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
<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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