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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,
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:
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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
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 CautionHello, 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
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
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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
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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:
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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 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
freesurfer@nmr.mgh.harvard.edu
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Azeez, Azeezat -
Bruce Fischl