Dont use --trgicoorder. Also, smooth the input, not the output (ie, use
--fwhm not --fwhm-trg). Don't use projfrac there (which will fix the
--sval-xyz error). Your 2nd command looks the same as the first
On 9/27/20 10:30 PM, 谢娆 wrote:
External Email - Use Caution
Hi,
To begin with, I want clarify my goal here: I want to resample my
resting-state functional data infsaverage5 and then do some
preprocessing before statistical analysis, and I get stuck in smooth now.
I tried the following command:
|mri_surf2surf --srcsubject sub-40 --srcsurfval
/home/disk2/Data/HC/HCprep/derivatives/fmriprep/sub-40/ses-1/func/sub-40_ses-1_task-rest_run-1_space-fsnative_hemi-L_bold.func.gii
--trgsubject fsaverage5 --trgicoorder 5 --trgsurfval
/home/disk2/Data/HC/HCprep/sub-40_smooth6_proj.mgh --hemi lh
--fwhm-trg 6 --projfrac white 0.5|
1.
--srcsubject: this is the freesurfer output folder from fmriprep
(in ...derivatives/freesurfer/...)
2.
--srcsurfval: I used fmriprep --output-space fsnative to resample
the resting data to subject native space.
3.
--trgsubject/--trgicoorder: I want to resample the data to a
fsaverage5 as I mentioned before
4.
--projfrac white 0.5: I followed your advice tosmooth
usemidthickness coordinates, but there is an error:
ERROR: cannot spec both --sval-xyz and --sval
then I tried to add these two parameters:
|mri_surf2surf --srcsubject sub-40 --srcsurfval
/home/disk2/Data/HC/HCprep/derivatives/fmriprep/sub-40/ses-1/func/sub-40_ses-1_task-rest_run-1_space-fsnative_hemi-L_bold.func.gii
--trgsubject fsaverage5 --trgicoorder 5 --trgsurfval
/home/disk2/Data/HC/HCprep/sub-40_smooth6_proj.mgh --hemi lh
--fwhm-trg 6 --projfrac white 0.5 --sval-xyz white --sval
/home/disk2/Data/HC/HCprep/derivatives/fmriprep/sub-40/ses-1/func/|
but the error still exist:
*ERROR: cannot spec both --sval-xyz and --sval*
I searched a lot but cannot found any useful help with it.
I also have another question about smooth: I can also smooth my data
with following command:
|mri_surf2surf --srcsubject fsaverage5 --srcsurfval
/home/disk2/Data/HC/HCprep/derivatives/fmriprep/sub-15/ses-1/func/sub-15_ses-1_task-rest_run-1_space-fsaverage5_hemi-L_bold.func.gii
--trgsubject fsaverage5 --trgsurfval
/home/disk2/Data/HC/HCprep/sub-40_smooth6_proj.mgh --hemi lh
--fwhm-trg 6 --projfrac white 0.5| (--projfrac didn't work here too)
--srcsurfval: I used fmriprep --output-space fsaverage5 to resample
the resting data to fsaverage5 in here
With |--srcsubject fsaverage5| specified here, will every subject use
the same coordinate/distance info when performing smooth?Willthe
command I used above performing smooth using every subjects' own
coordinate/distance info?And which command is better?
Any help will be appreciated, Thanks a lot!
rao
_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
