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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-4anPWQ...). 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

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