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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