External Email - Use Caution Awesome! Whatever is easiest for you 😉
-- Juan Eugenio Iglesias http://secure-web.cisco.com/1DRP30tSXMppp0KyzN8sBiVb_rbxRjFPmjNRpJ3ep6UGsmPgdFdL1PHpTB2HiZikT7mhDnrOSuMMNSyfWBC9ExkKF0npewjTGTJgEMsFLawYntgwWgMNuZX9F5v8wQsflOvhLxItA2W7jYwGI8Cq2vXFN4aiKieIWckGqFLsw8C0LJXSmsoAoKcQtCUEb549gkPIJD-OI9wJ_b9xR4nL2-29eow6o6Uz_ZrSOtwJGbb8aoGTToKo_15rmCrhx2wKl/http%3A%2F%2Fwww.jeiglesias.com From: Eric BARDINET <eric.bardi...@upmc.fr> Date: Thursday, August 24, 2023 at 11:53 AM To: Iglesias Gonzalez, Juan E. <jiglesiasgonza...@mgh.harvard.edu>, Freesurfer support list <freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] Easyreg > cortical parcels missing after SynthSeg with --parc option ? External Email - Use Caution Thanx ! It's running. How would you me to share the images with you? Best, Eric Le 23/08/2023 à 19:38, Iglesias Gonzalez, Juan E. a écrit : Got it! So: if you delete ima1_synthseg.nii.gz and ima2_synthseg.nii.gz, and then run the full command: 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 Then you should be fine. To be totally honest, I don’t understand why the combination of SynthSeg and EasyReg didn’t work. If you can share ima1.nii.gz and ima1_synthseg.nii.gz for me to take a look, that would be great. Greetings from Boston, /Eugenio -- Juan Eugenio Iglesias http://secure-web.cisco.com/1DRP30tSXMppp0KyzN8sBiVb_rbxRjFPmjNRpJ3ep6UGsmPgdFdL1PHpTB2HiZikT7mhDnrOSuMMNSyfWBC9ExkKF0npewjTGTJgEMsFLawYntgwWgMNuZX9F5v8wQsflOvhLxItA2W7jYwGI8Cq2vXFN4aiKieIWckGqFLsw8C0LJXSmsoAoKcQtCUEb549gkPIJD-OI9wJ_b9xR4nL2-29eow6o6Uz_ZrSOtwJGbb8aoGTToKo_15rmCrhx2wKl/http%3A%2F%2Fwww.jeiglesias.com<http://secure-web.cisco.com/18yHoTEILKnGtnBUCnNuKSYHRs2ij8OcPZlkLbaJ8Jvabvv4qO0cXQs-X_p7fXWZijTJCoL78kwHeSYlCoiwBwQTzhzK3uWdrj8F_cPOR5L59UoW5OaCx4ZtGjuoF0J87-hS7-IlMnyXAaxXl0tuMMdyWb4BG62cnyxVZ-97oO2NfTalDs6LAoE74sJhYsnQJbc4pdYn3i9XgXTbOJ8dThsUv7OBmFcp4Xyw5t_0maEDxYVIITGncLetpaNSYc18HpDtIT1tyCuAgOt_CfUUPmR-oVh5pfVE-SVELHhPVTx8PcN-pvJyBQoZBIbhOrTR0Rp3lt7e84EGGi9ChUnYYRA/http%3A%2F%2Fwww.jeiglesias.com> From: Eric BARDINET <eric.bardi...@upmc.fr><mailto:eric.bardi...@upmc.fr> Date: Wednesday, August 23, 2023 at 9:32 AM To: Iglesias Gonzalez, Juan E. <jiglesiasgonza...@mgh.harvard.edu><mailto:jiglesiasgonza...@mgh.harvard.edu>, Freesurfer support list <freesurfer@nmr.mgh.harvard.edu><mailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] Easyreg > cortical parcels missing after SynthSeg with --parc option ? External Email - Use Caution 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/1DRP30tSXMppp0KyzN8sBiVb_rbxRjFPmjNRpJ3ep6UGsmPgdFdL1PHpTB2HiZikT7mhDnrOSuMMNSyfWBC9ExkKF0npewjTGTJgEMsFLawYntgwWgMNuZX9F5v8wQsflOvhLxItA2W7jYwGI8Cq2vXFN4aiKieIWckGqFLsw8C0LJXSmsoAoKcQtCUEb549gkPIJD-OI9wJ_b9xR4nL2-29eow6o6Uz_ZrSOtwJGbb8aoGTToKo_15rmCrhx2wKl/http%3A%2F%2Fwww.jeiglesias.com<http://secure-web.cisco.com/1ssKgYjMYxrJv9Hj0FBi9rYzfz-tXASGLFLvLu3SfnKSfzvcDMiy5Bb3rHvOyzM2D7QrvQ1LbHRunFMbk_ZNoVqpqhDiHIfcjhWbAY9Yoepmffm9nHMJIlvM0RmnR2qsv1znV8XlOEwzE5buZQcbjwIt3GnV3NkaezGIf7U3PMWiKBvPxytY6Uq-mYkBZgQVVoMRyZvkJaZbLUNshEQ3L-tqSlvyE7xWWs95J00i2zzAit0oKmDvGaQvNFfXv6EIXFsaPV0eQsx68PhMDbqHCLUHNsjLx2UBBTNqYmW8xBQ6ZqLDSxG8CNxl-Zg7KCWbB1FpjsNUJGBgUlhgX7J69cw/http%3A%2F%2Fwww.jeiglesias.com> From: freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu> <freesurfer-boun...@nmr.mgh.harvard.edu><mailto:freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Eric BARDINET <eric.bardi...@upmc.fr><mailto:eric.bardi...@upmc.fr> Date: Tuesday, August 22, 2023 at 04:57 To: freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu> <freesurfer@nmr.mgh.harvard.edu><mailto: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. 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