External Email - Use Caution
I wanted to test the QuickNATv2 MATLAB and since I saw that it used freesufer, I used one of the samples in the subjects folder of freesurfer (sample-001.mgz), conformed it to 256^3( the QuickNAT required 256^3) and saved it as subject-0001.mgz. I'm sending you the screenshot of mri_info subject-0001.mgz. Oh i also forgot to send you the complete MATLAB error; it's complete form is like this: 'zcat' is not recognized as an internal or external command, operable program or batch file. ERROR: problem reading fname 'rm' is not recognized as an internal or external command, operable program or batch file. SWITCH expression must be a scalar or a character vector.
Error in load_mgh (line 158) switch type
Error in MRIread (line 87) [mri.vol, M, mr_parms, volsz] = load_mgh(fspec,[],[],headeronly);
Error in RunFile (line 15) DataVol = MRIread([DataPath,FileName]);
I saw somewhere that the problem might be from the .mgz file so i extracted it using Winrar and renamed it subject-0001.mgh and this time it showed this error: ERROR: could not open C:\Users\home\Desktop\Project code\QuickNATv2\SampleDatasample-0001.mgh for reading ERROR: loading C:\Users\home\Desktop\Project code\QuickNATv2\SampleDatasample-0001.mgh as MGH Dot indexing is not supported for variables of this type.
Error in RunFile (line 16) Data = DataVol.vol
On Sun, Dec 29, 2019 at 10:56 PM Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:
Hi Mahdi
can you run mri_info in a Linux shell on that file and send us the entire screen output?
cheers Bruce On Sun, 29 Dec 2019, mahdi mahdavi wrote:
External Email - Use CautionHi. I'm a medical student and I'm trying to use the QuickNATv2 MATLAB
code for
structural MRI segmentation for a paper. However, at the last step when
I want to
execute the Run command for this program, it returns an error related to
MRIRead
function from freesurfer. I'm, using windows so I Cloned freesurfer
library from
github and defined its path for MATLAB. The error is: SWITCH expression
must be a
scalar or a character vector; the MRI data is a .mgz file:
Error in load_mgh (line 166) switch type
Error in MRIread (line 94) [mri.vol, M, mr_parms, volsz] = load_mgh(fspec,[],[],headeronly);
Error in RunFile (line 15) DataVol = MRIread([DataPath,FileName]); I've also tried using linux shell for windows 10 and installed the
freesurfer with
it but i still get the same error. I didn't find any helpful guides on
various
forums so I'm mailing you hoping to find a solution cause I really need
to run
the QuickNAT for a paper. Regards Mahdi
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
