You can check the masks of each subject. There might be one whose mask is too small, and that will affect the final mask. If you run isxconcat-sess, it will create a file called masks.nii.gz with all the masks in them. You can load it up in freeview (or spm) and scroll through them.

On 7/11/2019 12:15 PM, Zhi Li wrote:

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It is group level, result of 2nd-level analysis. I preprocessed data of 50 subjects with FSFAST and SPM respectively, then I used SPM to do the 1st- and 2nd-level modelling. The version of FS now I use is 6.0 I think: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c.

Best,

Lizhi

On Thu, 11 Jul 2019 at 11:55, Greve, Douglas N.,Ph.D. <DGREVE@mgh.harvard.edu> wrote:

is this an individual or group? what version of FS are you running.

On 7/11/19 11:10 AM, Zhi Li wrote:
>
>         External Email - Use Caution
>
> Dear Freesurfer experts,
>
> Now I am using both FSFAST and SPM to preprocessed my functional image
> data. In FSFAST, I replaced the subcortical template with the whole
> brain in the folder "mri.2mm", to get the whole brain volumetric data.
> I have also diluted the whole brain template in FSFAST. However, as
> showed in attached files, the resampled data in FSFAST seems smaller
> than that of SPM. May I ask if it is normal? Would the mask creation
> step in FSFAST caused this difference? I read from a previous PPT
> which said "FSL BET run on the template" in mask creation. As far as I
> know, the default parameter in BET may strip some part of prefrontal
> lobe sometime. If FSFAST apply BET or similar algorithm to strip
> skull, may I ask how could I change the parameter? Looking forward to
> your kind suggestions.
>
> Thanks and best wishes,
>
> Lizhi
>
>
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