External Email - Use Caution        

I think a part of the problem is from this part in load_mgh.m:

% unzip if it is compressed
if (strcmpi(fname((strlen(fname)-3):strlen(fname)), '.MGZ') | ...
strcmpi(fname((strlen(fname)-3):strlen(fname)), '.GZ'))
  rand('state', sum(100*clock));
  gzipped =  round(rand(1)*10000000 + ...
  sum(int16(fname))) + round(cputime);
  %ind = findstr(fname, '.');
  %new_fname = sprintf('/tmp/tmp.load_mgh.%d.mgh', gzipped);
  new_fname = sprintf('%s.load_mgh.%d.mgh', tempname,gzipped);

  if(strcmp(computer,'MAC') || strcmp(computer,'MACI') || ismac)
    unix(sprintf('gunzip -c %s > %s', fname, new_fname)) ;
  else
    unix(sprintf('zcat %s > %s', fname, new_fname)) ;
  end
  fname = new_fname ;
else
  gzipped = -1 ;
end

there is no command for windows (just mac and linux it seems) and matlab cant recognize the zcat linux command (my linux shell, however, recognizes it). i  dont know how to modify this part to prevent the not recognized z cat error.

On Mon, Dec 30, 2019 at 11:39 AM mahdi mahdavi <mahdi.mahdavi74@gmail.com> wrote:

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 Caution        
>
> Hi. 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

_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer