[caret-users] Some remarks, whishes, questions

[Donna Dierker]

Hi Roland,

See inline replies below for a couple of answers.  John will be in later 
today and probably will know the remaining answers.

Donna

On 11/22/2007 05:31 AM, Roland Marcus Rutschmann wrote:
> Hi again,
>
> while working with the new caret version 5.5 I encountered some new (at least 
> to me) features that I have some questions to.
>
> Preprocessing-question:
> a) When I load a 1x1x1mm T1-nifti image with a q-form that has some angle to 
> it, the voxel-dimensions shown in caret are not 1x1x1 any more but eg 
> 0.96x1.02x0.99. How is the image resample if I use Volume->edit 
> Attributes->resample.
> -is it just a resampling in the 3 major dimensions or is the affine 
> transformation of the q-form used?
> -would you recommend this kind of resampling in this case?
>   
Don't know.  I know AFNI's 3dresample and FSL's flirt are alternatives.
> b) Rescaling-Wish: I use an unbiased T1-image that has a few outliers. What I 
> do now I only use voxels within a lower-upper threshold to rescale. Is there 
> some option within caret to do this? If not, I think it would be nice ;-)
>   

   VOLUME SCALE VOXELS 0 to 255 WITH PERCENTAGE OF MIN/MAX
      caret_command -volume-scale-percent-min-max-255 
         <input-volume-file-name>
         <output-volume-file-name>
         <percent-minimum>
         <percent-maximum>
        
         Scale voxels so that they are in the range 0 to 255 but
         map the first "percent-minimum" voxels to 0 and map the
         last "percent-maximum" voxels to 255.
        
         The "percent-minimum" and "percent-maximum" values should
         range from 0.0 to 100.0.  Setting the "percent-minimum" to
         2.0 and the "percent-maximum" to 3.0 will result in the first
         two percent of voxel values being mapped to zero and the last
         three percent of voxel values being mapped to two hundred
         fifty five.

> c) Remark: I often have a discrepancy of search handles and topology report of 
> the surfaces (both telling me no handles euler=2) on one hand and the 
> volume->segmentation->topology report on the other hand. In the latter I 
> often find euler=1, handles=1
>   
The volume: segmentation: topology report tells the truth, but sometimes 
the handles are so tiny (e.g., two voxels kissing at corners) that you 
can't see them on the inflated surface.  I'm not sure how the surface 
topology report works, but I'm not surprised it sometimes disagrees with 
the volume one.  Another common discrepancy is when Find Handles returns 
nothing in all three slice planes, but the topology error report still 
shows handles.  This is because Find Handles can only find "within 
slice" handles; handles resulting from voxels kissing at corners are not 
detected by Find Handles.

But my motto is to proceed to flattening if I can't see any handles on 
the inflated surface, and Find Handles can't find any, either.
> d) Remark-Question: Segmentation volumes seam to be saved as float32 not 
> gzipped per default. Is there a reason for this?
>   
Possibly because Wash U's "4dfp" format saves volumes this way, and our 
very first guinea pigs when John added volume support were wustl.edu 
users.  If there's a way to specify that segmentation volumes be 
gzipped, I'm unaware of it.
> e) separate brain extraction question: Do you think a brain extraction eg with 
> bet before segmentation is help/harmfull? 
>   
It is most helpful as a preprocessing step to bias correction, which can 
make a huge difference.  Otherwise, its effect is minimal.  Caret 
successfully removes the eye/skull without brain extraction most of the 
time; for the few times it fails, brain extraction may not solve your 
problems, because the eye fat is probably the culprit, and brain 
extraction may miss this, as well.  Most of the time, it shouldn't do 
any harm.  Turn off eye removal if it does.
> Sorry for the many questions but there's so much to explore in your wonderful 
> program.
>
> Regards and Thanks,
>
> Roland
>
>   
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