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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