Hi Miggy

can you cc the list so that others can answer? The two atlases we provide are described in:

https://surfer.nmr.mgh.harvard.edu/ftp/articles/fischl04-parcellation.pdf
https://surfer.nmr.mgh.harvard.edu/ftp/articles/desikan06-parcellation.pdf
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2937159/pdf/nihms213933.pdf


and yes, I guess you could edit the ribbon.mgz and then convert it back to wm.mgz. You'll need to make sure that the "on" edits are turned to 255 and the "off" ones to 1 (not 0) for things to work properly

cheers
Bruce
 On Wed, 4 Sep 2013, Miggy Chuapoco wrote:

Hi Bruce,
Thanks for the help. To explain a bit more about the first issue, we convert
ribbon.mgz into a a nifti file using a script in matlab, which we then edit
in ITK-SNAP to fix the segmentation. Typically from there we use a program
called mrVista to create meshes and do other data analysis depending on what
we need to do. However, we are doing group averaging for the first time and
we would like to use these fixed segmentations that we have in the group
averaging, and not the raw segmentations from recon-all. I was curious to
know that if I were able to convert the nifti file that we have edited back
into an .mgz file, would we be able to theoretically obtain a new wm.mgz
file and run autorecon2-wm. Let me know if that makes sense.

With regards to the second issue, which atlas is used in the
make_average_subject process and where would I be able to find a list of the
annotation files within each atlas?

Thanks for your help!
Miggy


On Wed, Sep 4, 2013 at 1:45 PM, Bruce Fischl <fischl@nmr.mgh.harvard.edu>
wrote:
      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




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