I'm so sorry, I don't know anything about programming... I downloaded it, copied it into my SUBJECTS_DIR as mris_anatomical_stats-doug and tried to run the whole thing again like this:
mris_anatomical_stats-doug -mgz -cortex $SUBJECTS_DIR/ZF1K.base/label/lh.cortex.label -f $SUBJECTS_DIR/ZF1K.base/stats/lh.aparc.pial.stats -b -a $SUBJECTS_DIR/ZF1K.base/label/lh.aparc.annot -c $SUBJECTS_DIR/ZF1K.base/label/aparc.annot.ctab ZF1K.base lh pial
but then I got this error:
bash: mris_anatomical_stats-doug: command not found
----- Ursprüngliche Mail ----- Von: "Douglas N Greve" greve@nmr.mgh.harvard.edu An: freesurfer@nmr.mgh.harvard.edu Gesendet: Mittwoch, 8. Februar 2017 17:08:26 Betreff: Re: [Freesurfer] extract area.pial stats
You don't need to open it. Just download it and put it in your path. You may want to call it something slightly differnt so that you don't confuse it with the v5.3 version
On 02/08/2017 10:53 AM, Clara Kühn wrote:
thanks. What kind of format is it? How do I open it?
Cheers Clara
----- Ursprüngliche Mail ----- Von: "Douglas N Greve" greve@nmr.mgh.harvard.edu An: freesurfer@nmr.mgh.harvard.edu Gesendet: Mittwoch, 8. Februar 2017 16:43:47 Betreff: Re: [Freesurfer] extract area.pial stats
Try this version (same as version 6)
https://gate.nmr.mgh.harvard.edu/safelinks/greve/mris_anatomical_stats
On 02/08/2017 04:55 AM, Clara Kühn wrote:
Hi Doug,
thanks for your reply. I tried it out and attached the lh.aparc.pial.stats file for you to take a look at. As far as I can tell it's still reporting the white surface area. Or am I reading it wrong?
Cheers Clara
----- Ursprüngliche Mail ----- Von: "Douglas Greve" greve@nmr.mgh.harvard.edu An: freesurfer@nmr.mgh.harvard.edu Gesendet: Mittwoch, 8. Februar 2017 00:15:22 Betreff: Re: [Freesurfer] extract area.pial stats
try
cd $SUBJECTS_DIR/subject/surf
mris_anatomical_stats -mgz -cortex ../label/lh.cortex.label -f ../stats/lh.aparc.pial.stats -b -a ../label/lh.aparc.annot -c ../label/aparc.annot.ctab subject lh pial
On 2/7/17 4:48 AM, Clara Kühn wrote:
Dear FreeSurfer experts,
I'm trying to extract a total Pial Surface Area like it is extracted for White Surface Area in the ?h.aparc.stats file. I have tried this command but it doesn't seem to include Pial Surface Area:
mris_anatomical_stats -a $SUBJECTS_DIR/ZF1K.base/label/lh.aparc.annot -f $SUBJECTS_DIR/ZF1K.base/stats/lh.aparc-areapial.stats -b ZF1K.base lh pial
How could I extract the total Pial Surface Area for each participant?
Thank you for you help! Clara _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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