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
>
>

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

--
Douglas N. Greve, Ph.D.
MGH-NMR Center
greve@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
www.nmr.mgh.harvard.edu/facility/filedrop/index.html
Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/

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


The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.