Hi,
I am a bit confused here. The images that seem problematic are *not* coming from the fslvbm 2nd step, but from the 3rd one?...
If all of the * _struc_GM_to_T_init images are ok, especially the two problematic ones, then there should not be any problem with template_4D_GM, as this is a mere concatenation of these images?...
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
--------------------------------------------------------------------
Dear Gwenaëlle,
Thank you very much for your response. To my surprise many of the original images from these 2 subjects are ok. e.g. the images from the subj which does not appear in the template are as follows:
_struc_
_GM_
_struc_GM_to_T
_struc_GM_to_T_init
_struc_GM_to_T_init_warp..., are ok when checking in fslview. However, the:
_struc_GM_to_template_GM
_struc_GM_to_template_GM_mod
_struc_GM_to_template_GM_warp
_struc_JAC_nl..., when oppened in fslview are NaNs. Do you have some clue what could have happened?
I will try anyway with fslroi/fslmerge to discard them, but it would be great if i can solve it in order not to make the sample too short.
Thanks again!
Juan Blas
Von: FSL - FMRIB's Software Library [mailto:[log in to unmask]]
Im Auftrag von Gwenaëlle DOUAUD
Gesendet: Dienstag, 10. April 2012 18:01
An: [log in to unmask]
Betreff: [FSL] Re : [FSL] template_GM_4D
not sure what's happening here, but quite likely flirt or fnirt (affine/NL registration) has failed for these two subjects. You need to have a look at the original _struc and _GM images
to understand why.
If there is no way of recovering these images, then you can just use fslroi/fslmerge on
template_GM_4D to edit these two out. Then average with fslmaths, flip the result with fslswapdim, and average the two to obtain a symmetric template.
--------------------------------------------------------------------
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
--------------------------------------------------------------------
Dear FSLers,
I´am quite new at FSL and have been trying the fslvbm script with a sample of 20 patients and 21 controls. After the fslvbm_2_template step had finished, I took a look at the file template_GM_4D with fslview motion loop tool, and realized there are two no proper
slices (number 7th: NaN, and number 37th: weird zoomed image). I would like to know how to edit this template in order to continue with step 3 of fslvbm, and if does any of you have any idea on why this errors occur?
Thanks in advance,
Cheers,
Juan Blas
