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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
Le 23/08/2023 à 02:20, Iglesias Gonzalez, Juan E. a écrit :
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
--
Juan Eugenio Iglesias
http://secure-web.cisco.com/16v5znE1wNC-7_G_i9djkPp5j413iMOQanH6o-5vxU6Z5h0Tj43vnYwvtWwinjQilegf3vRSAdPBdx1FXkznWRmwK01VTN_DyHxJk7mibil4d7INlfDix6V1k5lgngecb10bznHR1p4WGy7ba8v2vj_hamzv7kg1BbKIAAcmFCB_lWx3cvkJ02C7tpNXZn0PQ1wi_DLsQ5DA5WEnk4aglLVmNNPvD_IYZoHcUHQzOf1OBvFKf2iCsEaQM-M2KPQtfwc8dBkph4_K0y4o9tlMJ2wpYi1_jU7YwCS2Pj7ti8Q5eEvEp-WMUZLhTjv3cEdXd/http%3A%2F%2Fwww.jeiglesias.com
*From: *freesurfer-boun...@nmr.mgh.harvard.edu
<freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Eric BARDINET
<eric.bardi...@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 ?
External Email - Use Caution
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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