FSFAST: wrong brain mask in preproc

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Elmira Hassanzadeh

26 Apr 2023 26 Apr '23

12:22 p.m.

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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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Douglas N. Greve

26 Apr 26 Apr

6:43 p.m.

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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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Elmira Hassanzadeh

27 Apr 27 Apr

11:09 a.m.

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Thank you for clarifying.

Elmira

On Wed, Apr 26, 2023 at 6:44 PM Douglas N. Greve dgreve@mgh.harvard.edu 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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Douglas N. Greve
Elmira Hassanzadeh