Align ROI to FA map

AFNI Message Board
1

Hi Afni gurus,

I am trying to align an ROI from the IIT atlas V5 to FA maps. Both images were normalized to the IIT_mean_FA map.

I tried 3dresampling the ROI to the FAP maps, but they end up looking like this.

Any suggestions.

Best,
O

Screen Shot 2020-02-19 at 11.29.03 AM.png
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Hi Omar-

We’ll need some more information. Is the FA map in subject space? Standard space? Is it our version of the atlas or someone else’s?

3dresample just changes the grid. You’d want to apply the transform to get things to line up - via 3dAllineate or possibly 3dQwarp or both. But once we have additional info we can help with that.

-Peter

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  • We’ll need some more information. Is the FA map in subject space? Standard space? Is it our version of the atlas or someone else’s?

I ran 3dinfo on them and it says orig, but these images were warped to the IIT template (https://www.nitrc.org/projects/iit/). What I did was run 3drefit -space MNI so I could work with them.

The ROIs come from that same IIT link above.

Let me know if you need anything else.

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Please post all the commands you’ve run written out.

5

Peter Molfese Wrote:

Please post all the commands you’ve run written
out.

I ran auto_warp.py -base IITmean_FA.nii -input sub-control01.ses-01.FA.warped_5mm.resample.rotate.flipped.nii.gz -skull_strip_input no and it seemed like it worked.

Screen Shot 2020-02-20 at 1.07.59 PM.png
Screen Shot 2020-02-20 at 1.07.59 PM.png894×737 118 KB

6

That looks good. As Peter points out, the other commands you mentioned do not do any alignment at all. 3dresample just puts a dataset into another grid. 3drefit only changes the header of the dataset. To move data from one space to another, you have to use an alignment program as you did with auto_warp.py which calls @auto_tlrc and 3dQwarp to do the actual alignment. It also takes care of the resampling and setting the header attributes.