try typing:
rehash
then run it again
On Wed, 8 Feb 2017, Clara Kühn wrote:
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" <[email protected]>
An: [email protected]
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" <[email protected]>
An: [email protected]
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" <[email protected]>
An: [email protected]
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
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The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.
