It will be in the space that you analyzed it in. If you want the native space, then use -native when running preproc-sess and mkanalysis

Furthermore, the res-001.nii which is produce in produced in the res folder in not the same dimension of f.nii.

I would do the whole FAST preprocessing on f.nii., maintaining the same dimension and open it with FSL.

Thanks

Stefano

----Messaggio originale----
Da: stdp82@virgilio.it
Data: 5-apr-2017 23.39
A: "Freesurfer support list"<freesurfer@nmr.mgh.harvard.edu>
Ogg: [Freesurfer] R: Re: R: Re: Whole preprocessing with FAST without to perform a seed based analysis

Hi, 

as you advise I have run selxavg3-sess with the -svres option.

I found a folder called "res" which contain "res-001.nii". Is it the f.nii fully processed?

Thanks

Stefano

----Messaggio originale----
Da: "Douglas Greve" <greve@nmr.mgh.harvard.edu>
Data: 14-mar-2017 17.38
A: <freesurfer@nmr.mgh.harvard.edu>
Ogg: Re: [Freesurfer] R: Re: Whole preprocessing with FAST without to perform a seed based analysis

You can't  on either occasion just using preproc-sess. You can create an analysis with those components, then run selxavg3-sess with the -svres option. This will create a folder called eres with volumes that have had all the nuisance variables and low freqeuncies regressed out

On 3/14/17 12:32 PM, stdp82@virgilio.it wrote:

Thanks.

1- By using only preproc-sess, how can I perform "band pass filtering"?

2- And how can I take in account the nuisance variables: the CSF from which the top 5 principle components, the white matter from which the top 5 principle components, motion correction parameters (-mcextreg), 5th order polynomial. How can I eliminate the first 4 time points?

Regards

Stefano

----Messaggio originale----
Da: "Douglas Greve" <greve@nmr.mgh.harvard.edu>
Data: 14-mar-2017 16.14
A: <freesurfer@nmr.mgh.harvard.edu>
Ogg: Re: [Freesurfer] Whole preprocessing with FAST without to perform a seed based analysis

just use preproc-sess

On 3/14/17 10:45 AM, stdp82@virgilio.it wrote:

Hi list,

in FS-FAST, on rs-fMRI data, is possible to run selxavg3-sess without -a option?

I would use whole the FS-FAST to preprocess my data. I would include the mkanalysis-sess step but I would not perform a seed-based analysis. 

Thanks

Stefano

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