Can you run:
spatialsmooth-sess -i fmc -o fmcsm5 -fwhm 5 -fsd bold -s LD-functional
-d /Users/balajigoparaju/Desktop/subjectdata -update -noinorm
capture the terminal output and send it to me?
doug
Balaji Goparaju wrote:
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.
------------------------------------------------------------------------
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--
Douglas N. Greve, Ph.D.
MGH-NMR Center
[EMAIL PROTECTED]
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Fax: 617-726-7422
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