Re: [Freesurfer] Error in MATLAB while using freesurfer commands
You can unzip it outside of freesurfer and name it *.mgh then see if it works
cheers
Bruce
> On Dec 30, 2019, at 3:49 AM, mahdi mahdavi wrote:
>
>
> 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)*1000 + ...
> 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
>> 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
>>> 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
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Error in MATLAB while using freesurfer commands
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)*1000 + ...
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
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
> 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
Re: [Freesurfer] Error in MATLAB while using freesurfer commands
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] Error in MATLAB while using freesurfer commands
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
