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Instead of coregistering/averaging maps after DTIFIT, the more typical approach would be to simply concatenate ('fslmerge') the two original runs, concatenate the bvals/bvecs files, and then just run eddy_correct and dtifit using those concatenated files (i.e., as if all the data was collected in a single run in the first place).

cheers,
-MH

-- 
Michael Harms, Ph.D.
-----------------------------------------------------------
Conte Center for the Neuroscience of Mental Disorders
Washington University School of Medicine
Department of Psychiatry, Box 8134
660 South Euclid Ave. Tel: 314-747-6173
St. Louis, MO  63110 Email: [log in to unmask]

From: Tibor Auer <[log in to unmask]>
Reply-To: FSL - FMRIB's Software Library <[log in to unmask]>
Date: Tuesday, October 6, 2015 5:38 AM
To: FSL - FMRIB's Software Library <[log in to unmask]>
Subject: Re: [FSL] Having problems with DTIFIT with only two subjects...

Dear Rosalia,

 

How did you actually averaged the imagesin step e)? Are you sure there was no dimension reduction? Have you checked whether the output data.nii.gz is actually a 4D dataset with same amount of volumes as the number of entries in the bvals/bvecs.

 

However, there are some more conceptual issues:

1.       In step d), you first registered data_1 to data_2 and data_2 to data_1. So at the end, they are not aligned at all!

2.       Which bvals/bvecs have you used? The set from data_1 or from data_2?

 

And more importantly:

It is not advised to register raw DTI images, because then you disrupt the consistency between the geometry of the images and the geometry of the bvecs. One solution is to transform the bvecs, as well; but it is also suboptimal.

My recommendation is to analyse the two datasets separately without any registration, and coregister+average the metric images (e.g. FA maps) after DTIFIT.

 

Vale,

 

Auer, Tibor M.D. Ph.D.

MRC Cognition and Brain Sciences Unit
15 Chaucer Road
Cambridge
CB2 7EF

United Kingdom

Phone/Work: +44-(0)1223-273613

Mail: [log in to unmask]

 

From: Rosalia Dacosta Aguayo [mailto:[log in to unmask]]
Sent: Tuesday, October 06, 2015 11:05 AM
To: FSL - FMRIB's Software Library <[log in to unmask]>
Subject: Having problems with DTIFIT with only two subjects...

 

Dear FSL team,

I must be doing something wrong but I can not guess where is the problem. I have two groups of 12 subjects.

1. I have two DTI acquisitions (dti_1 and dti_2) from the same subject in the same scanner (the last two subjects to include in the study). And I did the following steps in order to prepare my two subjects.

a) From DICOM to NIFTI (dcm2nii)

b) eddy_correct dti_1 data_1 0

c) eddy_correct dti_2 data_2 0

d) Here I thing there is the problem...but I do not know to manage with them in order to ensure that both images are well aligned. I did the following for co-registration of the two images.
    

- flirt -in data_2.nii.gz -ref data_1.nii.gz -out data_2_registered -bins 256 -cost corratio -searchrx 0 0 -searchry 0 0 -searchrz 0 0 -dof 6 -interp trilinear

- flirt -in data_1.nii.gz -ref data_2_registered.nii.gz -out data_1_registered -bins 256 -cost corratio -searchrx 0 0 -searchry 0 0 -searchrz 0 0 -dof 6 -interp trilinear

 

 

e) Averaging of data_1_registered and data_2_registered  -out = data

f) Creation of the nodif.nii.gz with fslroi from data

g)Creation of nodif_brain_mask with BET

h) FSL --> DTIFIT Reconstruct diffusion tensors --> specify files manually (data, nodif_brain_mask, bvecs and bvals).

I get the following error message: Erros: Erro: data and bvals / bvecs do not contain the same number of entries

 

I hope I have explained well all I have done in order to facilitate the finding of my error...

 With my best regards,

Rosalia.

 

 

 

 

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