Print

Print

Hi Rosalia –

 

I have named the MD files the same as the files in the origdata. Thanks

 

Cheers,

kristen

 

From: FSL - FMRIB's Software Library [mailto:[log in to unmask]] On Behalf Of Rosalia Dacosta Aguayo
Sent: Tuesday, March 12, 2013 2:53 AM
To: [log in to unmask]
Subject: Re: [FSL] Problem opening files for tbss_non_FA

 

Dear Kristen,

 

Your MD files have to have the same names as your files in the origdata....So, copy your MD files into a MD folder and then, call these files as the one you have in the origdata folder.

 

Hope this helps,

Rosalia.

2013/3/12 Mark Jenkinson <[log in to unmask]>

Dear Kristen,

 

You need to do this within your FA directory.

So cd into the directory and then run the imglob command.

 

All the best,

Mark

 

 

 

On 8 Mar 2013, at 16:35, Kristen Mackiewicz Seghete <[log in to unmask]> wrote:



It outputs that it’s not a directory.

 

From: FSL - FMRIB's Software Library [mailto:[log in to unmask]] On Behalf Of Gwenaëlle DOUAUD
Sent: Friday, March 08, 2013 3:23 AM
To: [log in to unmask]
Subject: Re: [FSL] Problem opening files for tbss_non_FA

 

Hi Kristen,

what's the result of a $FSLDIR/bin/imglob *_FA.* in your FA directory?

Cheers,
Gwenaëlle

 

--------------------------------------------------------------------
Gwenaëlle Douaud, PhD
FMRIB Centre, University of Oxford
John Radcliffe Hospital, Headington 
OX3 9DU Oxford UK
Tel: +44 (0) 1865 222 523 
Fax: +44 (0) 1865 222 717
www.fmrib.ox.ac.uk/~douaud
--------------------------------------------------------------------

De : Kristen Mackiewicz Seghete <[log in to unmask]>
À : [log in to unmask] 
Envoyé le : Jeudi 7 mars 2013 18h36
Objet : [FSL] Problem opening files for tbss_non_FA


Hi All - 

I am having difficulty getting tbss_non_FA to run for MD data. I have run all the FA analyses, using tbss steps 1-4. I've had no problems running any of the FA analyses, or RD or AD analyses, using the DWI2DT files instead of the dtifit files. For each subject that I include, I get the following error message:

/usr/local/fsl/bin/tbss_non_FA: line 91: 30104 Aborted                $FSLDIR/bin/applywarp -i ../${ALTIM}/$f -o ${f}_to_target_${ALTIM} -r $FSLDIR/data/standard/FMRIB58_FA_1mm -w ${f}_FA_to_${best}_warp $postaffine
K0400-0709.DWI2DT_FA
** ERROR (nifti_image_read): failed to find header file for '../MD/K0400-0709.DWI2DT_FA'
** ERROR: nifti_image_open(../MD/K0400-0709.DWI2DT_FA): bad header info
Error: failed to open file ../MD/K0400-0709.DWI2DT_FA
ERROR: Could not open image ../MD/K0400-0709.DWI2DT_FA
Image Exception : #22 :: Failed to read volume ../MD/K0400-0709.DWI2DT_FA
terminate called after throwing an instance of 'RBD_COMMON::BaseException'
/usr/local/fsl/bin/tbss_non_FA: line 91: 30108 Aborted

I've checked the original files and header info to make sure the files are ok, and the files are there and in tact.

I am running analyses from my TBSS directory, which also contains my origdata, FA, and MD directories. Below is an example of the files in my origdata directory:

origdata:
D0001-0209.DWI2DT_FA.nii
D0002-0409.DWI2DT_FA.nii
D0003-0409.DWI2DT_FA.nii

I have copied my MD files (e.g., D0001-0209.DWI2DT_MD.nii) into the MD directory, and then named them identical to the files above.

I had read an earlier post that use of FA in the file names while using tbss_non_FA might confuse the script, so I tried just naming the files without FA (e.g., D0001-0209.DWI2DT.nii), but I got the same error. 

Any help with this problem would be greatly appreciated, as I'm not sure what to try next. Thanks!

cheers,
kristen