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Dear Christen,

I had the same problem. If your initial files were named 0708.DWI2DT_FA, when you run the different steps for TBSS...your FA appears two times: 0910.DWI2DT_FA_FA . This is a problem when you run the script.

The solution I got was: 

1) From DTIFIT process: you get : 0708.DWI2DT_FA

2) Copy these FA images from DTIFIT to mytbss directory (mkdir mytbss) and then rename these FA files: 0910.DWO2DT (you know they are FA) and go on with TBSS process.

3) Copy all your MD images from DTIFIT to mytbss and name them as the files you have in the origdata...(you know these are MD files)...and you can  go on...with the pipeline for tbss_non_fa images...

Hope this helps,

Rosalia.

1) Do not name your files with FA...just 0910.DWO2DT...(for example)...when  you run TBSS...origdata folder will have: 0910.DWO2DT



2013/3/12 Kristen Mackiewicz Seghete <[log in to unmask]>

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