Hi Doug,

The geometry of the input is correct in both freeview and tkmedit, and the outlines of the white and pial surfaces align well with with volume in freeview. Looking at the headers, I'm wondering if my initial transform of the image into the proper coordinates might be the problem. The DICOM wasn't oriented correctly at first, so I converted to nifti, and ran "mri_convert -c -iid 0 -1 0 -ijd 0 0 -1 -ikd 1 0 0 mprage.nii.gz mprage.mgz", which produced a conformed image with the correct orientation in freeview. Is there a chance that a problem here could produce the problems later down the pipeline? For example, I see now that mprage.nii.gz's header correctly lists the primary slice direction as axial, whereas the reoriented mprage.mgz incorrectly lists it as coronal. Also, orientation was originally listed as RAS, but changed to LIA after conversion. Is there a chance that this is affecting the later surface registration?

Thanks so much for any help you can provide. I've attached mri_info output for the nifti and mgz files below.

Best regards,

John

mri_info mprage.nii.gz
Volume information for mprage.nii.gz
          type: nii
    dimensions: 199 x 152 x 183
   voxel sizes: 1.0000, 1.0000, 1.0000
          type: FLOAT (3)
           fov: 199.000
           dof: 0
        xstart: -99.5, xend: 99.5
        ystart: -76.0, yend: 76.0
        zstart: -91.5, zend: 91.5
            TR: 8.42 msec, TE: 0.00 msec, TI: 0.00 msec, flip angle: 0.00 degrees
       nframes: 1
       PhEncDir: UNKNOWN
ras xform present
    xform info: x_r =   0.7324, y_r =   0.0361, z_r =   0.6799, c_r =     1.7748
              : x_a = -0.0157, y_a =   0.9992, z_a = -0.0361, c_a =    25.8853
              : x_s = -0.6807, y_s =   0.0157, z_s =   0.7324, c_s =    -8.5852
Orientation   : RAS
Primary Slice Direction: axial

voxel to ras transform:
                0.7324   0.0361   0.6799 -136.0543
               -0.0157   0.9992 -0.0361   -45.1875
               -0.6807   0.0157   0.7324    -9.0720
                0.0000   0.0000   0.0000     1.0000

voxel-to-ras determinant 0.999997

ras to voxel transform:
                0.7324 -0.0157 -0.6807    92.7637
                0.0361   0.9992   0.0157    50.2057
                0.6799 -0.0361   0.7324    97.5155
                0.0000   0.0000   0.0000     1.0000

______

mri_info mprage.mgz
Volume information for mprage.mgz
          type: MGH
    dimensions: 256 x 256 x 256
   voxel sizes: 1.0000, 1.0000, 1.0000
          type: UCHAR (0)
           fov: 256.000
           dof: 0
        xstart: -128.0, xend: 128.0
        ystart: -128.0, yend: 128.0
        zstart: -128.0, zend: 128.0
            TR: 8.42 msec, TE: 0.00 msec, TI: 0.00 msec, flip angle: 0.00 degrees
       nframes: 1
       PhEncDir: UNKNOWN
ras xform present
    xform info: x_r = -1.0000, y_r =   0.0000, z_r =   0.0000, c_r =     1.7748
              : x_a =   0.0000, y_a =   0.0000, z_a =   1.0000, c_a =    25.8853
              : x_s =   0.0000, y_s = -1.0000, z_s =   0.0000, c_s =    -8.5852

talairach xfm :
Orientation   : LIA
Primary Slice Direction: coronal

voxel to ras transform:
               -1.0000   0.0000   0.0000   129.7748
                0.0000   0.0000   1.0000 -102.1147
                0.0000 -1.0000   0.0000   119.4148
                0.0000   0.0000   0.0000     1.0000

voxel-to-ras determinant -1

ras to voxel transform:
               -1.0000   0.0000   0.0000   129.7748
               -0.0000 -0.0000 -1.0000   119.4148
               -0.0000   1.0000 -0.0000   102.1147
                0.0000   0.0000   0.0000     1.0000

---

John Plass

Ph.D. Candidate

Visual Perception, Neuroscience, and Cognition Lab
Northwestern University

On Wed, Jan 27, 2016 at 1:43 PM, Douglas N Greve <greve@nmr.mgh.harvard.edu> wrote:

I don't know how that could have happened. Is the geometry of the
exvivo input oriented correctly? Ie, if you load the orig.mgz into
freeview or tkmedit, is sag actually sagital, etc?

On 01/26/2016 06:08 PM, John Plass wrote:
> Hi Bruce,
> Thanks for your reply. The orientation is correct in freeview,
> although, digging further, I see that that it is misoriented when I
> view it in tkregister2. I ran tkregister --mgz --s {subID} --fstal
> --surf orig, and the orig volume is shown oriented correctly, but the
> orig surface appears to have some of the dimensions swapped. Any idea
> why this might be?
>
> Thanks for your help!
>
> John
>
> On Tuesday, January 26, 2016, Bruce Fischl <fischl@nmr.mgh.harvard.edu

> <mailto:fischl@nmr.mgh.harvard.edu>> wrote:
>
> Hi John
>
> does it come up in the correct orientation in freeview? If you didn't
> scan it in the orientation that a person would have been lying in the
> scanner, you will need to reorient the data so that we know what e.g.
> anterior is
>
> cheers
> Bruce
>
> On Tue, 26 Jan 2016, John Plass wrote:
>
> > Hello,
> > I've been following the Ex-Vivo Recon instructions
> > https://surfer.nmr.mgh.harvard.edu/fswiki/ExvivoRecon) with an
> MPRAGE scan
> > of a formalin-fixated brain. With considerable manual editing,
> I've been
> > able to produce convincing white and pial surfaces, but I am
> having trouble
> > getting a good parcellation. The labels are reversed from
> anterior to
> > posterior (e.g., superior parietal lobule area is labelled as
> middle frontal
> > gyrus). I am assuming this has to do with problems with the surface
> > registration. Also, when viewing the surfaces in Freeview, they
> appear
> > pretty dark (perhaps similar
> tohttps://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2011-June/018689.htm

> <http://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2011-June/018689.htm>
> > l), although the correspondence between red/green and gyri and
> sulci appears
> > to be correct. Might this be part of the problem?
> >
> > Any advice would be much appreciated! If you'd like to take a
> look at the
> > files, please let me know what and where to upload.
> >
> > Thanks very much for your help.
> >
> > Best regards,
> > John Plass
> >
> >
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> --
>
> ---
> John Plass
> Ph.D. Candidate
> Visual Perception, Neuroscience, and Cognition Lab
> Northwestern University
>
>
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--
Douglas N. Greve, Ph.D.
MGH-NMR Center
greve@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

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