External Email - Use Caution Hello FreeSurfer Developers,
I have explored a possible solution to my problem which would include coregistering my fifth scan to the template extracted from the first four scans through the function mri_coreg (described at: https://freesurfer.net/fswiki/mri_coreg). Although the function is listed on the website, it comes up as non existent when called. Is it deprecated? Is there a viable alternative which someone has explored? Il 2024-05-24 12:51 Tommaso Cusolito S319624 ha scritto: > External Email - Use Caution > > Hello FreeSurfer Developers, > > I'm attempting to extract cortical thickness from a fifth scan using a > template based on only the first four scans (obtained by following the > longitudinal pipeline available at > https://secure-web.cisco.com/1S7BQNmF9HghVT1XkcD-pYvMmoQDm0WTjg3-N1bP-4anPWQecP6BcEe1Czg5O1f2CwxkS5g6wvBC5ciP3B6fZBjHEArdfmqkQIDI1Gm7n0lLp1tjx4D4zvFYVzpSisw5KdAUrOc5MOZaTWLk0Hb2-gonhx3sqwRsmkWBznF1VYEORhfrW8ssC8QJg1j-KOTVg7occo24GF3AoarScmNgUSRTCutAjK6UGSDw2qbjT0jnd9Tmvg2TkPeAJETtQcmz2aYGEd5Pj7fs45UUqJB22CSonXUlpevMHJJfWtDO2FfuZm8dH-TQjj4u9kz8qeovL/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FLongitudinalProcessing). > Unfortunately, I don't have the option to run the longitudinal > processing from scratch including the fifth scan as I no longer have > access to the cross-sectionally processed single scan data (in format > patient_scan#) for scans 1 through 4 but only to the folders generated > by the recon-all function (in format > patient_scan#.long.patient_template). > I've made sure to generate .lta files (through mri_robust_register) > for forwards and backwards transformations from s5 to template and to > add the scan 5 to the "base-tps" file, but recon-all reports a later > error when using the function mri_fuse_segmentations as I no longer > have access to files for single scans (norm.mgz, > aseg.mgz,aseg.auto_noCCseg.mgz). > I acknowledge that the template data will be biased towards the first > four scans but I was looking for a way to use the function on only > data belonging to the "patient_scan#.long.patient_template" folders > together with the fifth scan data "patient_s5". > > Has anyone tried using this course of action and found a viable > solution? > > I've attached the recon-all.log in case it's of any use. > > 1) FreeSurfer version: > freesurfer-Linux-centos4_x86_64-stable-pub-v5.3.0 > > 2) Platform: 3.10.0-1160.92.1.el7.x86_64 > > 3) uname -a: Linux krusty 3.10.0-1160.92.1.el7.x86_64 #1 SMP Tue Jun > 20 11:48:01 UTC 2023 x86_64 x86_64 x86_64 GNU/Linux > > 4) recon-all.log: see attached > _______________________________________________ > 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. _______________________________________________ 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.
