On 5/27/2020 11:10 PM, Elizabeth Haris wrote:

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Hi guys,

 

I’m wanting to run segmentHA_T1.sh on an MNI152 registered brain. On my subject, I have run recon-all, then run mri_cvs_register to obtain a brain image registered in MNI152 space. My questions are:

 

  1. In recon-all, is there a way to specify registration to MNI152 space, or is it necessary to first run recon-all and then to run mri_cvs_register?
Yes, you must run recon-all first.

  1. Is it possible to run the segmentHA script on the brain registered in MNI152 space? I’m unable to find where I would specify the use the cvs/norm.mgz (instead of the mri/norm.mgz file). And from what I can see in the script, the parameters set in lines 179/180/181 (below) point to fsaverage brain files, which don’t appear to be the correct targets for the new MNI152 brain; however, there are no corresponding output files in the cvs folder, so I am unsure how to define these parameters.
Eugenio can answer better, but I think this will be hard. You'd have to make a "fake" subject using CVS to resample all the volumes segmentHA needs to do the segmentation. I think it would probably be a mess.
  1. Is there anything I have missed and would also need to do to run the segmentHA script on an MNI152 brain? (I have previously run the script on the average brain and all went well.)

 

179         set ATLASMESH="$FREESURFER_HOME/average/HippoSF/atlas/AtlasMesh.gz";

180         set ATLASDUMP="$FREESURFER_HOME/average/HippoSF/atlas/AtlasDump.mgz";

181         set LUT="$FREESURFER_HOME/average/HippoSF/atlas/compressionLookupTable.txt";

 

Thanks in advance,

 

Elizabeth


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