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Please ignore my last email. I added --out_type mgh and also changed the --out
to end with ?h.mgh and it's done the trick. Please do let me know if this isn’t
correct though!
Cheers,
Mason
Mason T Wells, MSc
PhD student
School of Optometry and Visio
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Sorry, just to follow up on this. The surface based analysis needs the outputs
in the format of MGH. I fear I may have missed a step here. Any advice would be
great.
Cheers,
Mason
Mason T Wells, MSc
PhD student
School of Optometry and Vision Science
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Great, thanks for this.
Am I right in thinking that the only outputs from this command are COR-.info
and COR-001 and that neither of these should have which hemisphere it was
created from in their name? I also notice the examples on the wiki page have
That looks good. The only thing to change is to specify the projection
fraction for vol2surf to --projfrac 0.5 (so that it samples in the
middle of the cortical ribbon rather than at the white/gray boundary)
On 4/17/2020 1:36 PM, Mason Wells wrote:
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>
> Hi,
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Hi,
Can I just double check this seems correct to you experts? I am not 100%
proficient in Freesurfer/FSL.
I ran:
bregister --s S1 --feat
Data/Feat2/LM/scans/Preprocessed_functionals/6_CMRRMB_run1_.feat/
Which seemed to give me what I needed, the
Yes, use the template.nii.gz as the registration target. A long time ago
we used to have some wrappers that would operate directly on feat
folders. Not sure if they still work but, check out
https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/FslFeatFreeSurfer
On 4/17/2020 10:43 AM, Mason Well
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Great, thanks again Bruce.
Doug, can you confirm this is the process for taking a filtered_func file and
getting it onto the freesurfer surface ready for analysis?
Mason T Wells, MSc
PhD student
School of Optometry and Vision Sciences
& Cardiff Univer
oh, then you probably want to use bbreg to register it and mri_vol2surf
to sample it onto the surface. Doug is the expert on this and can
add/correct if this is not the whole story :)
cheers
Bruce
On Fri, 17 Apr 2020, Mason
Wells wrote:
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Hi Bruce,
The on
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Hi Bruce,
The only pre-processing I have done is the motion correction, high pass
filtering and distortion correction. So, as far as I know it is still in the
volume and in the original functional space.
Best wishes,
Mason
Mason T Wells, MSc
PhD st
Hi Mason
is your filtered_func file already sampled onto the surface or is it a
volume?
cheers
Bruce
On Fri, 17 Apr 2020, Mason Wells wrote:
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Hi all,
I am trying to use an analysis package that works on surface based data
(SamSrf). I have ra
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Hi all,
I am trying to use an analysis package that works on surface based data
(SamSrf). I have ran Feat and have a filtered_func file which is of course the
motion corrected/unwarped version of my EPI. However, I need some advice on how
to get the
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