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

2016-03-04 Thread Douglas N Greve
Run preproc-sess instead. inorm-sess is no longer used On 03/04/2016 05:18 PM, Ji Won Bang wrote: > 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_reti

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

2016-03-04 Thread Ji Won Bang
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.

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

2016-03-04 Thread Douglas N Greve
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:

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

2016-03-04 Thread Douglas N Greve
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: > mkb

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

2016-03-04 Thread Ji Won Bang
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 : > Dear. Freesurfer experts. > > Hi. How are you? > > It might be very naive que

[Freesurfer] mkbrainmask-sess and inorm-sess

2016-03-04 Thread Ji Won Bang
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 in