Hi Melly,
You can use aparcstats2table from the file you created:
aparcstats2table --subjects …. --hemi lh --meas thickness --parc aparc_lgi --t summary_lgi.txt
Here you'll read the column "thickness" in the lh.aparc_lgi.stats file that you have created with mri_anatomical_stats (i.e. corresponding to lGI in this case, and not thickness). The name of the file can change, but has to start with ?h. for the hemi, and ends with .stats
Best,
Marie
On Aug 11, 2014, at 3:31 PM, melinda dora <mellydora@outlook.commailto:mellydora@outlook.com> wrote:
hi thank you marie. Ive tried this but it doesnt give me one single spreadsheet for the value of each subjects lgi, just produces a file in each subjects stats directory. How do I make a spreadsheet with everybody's lgi values in it?
Kind Wishes,
Melly
________________________________ From: Marie.Schaer@unige.chmailto:Marie.Schaer@unige.ch To: freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu; mellydora@outlook.commailto:mellydora@outlook.com Subject: Re: [Freesurfer] lobes gyrification Date: Mon, 21 Jul 2014 18:36:23 +0000
Hi Melly,
The LGI has the same format as the thickness files, so you can extract them using mris_anatomical_stats (providing you have your own annotation). The command will look something like:
mris_anatomical_stats -a $SUBJ/label/YOUR_ANNOT -t $SUBJ/surf/?h.pial_lgi -f $SUBJ/stats/OUTPUT_FILE $SUBJ ?h
Hope it helps,
Marie
On Jul 19, 2014, at 7:29 AM, melinda dora <mellydora@outlook.commailto:mellydora@outlook.com> wrote:
Dear freesurfer group, is there a command to extract lobar gyrification values for each subject? If so please what are the steps? if Ive already created the lobar annotation labels, can I extract gyrifaction with these if I have already passed the gyrification command?
Best,
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