what are you attempting to open it with? YOu didn't include that command
line
On Tue, 2 Jul 2019, Azeez, Azeezat wrote:

>
>         External Email - Use Caution        
>
> Hello  Bruce,
>
> Thank yo for the quick response.
>  
> I ran this script:
> mri_convert lRMFC.masked.mgh lRMFC.masked.nii --out_orientation RAS --apply_transform
> /media/disk2/COMBO_ABIDE_FS/FS_ABIDE1/fsaverage/mri/transforms/talairach.xfm
>
> This was output to the terminal, the .nii file was created
>
> $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $
> reading from lRMFC.masked.mgh...
> 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)
> INFO: Reading transformation from file
> /media/disk2/COMBO_ABIDE_FS/FS_ABIDE1/fsaverage/mri/transforms/talairach.xfm...
> Reading transform with LTAreadEx()
> Setting output orientation to RAS
> INFO: Applying transformation from file
> /media/disk2/COMBO_ABIDE_FS/FS_ABIDE1/fsaverage/mri/transforms/talairach.xfm...
> ---------------------------------
> INFO: Transform Matrix (linear_ras_to_ras)
>  1.000   0.000   0.000   0.000;
>  0.000   1.000   0.000   0.000;
>  0.000   0.000   1.000   0.000;
>  0.000   0.000   0.000   1.000;
> ---------------------------------
> Applying LTAtransformInterp (resample_type 1)
> INFO: Transform dst volume info is not used (valid flag = 0).
> Reslicing using trilinear interpolation
> writing to lRMFC.masked.nii...
>
>
> But attempting to open yield this
>
>  WARNING: Forced switch from 'Original View' to 'Talairach View' [#1]
> *+ WARNING: Forced switch from 'Talairach View' to 'Original View' [#2]
>
>
>
>
> On Tue, Jul 2, 2019 at 3:26 PM Bruce Fischl <fischl@nmr.mgh.harvard.edu> wrote:
>       Hi Azeezat
>
>       you need to give us more information than this. Did you try:
>
>       mri_convert file.mgh file.nii
>
>       did that give you an error? Where did the process fail? We need full screen
>       output of what you ran and what failed (in text format please, not as a
>       snapshot)
>
>       cheers
>       Bruce
>
>
>       On Tue, 2 Jul
>       2019, Azeez, Azeezat wrote:
>
>       >
>       >         External Email - Use Caution        
>       >
>       > Hello,
>       > I wish to convert a  .mgh file that can be opened in AFNI I've used mri_convert , yet
>       I am still
>       > unable to open the .nii file in AFNI.
>       > Any assistance in the matter would be greatly appreciated. 
>       >
>       > Thank You,
>       > -- 
>       > Azeezat Azeez
>       > PhD Student
>       > Brain Connectivity Lab
>       > Department of Biomedical Engineering || New Jersey Institute of Technology
>       > Graduate School of Biomedical Sciences || Rutgers University
>       > E: aka44@njit.edu
>       >
>       >_______________________________________________
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>
>
> --
> Azeezat Azeez
> PhD Student
> Brain Connectivity Lab
> Department of Biomedical Engineering || New Jersey Institute of Technology
> Graduate School of Biomedical Sciences || Rutgers University
> E: aka44@njit.edu
>
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