Hey Matthew,

 

I was suggested to change the filenames. So I tried to made them simpler… These are the same two old renamed nifty files.

 

As you can see, I have moved a new nifty file T1.nii(red marked) which results in the same. So I am sure the files are not the reason.

 

Rana Banik
Graduate Student
Dept. of Biomedical Engineering
Vanderbilt University
Contact: +16152756216

 

From: FSL - FMRIB's Software Library <[log in to unmask]> On Behalf Of Matthew Webster
Sent: Wednesday, June 5, 2019 3:51 AM
To: [log in to unmask]
Subject: Re: [FSL] regarding FSL in windows

 

Hi Rana,

Have you changed the filenames - in the screenshots the file was called CT-MRI-5639_MR_norm.<blah>, but you refer to 5639_nifti_file.nii in your latest command? Can you confirm there is a file called 5639_nifti_file.nii in your directory?

 

Kind regards

Matthew

--------------------------------
Dr Matthew Webster
FMRIB Centre 
John Radcliffe Hospital
University of Oxford



On 4 Jun 2019, at 21:46, Banik, Rana <[log in to unmask]> wrote:

 

I think the command line installed fslmaths properly(it launches now). But when I ran the following it doesn’t work. And also FSL GUI is unchanged.

<image001.png>

 

 

From: FSL - FMRIB's Software Library <[log in to unmask]> On Behalf Of Mark Jenkinson
Sent: Tuesday, June 4, 2019 3:31 PM
To: [log in to unmask]
Subject: Re: [FSL] regarding FSL in windows

 

Ah - that’s probably the key problem.

This came up on the list the other day and the following fix seemed to solve it:

 

sudo apt-get install libquadmath0 

So try that and see if it works.

All the best,

Mark

 




On 4 Jun 2019, at 21:15, Banik, Rana <[log in to unmask]> wrote:

 

Mark,

 

I am having the following errors when launching the FSLMATHS and FSLHD.

<image001.png>

 

 

From: FSL - FMRIB's Software Library <[log in to unmask]> On Behalf Of Mark Jenkinson
Sent: Tuesday, June 4, 2019 3:02 PM
To: [log in to unmask]
Subject: Re: [FSL] regarding FSL in windows

 

Hi, 

 

FSL doesn’t generally like it when there are two files with the same basename but different extensions.  Try using a totally different name.

 

If that still fails try:

  fslmaths original_name new_name

 

And then try bet on the new_name version.

It is possible that some fields in the file are not set to correct NIFTI settings and hence some tools complain.  Running it through fslmaths like this can fix that in certain circumstances.

 

If this also fails then see if fslhd will give you any useful output.

 

All the best,

Mark

 

 





On 4 Jun 2019, at 20:46, Banik, Rana <[log in to unmask]> wrote:

 

Hey Mark,

It was a gunzipped file then I unzipped it using Matlab and both files works pretty well in both Python(nibabel) and Matlab. Now as you have said I tried with .nii.gz extension which ends up the same. 

 

<image001.png>

 

 

From: FSL - FMRIB's Software Library <[log in to unmask]> On Behalf Of Mark Jenkinson
Sent: Tuesday, June 4, 2019 2:37 PM
To: [log in to unmask]
Subject: Re: [FSL] regarding FSL in windows

 

Hi, 

 

I’m not really sure what is going on here but some random things that might be worth trying, based on some past experiences on the list are:

 

 - Is it in fact a gzipped file that is misnamed?  

Try renaming it with the extension .nii.gz and see if that fixes it.

 

 - Are the weird non-standard characters in the filename?  

Try completely changing the name and see if that helps.

 

 - Do ‘ls -la’ in the directory and see if it is zero length or something odd (e.g. no read permission, broken alias, etc.)

 

 - Try reading it into python or matlab or with some other tool, to see if it is an FSL problem or a problem with the file itself.

 

All the best,

Mark

 






On 4 Jun 2019, at 20:10, Banik, Rana <[log in to unmask]> wrote:

 

The same things going on… Is there any syntax or file format/extension that I need to be aware of?

 

<image001.jpg>

 

 

From: FSL - FMRIB's Software Library <[log in to unmask]> On Behalf Of Braimah, Adebayo (Adebayo)
Sent: Tuesday, June 4, 2019 1:55 PM
To: [log in to unmask]
Subject: Re: [FSL] regarding FSL in windows

 

I am not exactly too sure of the behavior of the GUI in this case.

 

Try navigating to that directory and typing: `bet <input_image> <output_image> -m`

 

--

 

Thank You for Your Time

 

Adebayo Braimah
Research Assistant III

Pediatric Neuroimaging Research Consortium

Imaging Research Center

Cincinnati Children's
3333 Burnet Avenue, MLC 5033

Cincinnati, OH 45229

Phone: +1 (513) 636-3946

 

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