Could you post your bvecs and bvals files also?

In future studies, you will want to avoid having scanner interpolation on (the cause of your highly anisotropic voxels 0.85X0.85X2.3mm), as this is not ideal for tractography studies. This is not the cause of your current issue, however.

Peace,

Matt.

From: FSL - FMRIB's Software Library [mailto:[log in to unmask]] On Behalf Of cathyliu
Sent: Wednesday, March 25, 2009 12:00 PM
To: [log in to unmask]
Subject: Re: [FSL] white FA maps

Hi,

I have checked by bedpostx_datacheck, but I don't know what it means... Here is the results:

[yan@localhost ~]$ /opt/fsl/bin/bedpostx_datacheck /mnt/hgfs/Data/Yan/NeonatalDTI/AKBULUT/data/
/mnt/hgfs/Data/Yan/NeonatalDTI/AKBULUT/data//data
data_type      FLOAT32
dim1           116
dim2           160
dim3           45
dim4           33
datatype       16
pixdim1        0.8593750000
pixdim2        0.8593750000
pixdim3        2.3000710011
pixdim4        1.0000000000
cal_max        0.0000
cal_min        0.0000
file_type      NIFTI-1+
/mnt/hgfs/Data/Yan/NeonatalDTI/AKBULUT/data//nodif_brain_mask
data_type      INT16
dim1           116
dim2           160
dim3           45
dim4           1
datatype       4
pixdim1        0.8593750000
pixdim2        0.8593750000
pixdim3        2.3000710011
pixdim4        1.0000000000
cal_max        0.0000
cal_min        0.0000
file_type      NIFTI-1+
num lines in /mnt/hgfs/Data/Yan/NeonatalDTI/AKBULUT/data//bvals
1
num words in /mnt/hgfs/Data/Yan/NeonatalDTI/AKBULUT/data//bvals
33
num lines in /mnt/hgfs/Data/Yan/NeonatalDTI/AKBULUT/data//bvecs
3
num words in /mnt/hgfs/Data/Yan/NeonatalDTI/AKBULUT/data//bvecs
99

Regards,

Yan

Date: Wed, 25 Mar 2009 17:28:20 +0100
From: [log in to unmask]
Subject: Re: [FSL] white FA maps
To: [log in to unmask]

Ok, I see.

So seems that dtifit did not work...
Have you tried
bedpostx_datacheck <dtifit_directory>
?
Regards,
Markus

2009/3/25 cathyliu <[log in to unmask]>

Hi,

The white FA maps means that the FA value is 1.06592 everywhere in the brain mask, so it is quite high anisotropic.

The eddy corrected data look perfect, and the brain mask covers all the brain. As the FA maps are white, I don't continue to do the bedpostX yet.

Thank you so much!

Regards,

yan

Date: Wed, 25 Mar 2009 15:56:33 +0100
From: [log in to unmask]
Subject: Re: [FSL] white FA maps
To: [log in to unmask]

Hi!
What do you mean by white FA maps?
Is fslstat FAmap -R [0 0]?

How do the eddy_corrected data look like? How the brain mask?
What does "bedpostx_datacheck" on the dtifit directory return?

Could you give more information, please?

All the best,
Markus

2009/3/25 cathyliu <[log in to unmask]>

Hi,

We have some problems to make good FA maps, and L1,L2,L3,MD,V1,V2,V3...maps don't work either. We do the image preparation following your instructions, it works in most of our cases, but in 3 of them we have the white FA maps. We could view the oraginal data 32 directions without any problem, and there is not error information during the processing. We wonder if it is the problem of the old scanner version, or the wrong gradient table which FSL doesn't recognize. These three cases were examined in the machine:

Scanner software version: NT 9.1.1.3
scanner model: Gyroscan Intera
number of directions: 32
phase encoding direction: AP

Regards,

Yan

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--
Dr. med. Markus Gschwind, M.D.
Laboratory for Neurology and Imaging of Cognition
Dept of Neurosciences
University Medical Center (CMU)
1 Michel-Servet - 1211 GENEVA - CH

Tel 0041 (0) 22 379 5324
Fax 0041 (0) 22 379 5402
email: [log in to unmask]
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