[MINC-users] minctracc and mincresample question

[andrewkrause at ucla.edu]

Hello,

There's a lot of file conversion happening in the original workflow,  
so I thought it might be something like that. We received DICOM files  
from the scanner, converted them to Analyze format, skull-stripped,  
then converted them into MNC and registered with those files.

Here's what mincinfo gives on the skull-stripped version before registration:

image: unsigned short 0 to 65535
image dimensions: zspace yspace xspace
     dimension name         length     step     start
     --------------         ------     ----     -----
     zspace                    256        1         0
     yspace                    224        1         0
     xspace                    192        1         0

and after registration:

image: unsigned short 0 to 65535
image dimensions: yspace zspace xspace
     dimension name         length     step     start
     --------------         ------     ----     -----
     yspace                    230        1      -130
     zspace                    230        1       -92
     xspace                    230        1      -109



Here's mincinfo on the non-skull-stripped version before registration:

image: unsigned short 0 to 65535
image dimensions: zspace yspace xspace
     dimension name         length     step     start
     --------------         ------     ----     -----
     zspace                    256        1         0
     yspace                    224        1         0
     xspace                    192        1         0

and after registration (using the skull-stripped xfm file):

image: unsigned short 0 to 65535
image dimensions: zspace yspace xspace
     dimension name         length     step     start
     --------------         ------     ----     -----
     zspace                    181        1       -72
     yspace                    217        1      -126
     xspace                    181        1       -90


-- Andrew

Quoting Andrew Janke <a.janke at gmail.com>:

> Hi Andrew,
>
>> We've been using minctracc and mincresample to register skull-stripped
>> images as part of our workflow, but we recently found out that registration
>> might work better using the whole image before skullstripping. I was hoping
>> to save some work by registering the images with the skull on using
>> minctracc, and then take the xfm output file from that and apply it to the
>> skull-stripped versions with mincresample. However, when I do that, I end up
>> with blank registered images. Looking at the matrices in the xfm files of
>> the registered with skull on and registered with skull off images, I noticed
>> that the first three columns are fairly similar but the last column is very
>> different. Does anyone have any ideas as to why it's not working? I can post
>> the script I wrote to do this if it helps.
>
> The last column of a xfm matrix can be thought of as linear shifts in
> X, Y and Z. As such,
> my guess is that if you are using BET (via a conversion to NIFTI) to
> skull strip the images the co-ordinates of the stripped image is being
> altered along the way. The last column of a xfm matrix is the
> transformation parameters.
>
> Perhaps can you post the results of mincinfo on both your original and
> skull stripped images?  if they are different then you can do
> something hackish like this:
>
>    $ cp original.mnc final.mnc
>    $ minccopy stripped.mnc final.mnc
>
> To get your original co-ordinates back. This will just copy the data
> from the stripped image into final.mnc leaving the co-ordinate
> information intact.
>
> Thanks
>
>
> a
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