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: fischl@nmr.mgh.harvard.edu
> To: pvaltti@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
> > $SUBJECTS_DIR/AA/t1_icbm_normal_1mm_pn3_rf20.mnc
> > mincRead(): can't find file/home/esther/Freesufer/freesurfer/subjects/AA/t
> 1_icbm_normal_1mm_pn3_rf20.m
> > nc
> > -------I check in the directory enad the file is right there,
> > 
> > > Date: Fri, 15 Mar 2013 09:24:22 -0400
> > > From: fischl@nmr.mgh.harvard.edu
> > > To: pvaltti@hotmail.com
> > > CC: freesurfer@nmr.mgh.harvard.edu
> > > Subject: Re: [Freesurfer] mri_convert problem
> > >
> > > Hi Valtina
> > >
> > > you can convert directly without going through nii. What happens when yo
> u
> > > run ls -l on that file? Or mri_info?
> > >
> > > cheers
> > > Bruce
> > >
> > > On Fri, 15 Mar 2013, Valtina Pouegue wrote:
> > >
> > > > Hi, 
> > > >
> > > > I have a problem of conversion. I would like to convert mnc file to mg
> z.
> > But I think I shoul first convert mnc to nii then
> > > > nii to mgz. , 
> > > > so I try the command mri_convert and I have this error; 
> > > > -------------
> > > > [esther@m3012-04 ~]$ 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.
> > 
> >
> 
> _______________________________________________ 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.
> 
>