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Dear FSL users

I have one functional run of an fMRI task that I have preprocessed with feat to generate the appropriate first level feat directory. I want to register the statistics in the feat directory to standard space with the featregapply command so I can convert the standard space cope images to zstats. First, when I run the featregapply command on the feat directory it creates the cope and varcope files for each of my contrasts but doesn't create the FE_dof files for some of the subjects. I understand that I require the FE_dof for each cope image to perform the ttoz command. The preprocessing for each subject is identical by the way.

Any idea why this is happening?

Second, on the subjects where it does create the FE _dof files, I receive an error when I attempt to run the ttoz.

Command performed:

ttoz -zout zstat1.nii.gz varcope1.nii.gz cope1.nii.gz FEtdof_t1.nii.gz

Error received:

Error: failed to open file zstat1.nii.gz

Image Exception : #22 :: ERROR: Could not open image zstat1

An exception has been thrown

ERROR: Could not open image zstat1Trace: save_basic_volume4D.

terminate called after throwing an instance of 'RBD_COMMON::BaseException'

Aborted.

Any idea why this is happening?

Many thanks,

Liam.



---- Colin Hawco wrote ----

A wise colleague of mine once likened judging registrations to what the US supreme court said about art vs. ... explicit images which are not art: It may be hard to define but you know it when you see it.

I think the best practice is to look at it and make a judgement. Overlay the image on the template and see if there is any regions where it is a bad fit. The top of the brain should be smooth when you look at a sagittal view, not all bumpy and distorted (though check the unregistered MRI for unusual shape as well). Look at several scans together: if they are well normalized, they should overlap quite nicely. If the brains do not have a fairly consistent shape or one has a different shape/appearance than the other, this suggests a problem.

Good luck!


Colin Hawco, PhD
Neuranalysis Consulting
Neuroimaging analysis and consultation
www.neuranalysis.com
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-----Original Message-----
From: FSL - FMRIB's Software Library [mailto:[log in to unmask]] On Behalf Of Sam
Sent: March-16-16 5:13 AM
To: [log in to unmask]
Subject: [FSL] Nonlinear Registration Quality

Dear Experts,

I would like to understand more about what I should be looking for to help me know whether registration should be considered 'good' - particularly nonlinear. I have looked at the Wiki, FSL course and mailing list, but not found anywhere with any detail (ideally with pictures). Can anyone direct me to any resources please?

Thanks.
Sam.