Re: [Freesurfer] Issues processing brain hemispherectomized patients

[Bruce Fischl]

Hi Hinke

mri_em_register, mri_ca_label, mri_ca_register and mri_ca_normalize all 
take -lh and -rh commands to indicate that only one hemisphere exists. Try 
including them and see if it fixes things (you should be able to use expert 
options for this). We have only used it for ex vivo analysis in the past, 
but hopefully it will do the trick for you


cheers
Bruce


On Wed, 12 Oct 2016, Halbertsma, 
HN (ohk) wrote:



Dear all,
I’m having troubles getting a good Freesurfer output from a
hemispherectomised brain using recon-all. I was wondering whether there’s
someone that has experience with running Freesurfer on such an unusual
brain?

The first couple of issues I bumped into were failures regarding the
talaraich alignment which I solved using registration matrices from FSL. 

The issue I’m having now regards the labeling of subcortical structures.
Apparently Freesurfer cannot deal with the fact that there’s just one
hemisphere, and the fact that there is no clear corpus callosum. It looks
like it’s trying to divide one hemisphere into two, which obviously messes
up the subcortical labelling.
Any ideas on how to work around this issues? 

Is there maybe a way to mirror the intact hemisphere pretending to form a
full brain? Or are there any flags I can use to make sure the subcortical
labelling works fine? 

Thanks in advance

Hinke N. Halbertsma, MSc

PhD Student
University Medical Center Groningen (UMCG)
Department of Ophthalmology
NeuroImaging Center (Antonius Deusinglaan 2,  9713 AW Groningen), room 124
T. (+31) 050 363 4431
E. h.n.halbert...@umcg.nl








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[Freesurfer] Issues processing brain hemispherectomized patients

[Halbertsma, HN (ohk)]

Dear all,

I’m having troubles getting a good Freesurfer output from a hemispherectomised 
brain using recon-all. I was wondering whether there’s someone that has 
experience with running Freesurfer on such an unusual brain?

The first couple of issues I bumped into were failures regarding the talaraich 
alignment which I solved using registration matrices from FSL.

The issue I’m having now regards the labeling of subcortical structures. 
Apparently Freesurfer cannot deal with the fact that there’s just one 
hemisphere, and the fact that there is no clear corpus callosum. It looks like 
it’s trying to divide one hemisphere into two, which obviously messes up the 
subcortical labelling.
Any ideas on how to work around this issues?

Is there maybe a way to mirror the intact hemisphere pretending to form a full 
brain? Or are there any flags I can use to make sure the subcortical labelling 
works fine?

Thanks in advance

Hinke N. Halbertsma, MSc

PhD Student
University Medical Center Groningen (UMCG)
Department of Ophthalmology
NeuroImaging Center (Antonius Deusinglaan 2,  9713 AW Groningen), room 124
T. (+31) 050 363 4431
E. h.n.halbert...@umcg.nl








De inhoud van dit bericht is vertrouwelijk en alleen bestemd voor de 
geadresseerde(n). Anderen dan de geadresseerde(n) mogen geen gebruik maken van 
dit bericht, het niet openbaar maken of op enige wijze verspreiden of 
vermenigvuldigen. Het UMCG kan niet aansprakelijk gesteld worden voor een 
incomplete aankomst of vertraging van dit verzonden bericht.

The contents of this message are confidential and only intended for the eyes of 
the addressee(s). Others than the addressee(s) are not allowed to use this 
message, to make it public or to distribute or multiply this message in any 
way. The UMCG cannot be held responsible for incomplete reception or delay of 
this transferred message.
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.