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/1dfY0_iI3tMy2KScj5U-Me5vGZu7PR_1i3ceEoMc5Uwe_Pms3qhrrDDD9TDVDy-aIV47NDYjmikqxi2dFDWKvkgdnYUdP2g6Hn7X38CZCZpDfVCWhcjgf-F9QmodgsHUr9ATeuR0BnEC8qusqVX6_pYnL-bETKgyo55qvoQvbg7P1OWv7di1aDcVyGBtmkPall1kmEHyEsJ8MQFXi_rJw1yI6dI2lT85onXJXxNg93w00lXPHA82fy_vOTmPl6C3x3yiiLJO4v-X510SiLEH6ZB09DhzcKShOyWkAQHQLVoSBL4HqVUJdA-oxbEvuXEKo/http%3A%2F%2Fwww.jeiglesias.com
*From: *Eric BARDINET <eric.bardi...@upmc.fr>
*Date: *Wednesday, August 23, 2023 at 9:32 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 *
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/1dfY0_iI3tMy2KScj5U-Me5vGZu7PR_1i3ceEoMc5Uwe_Pms3qhrrDDD9TDVDy-aIV47NDYjmikqxi2dFDWKvkgdnYUdP2g6Hn7X38CZCZpDfVCWhcjgf-F9QmodgsHUr9ATeuR0BnEC8qusqVX6_pYnL-bETKgyo55qvoQvbg7P1OWv7di1aDcVyGBtmkPall1kmEHyEsJ8MQFXi_rJw1yI6dI2lT85onXJXxNg93w00lXPHA82fy_vOTmPl6C3x3yiiLJO4v-X510SiLEH6ZB09DhzcKShOyWkAQHQLVoSBL4HqVUJdA-oxbEvuXEKo/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
<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
<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.
Best,
Eric
_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://secure-web.cisco.com/1G46ROno2_m8rvD052SbQCvaHleHARPsHm09GSGyA2-8Lqo-w82C7mI545CPUfkmm57LgkxnfpbBkQNDiX8dqu2FALvjKbLOWtvZ1eNXIRYpfAiF9XeO1MorDFcfb59BIFk0oT07JPqrmfM7qqMoUzzcmvKAkMaZVUNV7wERDz2HtZF-l9qaHtwe44yLwsm7JWD5YN4_KQtg61nC6AVzOpW-sstMlhazYQPPyRCqrFQNPHsY1PZw_NQ_PrzTMUY-a3z6tAw9xRZBHfTrmOuVYVfNgx85MnGvLPkrdaydTZj-Oo5NhPTmfvtuLwD4VKsYbvWymXQ7-PwnIqLWsDL_9tg/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer
<https://secure-web.cisco.com/1zOiuJCeaTaqdeqpQvbW3s8qBLhbgAiv1xTCC08PbrGXQ_BpPXWhhBNRNrEosrlTtZy_OWGmXS9eRWe6DE07yc7yXjb5XID9OcV8xl5m3Rd9mnN22o2Qj25JpxFZOzS6MveuTtaRrI9MEXmfl24c1nvcRbuADnL2mqr2uTMu8TyagdxfKmJrI9x-uPA84NSVAKXj5kqEI7X6ATKtFYkIw3XZ_5CzZG4UrSaUtUHLG-hk07R3VCtLty4Ys949NycFgFDfsCmL7iRhlIjSmBX2ndszeTVD0NHnApJzq_1tDrLmD_dudCY7QkIpnN_CNm_9NKn_9x5ce3zjfQ_AsJpwmaQ/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer>
The information in this e-mail is intended only for the person to
whom it is addressed. If you believe this e-mail was sent to you
in error and the e-mail contains patient information, please
contact the Mass General Brigham Compliance HelpLine at
https://secure-web.cisco.com/1xkhqcce3GHUVfCewffcf2iBf0k_UWSwKzE6x8KfUbIzoP5WJ72SH14W3Q04dVoeef6ywJnfmGfv__NDHgTWiXC8SodKtOjeAwusW4RCcjjXrs1KY-Z3KwOWYr-BBX8YOzp_PzMRgpNAKGPXL2xk7WbtO8sTcr7iBsa5_FlxkpGuFWxcBz9iZ_Ey9rmkW6OvXp63TWs2FIgEJgkkrZy9qG1AxN5botUdnht-TDnLVQHjwPJ_rC8eXt_DYgNfa5KnMEhSzcYLehHhsT0T3_xRlHCf0avRNF38RuuxeUyfmlQR65DD-3VbjWqzg11UqKrBLCEEsn8zgRx6uYNRRJ06B2A/https%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline
<https://secure-web.cisco.com/15361bVrpPrFBAJiAssfrOrQqfmr6uE55rAnepcoNdfaghg52h8zNqDKredWWBY6GOtRluR-k80qIBL6qnIkYQiMj_rE_C_6sbZtD_JG0jtozoraRNOn21LklJds2oFehGNIAbflIXw7mr9JVDQHB31v3IEUDIme9Ch9Hi98dj2u0hGJeOJZNBUBFwXPFxL66qrV-_M1QVOvWysK5w48iPwVuL1W593YyCh5YJ01mb_OrOJ7BFGtS_cVS4b3HDaCeYeTFnZkpmfmx2CTi21jbVLsWISb2mgiKzgWZwgVyRVUNiUe_FCUO8PvJJsH5ylF_N8EzL4D1MFqdJUZk0QzAtg/https%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline>
.
Please note that this e-mail is not secure (encrypted). If you do
not wish to continue communication over unencrypted e-mail, please
notify the sender of this message immediately. Continuing to send
or respond to e-mail after receiving this message means you
understand and accept this risk and wish to continue to
communicate over unencrypted e-mail.
The information in this e-mail is intended only for the person to whom
it is addressed. If you believe this e-mail was sent to you in error
and the e-mail contains patient information, please contact the Mass
General Brigham Compliance HelpLine at
https://secure-web.cisco.com/1xkhqcce3GHUVfCewffcf2iBf0k_UWSwKzE6x8KfUbIzoP5WJ72SH14W3Q04dVoeef6ywJnfmGfv__NDHgTWiXC8SodKtOjeAwusW4RCcjjXrs1KY-Z3KwOWYr-BBX8YOzp_PzMRgpNAKGPXL2xk7WbtO8sTcr7iBsa5_FlxkpGuFWxcBz9iZ_Ey9rmkW6OvXp63TWs2FIgEJgkkrZy9qG1AxN5botUdnht-TDnLVQHjwPJ_rC8eXt_DYgNfa5KnMEhSzcYLehHhsT0T3_xRlHCf0avRNF38RuuxeUyfmlQR65DD-3VbjWqzg11UqKrBLCEEsn8zgRx6uYNRRJ06B2A/https%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline .
Please note that this e-mail is not secure (encrypted). If you do not
wish to continue communication over unencrypted e-mail, please notify
the sender of this message immediately. Continuing to send or respond
to e-mail after receiving this message means you understand and accept
this risk and wish to continue to communicate over unencrypted e-mail.
_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Please note that this e-mail is not secure (encrypted). If you do not wish to
continue communication over unencrypted e-mail, please notify the sender of
this message immediately. Continuing to send or respond to e-mail after
receiving this message means you understand and accept this risk and wish to
continue to communicate over unencrypted e-mail.
