Re: [Freesurfer] Freesurfer mkbrainmask-sess

Never mind, I believe I fixed the issue. Just missed a step. Thanks! --Rebecca Sheley On Wed, Oct 25, 2017 at 12:14 PM, Rebecca Sheley wrote: > Hello Freesurfer Team, > > I'm having trouble running preproc-sess, but only with the > mkbrainmask-sess step. I tried just

[Freesurfer] Freesurfer mkbrainmask-sess

Hello Freesurfer Team, I'm having trouble running preproc-sess, but only with the mkbrainmask-sess step. I tried just running this step and got this output. Do you have any insights on why this might be happening? My tmp folder is empty. The cwd directory is the folder where my data are located.

Re: [Freesurfer] mkbrainmask-sess: couldn't find register.dof6.lta

Yes, it does. Prior to v6, the brain mask was created by the FSL BET program, which did not depend on the registration. V6 now maps the brainmask from the FS analysis into the subject space, which does depend on the registration On 07/11/2017 02:36 PM, Li Guo wrote: > Dear freesurfer

[Freesurfer] mkbrainmask-sess: couldn't find register.dof6.lta

Dear freesurfer developers, I’d like to ask about an error I encountered in Freesurfer v6.0 with mkbrainmask-sess. I am using macOS Sierra. Here is the error: error:"ERROR: cannot find /Users/lguo15/Documents/MATLAB/fMRI_P3/Fisch_P3_01/bold/register.dof6.lta, you might need to run

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

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 >

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

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

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

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

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: >

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

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

[Freesurfer] mkbrainmask-sess and inorm-sess

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

Re: [Freesurfer] mkbrainmask-sess

I imagine this issue has been solved by now but just for the record I ran into a similar issue. In my case the problem turned out to be that FSL installs by default in /usr/local/fsl/bin but FSFAST was looking for it in /bin This was on OS X 10.8.2 with FSL Installer - Version 2.0.10 and

Re: [Freesurfer] mkbrainmask-sess

Hi again, Could this error be due to the fact that I don't have a full version of fsl installed and configured on my ubuntu virtual machine? i.e. does fsfast require fsl to be installed? Thanks K From: Kiley Seymour kiley_seym...@yahoo.com.au To:

Re: [Freesurfer] mkbrainmask-sess

It could be. It uses fsl only to create a mask of the brain, so it probably does not need a full fsl install, but it might need more than you have. doug On 3/25/12 7:05 AM, Kiley Seymour wrote: Hi again, Could this error be due to the fact that I don't have a full version of fsl installed

[Freesurfer] mkbrainmask-sess

Dear Freesurfers, I am currently trying to do some retinotopic mapping. I have been successful in running the reconstruction commands and setting everything up for the analysis, but I have run into problems when using the selxavg3-sess command. i.e. selxavg3-sess -a rtopy.self.lh -s IFEE2211

Re: [Freesurfer] mkbrainmask-sess

HI Sebastian, I made a mod to this in development version, but it operates slightly differently in that you set the nth run with -run. Eg, -run 2 would mean to use the 2nd run. Otherwise, if you run it on more than one session, the run that you specify might not exist. Would this work for

Re: [Freesurfer] mkbrainmask-sess

Hi Doug, On 26. Jun 2006, at 21:19 Uhr, Doug Greve wrote: HI Sebastian, I made a mod to this in development version, but it operates slightly differently in that you set the nth run with -run. Eg, -run 2 would mean to use the 2nd run. Otherwise, if you run it on more than one session, the

[Freesurfer] mkbrainmask-sess

Hi List, to follow up my mail from several days ago, all mkbrainmask-sess (v3.0.2 centos4 x86_64) really needs to be able to select the run from which to take the run-number are the following lines: case -run set run = $argv[1]; shift; breaksw somewhere between the label

[Freesurfer] mkbrainmask-sess

Hi All, just a quick note to let you know that 3.0.2's (centos4 x86_64) mkbrainmask-sess does not really parse the -run nth parameter it specifies in its help text. Haven't found time to implement a fix yet, but it is a minor issue anyway... Ahoi Sebastian -- Sebastian Moeller

[Freesurfer] mkbrainmask-sess failed

Dear all, When I used mkbrainmask-sess, an error occurred shown below. I am using the latest FreeSurfer, and the bet command is included in the distribution. Could anyone tell me how to fix it? thanks, Jia ++begin of error message+