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FSL  June 2012

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Subject:

Re: sienax issues during TIC

From:

Mark Jenkinson <[log in to unmask]>

Reply-To:

FSL - FMRIB's Software Library <[log in to unmask]>

Date:

Sat, 9 Jun 2012 21:56:40 +0800

Content-Type:

text/plain

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text/plain (33 lines)

Hi Roberto,

This looks like you have a very old version of FSL and sienax.
Please update to the most recent version.
The command avwmaths became fslmaths many years ago.

All the best,
	Mark


On 9 Jun 2012, at 06:22, Roberto wrote:

> Hello,
> 
> I am trying to use SIENAX to obtain total intracranial volume for some T1 niftii images. 
> 
> I am using the sienax command (running it off the terminal on a PC) and i receive an error message as follows: 
> 
> ERROR (nifti_image_read): failed to fined header file for '/software/fsl4/etc/standard/avg152T1_brain_mask_dil_. 
> 
> Indeed when I go to that folder, I do not find that particular file but I do have a lot of other 152 templates. Does this have to do with the version I have or the add-ons I have installed? (Note: I also have an error with that it cannot find avwmaths from the bin subfolder in fsl4.) 
> 
> If not, should I be using a different MNI template and if so, how can I specify, via command, which template to use. Also, I only assumed my input file should be a .nii. Is this ok?
> 
> I ran the command as: 
> 
> sienax 3dvol.nii -d -2
> 
> I am using t1 images 
> 
> Many thanks, 
> Robert
> 

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