Thanks for your reply. It works.
I have 1 more general question.
When running: mktemplate-sess -s $SUBJECT -df sessdirfile -fsd bold_day1
I get 2 files (template.log & template.nii.gz) under the functional subdirectory(bold_day1) and under each run(001, 002 etc).
When I run: mc-sess -s $SUBJECT -df sessdirfile -fsd bold_day1 -per-run
Does that command use the template for motion correction that was created under each run? Not the one under the functional subdirectory?
My understanding of mktemplate-sess and mc-sess is that mktemplate-sess produces the template per each run (saves the template file under each run) and/or the template per session(?) (saves the template file under the functional subdirectory).
Then mc-sess utilizes the template for motion correction. If I use -per-run, mc-sess utilizes the template file created per each run and if I use -per-session, mc-see utilizes the template file created per session(file under the functional subdirectory).
Is my understanding correct?
Thanks a lot!
Best, Ji Won
2016-03-03 12:36 GMT-05:00 Douglas N Greve greve@nmr.mgh.harvard.edu:
you have to use -per-run not -per-session
On 03/03/2016 12:27 PM, Ji Won Bang wrote:
The command I used is:
mktemplate-sess -s $SUBJECT -df sessdirfile -fsd bold_retino
mc-sess -s $SUBJECT -df sessdirfile -fsd bold_retino -per-session
Thank you.
Best, Ji Won
2016-03-03 12:22 GMT-05:00 Ji Won Bang <kirstens03@gmail.com mailto:kirstens03@gmail.com>:
Dear. freesurfer experts. Hi. I'm using freesurfer version 5.3.0. I tried mc-sess onto runs that have different number of slices. However, due to this different number of slices in different runs, mc-sess gives an error. I expected that running mc-sess in freesurfer version 5.3.0 would handle this issue. If you can share your idea to fix this problem, that would be a great help. Thank you! Best, Ji Won
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