Hi Paul, this mostly looks right. I think the problem may be that you are including the unknown label on the command line. I think that mris_label2annot will ignore the 0 inthe ctab file, which means that it assign the first label passed (lh.unknown.label) to the the first non-zero ROI in the ctab file (banksts). Try that and see if it works. doug

On 01/30/2013 03:03 PM, Paul Beach wrote:

Hi Doug,

I've been attempting to utilize the programs suggested by you to create manual labels (ROIs) on the cortical surface of tksurfer to be able to export certain ones to AFNI. The problem I was having originally was that the cortical ribbon was not fully covered by surface drawn labels that were changed to volumes by MRI_label2vol.

You suggested first using mri_annotation2label to extract the labels within the aparc.annot files (left and right hemispheres), putting my created labels into the same folder (replacing, for example, the "insula" label with anterior, middle, and posterior insula labels) and then using mris_label2annotation to make a new annotated file to be sent into a re-ran mri_aparc2aseg.

The problem I'm running into now, after extracting all the labels, putting in my own, and running mris_label2annotis that the resultant annotation's labels are highly out of place and disorganized. For example, the label for the cuneus is where the corpus callosum is.

I'm wondering if this has something to do with the order of labels in the mris_label2annot script of possibly with my .ctab file. The latter was created based on what I found here https://surfer.nmr.mgh.harvard.edu/fswiki/tksurfer_labeledit on the Freesurfer wiki. I simply added my six manual labels/ROIs at the end. I tried to use their GWFSAnnotToLUT https://surfer.nmr.mgh.harvard.edu/fswiki/tksurfer_labeledit?action=AttachFile&do=view&target=GWFSAnnotToLUT program, but could not get it to work, so I'm not sure if the .ctab file accurately represents tksurfer's Lookup Table.

I'm also not sure if it has something to do with overlapping vertices of different labels. For example, will leaving the "insula" label in mess things up when I also try to include the anterior, middle, and posterior insula labels? If so, would simply removing labels that overlap, vertex-wise, help?

I have attached the setup of the .ctab file as well as my mris_label2annot script.

Thanks for your advice, Paul

On Tue, Jan 22, 2013 at 2:52 PM, Paul Beach <pabeach1@gmail.com mailto:pabeach1@gmail.com> wrote:

Thanks for your help!



On Tue, Jan 22, 2013 at 11:12 AM, Douglas N Greve
<greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> wrote:

     mri_annotation2label breaks them appart
    mris_label2annot puts them back together again
    doug

    On 01/22/2013 11:09 AM, Paul Beach wrote:

        Hi Doug,

        Thank you for this. However, can you give me a hint as to
        how I can go about breaking apart the aparc.annot files
        into their constituent label files? Are there a particular
        commands for doing this and eventually recombining the
        labels into the overall aparc.annot file?


        Thanks!



        On Wed, Jan 16, 2013 at 3:15 PM, Douglas N Greve
        <greve@nmr.mgh.harvard.edu
        <mailto:greve@nmr.mgh.harvard.edu>
        <mailto:greve@nmr.mgh.harvard.edu
        <mailto:greve@nmr.mgh.harvard.edu>>> wrote:


            The "annotation" is the name we give to a surface
        segmentation
            (eg, lh.aparc.annot). You can break lh.aparc.annot
        into its
            constituent label files. You can then replace the
        insula label
            file with posterior and anterior labels that you
        create. You can
            then recombine the labels back into a new annotation.
        Once you
            have the new annotation, you can run mri_aparc2aseg to
        map the
            annotation into the volume. This method will do better
        at filling
            in the cortical ribbon than mri_surf2vol or mri_label2vol.

            doug



            On 01/16/2013 01:25 PM, Paul Beach wrote:

                Hi Doug,

                Thanks a lot for the reply. I'm relatively new to
        freesurfer
                and it's great to see such a helpful community.

                I'm a little fuzzy on what you mean with your second
                suggestion, related to the manual ROI
        creation/export to AFNI.
                Could you explain a bit more about creating "a new
        annotation
                and then run mri_aparc2aseg."

                First, I'm not sure what you mean by "new annotation."

                Second, my understanding is that mri_aparc2aseg
        normally deals
                with ROIs in the LUT. However, looking at the wiki
        for this
                command, it seems as though I can utilize my
        created label
                using the "--annot argName" option.
                How does this look:
                mri_aparc2aseg --s [subj] --annot lh.aIns.label
        --o lh.aIns_aparc


                Cheers,
                Paul



                On Wed, Jan 16, 2013 at 10:56 AM, Douglas N Greve
                <greve@nmr.mgh.harvard.edu
        <mailto:greve@nmr.mgh.harvard.edu>
        <mailto:greve@nmr.mgh.harvard.edu
        <mailto:greve@nmr.mgh.harvard.edu>>
                <mailto:greve@nmr.mgh.harvard.edu
        <mailto:greve@nmr.mgh.harvard.edu>

                <mailto:greve@nmr.mgh.harvard.edu
        <mailto:greve@nmr.mgh.harvard.edu>>>> wrote:

                    Hi Paul,

                    On 01/16/2013 10:27 AM, Paul Beach wrote:
                    > Hello,
                    >
                    > I have two issues, currently.
                    >
                    > First, I was wondering if it would be
        possible to create
                separate
                    > FSAverage brains for different subject
        groups. I am
                working with
                    > healthy seniors and various stages of
        Alzheimer's
                disease, so
                    doing so
                    > would be very helpful from the perspective
        of not
                conflating the
                    > differences in neuroanatomy between the
        these groups.
                One idea
                    we had
                    > was to create separate HOME directories for
        each group,
                but we
                    wanted
                    > to know if there was an easier way. I can't find
                anything in the
                    > interwebs about this.
                    You can create your own fsaverage subject using
                make_average_subject.
                    Note that when you run recon-all it registers
        to the standard
                    fsaverage
                    space. If you want to register to a different
        space, you
                will need to
                    re-run mris_register. Once you do this, you
        will not be
                able to
                    compare
                    groups.
                    >
                    > Second, I utilize some ROIs that are not
        specified by FS
                (such as
                    > secondary somatosensory cortex and anterior
        vs. posterior
                    insula). My
                    > means of getting around this was to use
        FSAverage and
                tksurfer to
                    > hand-draw them, save them as '.label' files,
        map them to
                individual
                    > subjects, and export them to AFNI since much
        of our
                correlation
                    > analysis is done on that platform. However,
        I've noticed
                that when I
                    > view these hand-drawn ROIs in AFNI they only
        show up at the
                    border of
                    > the gray and white matter, rather than
        filling the
                entirety of the
                    > gray matter. Note that this problem does not
        occur for
                ROIs in the
                    > look up table (like the caudal ACC).
        Exporting these to AFNI
                    gives you
                    > a nice ROI that fills all the gray matter in
        the defined
                region.
                    Try using --proj frac 0 1 .1 with
        mri_label2vol. Or you
                can create
                    a new
                    annotation and then run  mri_aparc2aseg. The
        2nd method
                works a little
                    better since the 1st method can leave some holes.

                    doug
                    >
                    > _Code I'm using_:
                    > For the latter problem, what I first use is
                mri_label2label to
                    map the
                    > fsaverage-based ROI onto individual
        subjects, for
                example with the
                    > left anterior insula, before using
        mri_label2vol:
                    > *mri_label2label --srclabel lh.aIns.label
        --srcsubject
                fsaverage
                    > --trglabel lh.aIns.label --trgsubject [subj]
        --regmethod
                surface
                    > --hemi lh*
                    >
                    > *mri_label2vol --label
        ../label/lh.aIns.label --regheader
                    > aparc+aseg.mgz --o gmroi_volume.nii.gz
        --temp orig/001.mgz*
                    >
                    >
                    > Then I copy the new volume file to their
        AFNI folder,
                rename it, and
                    > run my correlation analysis on them.
                    >
                    > Note, that for those ROIs that are in the
        look up table
                (those
                    > parcellated by freesurfer) I simply use
        mri_label2vol before
                    > extracting them using 3dcalc (for example,
        the caudal
                anterior
                    > cingulate)...
                    > *mri_label2vol --seg aparc+aseg.mgz --regheader
                aparc+aseg.mgz --o
                    > gmroi_volume.nii.gz --temp orig/001.mgz*
                    >
                    > *3dcalc -a gmroi_volume.nii.gz -expr
        'equals(a,1002)'
                -prefix
                    > ROI_FS_lh.caudalACC.nii.gz*
                    >
                    >
                    >
                    > tl:dr
                    > Is it possible to "easily" create multiple
        FSAverages
                based on
                    > selected subjects (in my case, subject
        groups separated by
                    disease state)?
                    >
                    > and
                    >
                    > Does anyone have any advice on how to get
        hand-drawn
                surface-based
                    > ROIs from Freesurfer's tksurfer into AFNI
        that full
                cover the
                    entirety
                    > of the gray matter?
                    >
                    >
                    > Cheers and thanks!
                    > --
                    > Paul Beach
                    >
                    >
                    >
                    > _______________________________________________
                    > Freesurfer mailing list
                    > Freesurfer@nmr.mgh.harvard.edu
        <mailto:Freesurfer@nmr.mgh.harvard.edu>
                <mailto:Freesurfer@nmr.mgh.harvard.edu
        <mailto:Freesurfer@nmr.mgh.harvard.edu>>
                    <mailto:Freesurfer@nmr.mgh.harvard.edu
        <mailto:Freesurfer@nmr.mgh.harvard.edu>

                <mailto:Freesurfer@nmr.mgh.harvard.edu
        <mailto:Freesurfer@nmr.mgh.harvard.edu>>>

                    >
        https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

                    --
                    Douglas N. Greve, Ph.D.
                    MGH-NMR Center
        greve@nmr.mgh.harvard.edu
        <mailto:greve@nmr.mgh.harvard.edu>
        <mailto:greve@nmr.mgh.harvard.edu
        <mailto:greve@nmr.mgh.harvard.edu>>
                <mailto:greve@nmr.mgh.harvard.edu
        <mailto:greve@nmr.mgh.harvard.edu>

                <mailto:greve@nmr.mgh.harvard.edu
        <mailto:greve@nmr.mgh.harvard.edu>>>
                    Phone Number: 617-724-2358 <tel:617-724-2358>
        <tel:617-724-2358 <tel:617-724-2358>>
                <tel:617-724-2358 <tel:617-724-2358>
        <tel:617-724-2358 <tel:617-724-2358>>>
                    Fax: 617-726-7422 <tel:617-726-7422>
        <tel:617-726-7422 <tel:617-726-7422>> <tel:617-726-7422
        <tel:617-726-7422>

                <tel:617-726-7422 <tel:617-726-7422>>>

                    Bugs:
        surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
        <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting>

        <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting>

        <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting>
                    FileDrop:
        www.nmr.mgh.harvard.edu/facility/filedrop/index.html
        <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html>

        <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html>

        <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html>

                    Outgoing:
        ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/

                    _______________________________________________
                    Freesurfer mailing list
        Freesurfer@nmr.mgh.harvard.edu
        <mailto:Freesurfer@nmr.mgh.harvard.edu>
                <mailto:Freesurfer@nmr.mgh.harvard.edu
        <mailto:Freesurfer@nmr.mgh.harvard.edu>>
                <mailto:Freesurfer@nmr.mgh.harvard.edu
        <mailto:Freesurfer@nmr.mgh.harvard.edu>

                <mailto:Freesurfer@nmr.mgh.harvard.edu
        <mailto: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.




                --         Paul Beach
                DO/PhD candidate - Year V
                Michigan State University
                - College of Osteopathic Medicine - OMS V
                - Neuroscience Program
                   - Bozoki Lab: Neurology/Radiology
                - President: American Physician Scientist
        Association, MSU COM
                Chapter


            --     Douglas N. Greve, Ph.D.
            MGH-NMR Center
        greve@nmr.mgh.harvard.edu
        <mailto:greve@nmr.mgh.harvard.edu>
        <mailto:greve@nmr.mgh.harvard.edu
        <mailto:greve@nmr.mgh.harvard.edu>>
            Phone Number: 617-724-2358 <tel:617-724-2358>
        <tel:617-724-2358 <tel:617-724-2358>>
            Fax: 617-726-7422 <tel:617-726-7422> <tel:617-726-7422
        <tel:617-726-7422>>

            Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
        <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting>
            <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting>
            FileDrop:
        www.nmr.mgh.harvard.edu/facility/filedrop/index.html
        <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html>

        <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html>
            Outgoing:
        ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/




        -- 
        Paul Beach
        DO/PhD candidate - Year V
        Michigan State University
        - College of Osteopathic Medicine - OMS V
        - Neuroscience Program
           - Bozoki Lab: Neurology/Radiology
        - President: American Physician Scientist Association, MSU
        COM Chapter


    -- 
    Douglas N. Greve, Ph.D.
    MGH-NMR Center
    greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>
    Phone Number: 617-724-2358 <tel:617-724-2358>
    Fax: 617-726-7422 <tel:617-726-7422>

    Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
    <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting>
    FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html
    <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html>
    Outgoing:
    ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/




-- 
Paul Beach
DO/PhD candidate - Year V
Michigan State University
- College of Osteopathic Medicine - OMS V
- Neuroscience Program
   - Bozoki Lab: Neurology/Radiology
- President: American Physician Scientist Association, MSU COM Chapter

-- Paul Beach DO/PhD candidate - Year V Michigan State University

• College of Osteopathic Medicine - OMS V
• Neuroscience Program
  • Bozoki Lab: Neurology/Radiology
• President: American Physician Scientist Association, MSU COM Chapter