Hi Linette,

just noticed that this slipped through.

-qcache from cross cannot be used.

The preproc command is fine, but qcache does more (which you may not need). With qcache it smoothes at different levels, so that you can select the smoothing level later. The preproc command below only smoothes at 10 fwhm. Sometimes you may need more (like 15).

Best, Martin

On 08/18/2016 02:20 PM, Linette Savage wrote:

Hello Freesurfers,

My ultimate goal is a MLE analysis of 2 groups (n~25) at 2 time points.

I have followed the longitudinal processing stream (cross, base, long) although only ran -qcache at the cross stage. Do I need to add this flag to the base and/or long recon-all command? Or is the same thing achieved by running this code (described in the LME wiki page under Preparing your data):

mris_preproc --qdec-long long.qdec.table.dat --target fsaverage --hemi lh --meas thickness --out lh.thickness.stack.mgh mri_surf2surf --hemi lh --s fsaverage --sval lh.thickness.stack.mgh --tval lh.thickness.stack.fwhm10.mgh --fwhm-trg 10 --cortex --noreshape

I'm using Freesurferv5.3.0 on OS X El Capitan although about to move to a Linux system.

Thanks kindly,

Linette Savage

University of Calgary

Brain Training Study

www.braintrainingstudy.ca http://www.braintrainingstudy.ca

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