Hi all,
I'm trying to make a group average of a set of subjects that we've collected various functional data on and use anatomical landmarks of the group average surface to predict the locations of functional areas that we've found to be correlated to the anatomy of the ventral cortex. As such, we'd like to get as accurate of an average surface as possible. I've come up on two problems that I'd like to address and was wondering if anyone could help come up with a solution.
I ran the recon-all command on all the subjects and created a segmentation, however we made edits to the segmentation using ITK-SNAP, and not tkmedit. Some of the changes were fairly drastic and we'd like to use the fixed segmentations in the averaging process. I've considered perhaps running the -autorecon2-wm flag, but unfortunately using ITK-SNAP essentially makes edits to ribbon.mgz, and not wm.mgz. I was wondering if there was a way to "extract" a new wm.mgz from an edited ribbon.mgz.
My second problem involves trying to anchor a sulcus on the ventral surface during the averaging process (the mid-fusiform sulcus) in hopes of getting a more accurate representation of the sulcus on the average surface. As it stands there is a bit too much variability of the average MFS location when compared to the individual subjects' MFS location, and we'd like to reduce that if possible. Is there any way of using a label, or something similar, that can be considered as an "anchor" during the averaging process?
Thanks and regards, Miggy Chuapoco
Hi Miggy,
not sure about your first issue as the ribbon is the gray matter and the wm.mgz is white matter, so how would edits in one change the other?
For the second one, there is a flag in mris_register that allows you to draw a label on an individual subject and indicate what parcellation unit is should be in the average. The syntax is:
mris_register -l <label file> <gcsa file> <annotation name> ...
where
<label_file> is the label you draw on the individual (e.g. in tksurfer) <gcas_file> is one of our standard atlases, listed in $FREESURFER_HOME/average/*.gcs <annotation name> is the name of the annotation in the atlas that the label should map to (e.g. S_central in the Destrieux atlas)
cheers Bruce
On Wed, 4 Sep 2013, Miggy Chuapoco wrote:
Hi all, I'm trying to make a group average of a set of subjects that we've collected various functional data on and use anatomical landmarks of the group average surface to predict the locations of functional areas that we've found to be correlated to the anatomy of the ventral cortex. As such, we'd like to get as accurate of an average surface as possible. I've come up on two problems that I'd like to address and was wondering if anyone could help come up with a solution.
I ran the recon-all command on all the subjects and created a segmentation, however we made edits to the segmentation using ITK-SNAP, and not tkmedit. Some of the changes were fairly drastic and we'd like to use the fixed segmentations in the averaging process. I've considered perhaps running the -autorecon2-wm flag, but unfortunately using ITK-SNAP essentially makes edits to ribbon.mgz, and not wm.mgz. I was wondering if there was a way to "extract" a new wm.mgz from an edited ribbon.mgz.
My second problem involves trying to anchor a sulcus on the ventral surface during the averaging process (the mid-fusiform sulcus) in hopes of getting a more accurate representation of the sulcus on the average surface. As it stands there is a bit too much variability of the average MFS location when compared to the individual subjects' MFS location, and we'd like to reduce that if possible. Is there any way of using a label, or something similar, that can be considered as an "anchor" during the averaging process?
Thanks and regards, Miggy Chuapoco
freesurfer@nmr.mgh.harvard.edu
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Bruce Fischl -
Miggy Chuapoco