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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Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Thanks for your help!

I'd like to run mkbrainmask-sess & inorm-sess under version 5.3.0

What I used to run are: mkbrainmask-sess -s $SUBJECT -funcstem fmc -df sessdirfile -fsd bold_retino inorm-sess -s $SUBJECT -motioncor -funcstem fmc -df sessdirfile -fsd bold_retino

However, since version 5.3.0 changed a lot, I tried: mkbrainmask-sess -s $SUBJECT -df sessdirfile -fsd bold_retino inorm-sess -s $SUBJECT -motioncor -df sessdirfile -fsd bold_retino

It gives me an error: ERROR: could not determine file for /home/jbang/Projects/replay/epi/replay06/bold_retino/023/fmc ERROR: inorm failed

Which part am I doing wrong?

Thank you so much.

Best, Ji Won

2016-03-04 17:13 GMT-05:00 Douglas N Greve greve@nmr.mgh.harvard.edu:

The functional stream changed a lot from version 4 to version 5. The commands and workflow are very different now

On 03/04/2016 04:31 PM, Ji Won Bang wrote:

...

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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