Re: [Freesurfer] Fwd: Anatomical segmentation - question

Hi Rotem, can you repost the question? The email got reformatted and is impossible to read. thanks doug

On 01/09/2014 01:16 AM, Rotem Saar wrote:

Hi Doug,

Can u help ?

Thanks Rotem

Rotem Saar-Ashkenazy Department of Brain and Cognitive Science Ben Gurion University of the Negev Beer-Sheva 84105 Israel

2014/1/6 Bruce Fischl <fischl@nmr.mgh.harvard.edu mailto:fischl@nmr.mgh.harvard.edu>

it probably doesn't matter, but Doug is the Talairach expert, so
perhaps he can comment
Bruce


On Mon, 6 Jan 2014, Rotem Saar wrote:

    Dear freesurfer experts,

    I'm performing anatomical segmentation for Philips dicoms (3T
    scanner). I
    got these two images from the same slice while performing step
    number 4 in
    the script below – from some reason, the two images don't fit.
    Should I use
    "scale brain" ? I know this is not recommended thus want to
    consult with u
    first – Can u please comment on why this is happening? Is
    there any value
    that corresponds to "how good is the segmentation" ? if yes,
    where can I
    find it ?

    My script is written below.

    Thanks,

    Rotem

    Anatomical segmentation:

    first step- 23 hours:

    recon-all -autorecon-all -i ~/Desktop/ FOLDER-NAME /I00001.dcm -s
    FOLDER-NAME

    second step:(gyrus=green, sulcus=red)

    tksurfer -curv FOLDER-NAME lh/rh inflated

    third step: (talairch registretion)

    tkmedit FOLDER-NAME brainmask.mgz

    File-> transforms-> load transform AUX-> Browse-> talairch.xfm

    forth step: (simetry - allows changing 12df transformation. if
    we made any
    changes we should click "save reg" and run this command again)

    tkregister2 --mgz --s FOLDER-NAME --fstal --surf orig

    IF WE CHANGE ANYTHING, CLICK "SAVE REG" AND RUN FROM STARTING
    POING:
    recon-all -all -subjectid FOLDER-NAME

    fifth step: (scalp removal: if removed too much, rise up from
    the value 25:

    recon-all -skullstrip -wsthresh 25 -clean-bm -no-wsgcaatlas -s
    FOLDER-NAME

    to check the result press: tkmedit FOLDER-NAME brainmask.mgz
    lh.white -aux
    T1.mgz -aux-surface rh.white )

    for hand correction: tkmedit FOLDER-NAME brainmask.mgz -aux T1.mgz

    tools-> configure volume brush -> MARK: mode=clone, source=Aux

    tools-> configure brush info (for choosing brush size)

    click on edit voxels: click in MIDDLE for adding voxels, RIGHT
    for removing
    voxels : slice by slice.

    when finish, click: File-> save main volume

    sisxt step: (cp for correcting segmentation)

    tkmedit FOLDER-NAME brainmask.mgz lh.white -aux T1.mgz
    -aux-surface rh.white

    seventh step: (done)

    recon-all -autorecon2-cp -autorecon3 -s FOLDER-NAME






    Rotem Saar-Ashkenazy
    Department of Brain and Cognitive Science
    Ben Gurion University of the Negev
    Beer-Sheva 84105
    Israel




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