Jenifer,

Hi, you can do this:

recon-all -qcache -measure your_measure

where you replace 'your_measure' with the name of the measure, for instance:

recon-all -qcache -measure lgi_pial

normally the -qcache function defaults to a set of known measures (thickness, curv, area, etc.), but if the -measure flag is added, then it just uses whatever is specified as the arg. you can only specify one measure. there is also a -fwhm flag and -average flag to override those params if you dont like the defaults (see -qcache help section in recon- all -help).

Then, to add this new measure to the drop-down menu on the Design tab of qdec, add this to your .Qdecrc file:

MEASURE1 = lgi_pial

you can add more custom measures like this:

MEASURE2 = thickness_new MEASURE3 = jacobian_new

Nick

On Mon, 2009-02-09 at 12:44 -0600, Juranek, Jenifer wrote:

Hi,

Running FSv4.2.0 on RHEL4.

I’d like to add a variable such as lgi to qdec analyses. I created a .Qdecrc and .fsgd file, ran the lgi files through mris_preproc & mri_surf2surf (following instructions for Uncached Data posted under Group Analysis of the FsTutorial). While the output of mri_glmfit displays nicely in tksurfer, I’d like to look at the data within qdec (where scatter plots are easily viewed). The error I receive within qdec is as follows:

<1st subject in fsgd file>/surf/?h.<var_name>.fwhm<smoothing factor>.fsaverage.mgh does not exist

Is there an easy (e.g. scripted) way to generate the files within each subjects’ /surf dir for a new variable not already recognized by the - qcache script for use by qdec?

Many Thanks for any suggestions/solutions,

Jenifer

---

Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer