just:
mri_convert <full path to minc file> volume.mgz
cheers
Bruce
On Fri, 15 Mar 2013, Valtina Pouegue wrote:
Sorry, I am also a beginner in Linux environment. Now it works.
I try :
-------------
esther@m3012-04 ~]$ ls -l $SUBJECTS_DIR/AA
total 13892
-rwxr--r-- 1 esther esther 14224696 12 mar 23:33
t1_icbm_normal_1mm_pn3_rf20.mnc
[esther@m3012-04 ~]$ ls -l $SUBJECTS_DIR/AA/t1_icbm_normal_1mm_pn3_rf20.mnc
-rwxr--r-- 1 esther esther 14224696 12 mar
23:33/home/esther/Freesurfer/freesurfer/subjects/AA/t1_icbm_normal_1mm_pn3_rf20.
mnc
----------------
And this
----------
Volume information
for/home/esther/Freesurfer/freesurfer/subjects/AA/t1_icbm_normal_1mm_pn3_rf20.
mnc
type: MINC
dimensions: 181 x 217 x 181
voxel sizes: 1.0000, 1.0000, 1.0000
type: SHORT (4)
fov: 217.000
dof: 0
xstart: -90.5, xend: 90.5
ystart: -108.5, yend: 108.5
zstart: -90.5, zend: 90.5
TR: 0.00 msec, TE: 0.00 msec, TI: 0.00 msec, flip angle: 0.00
degrees
nframes: 1
PhEncDir: UNKNOWN
ras xform present
xform info: x_r = 1.0000, y_r = 0.0000, z_r = 0.0000, c_r =
0.5000
: x_a = 0.0000, y_a = 1.0000, z_a = 0.0000, c_a =
-17.5000
: x_s = 0.0000, y_s = 0.0000, z_s = 1.0000, c_s =
18.5000
Orientation : RAS
Primary Slice Direction: axial
voxel to ras transform:
1.0000 0.0000 0.0000 -90.0000
0.0000 1.0000 0.0000 -126.0000
0.0000 0.0000 1.0000 -72.0000
0.0000 0.0000 0.0000 1.0000
voxel-to-ras determinant 1
ras to voxel transform:
1.0000 -0.0000 -0.0000 90.0000
-0.0000 1.0000 -0.0000 126.0000
-0.0000 -0.0000 1.0000 72.0000
0.0000 0.0000 0.0000 1.0000
-------------------
which command shoul I use for convert direct from MNC to mgz^
Thanks
Date: Fri, 15 Mar 2013 10:00:04 -0400
From: fis...@nmr.mgh.harvard.edu
To: pval...@hotmail.com
CC: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] mri_convert problem
can you run ls -l and mri_info on it?
On Fri, 15 Mar 2013, Valtina Pouegue
wrote:
> I get this error-------------
> esther@m3012-04 ~]$ mri_info
> $SUBJECTS_DIR/AA/t1_icbm_normal_1mm_pn3_rf20.mnc
> mincRead(): can't find file/home/esther/Freesufer/freesurfer/subjects/AA/t
1_icbm_normal_1mm_pn3_rf20.m
> nc
> -------I check in the directory enad the file is right there,
>
> > Date: Fri, 15 Mar 2013 09:24:22 -0400
> > From: fis...@nmr.mgh.harvard.edu
> > To: pval...@hotmail.com
> > CC: freesurfer@nmr.mgh.harvard.edu
> > Subject: Re: [Freesurfer] mri_convert problem
> >
> > Hi Valtina
> >
> > you can convert directly without going through nii. What happens when yo
u
> > run ls -l on that file? Or mri_info?
> >
> > cheers
> > Bruce
> >
> > On Fri, 15 Mar 2013, Valtina Pouegue wrote:
> >
> > > Hi,
> > >
> > > I have a problem of conversion. I would like to convert mnc file to mg
z.
> But I think I shoul first convert mnc to nii then
> > > nii to mgz. ,
> > > so I try the command mri_convert and I have this error;
> > > -------------
> > > [esther@m3012-04 ~]$ mri_convert $SUBJECTS_DIR/Patient1/fichierMnc.mnc
> Folder1.nii.gz
> > > mri_convert
> /home/esther/Freesufer/freesurfer/subjects/Patient1/fichierMnc.mnc
> Folder1.nii.gz
> > > $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $
> > > reading from
> /home/esther/Freesufer/freesurfer/subjects/Patient1/fichierMnc.mnc...
> > > mincRead(): can't find file
> /home/esther/Freesufer/freesurfer/subjects/Patient1/fichierMnc.mnc
> > > [esther@m3012-04 ~]$
> > > --------------------
> > > I look up, and the file is at the rith place.... Could you help me..
> > > Thanks
> > >
> > > VP]
> > >
> > >
> >
> >
> > The information in this e-mail is intended only for the person to whom i
t
> 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 i
n
> error
> > but does not contain patient information, please contact the sender and
> properly
> > dispose of the e-mail.
>
>
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error but does not contain patient information, please contact the sender
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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.
