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, freesurfer-request@nmr.mgh.harvard.edu wrote:

Message: 4 Date: Mon, 21 Jul 2008 09:43:54 -0400 From: "Balaji Goparaju" balaji.goparaju@gmail.com Subject: [Freesurfer] Preproc-sess: Spatial smoothing and brain masking To: freesurfer@nmr.mgh.harvard.edu Message-ID: 4002c9df0807210643q88b079blf1511f4eaf49e570@mail.gmail.com 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.