External Email - Use Caution Dear Experts,
I am working with FreeSurfer infant_recon_all and I need to correct the pial surface for most of the analyzed subjects. I would like to implement this correction by fixing the intensity normalization using control points, as well as for the adult subjects with tkmedit, but I can not understand if it is then possible to re-run the infant_recon_all pipeline (or how) after the cp definition, since it seems to me that it does not exist the possibility to add -autorecon2-cp and -autorecon3 flags to infant_recon_all, like with the pipeline for adults. So, I am asking if you have some suggestion to do that. I have already tried to normalize the intensity with flag --intnormFSL, specific for infant_recon_all. The result is better but not the best. Is there any other possibility? For example: - to launch mri_nu_correct.mni --i $infile --o $nufile Then, should I add the --masked flag at the infant_recon_all command by passing $nufile as input? Which is the difference between this one and the --intnormFSL option? - Is there something similar to the adult -autorecon2-cp also for infants? - Do you think that the application of AntsN4BiasFieldCorrectionFs is a good idea? And what about the possibility of applying newborn FLAIR sequence to the Bias Field corrected images? - Could it be better to create my own atlas and to use that to obtain a better segmentation? Thank you very much for any kind suggestion. Best Regards, Laura Mazzocchi --- La ricerca neurologica ha bisogno anche di te SOSTIENI LA FONDAZIONE MONDINO CON IL TUO 5 X MILLE http://secure-web.cisco.com/1OcBqU8Yy68wxtJrh1xuYaYanoYCq1G_wyTWR4VlJonLrJ1DIA8MfYXcTCbwJ8F7Rw12vz9YfnRQdQNSfEq3aZIzMUd-d_gNvL-GztvV0MFcxklHxOpvbpqihjXkl5wZxl_-Isr1k7xY6NIV0X5lx1US__Nr8ZnoE0DdYHmC5HeMqcxUhcxK-82i67WPr9Fm6-O4rqYa7G7yMYgm1EM71pAQn2tImIe2jWZKBFm9fcbiODUgQdyC-cNvvIDE9L8jLc-pxhaTntpDFgg0MgBP8QMGkhcu7EUezmgaSLTdpEgHlwT9Guyy69WV7dJC1WmKoKAm9PJToLnRxSrULeumcnA/http%3A%2F%2Fwww.mondino.it%2Fistituto-neurologico-casimiro-mondino-pavia%2Fcome-sostenerci%2F _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer 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://www.massgeneralbrigham.org/complianceline <https://www.massgeneralbrigham.org/complianceline> . 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.
