Sorry, I always use 'dcm2nii' at the Linux command line, not a GUI version.  What platform are you using?

'dtifit' will not perform any correction for angulation.  That needs to be done by 'dcm2nii'.  But again, I'm used to that being the default setting anyway (at least at the command line).  Don't you get output to the terminal indicating that the bvecs are being rotated?

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: "Raphael F.C." <[log in to unmask]>
Reply-To: FSL - FMRIB's Software Library <[log in to unmask]>
Date: Friday, May 8, 2015 10:21 AM
To: FSL - FMRIB's Software Library <[log in to unmask]>
Subject: Re: [FSL] TBSS - FOV angulation

Thank you, Michael!

Just to understand it better:

In dcm2nii, Help->Preferences, there is the checkbox 'Reorient large images to the nearest orthogonal plane'. And it says that it will not have any effect on DTI images to avoid 'disrupting interpretation of the principle vectors'.
Does this mean that I can either check or uncheck this box, and this will not affect the DTI?


"If your acquisition was angled, then yes, you want to account for that in the bvecs if using 'dtifit'"
Does it mean that bvec file will be corrected after transformation so that I don't need to worry with converted DTI images, i.e., that I can just input these images into dtifit? O should I expect dtifit to perform that correction (The later is what I understood from the quotation above).

2015-04-28 11:09 GMT-03:00 Harms, Michael <[log in to unmask]>:

Hi,

If you are using the default settings, then yes, 'dcm2nii' should correct the bvecs for the slice angulation.  If you pay attention to the output to the terminal (if using command line 'dcm2nii') you can confirm that this is indeed the case.

If your acquisition was angled, then yes, you want to account for that in the bvecs if using 'dtifit'.

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: "Raphael F.C." <[log in to unmask]>
Reply-To: FSL - FMRIB's Software Library <[log in to unmask]>
Date: Tuesday, April 28, 2015 6:26 AM
To: FSL - FMRIB's Software Library <[log in to unmask]>
Subject: Re: [FSL] TBSS - FOV angulation

Dear Andreas,

Just to be crystal clear:

1) dcm2nii will correct the gradient table by the angulation used in the FOV. Is that right? Is there any special option that I need to check in order to do so? Because I have already converted DICOM images to nifti used mricron (dcm2nii), but I didn't check any option box in particular.

2) If I don't do it, do you think there is going to be any problem?

Thank once more,
Raphael

2014-12-11 9:54 GMT-02:00 Andreas Bartsch <[log in to unmask]>:
No, dtifit itself doesn't. You may do that with the DICOM to NIFTI conversion, e.g. using dcm2nii or MRIConvert.
Cheers,
Andreas

Von: "Raphael F.C." <[log in to unmask]>
Antworten an: FSL - FMRIB's Software Library <[log in to unmask]>
Datum: Donnerstag, 11. Dezember 2014 12:15
An: <[log in to unmask]>
Betreff: [FSL] TBSS - FOV angulation

Dear all,

Does anybody know if the DTIfit tool corrects the gradient direction table when I use an angulated FOV? Does it matter for TBSS?

I was talking to some researches that I know and they all used a non angulated FOV, but they were not sure if in the TBSS processing (or preprocessing steps, like DTIfit) the algorithm would correct the gradient table for this angulation.

Thank you very much,
Raphael
--
Raphael F. Casseb
Medical Physicist, Ph.D. Student 
Medical Physics Lab - State University of Campinas



--
Raphael F. Casseb
Medical Physicist, Ph.D. Student 
Medical Physics Lab - State University of Campinas

 

The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail.




--
Raphael F. Casseb
Medical Physicist, Ph.D. Student 
Medical Physics Lab - State University of Campinas
Contact: +55 19 3521-8246

 

The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail.