Re: [Freesurfer] Functional connectivity preprocessing and seed analysis

On 9/15/2020 11:26 AM, Wenzhen Zhao wrote:

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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.

Yes, it just inverts the transform to go in the opposite direction

# 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?

No, once it has a transformation in one direction, it has it in both directions

I deeply appreciate your help.

Sincerely,

Wenzhen

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