On 5/31/2020 8:48 AM, Elizabeth Haris wrote:
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Hi Eugenio,
Just to double check I understand:
- If I run segmentHA_T1.sh on the output from recon-all, then the output from segmentHA_T1.sh is also in fsaverage space (not native space)?
None of the output is in fsaverage space
- If this is correct, then can I just warp this segmentation (from fsaverage space to MNI152 space) using mri_cvs_register?
i.How would I specify that mri_cvs_register should run on the registration given by cvs for each subject (in the flagged arguments it only shows how to specify registration to MNI152 space)?
OR
- Did you mean that I can specify segmentHA_T1.sh to run in native space (I couldn’t find anything on how to do this) and then warp this native segmentation to MNI152 space?
It always runs in native space. You can use CVS to warp ti to MNI space with mri_convert lh.hippoAmygLabels-T1.v21.CA.FSvoxelSpace.mgz final_CVSmorph_tocvs_avg35_inMNI152.m3z output-in-mni152.mgz
Many thanks for the help and clarification,
Elizabeth
*From: *freesurfer-bounces@nmr.mgh.harvard.edu on behalf of "Iglesias Gonzalez, Juan E." JIGLESIASGONZALEZ@mgh.harvard.edu *Reply to: *Freesurfer support list freesurfer@nmr.mgh.harvard.edu *Date: *Thursday, 28 May 2020 at 10:20 pm *To: *Freesurfer support list freesurfer@nmr.mgh.harvard.edu *Subject: *Re: [Freesurfer] Running amygdala segmentation on a warped brain (fsaverage-to-MNI152)
Hi Elizabeth,
segment_T1.sh uses a bunch of files in native space for initialization that you’d also have to deform, if you wanted to run it in MNI space.
I think the easiest would be to run it in native space, and then warp the segmentation to MNI, using e.g., the registration given by CVS.
Cheers,
/Eugenio
Juan Eugenio Iglesias
Senior research fellow
CMIC (UCL), MGH (HMS) and CSAIL (MIT)
*From: *freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Elizabeth Haris e.haris@unsw.edu.au *Reply-To: *Freesurfer support list freesurfer@nmr.mgh.harvard.edu *Date: *Wednesday, May 27, 2020 at 23:11 *To: *"freesurfer@nmr.mgh.harvard.edu" freesurfer@nmr.mgh.harvard.edu *Subject: *[Freesurfer] Running amygdala segmentation on a warped brain (fsaverage-to-MNI152)
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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:
- 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?
- 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.
- 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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