Hi FreeSurfer experts,
I have two different ways to do functional connectivity, and was wondering
which one is optimal since they produce different results. The first is handed
down to me from a previous coordinator. However a few of the steps seemed
overly complicated, so I looked into a more direct method. Both methods use
single vertex as a seed, so we smooth in order to include enough vertexes for
fcseed-sess.
Option 1 (the old version):
Creating the mask, smoothing, and binarizing it:
~ mri_label2label --s fsaverage --regmethod surface --hemi lh --srclabel
$SUBJECTS_DIR/$subject/label/$label.label --trglabel
$SUBJECTS_DIR/$subject/label/junk.label--outmask
$SUBJECTS_DIR/$subject/mri/{$label}_sm00.mgh
~ mris_fwhm --i $SUBJECTS_DIR/$subject/mri/{$label}_sm00.mgh --fwhm 4
--smooth-only --o $SUBJECTS_DIR/$subject/mri/{$label}_sm04.mgh --s fsaverage
--hemi lh
~ mri_binarize --i $SUBJECTS_DIR/$subject/mri/${label}_sm04.mgh --min 10e-10
--o $SUBJECTS_DIR/$subject/mri/{$label}_sm04.10e-10.bin.mgh
Switching to dev in order to convert the mask into a volume:
~ source /usr/local/freesurfer/nmr-dev-env
~ mri_surf2vol --so $SUBJECTS_DIR/fsaverage1/surf/lh.pial
$SUBJECTS_DIR/$subject/mri/${label}_sm04.10e-10.bin.mgh --subject fsaverage --o
$SUBJECTS_DIR/$subject/mri/{$label}_sm04.10e-10.bin.vol.mgz
We then move back into 5.3 and use this volume as segmentation in fcseed-config
and -sess
Option 2:
Turning label into a volume, smoothing it, and binarizing it:
~ mri_label2vol --label $SUBJECTS_DIR/fsaverage1/label/{$label} --temp
$SUBJECTS_DIR/fsaverage1/orig.mgz --regheader $SUBJECTS_DIR/fsaverage1/orig.mgz
--hemi lh --subject fsaverage --proj frac 0 1 .1 --o
$SUBJECTS_DIR/{$subject}/{$label}.vol.mgz
~ mri_fwhm --i $SUBJECTS_DIR/{$subject}/{$label}.vol.mgz --fwhm 4 --smooth-only
--o $SUBJECTS_DIR/{$subject}/{$label}.sm4.vol.mgz
~ mri_binarize --i $SUBJECTS_DIR/{$subject}/{$label}.sm4.vol.mgz --min 10e-10
--o $SUBJECTS_DIR/{$subject}/{$label}.sm4.bin.vol.mgz
We then use this volume as segmentation in fcseed-config and -sess.
I would prefer to use the second method since it is more straightforward, but I
wanted to make sure that a) it is sound and b) it is more optimal than option
1.
Thank you for your help!
Anais Rodriguez-Thompson
Clinical Research Coordinator
Brain Genomics Laboratory
Martinos Center for Biomedical Imaging
Massachusetts General Hospital
Phone: (617) 643-3215
_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.
