[Freesurfer] Re: Individual pre- and post-values for cortical thickness after a paired analysis

Yes, you can run something like mri_segstats --i stack1.mgz --seg ocn.mgz --avgwf  subject.vals1.dat --excludeid 0 --sum sum1.dat where stack1.mgz is the stack of subjects in fsaverage space from time point 1 The output subject.val1.dat will have a row for each subject and a column for each cluster. The value will be the average value from that subject over the voxels in that cluster

On 7/31/2025 9:26 AM, Franziska Mund wrote:

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Dear FreeSurfer Developers,

we have a longitudinal study design with one group and ran a paired analysis in FreeSurfer V6 (as described here: https://surfer.nmr.mgh.harvard.edu/fswiki/PairedAnalysis https://secure-web.cisco.com/1V0gSNyIvhCtX3j8K-mzIp_bu0OnK1ZDZxKlOeenlA2T-l0CCdlEjkvqSe_5KXnd2BsF6h2tMQlWydqH1m8dKAmoCEpn-TbkFaHJWOqGpSYtRU8YvMgQzcP2QDPVw3azcRBFW9C1XlQKk7m8bMYYozP3nmdcvhYw0JYyhHjkoxQOgcnd0zYH4S7XaSVtvWRFD4r_MjbvM8iG-0t0lmqJbYtixgRh3XHMAtobqfTEdgrqNk_fjPSL2M5iEDFemk9Hrlavuirl3qGaFh1WcfeX9q_SI8y8ZY4bIoYk8BnOINqrgvbl8EIJ2YvLhfqSqnz1c6lWT0TuWLUcnXChPRCK_YQ/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FPairedAnalysis). Afterwards we corrected for multiple comparisons (as described here: https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/MultipleComparisonsV6.0 https://secure-web.cisco.com/1kF3xxriMcabTqMwlV5PjrV7Bz3-ihiWEkX08AlNLpslyHgUOXeF8fr5ulAvLPcyf8uMHq8hloj1Y0krgnu9ohcGi3EnBNppfRwRcB9TLq05apD-eGE0K0CzTmSAcVmw2etFiVP5PgwWAwPHUk7JIZrQVUVLi2EUia9T1UWuxO0p9FoioElKpdbAyBIeUJ7NH1O8Ihf4t4SWLnIDfP9Q5N_iL13R5ypa0TFVO14wZu8IhSGemg9TvCJHE2p5ES8a9ByJ1j715uelFLXsf_fr8VmOnWc-UAAujQ7EcU9n-yoDUBI_EAwXM5TAJJX57AVmv5Kmp850i96_x9yuV1H5kxw/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FFsTutorial%2FMultipleComparisonsV6.0).

One cluster showed a significant change for cortical thickness and the average values of each subject were located in the “y.ocn.dat”.

However, we are now wondering how it is possible to get the individual pre- and post-values for that specific cluster for all subjects. Is there any method to do so?

Any assistance is very much appreciated!

Thanks in advance.

Best,

Franziska

*Dr. Franziska Mund *

Wissenschaftliche Mitarbeiterin

Sportmedizinisches Institut

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