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sorry this the command I used in the terminal afni avg152T1_brain.nii.gz lRMFC.masked.nii
On Tue, Jul 2, 2019 at 4:14 PM Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:
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 CautionHello 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 needfull screen
output of what you ran and what failed (in text format please, notas 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'veused 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 ofTechnology
> Graduate School of Biomedical Sciences || Rutgers University > E: aka44@njit.edu > >_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer-- 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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