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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