Hi Marie:

Thanks so much. I used your command and got the average LGI values for each region for each subject. However when ran the second script, I get the following message:

csh::alanf@cerebro [/media/Alan_WORK/WORK/De_LISI_Final/LGI_HSF] : aparcstats2table --subjects HM0403 /HM0503 /HM0603 /HM0703 /HM0903 /HM1003 /HM1103 /HM1203 /HM1303 /HM1403 /HM1703 /HM1903 /HM2003 /HM2103 /HM2203 /HM2303 /HM2403 /HM2503 /HM2803 /HM2903 /HM3003 /HM3103 /HM3203 /HM3303 /HM3403 /HM3603 /HM3703 /HM3903 /HM4003 /HM4203 /HM4303 /HM4403 /HM4503 /HM4603 /HM4703 /HM4803 /HM4903 /HM5103 /HM5203 /HM5303 /HM5403 /HM5503 /HM5603 /HM5703 /HM5903 /HM6003 /HM6103 /HM6203 /HM6303 /HM6403 /HM6503 /HM6603 /HM6703 /HM6803 /HM6903 /HM7003 /HM7103 /HM7203 /HM7303 /HM7403 /HM7503 /HM7603 /HM7703 /HM7903 /HM8003 /HM8103 /HM8203 /HM8303 /HM8403 /HM8503 /HM8603 /HM8703 /HM8803 /HM8903 /HM9003 --hemi lh --meas thickness --parc aparc_lgi --tablefile aparc_lgi_lh.txt

SUBJECTS_DIR : /media/Alan_WORK/WORK/De_LISI_Final/LGI_HSF/
Parsing the .stats files
Traceback (most recent call last):
  File "/usr/local/freesurfer/stable5_0_0//bin/aparcstats2table", line 321, in <module>
    parc_measure_map = parsed.parse(options.meas)
  File "/autofs/cluster/freesurfer/centos4.0_x86_64/stable5_0_0/bin/fsutils.py", line 189, in parse
    val = float(strlist[self.measure_column_map[measure]])
ValueError: invalid literal for float(): ThickAvg

Am I doing something wrong?

Thanks again,

Alan


On Tue, Sep 3, 2013 at 5:11 PM, Marie Schaer <Marie.Schaer@unige.ch> wrote:

Hi Alan,

lGI is different from the folding index. lGI is not yet extracted automatically in the different regions, because it's more meant to be use at the vertexwise level. But you can easily obtain the lGI values averaged over the Desikan's ROI using the following command:

mris_anatomical_stats -a SUBJ/label/?h.aparc.annot -t SUBJ/surf/?h.pial_lgi -f SUBJ/stats/lh.aparc_lgi.stats SUBJ ?h

Please note than then you will get the average lGI values for each region for each subject under the thickness column, and that the volume in this same text file will not mean anything relevant anymore.

Then you can go for:

aparcstats2table --subjects ALL_YOUR_SUBJECTS --hemi ?h --meas thickness --parc aparc_lgi --tablefile aparc_lgi_?h.txt


Let me know if you have difficulties,

Marie


On Sep 3, 2013, at 1:53 PM, Alan Francis <alandarkenergy@gmail.com>
 wrote:

> Hi Marie et al,
>
> I have run recon all on the data and calculated LGI for all the brains in my dataset. How does one go about extracting LGI values for each region (eg left Pars Triangularis). Is the Folding index given in the aparc stats sheet the same as LGI?
>
> thanks so much,
>
> Alan