Hi,

I would like to ask for your help as I have encountered some problems in EV quantification. Its says:

Error using xform_nii>change_hdr (line 350)
Non-orthogonal rotation or shearing found inside the affine matrix
in this NIfTI file. You have 3 options:

1. Using included 'reslice_nii.m' program to reslice the NIfTI
file. I strongly recommand this, because it will not cause
negative effect, as long as you remember not to do slice
time correction after using 'reslice_nii.m'.

2. Using included 'load_untouch_nii.m' program to load image
without applying any affine geometric transformation or
voxel intensity scaling. This is only for people who want
to do some image processing regardless of image orientation
and to save data back with the same NIfTI header.

3. Increasing the tolerance to allow more distortion in loaded
image, but I don't suggest this.
To get help, please type:
help reslice_nii.m
help load_untouch_nii.m
help load_nii.m

Error in xform_nii (line 154)
[hdr,orient]=change_hdr(hdr,tolerance,preferredForm);

Error in load_nii (line 135)
nii = xform_nii(nii, tolerance, preferredForm);
Error in WhyD_preproc (line 101)
wm_mask = load_nii(sprintf('%s/c2rFLAIR_%s.nii',names.directory_path,names.folder_id));
Error in WhyD_setup (line 125)
if check_preproc_vals(n) == 0 names = names_stack{n,1}; names_stack{n,1} = WhyD_preproc(names, spmtoolbox_path); end
Error in WhyD_GUI>run_button_Callback (line 281)
WhyD_setup(arg0,arg1,arg2,arg3,arg4,arg5,arg7,arg8,arg9,2);
Error in gui_mainfcn (line 96)
feval(varargin{:});
Error in WhyD_GUI (line 28)
gui_mainfcn(gui_State, varargin{:});
Error in guidemfile/@(hObject,eventdata)WhyD_GUI('run_button_Callback',hObject,eventdata,guidata(hObject))
Error while evaluating uicontrol Callback

I have resliced the nii image (option 1) using NIFTI toolbox. Converted the hdr format back to nii and used W2MHS to calculate the EV volume again. It went smoothly and all the output nii images were fine but in the RFREG_ev_660t.txt shows that
Study: W2MHS Subject: 660t
EV: NaN
EV-Deep: NaN
EV-Periventricular: NaN

Why did it show NaN? Did I do something wrong?
I have tried to reslice a few subjects that gave the same error message but in the end, they all gave NaN as the EV, EV-Deep and EV-Periventricular too.

The attachment contains all the output files from W2MHS and reslicing of this study.

Thanks for your help.