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
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
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://secure-web.cisco.com/1S4AQ0YxeConff8GRPGc3ftgLd1ikrq2bAY0qt_tN2AQguO...
freesurfer@nmr.mgh.harvard.edu
-
Douglas N. Greve -
wangzhiwei3233