Re: [Freesurfer] Ex-Vivo Surface Misoriented in tkmedit, but not Freeview

[John Plass]

Hi Bruce,
When I run the last stage of the ex-vivo processing (recon-all -cortribbon
-sphere -surfreg -cortparc -parcstats -subjid $SUBID -noaseg), the
parcellation labels come out in the wrong place. I haven't been able to
figure out why this is happening, so I was wondering if its possible that
the surface registration is starting with the surface misoriented like it
is in tkmedit.

John


---
John Plass
Ph.D. Candidate
Visual Perception, Neuroscience, and Cognition Lab
Northwestern University

On Tue, Mar 1, 2016 at 7:38 AM, Bruce Fischl 
wrote:

> Hi John
>
> this is pretty puzzling. Is it causing any problems? tkmedit has been
> deprecated and it may just not be properly reading some header information
> or other. If nothing else is affected you can probably ignore it
>
> cheers
> Bruce
>
>
>
> On Mon, 29 Feb 2016, John Plass wrote:
>
> Hi Bruce,
>> Thanks for your help. In freeview, the surface outline overlays on the
>> volume correctly, and both the volume and the surface are oriented
>> correctly
>> in terms of R-L, A-P, and S-I axes. In tkmedit, the volume is oriented
>> correctly, but the surface appears to be oriented with some of the axes
>> swapped. E.g., from the coronal view in tkmedit, I see a coronal slice of
>> the volume, but the outline of an axial slice of the surface, with the
>> anterior part pointing down.
>>
>> John
>>
>>
>>
>
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Re: [Freesurfer] Ex-Vivo Surface Misoriented in tkmedit, but not Freeview

[Bruce Fischl]

Hi John

this is pretty puzzling. Is it causing any problems? tkmedit has been 
deprecated and it may just not be properly reading some header information 
or other. If nothing else is affected you can probably ignore it

cheers
Bruce


On Mon, 29 Feb 2016, 
John Plass wrote:

> Hi Bruce,
> Thanks for your help. In freeview, the surface outline overlays on the
> volume correctly, and both the volume and the surface are oriented correctly
> in terms of R-L, A-P, and S-I axes. In tkmedit, the volume is oriented
> correctly, but the surface appears to be oriented with some of the axes
> swapped. E.g., from the coronal view in tkmedit, I see a coronal slice of
> the volume, but the outline of an axial slice of the surface, with the
> anterior part pointing down.
> 
> John
> 
>
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Re: [Freesurfer] Ex-Vivo Surface Misoriented in tkmedit, but not Freeview

[John Plass]

Hi Bruce,
Thanks for your help. In freeview, the surface outline overlays on the
volume correctly, and both the volume and the surface are oriented
correctly in terms of R-L, A-P, and S-I axes. In tkmedit, the volume is
oriented correctly, but the surface appears to be oriented with some of the
axes swapped. E.g., from the coronal view in tkmedit, I see a coronal slice
of the volume, but the outline of an axial slice of the surface, with the
anterior part pointing down.

John
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Re: [Freesurfer] Ex-Vivo Surface Misoriented in tkmedit, but not Freeview

[Bruce Fischl]

Hi John

when you say that they are oriented correctly in freeview, does that mean 
that they just overlay properly on the volume? Or that e.g. what freeview 
thinks is anterior is actually anterior, etc...?


cheers
Bruce


On Mon, 29 Feb 2016, John 
Plass wrote:



Hello Freesurfer Experts,
I wrote in recently about my parcellation troubles with an ex-vivo scan
(link). Digging further, I've found that the surfaces I've produced
following the Ex-Vivo recon instructions are oriented properly when viewed
in freeview (freeview -v mri/orig.mgz -f surf/rh.white:edgecolor=blue
surf/rh.pial:edgecolor=red), but are misoriented in tkmedit (tkmedit $SUBID
orig.mgz rh.white). I suspect that something related this might be the
source of the parcellation problems. Any idea why this might be and how I
can fix it?

Relevant background information:
*volumes were reoriented before FS processing using the command "mri_convert
-c -iid 0 -1 0 -ijd 0 0 -1 -ikd 1 0 0 mprage.nii.gz  mprage.mgz"
*running freesurfer-Linux-centos4_x86_64-stable-pub-v5.3.0 on Ubuntu 14.04

As always, I'm very grateful for any help you can provide.

John



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[Freesurfer] Ex-Vivo Surface Misoriented in tkmedit, but not Freeview

[John Plass]

Hello Freesurfer Experts,
I wrote in recently about my parcellation troubles with an ex-vivo scan (
link
).
Digging further, I've found that the surfaces I've produced following
the Ex-Vivo
recon instructions 
are oriented properly when viewed in freeview (freeview -v mri/orig.mgz -f
surf/rh.white:edgecolor=blue surf/rh.pial:edgecolor=red), but are
misoriented in tkmedit (tkmedit $SUBID orig.mgz rh.white). I suspect that
something related this might be the source of the parcellation problems.
Any idea why this might be and how I can fix it?

Relevant background information:
*volumes were reoriented before FS processing using the command
"mri_convert -c -iid 0 -1 0 -ijd 0 0 -1 -ikd 1 0 0 mprage.nii.gz
mprage.mgz"
*running freesurfer-Linux-centos4_x86_64-stable-pub-v5.3.0 on Ubuntu 14.04

As always, I'm very grateful for any help you can provide.

John
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