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Hi Douglas,
This time, I tried to smooth one single image. Here occurs the error that the number of surface vertices (10242) and the number of value vertices (1) do not match. However, the image we want to smooth indeed has 10242 vertices. [image: Screenshot 2021-11-09 at 23.43.57.png]
The following is the command line and the terminal output.
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/SeedBasedRSFC/UA-Intersect-L-ILOTC/sub-eb01/sub-eb01_space-fsaverage5_hemi-L_Seed-UA-Intersect-L-ILOTC_RSFC.func.gii --fwhm 6 --tval /Volumes/NatureNurtu/NatureNurture/Neuroimaging/RSFC/Smoothing/UA-Intersect-L-ILOTC/sub-eb01/sub-eb01_space-fsaverage5_hemi-L_Seed-UA-Intersect-L-ILOTC_RSFC_Smoothed.func.gii
7.2.0
setenv SUBJECTS_DIR /Applications/freesurfer/7.2.0/subjects cd /Volumes/NatureNurtu/NatureNurture/Neuroimaging/RSFC/Smoothing mri_surf2surf --s fsaverage5 --hemi lh --cortex --sval /Volumes/NatureNurtu/NatureNurture/Neuroimaging/RSFC/SeedBasedRSFC/UA-Intersect-L-ILOTC/sub-eb01/sub-eb01_space-fsaverage5_hemi-L_Seed-UA-Intersect-L-ILOTC_RSFC.func.gii --fwhm 6 --tval /Volumes/NatureNurtu/NatureNurture/Neuroimaging/RSFC/Smoothing/UA-Intersect-L-ILOTC/sub-eb01/sub-eb01_space-fsaverage5_hemi-L_Seed-UA-Intersect-L-ILOTC_RSFC_Smoothed.func.gii
sysname Darwin hostname Yangwens-MBP.homenet.telecomitalia.it machine x86_64 user yangwenxu srcsubject = fsaverage5 srcval = /Volumes/NatureNurtu/NatureNurture/Neuroimaging/RSFC/SeedBasedRSFC/UA-Intersect-L-ILOTC/sub-eb01/sub-eb01_space-fsaverage5_hemi-L_Seed-UA-Intersect-L-ILOTC_RSFC.func.gii srctype = trgsubject = fsaverage5 trgval = /Volumes/NatureNurtu/NatureNurture/Neuroimaging/RSFC/Smoothing/UA-Intersect-L-ILOTC/sub-eb01/sub-eb01_space-fsaverage5_hemi-L_Seed-UA-Intersect-L-ILOTC_RSFC_Smoothed.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 ERROR: dimension inconsistency in source data Number of surface vertices = 10242 Number of value vertices = 1
On Tue, 9 Nov 2021 at 19:10, Douglas N. Greve dgreve@mgh.harvard.edu wrote:
I have a feeling that it may be ignoring the extra frames in the gii file. Can you send the result of:
mri_info sub-eb01_task-resting_space-fsaverage5_hemi-L_desc-regressedFiltered.func.gii
On 11/9/2021 10:51 AM, Yangwen Xu wrote:
External Email - Use CautionYes! It's simply a gifti image with 10242 vertices and 475 time points. The following is the information:
[image: Screenshot 2021-11-09 at 16.47.58.png]
Do I need to transfer the images to you?
On Tue, 9 Nov 2021 at 16:26, Douglas N. Greve dgreve@mgh.harvard.edu wrote:
I have a feeling that it may be ignoring the extra frames in the gii file. Can you send the result of mri_info sub-eb01_task-resting_space-fsaverage5_hemi-L_desc-regressedFiltered.func.gii
On 11/9/2021 10:17 AM, Yangwen Xu wrote:
External Email - Use CautionHi 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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