Hi William,
you can use freesurfer's pctsurfcon to compute the gray/white contrast on the longitudinal directories. This will produce a surface overlay at: tp.long.base/surf/?h.w-g.pct.mgh
I don't think the long_mris_slopes script can deal with those files directly, so you have two options:
- take a look at that script and run the same commands manually for the w-g.pct.mgh files
- convert the pct.mgh files to thickness format, rename volume to something else, rename the w-g.pct to volume , run long_mris_slopes and rename everything back.
Best, Martin
On Mon, 2019-05-06 at 16:41 -0700, WON JONG CHWA wrote:
External Email - Use CautionDear FreeSurfer experts,
I am currently running a longitudinal analysis in FreeSurfer v5.3 to look at changes in volume and gray/white contrast. I ran all the processing steps and used this command below to look at results for volume:
long_mris_slopes --qdec ./qdec/qdec.table.dat --meas volume --hemi lh --do-label --do-rate --time years --qcache fsaverage --sd $SUBJECTS_DIR
We also would like to look at change in gray-white matter intensity ratio over time (between 2 timepoints) as well, but there is no separate measure defined for it. I was wondering what we can do to calculate this.
Thank you. William _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer