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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