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