[MINC-users] minctracc and mincresample question

[andrewkrause at ucla.edu]

And of course now I see that somehow the resizing during resampling  
got lost in the many edits to the script, and that might be what's  
causing the problem. Thanks for your help!

-- Andrew

Quoting 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
>> _______________________________________________
>> MINC-users at bic.mni.mcgill.ca
>> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users
>>
>
>
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