Thanks a lot help, Marie.
Indeed the -t switch worked.
Now, the lh.aparc.stats (thickness) and my generated lh.lgi.stats (lGI) differ in the columns 4,5,6, which correspond to GrayVol, AverageThk, and StdevThk. Could you please help me to understand these values?
1. Why is the GM volume different in the two files (column 4)?
2. Is the average lGI in the column 5?
3. My impression is that the lGI is a property of an area, e.i. of the lateraloccipital cortex, so I would expect to get only a single value for the area.
Thanks a lot in advance,
Martin
On Friday 09 May 2008 10:53:13 Marie Schaer wrote:
Martin,
Try instead the option -t pial_lgi as follows:
mris_anatomical_stats -mgz -f lh.lgi.stats -b -a ../label/lh.aparc.annot -c ../label/ lgi.annot.ctab -t pial_lgi $SUBJECT lh
Otherwise it will read lh.pial_lgi as a surface file, whereas it is indeed a thickness / curv file
Have a nice day,
Marie
On 9 mai 08, at 10:29, Martin Kavec wrote:
Thanks for responce, Dough.
I've looked at recon-all as you suggested, and came up with the following commandline:
mris_anatomical_stats -mgz -f lh.lgi.stats -b -a ../label/lh.aparc.annot -c ../label/lgi.annot.ctab $SUBJECT lh pial_lgi
This, however yields segfault:
INFO: assuming MGZ format for volumes. computing statistics for each annotation in ../label/lh.aparc.annot. reading volume $SUBJECT/mri/wm.mgz... reading input surface $SUBJECT/surf/lh.pial_lgi... Segmentation fault
I'm wondering whether this could be related to the fact that mris_anatomical_stats, calculates mean and stdev on the per-vertex basis over the defined label, while here we want it to calculate LGI, which is not calculated in this manner.
Thanks,
Martin
On Thursday 08 May 2008 18:32:28 Doug Greve wrote:
use mris_anatomical_stats. Look in recon-all to see how to invoke it. You can create another stats file (can't add it to the one that is already there).
doug
Martin Kavec wrote:
Hi,
is it possible to obtain LGI values of cortices, similarly as curvature indices in ?h.aparc.stats? Could this value possibly be included in the ?h.aparc.stats files?
Thanks in advance,
Martin
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