Hi again,

After I renamed all the files as needed, I got another error :

ERROR (nifti_image_read): failed to find header file for /usr/local/fsl/date/dti20/./nodif_brain_mask

ERROR nifti_image_open ( /usr/local/fsl/date/dti20/./nodif_brain_mask): bad header info

ERROR failed to open /usr/local/fsl/date/dti20/./nodif_brain_mask

ERROR could not open image /usr/local/fsl/date/dti20/./nodif_brain_mask

Image exception: #22: Failed to read volume  /usr/local/fsl/date/dti20/./nodif_brain_mask

terminate called after throwing an instance of 'RBD_COMMON:BaseException'

I think my "nodif_brain_mask" is not the correct file. I created a brain mask using BET GUI for the dti data I have, named "dti20.nii.gz". I looked up how to create the brain mask for the reference volume only (nodif), but I didn't understand how to do this.

Thanks,

Irina

 

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From: Stamatios Sotiropoulos <[log in to unmask]>
To: [log in to unmask]
Sent: Friday, April 26, 2013 8:51 PM
Subject: Re: [FSL] bedpostx error

Hi 

you need to provide as input to bedpostx a folder, in which the following files are expected (named exactly as):

data 

nodif_brain_mask 

bvals 

bvecs

Cheers

Stam

On 26 Apr 2013, at 07:39, Serbu Irina wrote:

Dear FSL experts,

I tried to use FDT on a dataset and when I got to the bedpostx step, I got the following message: "data not found". I copied the entire sequence below:

switching from /usr/local/fsl/date to /usr/local/fsl/date

bedpostx /usr/local/fsl/date/dti20 -n 2 -w 1  -b 1000

/usr/local/fsl/bin/bedpostx /usr/local/fsl/date/dti20 -n 2 -w 1  -b 1000

subjectdir is /usr/local/fsl/date/dti20

/usr/local/fsl/date/dti20/data not found

bedpostx_datacheck didn't return anything in the terminal.

Also, I have a problem with fslview. It doesn't show anything but a gray screen. I attached the screenshot so you can see the exact problem.

Thanks in advance,

Irina Serbu

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