Thank you kindly Martin, saved me a lot of trouble and time starting from scratch!

On Wed, Oct 18, 2017 at 9:45 AM, Martin Reuter mreuter@nmr.mgh.harvard.edu wrote:

Hi Garret,

sure, there is no need to run qcache at all. Assuming you do a thickness analysis, you can directly use mris_preproc to register all thickness maps from only the first time point to fsaverage and smooth them (there you need to pass a list of only the first longidutinal time points: sidtp1.long.base ) . Then you can run mri_glmfit the same way as in any other cross sectional analysis.

Take a look at this page (Uncached Data):

https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis

Usually it is a good idea to separate the mapping and smoothing steps (as described in the tutorial) by splitting into mris_preproc and mris_surf2surf (for smoothing). The reason is that you can later easily smooth at a different smoothing level and avoid a second time-consuming mapping of all the thickness files.

Best, Martin

Am 17.10.2017 um 16:59 schrieb Garret O'Connell:

Hello FreeSurfer experts,

I am trying to do a cross-sectional baseline analysis from the outputs of the longitudinal processing stream, following the advice on a previous question's thread:

https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2016- March/044681.html

From my reading of the issue, I need to run the following command, entering the cross-sectional title folder as the first input.

recon-all -long "subj_crossfolder" "subj_base" -qcache

For this step, i know it is necessary that recon-all knows where the cross folders are located, although from my understanding, it does not actually use data from these folders., instead using the data in the .long folders.

My issue is that I do not have access to the cross folders anymore, and was wondering if there was a work around to do the cross sectional analysis without them?

Thanks for any help! Garret

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