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Yes! It's simply a gifti image with 10242 vertices and 475 time points. The
following is the information when I run the gifti function in matlab:
>>
gifti('sub-eb01_task-resting_space-fsaverage5_hemi-L_desc-regressedFiltered.func.gii')
ans =
struct with fields:
cdata: [10242×475 single]
On Tue, 9 Nov 2021 at 19:10, Douglas N. Greve <[email protected]>
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:
>
> [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 <[email protected]>
> 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 <[email protected]>
>> 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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