line 160, there is the
following test:
test $infunc -nt $outfunc
This is used to skip processing if -update is specified, the test
evaluates to 1 if $infunc exists and is older than $outfunc it
evaluates to 0 if $infunc truely is newer than $outfunc; it ALSO
evaluates to 1 if $outfunc does not exist (tested with macosx 10.5.4).
So if $outfunc does not exist (and 'ls: 017/fmcsm5.nii: No such file
or directory' is exactly pointing to ths configuration), then the
processing is skipped. I would assume that running without the "-
update" option should solve the problem...
Or exchanging line 159 with something along the ines of:
if ($UpdateOnly & !(-e $outfunc)) then
So that the critical test is only run, if no $outfunc exists...
Then again, I could be completely out to lunch, as I still use FS
3.0.5, and only looked at the 4.0.5 code...
ahoi
Sebastian
On Jul 21, 2008, at 3:51 PM, [EMAIL PROTECTED]
wrote:
Message: 4
Date: Mon, 21 Jul 2008 09:43:54 -0400
From: "Balaji Goparaju" <[EMAIL PROTECTED]>
Subject: [Freesurfer] Preproc-sess: Spatial smoothing and brain
masking
To: freesurfer@nmr.mgh.harvard.edu
Message-ID:
<[EMAIL PROTECTED]>
Content-Type: text/plain; charset="iso-8859-1"
Hi,
I used the command
preproc-sess -s LD-functional -fwhm 5
However, the command does not seem create the fmcsm5.nii file. The
process
completes motion correction successfully, but it
does not complete the spatial smoothing and brain masking. I get a
"Motion
correction SUCCESSFULLY completed" message but
I only get a "Spatial smoothing done" message. I have already asked
this
question in the mailing list. and i was asked to check the
writing permissions of the directories. I have changed the "bold"
directory
and freesurfer directory to have read, write and execute
permisions using the "chmod -R 777" command.
I get the following output:
--------------------------------------------------------------
preproc-sess logfile is log/preproc-sess.log
--------------------------------------------------------------
instem f
mc 1 f fmc
stc 0 fmc
sm 1 fmc fmcsm5
mask 1 brain
LD-functional MC -----------------------------
Mon Jul 21 09:32:56 EDT 2008
/Users/balajigoparaju/Desktop/subjectdata
mc-sess -fstem f -fmcstem fmc -s LD-functional -d
/Users/balajigoparaju/Desktop/subjectdata -fsd bold -new -update -no-
inorm
----------------------------------------
Logfile is
/Users/balajigoparaju/Desktop/subjectdata/log/mc-LD-functional-
bold.log
-------------------------------------------
/Users/balajigoparaju/Desktop/subjectdata/LD-functional
RunList: 006 010 017 019
Targ Stem is 006/f
Update not needed
-rwxrwxrwx 1 balajigo admin 41091424 Jul 11 10:15 006/fmc.nii
-rwxrwxrwx 1 balajigo admin 523 Jul 7 09:57 006/f.bhdr
Update not needed
-rwxrwxrwx 1 balajigo admin 41091424 Jul 13 08:26 010/fmc.nii
-rwxrwxrwx 1 balajigo admin 523 Jul 7 09:57 010/f.bhdr
Update not needed
-rwxrwxrwx 1 balajigo admin 41091424 Jul 13 17:03 017/fmc.nii
-rwxrwxrwx 1 balajigo admin 523 Jul 7 09:57 017/f.bhdr
Update not needed
-rwxrwxrwx 1 balajigo admin 41091424 Jul 13 17:07 019/fmc.nii
-rwxrwxrwx 1 balajigo admin 523 Jul 7 09:57 019/f.bhdr
Mon Jul 21 09:32:57 EDT 2008
mc-sess completed SUCCESSFULLY
LD-functional Smooth ------------------------
Mon Jul 21 09:32:57 EDT 2008
/Users/balajigoparaju/Desktop/subjectdata
spatialsmooth-sess -i fmc -o fmcsm5 -fwhm 5 -fsd bold -s LD-
functional -d
/Users/balajigoparaju/Desktop/subjectdata -update -noinorm
----------------------------------------
------------------------------------------------
------------------------------------------------
/Users/balajigoparaju/Desktop/subjectdata/LD-functional
Mon Jul 21 09:32:57 EDT 2008
~/Desktop/subjectdata/LD-functional/bold ~/Desktop/subjectdata
RunList 006 010 017 019
/Users/balajigoparaju/Desktop/subjectdata/LD-functional/bold
ls: 006/fmcsm5.nii: No such file or directory
-rwxrwxrwx 1 balajigo admin 41091424 Jul 11 10:15 006/fmc.nii
Update not needed
/Users/balajigoparaju/Desktop/subjectdata/LD-functional/bold
ls: 010/fmcsm5.nii: No such file or directory
-rwxrwxrwx 1 balajigo admin 41091424 Jul 13 08:26 010/fmc.nii
Update not needed
/Users/balajigoparaju/Desktop/subjectdata/LD-functional/bold
ls: 017/fmcsm5.nii: No such file or directory
-rwxrwxrwx 1 balajigo admin 41091424 Jul 13 17:03 017/fmc.nii
Update not needed
/Users/balajigoparaju/Desktop/subjectdata/LD-functional/bold
ls: 019/fmcsm5.nii: No such file or directory
-rwxrwxrwx 1 balajigo admin 41091424 Jul 13 17:07 019/fmc.nii
Update not needed
Started at Mon Jul 21 09:32:57 EDT 2008
Ended at Mon Jul 21 09:32:59 EDT 2008
spatiallysmooth-sess Done
LD-functional Inorm ------------------------
Mon Jul 21 09:32:59 EDT 2008
/Users/balajigoparaju/Desktop/subjectdata
mkbrainmask-sess -maskstem brain -fsd bold -s LD-functional -d
/Users/balajigoparaju/Desktop/subjectdata -update
----------------------------------------
------------------------------------------------
------------------------------------------------
/Users/balajigoparaju/Desktop/subjectdata/LD-functional
Mon Jul 21 09:32:59 EDT 2008
/Users/balajigoparaju/Desktop/subjectdata/LD-functional/bold
ls: masks/brain.nii: No such file or directory
-rwxrwxrwx 1 balajigo admin 523 Jul 7 09:57 006/f.bhdr
Update not needed
Mon Jul 21 09:33:00 EDT 2008
mkbrainmask-sess done
----------------------------------------
Started at Mon Jul 21 09:32:56 EDT 2008
Ended at Mon Jul 21 09:33:00 EDT 2008
preproc-sess done
Any help is appreciated.
Thank you.
--
Sebastian Moeller
Tel.: 04 21 - 2 18 - 78 38 oder 96 91
Fax.: 04 21 - 2 18 - 90 04
GSM: 0 15 77 - 1 90 31 41
[EMAIL PROTECTED]
AG Kreiter / FB 2
Institut fuer Hirnforschung III
Abteilung Theoretische Neurobiologie
Universitaet Bremen
Biogarten
Hochschulring 16a
Postfach 33 04 40
28359 Bremen
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