[Brains-users] Re: [Fwd: Hippocampal Traces on 6 healthy controls.]

[Steve Pieper]

Hi Hans -

That looks great - and much simpler than rolling a new tool to do the 
same thing!

One question:  John said they rotated the images first so they could 
draw their contours along the long axis of the hippocampus.  Do you have 
a way to get the label map back in the original SPGR acquisition space?

Thanks,
Steve



Hans Johnson wrote:

> Steve,
> 
> If I understand your problem correctly, this would also be trivial in
> BRAINS. Just off the top of my head, here is what the code may look like
> in the simplest terms:
> 
> 
> ====================================================================================
> ## This script assumes that you are in the directory with all the roi's
> ##
> proc CreateCodeImageFromROI { DirectoryName } {
>   foreach roiFile [ glob ${DirectoryName}/*.xroi ] {
>     set temproi [ b2 load roi $roiFile ]
>     lappend myMasks [ b2 convert roi to mask $temproi ]
>     #just to keep memory nice and clean, the roi is no longer needed
>     b2 destroy roi $temproi
>   }
> 
>   set myImage [ b2 convert mask-set to code-image $myMasks ]
> #Again just to keep memory nice and clean, the Masks are no longer
>   needed
>   foreach delMask $myMasks {
>      b2 destroy mask $delMask
>   }
>   return $myImage
> }
> 
> set imageToDelete [ CreateCodeImageFromROI
> /raid1/structural/MR/testpat/testscan/10_ACPC/hjohnson ]
> b2 save image $myImage MyOutputCodeImage.hdr strictAnalyze75 data-type=
> unsigned-8bit
> b2 destroy image $imageToDelete
> 
> 
> ====================================================================================
> 
> I have run this script on a set of cerebellar ROI's (a set of coplanar
> contour ROIS). The resulting image is shown in the attached image.
> 
> Hans
> 
> On Jun 03, 2005 09:18 AM, Steve Pieper <pieper at bwh.harvard.edu> wrote:
> 
> 
>>Hi -
>>
>>Yesterday on the engineering tcon Bill Lorensen and Jim Miller said
>>they
>>have code to batch-convert contour ROIs into labelmaps -- this would
>>be
>>great to work on the files that Dartmouth generated with BRAINS.
>>
>>Here's the background info from John West. He also told me that there
>>is a transform file from Brains, but I don't have an example of that
>>--
>>John, can you provide them?
>>
>>I'm cc'ing Hans Johnson from Iowa so he knows what's up... perhaps he 
>>already has a program to do this? If not, maybe he'll want this
>>feature
>>too.
>>
>>Best,
>>Steve
>>
>>
>>
>>-------- Original Message --------
>>Subject: Hippocampal Traces on 6 healthy controls.
>>Date: 3 May 2005 12:37:00 -0400
>>From: John D. West <John.D.West at Dartmouth.EDU>
>>To: "Steve Pieper" <pieper at bwh.harvard.edu>
>>CC: Andrew J. Saykin <Andrew.J.Saykin at Dartmouth.EDU>
>>
>>Hi Steve.
>>
>>I just uploaded the hippocampal traces for our 6 HCs.  You can get to 
>>the data from the Wiki.
>>
>>Couple of things I should mentions. First, the traces were not made on
>>the original SPGR. They were made on an SPGR realigned along the long
>>axis of the hippocampus, and resampled to 1.01562 mm3 isotropic
>>voxels.
>>  We have these resampled images in analyze format if you need them.
>>
>>Second, the point list in the files are x and y pixel coordinates. The
>>.zroi file name itself tells you the z pixel coordinate.  The list of 
>>points in each .zroi file is listed as follows:
>>
>>the first entry is the # of coordinates x1,y1, x2, y2, etc. i.e. if 
>>there are 4 points this number would be 8
>>x1
>>y1
>>x2
>>y2
>>etc.
>>header info which I have anonymized
>>
>>If you need any other info on those files, please let me know.
>>
>>Thanks.
>>-John
>>
> 
> 
> 
> 
> Hans Johnson
> hans-johnson at uiowa.edu
> 
> 
> ------------------------------------------------------------------------
>