Qcache is a FreeSurfer term meaning to "cache" (or, store) your data to prepare it to be analyzed with QDEC. This flag is intended to speed up later processing and allow for rapid analysis of group data. Since caching your data takes about 5 minutes, the idea was to make pre-cached files ready to be analyzed in QDEC, as opposed to waiting 5 minutes every time you want to run an analysis in QDEC.
The Qcache recon-all flag completes the following:
- resample data onto the average subject (called fsaverage)
- smooth it at a range of FWHM (full-width/half-max) values, usually 0, 5, 10, 15, 20, and 25mm.
The QDEC utility for group analysis requires pre-cached files as an input. These files are created by running mris_preproc, which creates smoothed surface data files sampled to the 'fsaverage' common-space surface. By default, the surface data for thickness, curv, sulc, area and jacobian_white are smoothed at 0, 5, 10, 15, 20, and 25 mm FWHM. If just one set of surface data needs to be processed, then the option -measure <surfmeas> can follow -qcache, where <surfmeas> is one of: thickness, curv, sulc, area, jacobian_white or any surface measure. Multiple instances of -measure <meas> is supported. The -measuredir option allows specifying a directory other than the default of surf. Another option is -fwhm <num> where <num> is a value in mm. Also, -target <name> allows specifying a common-space target other than fsaverage (the default). Qcache is also a target for make, eg. recon-all -make qcache.
Common questions:
If I ran qcache on my data and then made manual edits, do I have to re-run qcache? Yes, but re-running it will only take a few minutes max.
If I ran qcache on my data, how do I assemble my data for group analysis? You would still have to run mris_preproc, but since your data is already smoothed at a range of FWHM values, you do not have to run mri_surf2surf. Your command would look something like the following. Once this is run, you can proceed with mri_glmfit.
mris_preproc --fsgd gender_age.fsgd \ --cache-in thickness.fwhm10.fsaverage \ --target fsaverage \ --hemi lh \ --out lh.gender_age.thickness.10.mgh