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Hi Douglas,
Thanks for the reply. Here are my command line and the output from the terminal. Please tell me if you need further information.
export FREESURFER_HOME=/Applications/freesurfer/7.2.0 export SUBJECTS_DIR=/Applications/freesurfer/7.2.0/subjects source $FREESURFER_HOME/SetUpFreeSurfer.sh
mri_surf2surf --s fsaverage5 --hemi lh --cortex --sval /Volumes/NatureNurtu/NatureNurture/Neuroimaging/RSFC/Preprocessing/fmriprepRF/sub-eb01/sub-eb01_task-resting_space-fsaverage5_hemi-L_desc-regressedFiltered.func.gii --fwhm 6 --tval /Volumes/NatureNurtu/NatureNurture/Neuroimaging/RSFC/Preprocessing/fmriprepRFS/sub-eb01/sub-eb01_task-resting_space-fsaverage5_hemi-L_desc-regressedFilteredSmoothed.func.gii
7.2.0
setenv SUBJECTS_DIR /Applications/freesurfer/7.2.0/subjects cd /Volumes/NatureNurtu/NatureNurture/Neuroimaging/RSFC/Preprocessing mri_surf2surf --s fsaverage5 --hemi lh --cortex --sval /Volumes/NatureNurtu/NatureNurture/Neuroimaging/RSFC/Preprocessing/fmriprepRF/sub-eb01/sub-eb01_task-resting_space-fsaverage5_hemi-L_desc-regressedFiltered.func.gii --fwhm 6 --tval /Volumes/NatureNurtu/NatureNurture/Neuroimaging/RSFC/Preprocessing/fmriprepRFS/sub-eb01/sub-eb01_task-resting_space-fsaverage5_hemi-L_desc-regressedFilteredSmoothed.func.gii
sysname Darwin hostname Yangwens-MacBook-Pro.local machine x86_64 user yangwenxu srcsubject = fsaverage5 srcval = /Volumes/NatureNurtu/NatureNurture/Neuroimaging/RSFC/Preprocessing/fmriprepRF/sub-eb01/sub-eb01_task-resting_space-fsaverage5_hemi-L_desc-regressedFiltered.func.gii srctype = trgsubject = fsaverage5 trgval = /Volumes/NatureNurtu/NatureNurture/Neuroimaging/RSFC/Preprocessing/fmriprepRFS/sub-eb01/sub-eb01_task-resting_space-fsaverage5_hemi-L_desc-regressedFilteredSmoothed.func.gii trgtype = srcsurfreg = sphere.reg trgsurfreg = sphere.reg srchemi = lh trghemi = lh frame = 0 fwhm-in = 0 fwhm-out = 6 label-src = lh.cortex.label label-trg = lh.cortex.label OKToRevFaceOrder = 1 UseDualHemi = 0 Reading source surface reg /Applications/freesurfer/7.2.0/subjects/fsaverage5/surf/lh.sphere.reg Loading source data Reading source subject label mask lh.cortex.label masking the input INFO: trgsubject = srcsubject Approximating gaussian smoothing of target with fwhm = 6.000000, std = 2.547965, with 2 iterations of nearest-neighbor smoothing Reading target space mask label lh.cortex.label NN smoothing output with n = 2 Saving target data Saving to /Volumes/NatureNurtu/NatureNurture/Neuroimaging/RSFC/Preprocessing/fmriprepRFS/sub-eb01/sub-eb01_task-resting_space-fsaverage5_hemi-L_desc-regressedFilteredSmoothed.func.gii
Best, Yangwen
On Tue, 9 Nov 2021 at 15:49, Douglas N. Greve dgreve@mgh.harvard.edu wrote:
please send your command line and terminal output
On 11/9/2021 6:05 AM, Yangwen Xu wrote:
External Email - Use CautionHello FreeSurfer Developers,
I am trying to smooth images using mri_surf2surf. Here is the command line: 'mri_surf2surf --s fsaverage5 --hemi lh --cortex --sval ',InputImagePath,' --fwhm 6 --tval ', OutputImagePath
The Input Image is 10242 (number of vertices) * 475 (number of time points) in the func.gii format. The output image is supposed to be in the same dimensions. However, it only smoothed the image of the first time point, i.e., the dimension of the output Image is 10242 * 1.
I have implemented this before but never met this problem. The only difference seems that I am now using freesurfer-darwin-macOS-7.2.0. Does anyone have any thoughts on how to solve this problem?
Thanks for the help, Yangwen
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