External Email - Use Caution
Hi,
To begin with, I want clarify my goal here: I want to resample my resting-state functional data in fsaverage5 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
--srcsubject: this is the freesurfer output folder from fmriprep (in ...derivatives/freesurfer/...)
--srcsurfval: I used fmriprep --output-space fsnative to resample the resting data to subject native space.
--trgsubject/--trgicoorder: I want to resample the data to a fsaverage5 as I mentioned before
--projfrac white 0.5: I followed your advice to smooth use midthickness 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? Will the 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
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|
--srcsubject: this is the freesurfer output folder from fmriprep (in ...derivatives/freesurfer/...)
--srcsurfval: I used fmriprep --output-space fsnative to resample the resting data to subject native space.
--trgsubject/--trgicoorder: I want to resample the data to a fsaverage5 as I mentioned before
--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
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freesurfer@nmr.mgh.harvard.edu
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Douglas Greve -
谢娆