no, the stats file has partial-volume corrected estimates in it, so
simply counting the number of voxels in the volume won't match it
On Mon, 3
Aug 2015, Jonathan Plasencia wrote:
That is partly correct. The nii is not matching the stats file (which it is
my understanding the stats file is based off the mgz file. If this is the
case then yes to your first question).
I'll send a mgz file and its stats file directly to your personal email in a
minute:
fis...@nmr.mgh.harvard.edu
Best,
Jon
On Mon, Aug 3, 2015 at 1:18 PM, Bruce Fischl <fis...@nmr.mgh.harvard.edu>
wrote:
and you are saying that aseg.nii does *not* match the voxel
counts in aseg.mgz? That is surprising. Can you email me the
aseg.mgz?
On Mon, 3 Aug 2015, Jonathan Plasencia wrote:
I've given it a try in which I do not include
" --out_orientation RAS" for
writting an nii file (see output below). In doing so
the new aseg.nii file
appears to be the exact same as the original nii
files I created (i.e. the
number of voxels for a given segmentation ID did not
change between the old
and new nii file and neither of these are matching
the stats file). Do you
have another suggestion for fixing this? I ask
because some of the smaller
structures can have up to a 30% change in the number
of voxels representing
a given structure (comparing the nii file to the
stats file).
r500711$ mri_convert aseg.mgz aseg.nii
mri_convert aseg.mgz aseg.nii
$Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16
mreuter Exp $
reading from aseg.mgz...
TR=0.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-1, 0, 0)
j_ras = (0, 0, -1)
k_ras = (0, 1, 0)
writing to aseg.nii...
On Fri, Jul 31, 2015 at 2:31 PM, Jonathan Plasencia
<jplas...@asu.edu>
wrote:
Ok, I will give this a look. Thank you
everyone.Best,
Jon
cheers
Bruce
On Fri, 31 Jul 2015, Jonathan Plasencia wrote:
This is what we did from terminal:
mri_convert aseg.mgz aseg.nii
--out_orientation RAS
mri_convert aseg.mgz aseg.nii
--out_orientation RAS
$Id: mri_convert.c,v 1.179.2.7
2012/09/05
21:55:16 mreuter Exp $
reading from aseg.mgz...
TR=0.00, TE=0.00, TI=0.00, flip
angle=0.00
i_ras = (-1, 0, 0)
j_ras = (0, 0, -1)
k_ras = (0, 1, 0)
Setting output orientation to RAS
Reslicing using trilinear interpolation
writing to aseg.nii...
** I ran this command from within the
subject's mri folder.
Should we try this
without --out_orientation
RAS ?
Best,
Jonathan Plasencia
Graduate Student
NSF Graduate Research Fellow
School of Biological and Health Systems
Engineering
Arizona State University
Email: jplas...@asu.edu
Phone: (480)861-7017
On Fri, Jul 31, 2015 at 12:54 PM, Bruce
Fischl
<fis...@nmr.mgh.harvard.edu>
wrote:
why are you specifying the output
orientation? That is probably
causing
resampling
On Fri, 31 Jul 2015,
Jonathan Plasencia wrote:
>
> We are using the following line:
>
>
> mri_convert aseg.mgz aseg.nii
--out_orientation RAS
>
>
>
> Best,
>
> Jonathan Plasencia
> Graduate Student
> NSF Graduate Research Fellow
> School of Biological and Health
Systems Engineering
> Arizona State University
> Email: jplas...@asu.edu
> Phone: (480)861-7017
>
> On Fri, Jul 31, 2015 at 12:31
PM,
Lilla Zollei
<lzol...@nmr.mgh.harvard.edu>
> wrote:
>
> Hi Jon,
>
> What is the exact command
that
you used for the below
described
> conversion?
>
> Lilla
>
> On Fri, 31 Jul 2015,
Jonathan
Plasencia wrote:
>
> > I've converted the
aseg.mgz
file to .nii (need data in
nii to
> do some further work on
the
data). However, the number
of voxels
> for a given structure
changes
when comparing the stats
file
> (from freesurfer) to the
created
.nii file. What is
happening
> here? Is there a fix for
this? I
would expect the number
of
> > voxels for a given
structure
should be the same
between the
> stats file and the .nii
file.
> > Note: I get the voxel
values
in the stats file from
the
> NVoxels column. I get the
voxel
values in the generated
.nii
> file by using matlab to
count
the number pixels with a
given
> SegId value (i.e. given
intensity value).
> >
> >
> > Best,
> >
> > Jon
> >
> >
>
_______________________________________________
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
>
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
> 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.
>
>
>
>
_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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.
_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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.
_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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.
