External Email - Use Caution
Dear Doug,
Thank you for your replying.
I collected the data by myself using a SIEMENS machine. Sorry, what do you mean
by mapping the time course. I guess I am not trying to do that. I would like
to do beta series analysis.
I used the command in its old way, and I mapped it to 2mm template. It is OK
now. The time and space are both acceptable. The code is as follows, I will
really appricate it if you can help me to check the code.
mri_surf2vol --hemi ${hemi} --o
${ROOTDIR}/$isub/bold/${irun}/spmRibbon${hemi}/${iVolume} --projfrac 0
--fillribbon --template ${SUBJECTS_DIR}/fsaverage/mri.2mm/brain.mgz \
--reg ${SUBJECTS_DIR}/fsaverage/mri.2mm/reg.2mm.dat --surfval
${ROOTDIR}/$isub/bold/${irun}/spm${hemi}/${iVolume}
Best,
Zhiwei
>Message: 5
>Date: Sun, 20 Aug 2023 17:23:52 -0400
>From: "Douglas N. Greve" <dgr...@mgh.harvard.edu>
>Subject: Re: [Freesurfer] converting preprocessed surface functional
> data to volume
>To: freesurfer@nmr.mgh.harvard.edu
>Message-ID: <c31ec38b-fcd6-c47a-8b29-f32857181...@mgh.harvard.edu>
>Content-Type: text/plain; charset="utf-8"
>
> External Email - Use Caution
>
>where did the functional data come from? Are you trying to map the time
>courses? That usually does not work that well as your resulting image
>will be huge. One thing to do is to map it to a cropped volume (most of
>the 256^3 is outside the brain) and or also map it to 2mm instead of 1mm.
>
>On 8/13/2023 11:02 PM, wangzhiwei3233 wrote:
>>
>> ????????External Email - Use Caution
>>
>> Dear Freesurfer experts,
>> I am going to convert the preprocessed surface functional data to
>> volume in fsaverage space so that I can used the processed data in SPM
>> for further analysis, for example, beta series analysis. I tried
>> mri_surf2vol, it worked. But it is time consuming. It takes around 5
>> minutes per 10 volumes. In addition, the result volume is too big
>> (67MB/ volume for 256*256*256 matrix, 1mm resolution). My data
>> contains about??70800 brain volumes, so the needed time is about
>> 40days and the storage space is about 7TB , which is unacceptable. The
>> code is? as follows:
>>
>> /mri_surf2vol --o
>> ${Dir_Subj_fMRI}/$isub/bold/${irun}/Ribbon/${iVolume} --subject
>> fsaverage --so ${SUBJECTS_DIR}/fsaverage/surf/lh.white
>> ${Dir_Subj_fMRI}/$isub/bold/${irun}/LH/${iVolume} --so
>> ${SUBJECTS_DIR}/fsaverage/surf/rh.white
>> ${Dir_Subj_fMRI}/$isub/bold/${irun}/RH/${iVolume} /
>> /
>> /
>> Are there methods with faster speed and outputing volumes with lower
>> resolution?
>>
>> Best,
>> Zhiwei
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