[Freesurfer] nmr-std-env error on seychelles

Hi Freesurfers, I have an issue with a job I launch on seychelles. I get this error message: /usr/local/freesurfer/nmr-std-env: line 98: syntax error near unexpected token `(' /usr/local/freesurfer/nmr-std-env: line 98: ` set path = ( /usr/pubsw/bin $path )' /var/spool/PBS/mom_priv/jobs/1258634.s

[Freesurfer] design is ill-conditioned

Hi freesurfers, I'm trying to run an estimation with my last subject and get stuck with a ERROR: design is ill-conditioned I can imagine this means that my design misses something bu I can't find what. Conditions all have events in all runs, time points are equally spaced. Here's the log of the se

Re: [Freesurfer] FSfast - excluding time points from my analysis

Sent that earlier but seems like it didn't post. Sorry if it's a second posting. Hi Freesurfers, I would like to be able to regress out specific time points from my functionals using FSfast. I thought I should do it with the -extreg option to mkanalysis-sess but I don't know how to create the req

[Freesurfer] FSfast - excluding time points from my analysis

Hi Freesurfers, I would like to be able to regress out specific time points from my functionals using FSfast. I thought I should do it with the -extreg option to mkanalysis-sess but I don't know how to create the required extregstem_000.bfloat file. How can I create this file? Thanks, Max ___

Re: [Freesurfer] isxconcat-sess

SF_gabor__LSF_gabor/tal.ces.nii > > You can then use this as input to mri_glmfit passing it with > the --y option. You can get more help from the FS FAST tutorial. Go to > the wiki, type "isxconcat-sess" in the Search field, then hit the > "Text" button. >

Re: [Freesurfer] isxconcat-sess

Hi freesurfers, I've been running isxconcat-sess with this line chaumon[/homes/11/chaumon/data] (nmr-std-env) isxconcat-sess -sf subjlist.txt -analysis Analyse_Simple_Confidence -c High_confidence__Low_confidence_vs_HSF_gabor__LSF_gabor -o AVG08 I was expecting to find a directory called osgm in

[Freesurfer] Matrix is singluar to working precision

Hi Freesurfers, I'm trying to selxavg3 my data. My design includes 6 conditions including a 0 rest condition. 3 contrasts have been defined using mkcontrast. The analysis too using mkanalysis. I use this command line : [/homes/11/chaumon/data] (nmr-std-env) selxavg3-sess -analysis "Analyse_Simpl