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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On 03/03/2016 02:46 PM, Ji Won Bang wrote:

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?

It uses the one under each run.

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?

Yes

Thanks a lot!

Best, Ji Won

2016-03-03 12:36 GMT-05:00 Douglas N Greve <greve@nmr.mgh.harvard.edu mailto: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>
> <mailto: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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