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Dear FreeSurfers!
I'm currently trying to do seed-based analysis. Therefore I'm using fcseed-config and fcseed-sess to configure my seed region. However, since I'm using a dataset that has been preprocessed with fMRIPrep, I'm having a lot of trouble doing this. Although I'm doing surface analyses, it seems that fcseed-sess is deriving the seed time course from the volumetric space (which of course makes sense since aparc+aseg is in volumetric space). I was wondering whether there is any way to use these functions with data, that has already been mapped onto the surface (i.e., fmcpr.sm0.fsaverage.lh)? The fMRIPrep output doesn't produce a template file, that seems to be indispensable for the formation of such a seed region.
This is the code I used:
fcseed-config -segid 1035 -fcname lh_insula_new.dat -fsd bold -mean -cfg mean.lh_insula_new.config -funcstem fmcpr.sm0.fsaverage.lh (I'm using funcstem since I don't have fmcpr.nii in my folders, only fmcpr.sm0.fsaverage.lh).
fcseed-sess -sf sessid -cfg mean.lh_insula_new.config
And this is my error:
fcseed-sess -sf sessid -cfg mean.lh_insula_1010.config Logfile is /storage/marilena/freesurfer_data/Study_3/Excite_data_3/Project/log/fcseed-sess.lh_insula_1010.dat.log Mon 07 Mar 2022 01:24:38 PM UTC Linux pslg067035.pers.ad.uni-graz.at 5.4.0-100-generic #113-Ubuntu SMP Thu Feb 3 18:43:29 UTC 2022 x86_64 x86_64 x86_64 GNU/Linux setenv SUBJECTS_DIR /storage/marilena/freesurfer_data/Study_3/Excite_data_3/Project/structural/ cd /storage/marilena/freesurfer_data/Study_3/Excite_data_3/Project /usr/local/freesurfer/fsfast/bin/fcseed-sess -sf sessid -cfg mean.lh_insula_1010.config freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b Mon 07 Mar 2022 01:24:38 PM UTC Linux pslg067035.pers.ad.uni-graz.at 5.4.0-100-generic #113-Ubuntu SMP Thu Feb 3 18:43:29 UTC 2022 x86_64 x86_64 x86_64 GNU/Linux setenv SUBJECTS_DIR /storage/marilena/freesurfer_data/Study_3/Excite_data_3/Project/structural/ cd /storage/marilena/freesurfer_data/Study_3/Excite_data_3/Project /usr/local/freesurfer/fsfast/bin/fcseed-sess -sf sessid -cfg mean.lh_insula_1010.config freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b
mri_label2vol --seg /storage/marilena/freesurfer_data/Study_3/Excite_data_3/Project/structural//01/mri/aparc+aseg.mgz --reg /storage/marilena/freesurfer_data/Study_3/Excite_data_3/Project/01/bold/001/register.dof6.lta --temp ERROR: could not determine file for /storage/marilena/freesurfer_data/Study_3/Excite_data_3/Project/01/bold/001/template --fillthresh .5 --o /storage/marilena/freesurfer_data/Study_3/Excite_data_3/Project/01/bold/001/tmp.fcseed-sess.470390/seg.nii.gz --pvf /storage/marilena/freesurfer_data/Study_3/Excite_data_3/Project/01/bold/001/tmp.fcseed-sess.470390/pvf.nii.gz ERROR: Option could unknown
Thank you a lot in advance!!
Best, Marilena