2 Jul
2019
2 Jul
'19
4:25 p.m.
Try loading it in freeview instead. If that works fine, then I think you will have to ask the afni folks for help. Bruce
On Tue, 2 Jul 2019, Azeez, Azeezat wrote:
External Email - Use Caution
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 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 > > > >_______________________________________________ > 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 > >_______________________________________________ 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