Hi,

Using bet (the brain extraction tool) with the -m flag will create a new image with the skull removed and supply a binary brain mask.

Jeanette

2011/11/1 ·ëè´ <[log in to unmask]>

Dear Mark,

 

         So kind you are. I found your code was very useful. And using fslmerge, I can convert 3D files to one 4D file. Here is what I typed in the terminal.

                   fslmerge -t 4D.nii 01.nii.gz 02.nii.gz

         Is it correct? Should I specify TR explicitly? Or should I use fslmerge ¨Ctr ¡­¡­.. instead?

 

         ANOTHER QUESTION may be not related to the one above. Can FSL create a mask for inside-brain voxels? How?

 

         Thank you very much!

 

Best wishes!

 

     Lu FENG

[log in to unmask]

 

From: FSL - FMRIB's Software Library [mailto:[log in to unmask]] On Behalf Of Mark Jenkinson
Sent: 2011Äê11ÔÂ1ÈÕ 16:39
To: [log in to unmask]
Subject: Re: [FSL] Can 'fslchfiletype' change a series of .img/.hdr files into one 4D NIFTI file?

 

Dear Lu Feng,

 

The second command is not for doing multiple images, it is for renaming

an image at the same time as changing its type.  If you did do:

  fslchfiletype NIFTI_GZ filename1 filename2

then you will have lost the contents of filename2 (if it existed before) and

have replaced it with a version of the contents of filename1.  So I think you

need to avoid this in your case.

 

If what you want to do is take a set of images and simply convert them

from .hdr/.img pairs into .nii.gz format then you need to script this.  A

simple version is the following:

 

  for fn in *.img ; do  fslchfiletype NIFTI_GZ $fn $fn ; done

 

This will run it on all the files that match *.img in the present working

directory.  You can replace this *.img term with any other you prefer

(e.g. control*.img would only do images that started with "control" in

their filenames).  

 

Note that you only need to have the for loop find the .img files, as 

fslchfiletype will automatically find the matching .hdr file.  It could

also be rewritten to use .hdr instead of .img (it doesn't matter - it 

should just make sure that it only picks one and not both - as doing

for fn in * ; do ... would be bad as it could do both .hdr and .img which

would confuse things).

 

I hope this is clear and helpful.

 

All the best,

    Mark

 

 

 

On 1 Nov 2011, at 08:20, ·ëè´ wrote:

Dear experts,

 

Since I¡¯m new to FSL, please bear my questions which seem to be something silly to skilled ones.

 

When I typed in the terminal

                   fslchfiletype NIFTI_GZ filename1

it worked well and changed a pair of filename1.hdr and filename1.img into filename1.nii.gz. But when I typed in the terminal as the document suggested

                   fslchfiletype NIFTI_GZ filename1 filename2

it only changed the latter pair into filename2.nii.gz. What I wondered is how to change a series of pairs into a 4D NIFTI file.

 

I have tried a 3D to 4D convertor provided by SPM. But the final file can't be recognized by FSLView.

 

ANOTHER QUESTION: Can FSL create a mask for inside-brain voxels? How?

 

Thanks in advance~~~~

 

Best wishes!

 

     Lu FENG

[log in to unmask]

 

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