[caret-users] Distorted COMPMEDWALL

donna at brainvis.wustl.edu donna at brainvis.wustl.edu
Wed Feb 19 11:51:02 CST 2014


I've looked at this some more, because it was bugging me.  More thoughts:

* The volume headers are incomplete, as though they are old-fashioned
Analyze volumes, rather than NIFTI.  AFNI's 3dinfo remarks:

*+ WARNING: Assuming ANALYZE orientaion is LPI.
++    To change orientation or silence this message,
++    Set AFNI_ANALYZE_ORIENT to the proper orientation
++    in your .afnirc file.
++      e.g.: AFNI_ANALYZE_ORIENT = LPI
*+ WARNING: Assuming view is +orig.
++    To change view or silence this message,
++    Set AFNI_ANALYZE_VIEW to the proper view
++    in your .afnirc file.
++      e.g.: AFNI_ANALYZE_VIEW = orig
*+ WARNING: No ANALYZE origin found in file B_T2_Rhem_noStemBulb255.hdr

* That said, the volume and surface *orientation* seem to be in sync; the
scale, however, is not.  See attached capture.

* Comparing your image to online ferret images, I think the orientation
may be okay, but the hemisphere appears rotated left ear downward
somewhat, which might create problems like this.

* A much bigger problem, is that your so-called left hemisphere is on the
right, which could definitely explain your CMW problems, not to mention
why my medial view looks lateral to me.

Caret needs left to be on left, right on right.  The surface can be
x-flipped with an affine transform (command line or GUI), but the image
needs flipping, too, if they shall align.

It's making more sense now.  Sorry I didn't notice this before.

> There were two problems in the previous email, one of which appears not to
> be sorted:
>
> * hole in what looked like the medial wall, but which caret thought was
> ventral view
> * surface does not appear to be in LPI orientation
>
> Until the surface is in the right orientation, this isn't going to work.
> The medial wall won't be where caret expects it to be.
>
>
> On Feb 18, 2014, at 8:26 PM, Ahmad Khan <110ahmadkhan at gmail.com> wrote:
>
>> Hi Donna,
>>
>> Thanks for the help. That problem has been sorted out, but now the
>> COMPMEDWALL orientation is like the figure
>> given below (front view and back view) . Please help!
>>
>> With Best Regards
>> Ahmad
>>
>> <image.png><image.png>
>>
>>  Ahmad Raza Khan
>> (Postdoctoral fellow)
>> Advanced Imaging Research Center (AIRC),Division of Neuroscience
>> Oregon National Primate Research Center (ONPRC)
>> Oregon Health and Science University (OSHU),Portland
>> Oregon- 97006
>> Ph no.    503-614-3755
>> Mob No.-503-799-7204
>>
>>
>> On Thu, Feb 13, 2014 at 9:02 AM, Donna Dierker
>> <donna at brainvis.wustl.edu> wrote:
>> Hi Ahmad,
>>
>> Even if your anatomical volume is in LPI orientation, I don't think your
>> surface is.  Does the segmentation volume used to generate that surface
>> align properly with the anatomical volume (T1/T2)?
>>
>> The attached capture shows what I see when I set your fiducial surface
>> to medial view (ferret_medial.jpg).  It doesn't look medial to me.
>>
>> But the source of your compressed medial wall woes is the hole shown in
>> the ventral view (ventral_hole.jpg).  I'm not sure this really is
>> ventral; I suspect it might be the real medial view, but it is closer to
>> what you see when you press the V button on the toolbar.  The fact that
>> the subcortical stuff isn't filled in the segmentation used to generate
>> the surface means your surface is more topologically equivalent to a
>> sheet than a sphere, and Caret needs the latter to do its
>> CMW/registration thing.
>>
>> So can you fill the subcortical stuff and regenerate the surface, so
>> it's more sphere-like?
>>
>> Donna
>> <ferret_medial.jpg>
>> <ventral_hole.jpg>
>>
>>
>>
>> On Feb 12, 2014, at 4:54 PM, Ahmad Khan <110ahmadkhan at gmail.com> wrote:
>>
>>> Hi Donna,
>>>
>>> I have uploaded the file as zip file name Data_Ferret.
>>> Thanks for your timely help.
>>>
>>> With Regards
>>> Ahmad
>>>  Ahmad Raza Khan
>>> (Postdoctoral fellow)
>>> Advanced Imaging Research Center (AIRC),Division of Neuroscience
>>> Oregon National Primate Research Center (ONPRC)
>>> Oregon Health and Science University (OSHU),Portland
>>> Oregon- 97006
>>> Ph no.    503-614-3755
>>> Mob No.-503-799-7204
>>>
>>>
>>> On Wed, Feb 12, 2014 at 6:41 AM, Donna Dierker
>>> <donna at brainvis.wustl.edu> wrote:
>>> Can you trim your working directory down to a gigabyte zipped and
>>> upload it here:
>>>
>>> http://pulvinar.wustl.edu/cgi-bin/upload.cgi
>>>
>>> The only other thing that comes to mind is that maybe your mesh density
>>> is so high that inflation isn't taking out enough folds for the
>>> projection to sphere / compressed medial wall thing to happen properly.
>>>
>>> Looking at the data seems like the most efficient way to troubleshoot.
>>>
>>>
>>> On Feb 11, 2014, at 6:19 PM, Ahmad Khan <110ahmadkhan at gmail.com> wrote:
>>>
>>> > Hi,
>>> >
>>> > I am still getting the same problem and the orientation is
>>> > x axis: increases left to right
>>> > y axis: increases posterior to anterior
>>> > z axis: increases inferior to superior.
>>> > Surface don't have any topological defects or other defects.
>>> >
>>> > Please help!
>>> >
>>> >
>>> > <image.png>
>>> >
>>> >  Ahmad Raza Khan
>>> > (Postdoctoral fellow)
>>> > Advanced Imaging Research Center (AIRC),Division of Neuroscience
>>> > Oregon National Primate Research Center (ONPRC)
>>> > Oregon Health and Science University (OSHU),Portland
>>> > Oregon- 97006
>>> > Ph no.    503-614-3755
>>> > Mob No.-503-799-7204
>>> >
>>> >
>>> > On Thu, Jan 16, 2014 at 5:42 PM, Donna Dierker
>>> <donna.dierker at sbcglobal.net> wrote:
>>> > When I see something like that, I wonder if your fiducial surface was
>>> in the right orientation:
>>> >
>>> > x axis: increases left to right
>>> > y axis: increases posterior to anterior
>>> > z axis: increases inferior to superior
>>> >
>>> >
>>> > On Jan 16, 2014, at 6:45 PM, Ahmad Khan <khaah at ohsu.edu> wrote:
>>> >
>>> > > Hi,
>>> > >
>>> > > I am  wondering that despite of having good fiducial surface , when
>>> I try to make inflated and ellipsoidal surface from fiducial.
>>> > > I get this type of COMPMEDWAL surface. Please help me in this
>>> regard.
>>> > >
>>> > >
>>> > > Thanks
>>> > > Ahmad
>>> > >
>>> > > <image003.png>
>>> > > _______________________________________________
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>>> >
>>> >
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