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Juan Eugenio Iglesias

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Hola Eugenio,

I first tried > mri_easyreg --ref ima1.nii.gz --flo ima2.nii.gz

Answer > Error : Reference segmentation must be provided

Comment > Warning : TF-TRT Warning: Could not find TensorRT

Then I ran mri_synthseg > mri_synthseg --i ima1.nii.gz --o ima1_synthseg.nii.gz -- vol ROIs.csv --qc QC.csv --post postprob.nii.gz --parc (same for ima2)

I've got lots of cortical ROis, seen in ROIs.csv

Finally, I tried again > mri_easyreg --ref ima1.nii.gz --flo ima2.nii.gz --ref_seg ima1_synthseg.nii.gz --flo_seg ima2_synthseg.nii.gz --ref_reg ima1-reg.nii.gz --flo_reg ima2-reg.nii.gz --fwd_field FWF.nii.gz --bak_field BWF.nii?gz

And I get >

Segmentation of reference image already exists; reading from disk

Segmentation of floating image already exists; reading from disk

Error: no cortical labels found; does the segmentation include cortical parcels?

Thanx !

Eric

Dear Eric,

Thanks for the interest in our tool!

Can you please send us the exact command line that you used, and the full output of  mri_easyreg?

Cheers,

/Eugenio

 

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Juan Eugenio Iglesias

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From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Eric BARDINET <eric.bardinet@upmc.fr>
Date: Tuesday, August 22, 2023 at 04:57
To: freesurfer@nmr.mgh.harvard.edu <freesurfer@nmr.mgh.harvard.edu>
Subject: [Freesurfer] Easyreg > cortical parcels missing after SynthSeg with --parc option ?

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Hello Freesurfer Developpers,

I attempted to run mri_easyreg (Freesurfer 7.4) between two MP2RAGE UNI
images (acquired on a SIEMENS PRISMA 3T).

First, I did not include segmentations, as I understood that EasyReg
would run it for me.

But it didn't. I don't know why.

Then I first ran mri_synthseg with the --parc option on the two images.

I checked the results, and saw cortical labels on both hemispheres.

But when I ran again mri-easyreg adding these images (--ref_seg
--flo_reg), I get again the > no cortical parcels.

What did I do wong?

Any hints?

Thanks in advance for your help.

Best,

Eric




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