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> Dear freesurfer developers, > > I’m attempting to analyze my resting -state fMRI data, and I followed > procedures on your functional connectivity page. When I tried to run > preprocessing with my data, but it turns out that default mri_coreg did not > register my fMRI template volume onto anatomical scan well. So, I went on > to register fMRI to anatomical space on my own using bbregister with > (init-rr method - rigid transformation). I re-ran preprocessing without > registration (-noreg) to correct motion and slice-timing. My commands > looked like below: > #bbregister —mov fMRI_template_volume —bold —s subject —init-rr —lta > functional2anatomical.lta > #preproc-sess -s sess01 -fsd rest -stc siemens -noreg -surface fsaverage > lhrh -surf-fwhm 5 -mni305-2mm -vol-fwhm 0 -per-run -force > > Then, I configured seeds (ex. Hippocampus), and ran following commands: > #fcseed-config -segid 17 -fcname left_hippocampus.dat -fsd rest -mean > -cfg left_hippocampus.config > #fcseed-sess -s sess01 -cfg left_hippocampus.config > > It did run smoothly, but what I noticed from fcseed-sess script was it was > transforming anatomical aseg mask into functional space. I am confused on > this part, because during processing step, we only make registration file > for transformation from functional space to anatomical space, but > fcseed-sess command needs registration file that moves anatomical scan to > functional scan. > > # Convert segmentation to native functional space (##from fcseed-sess > script##) > > set cmd = (mri_label2vol --seg $seganat \ > > --reg $reg --temp $template --fillthresh $FillThresh \ > > --o $seg --pvf $pvf); > > echo $cmd | tee -a $LLF > > > Then, Later, during mkanalysis-sess step, the command seems to use functional > 2 anatomical transformation. Could you please clarify which registration file > it uses to process each step that I talked about above? Do I also need to > make anatomical to functional transformation registration? > > > I deeply appreciate your help. > > > Sincerely, > > Wenzhen > >
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