hmmm, not sure why. If this is a problem we can certainly change it, just
let us know
On Thu, 5 Mar 2015, Krieger, Donald N. wrote:
Hi Zack,
It looks like mris_info send that matrix out on the error output rather than
the standard output.
I just tried it and you can get it by redirecting both to your file like
this:
Try mris_info lh.pial >& lh_info.txt
Regards,
Don
Signature0001
Don Krieger, Ph.D.
Department of Neurological Surgery
University of Pittsburgh
From: freesurfer-boun...@nmr.mgh.harvard.edu
[mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Zachary
Greenberg
Sent: Wednesday, March 04, 2015 7:05 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] mris_convert lh.pial to lh.pial.asc coordinate
shift
Thanks bruce. It will work out fine if I can just pull out that c_(ras)
array in a pipelined way to apply it to the ascii data.
I'm struggling a bit to achieve that though. I think because mris_info
outputs the tables of *_(ras) info in a strange way. For example, if I try
to cat the output of mris_info to a txt file: 'mris_info lh.pial >
lh_info.txt', the text file will contain everything except the *_(ras) info
table that you see if you just call the command by itself:
volume geometry:
extent : (256, 256, 256)
voxel : ( 1.0000, 1.0000, 1.0000)
x_(ras) : (-1.0000, 0.0000, 0.0000)
y_(ras) : ( 0.0000, 0.0000, -1.0000)
z_(ras) : ( 0.0000, 1.0000, 0.0000)
c_(ras) : (-1.6000, -5.1750, -15.3313)
file : ../mri/filled-pretess255.mgz
Are there any mris_info experts on the team who might know how to circumvent
this?
thanks again for your help!
-zack
On Wed, Mar 4, 2015 at 2:54 PM, Bruce Fischl <fis...@nmr.mgh.harvard.edu>
wrote:
Hi Zack
the ascii format I don't think supports the c_ras info, which is why you see
a shift
cheers
Bruce
On Wed, 4 Mar 2015, Zachary Greenberg wrote:
Ok I figured out that this shift corresponds to the c_(RAS) value in the
header of lh.pial, which you can get with 'mris_info lh.pial'
Alternatively you can get the first coordinate and subtract it from the
first coordinate of lh.pial.asc with 'mris_info lh.pial --v 0'
Is there a way I'm not thinking of to output c_(RAS) directly using
mris_info or a bash command (cat grep)?
Thanks again,
-zack
On Wed, Mar 4, 2015 at 12:54 PM, Zachary Greenberg
<zacharyigreenb...@gmail.com> wrote:
Hi all,
I discovered that converting the mesh data from freesurfer lh.pial
format to ascii (.asc) causes a shift in the coordinates of the mesh.
You can see this by overlaying the two surfaces in freeview, and
looking at the difference between the [0 0 0] surface RAS coordinate
in lh.pial vs lh.pial.asc.
The shift is not consistent across different subjects. I'm wondering
if there is a way to fix this, or if there is some regularity in the
coordinate shift that can be used to correct (that I'm not seeing).
For example the difference coordinates between lh.pial and lh.pial.asc
in two different subjects are:
[ 1.6 , 5.18, 15.33]
[2.02, -15.80, 0.18]
Thanks for any help you can offer!
-zack
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Zachary Greenberg
Imaging Specialist
Department of Neurological Surgery
University of California, San Francisco
Email: zachary.greenb...@ucsf.edu
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