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 <fis...@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: ak...@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: ak...@njit.edu
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