Re: [Freesurfer] per-run and Native space

Hi Shahin, preproc-sess is written in a funny way that turns off volume smoothing with -per-run. The work-around is to put -fwhm after -per-run

doug

On 03/14/2014 11:36 PM, SHAHIN NASR wrote:

I am trying to preproc-sess my data (fwhm 1.5, per-run, native space) with this command

preproc-sess -fwhm 1.5 -fsd bold -per-run

I expect it to generate fmcpr.sm1.5.nii.gz for each run of my dataset. Although preproc-sess finishes without any error, it only generates fmcpr.nii.gz and when I run selxavg3-sess, it returns an error that

...

cannot determine format of test/bold/013/fmcpr.sm1.5

and exits. Would you tell me why those files are not generated?

Regards

-- Shahin Nasr

PhD in Cognitive Neuroscience Martinos Imaging Center, MGH Harvard Medical School