Re: [Freesurfer] FSFAST: wrong brain mask in preproc

2023-04-27 Thread Elmira Hassanzadeh 
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Thank you for clarifying.

Elmira

On Wed, Apr 26, 2023 at 6:44 PM Douglas N. Greve 
wrote:

> External Email - Use Caution
>
> Yes, this is the expected behavior, ie, it should cover only subcortical
> GM regions. It is expected that cortical regions will be handled with the
> surface based analysis. You can recombine the results at the end with
> vlrmerge.
>
> On 4/26/2023 12:22 PM, Elmira Hassanzadeh wrote:
>
> External Email - Use Caution
> Hi everyone,
>
> We preprocessed resting-state data with preproc-sess. In the output, I
> noticed although *fmcpr.nii* covers the whole brain,*
> fmcpr.sm6.mni305.2mm.nii* is only covering brain stem+cerebellum
> (screenshots attached).
>
> Any clue what went wrong? This is an example of the command we ran for one
> of our subjects(R19):
>
> *preproc-sess -surface R19 lhrh -s R19 -fwhm 6 -fsd rest -mni305 -per-run*
>
> Thanks,
> Elmira
>
>
>
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Re: [Freesurfer] FSFAST: wrong brain mask in preproc

2023-04-26 Thread Douglas N. Greve 
   External Email - Use Caution

Yes, this is the expected behavior, ie, it should cover only subcortical 
GM regions. It is expected that cortical regions will be handled with 
the surface based analysis. You can recombine the results at the end 
with vlrmerge.


On 4/26/2023 12:22 PM, Elmira Hassanzadeh wrote:


External Email - Use Caution

Hi everyone,

We preprocessed resting-state data with preproc-sess. In the output, I 
noticed although *fmcpr.nii* covers the whole 
brain,*fmcpr.sm6.mni305.2mm.nii* is only covering brain 
stem+cerebellum (screenshots attached).


Any clue what went wrong? This is an example of the command we ran for 
one of our subjects(R19):


*preproc-sess -surface R19 lhrh -s R19 -fwhm 6 -fsd rest -mni305 -per-run*

Thanks,
Elmira



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