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Dear FreeSurfer Developers,

We are doing research on cortical changes after radiation therapy to the brain. We are trying to compare the thickness of the cortex at the beginning of the radiation (T0) and after one year of treatment (T1). Subsequently, we would like to correlate the thickness change to the dose given to the specific brain areas.

We ran the ‘recon-all’ commands for longitudinal data. All the commands executed without errors according to the log file.

“recon-all -all -i IM1.DCM -s Subj001_MR1”

“recon-all -all -i IM1.DCM -s Subj001_MR2”

“recon-all -base Subj001 -tp Subj001_MR1 -tp Subj001_MR2 –all”

“recon-all -long Subj001_MR1 Subj001 –all”

“recon-all -long Subj001_MR2 Subj001 –all”

We could find cortical changes and load them into qdec. However, the problem now is that we want to correlate the dose distribution to these thickness changes. We encounter the next issues:

How to insert the dose files (DICOM-format) into FreeSurfer/qdec to make it part of the analysis?

We have searched for instructions, both in the archives and in the tutorials, how to import the dose files into FreeSurfer but we cannot find any documentation. Does anybody have experience with loading dose-files into FreeSurfer software?

How to execute statistical analysis within a subject? In this case, correlate thickness changes and dose distribution from one patient?

In the tutorials and the archives we couldn’t find any within-subject analysis. Nevertheless, in the paper ‘Dose-Dependent Cortical Thinning After Partial Brain Irradiation in High-Grade Glioma’ of Karunamuni et al. (2016) (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4747044/) this type of analysis is done, so we know it is possible. We already contacted the authors of this paper but they do not respond.

The version of Freesurfer we are using is: Freesurfer-Darwin-OSX-stable-pub-v6.0.0-2beb96c on a macOS Mojave operating system.

Thank you very much in advance, it would be of great help if you could advise us regarding this experiment.

We are looking forward to your response.

Kind regards,

Janneke Janssens and Piotr Andrzejewski

E: janneke.janssens@medaustron.at

T: +43 2622 26 100 660