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 Creating a mask from the AAL template		  New Topic  Reply to Topic
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crozier
New Member

19 Posts
Posted - Jun 11 2007 :  5:13:07 PM  Show Profile  Reply with Quote
Hi,

I am trying to make a mask from the AAL template that's in the SPM2 directory. The file name is aal_MNI_V4.hdr/.img The region I am interested in has the value 41. To create the mask I first used avwchfiletype to change the image file to NIFTI_GZ. Then I tried to use avwmaths++ with the following command:
avwmaths++ aal_MNI_V4.nii.gz -thr 40.9 -uthr 41.1 left_amygdala.nii.gz

However, I get the following error:
** ERROR: nifti_image_read(aal_MNI_V4): can't open header file
** ERROR: nifti_image_open(aal_MNI_V4): bad header info
Error: failed to open file aal_MNI_V4
Cannot open volume aal_MNI_V4 for reading!

I also tried to run avwmaths++ on the ANALYZE version of the file and got the same message along with the following:
Error:: FslGetIntensityScaling: Null pointer passed for FSLIO

I am able to open the image with FSLView without any problems. Any ideas about how to do this?

Thanks,
Joe

syam.gadde
BIAC Staff

USA
421 Posts
Posted - Jun 11 2007 :  5:21:34 PM  Show Profile  Reply with Quote
I ran it on golgi on the original analyze files and it worked without error:

env FSLOUTPUTTYPE=NIFTI_GZ avwmaths++ aal_MNI_V4.hdr -thr 40.9 -uthr 41.1 left_amygdala.nii.gz

(the env FSLOUTPUTTYPE=NIFTI_GZ is in case you haven't set up your FSL environment, but you must have had it set already since it didn't complain)
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crozier
New Member

19 Posts
Posted - Jun 11 2007 :  5:28:20 PM  Show Profile  Reply with Quote
Hey Syam,

I just copied your text exactly and pasted it and still got the same error. I don't get it...

Joe
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crozier
New Member

19 Posts
Posted - Jun 11 2007 :  5:31:52 PM  Show Profile  Reply with Quote
It got it to work now.

Joe
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syam.gadde
BIAC Staff

USA
421 Posts
Posted - Jun 11 2007 :  5:31:52 PM  Show Profile  Reply with Quote
Maybe you're using a different avwmaths++ than I am:

which avwmaths++

will tell you what you're using.

Try this:

/usr/local/packages/fsl/bin/avwmaths++ aal_MNI_V4.hdr -thr 40.9 -uthr 41.1 left_amygdala.nii.gz
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