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FSL  August 2011

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Subject:

Re: TBSS exception

From:

Mark Jenkinson <[log in to unmask]>

Reply-To:

FSL - FMRIB's Software Library <[log in to unmask]>

Date:

Mon, 22 Aug 2011 08:41:11 +0100

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text/plain

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Dear Christine,

When you say "left-right reversed" this is only about the storage and
not the coordinates or the labels.  As it is only the coordinates and
the labels that count in FSL then it is unimportant what the storage type
is, and it does not reflect the fact that there is any flipping of any 
sort involved.  It does not matter whether images are stored as "neurological"
or "radiological" for pipelines within FSL.  However, when mixing FSL
with other tools it is very possible that there might be problems, especially
if you create pipelines involving a mix of images that are "radiological"
and "neurological".  I cannot comment more on the specifics as it no
doubt depends exactly on how you are using FSL and AFNI, but I would
like to again confirm the fact that users of FSL alone do not need to 
worry about flipping of their data as long as the original labels are correct.

All the best,
	Mark


On 21 Aug 2011, at 04:55, Christine Zakrzewski wrote:

> Dear Mark, 
> First of all, thanks to you and all the rest of the gurus in providing me an invaluable education, simply by reading the posts to this forum.
> I originally commented that the templates included with FSL tend to be left-right reversed from orthogonal space (ie, the template matrix is -2 0 0; 0 2 0; 0 0 2 instead of 2 0 0; 0 2 0; 0 0 2). The user had mentioned that he was using nifti files--their native orientation is neurological. However, wouldn't the negative determinant of the matrix associated with the FSL template reverse the orientation of the images applied to it in the non-linear transform?
> We have experienced a similar issue in our lab--left/right flipping--when using nifti files (converted from dicom with Chris Rorden's script, preprocessed with tbss, between-subjects analysis with AFNI) when switching between AFNI and FSL. We have been unable to identify the exact source of the issue until now. Users of (f)MRI data should be aware of theses issues during all steps of the pipeline, especially when switching between platforms.
> Thank you for this detailed response, and bringing us closer to the answer.
> Christine
> 
>>>> Mark Jenkinson <[log in to unmask]> 08/20/11 3:23 AM >>>
> Dear Christine,
> 
> We have been *extremely* careful about the left-right issue in FSL and have gone to a great deal of trouble to test and verify the fact that FSL will not flip data.  So this is *NOT* something that people need to worry about. I have not seen any instance of this problem and I have done a *lot* of checking.
> 
> It is also incorrect to say that we ignore the sform and qform.  We in fact always take into account the sign of the determinant, which determines whether it is a right-handed or left-handed coordinate system.  If it is different from the templates (which are the FSL "native" handedness, or what we have also called "radiological" storage) then we take this into account in *all* of the FSL tools.
> 
> What is absolutely crucial is that all users check is that the original images that they are using and *labelled* correctly - including for left and right.  This ensures that the sform/qform information is correct.  This can be checked by looking at the labels in FSLView (and is best if there is a marker, like a vitamin capsule, so that left and right can be distinguished by simply looking at the image).
> 
> If the labelling is correct then we are *extremely* confident that FSL will not flip left and right at any point in any tool in our pipelines.  If it is not correct then it needs to fixed at this point and *no* analysis should be done using these images until the labels are fixed.  I would like all users of FSL to understand this and know that as long as the labels are correct then everything will work fine and that we have put a lot of effort into ensuring that this is true.
> 
> The fact that the templates use a negative determinant matrix is not important as we can deal just as happily with a positive determinant version.  We have carefully checked this, as I've said above.  The statement that the templates "tend to be left-right reversed from orthogonal space" isn't accurate.  There is no such thing as a standard "orthogonal space", although maybe you are referring to the x,y,z (mm) NIfTI coordinate system (which is an arbitrary choice, but at least a standardised one).  It is true that the voxel coordinates space of these template images is different in left-right orientation, but this is exactly what the sform and qform are there to give information about.  And because we use the information from them in *all* tools and have checked all the combinations of handedness and orientation *very carefully* then we are *extremely* confident that everything works correctly in FSL.
> 
> I would like to reassure all users that flipping is not going to happen, not in non-linear registration and not in any other case (with the one exception of fslswapdim which can deliberately do this but because of that we strongly discourage people from using it - they can use fslreorient2std instead which will never swap left-right).
> 
> I hope this is clear and reassures everyone about the status of left-right flipping and FSL.
> 
> All the best,
> 	Mark
> 
> 
> 
> On 20 Aug 2011, at 07:20, Christine Zakrzewski wrote:
> 
>> Most of the FSL tools ignore the NIfTI spatial transforms (both QForm and SForm). Additionally, the templates included with FSL tend to be left-right reversed from orthogonal space (ie, the template matrix is -2 0 0; 0 2 0; 0 0 2 instead of 2 0 0; 0 2 0; 0 0 2). Therefore, you need to be very careful when using FSL for normalization. I would ensure the images are not flipped during the non-linear registration. 
>> 
>> 
>>>>> Morten Bruvold <[log in to unmask]> 08/19/11 9:54 AM >>>
>> Hi, I receive this error message when trying to run randomise on tbss_sym data from the tool "Testing left vs. right in TBSS":
>> randomise -i all_FA_skeletonised_left_minus_reight.nii.gz -o randomiseLRdiff -1 -v 5 -T
>> 
>> ERROR: Program failed
>> 
>> An exception has been thrown
>> Data mask is blank.
>> 
>> Exiting
>> 
>> I tried first dcm2nii and then MRIconvert for conversion of data to nifti. Both give the same error. When viewing the mean_FA_skeleton_mask i can see the proper mask image.
>> Do anyone have a clue about what could be wrong?
>> Regards,
>> Morten
>> 
>> 
>> The information in this transmission is intended for official use of the Kessler Foundation.  It is intended for the exclusive use of the persons or entities to which it is addressed.  If you are not an intended recipient or the employee or agent responsible for delivering this transmission to an intended recipient, be aware that any disclosure, dissemination, distribution or copying of this communication, or the use of its contents, is strictly prohibited.  If you received this transmission in error, please notify the sender by return e-mail and delete the material from any computer.
>> 
> 

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