Re: [Freesurfer] mkbrainmask-sess and inorm-sess

You specify it when you run mkanalysis-sess

On 03/04/2016 04:36 PM, Ji Won Bang wrote:

In a simple word, my question is:

under version 5.3.0, how can I specify funcstem (stem of functional volume)? I don't see any argument for that..

Thanks a lot.

Best, Ji Won

2016-03-04 16:31 GMT-05:00 Ji Won Bang <kirstens03@gmail.com mailto:kirstens03@gmail.com>:

Dear. Freesurfer experts.

Hi. How are you?

It might be very naive question.

When using version 4.5.0 I used the command:
mkbrainmask-sess -s $SUBJECT -funcstem fmc -df sessdirfile -fsd
bold_retino

However under the version 5.3.0, mkbrainmask-sess does not have
-funcstem.

May I use -maskstem instead of -funcstem?

If so, after that, I tried:
inorm-sess -s $SUBJECT -motioncor -funcstem fmc -df sessdirfile
-fsd bold_retino

However, it complains that:
ERROR: cannot find
/home/jbang/Projects/replay/epi/replay06/bold_retino/masks/brain
You may need to run preproc-sess or mkbrainmask-sess to create a
brain mask

Could you please help?

Thank you very much.

Best,
Ji Won

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