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.

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 Caution

Yes! It's simply a gifti image with 10242 vertices and 475 time points. The following is the information:

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 Caution

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 Caution

Hello 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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