So the T2w image is already having the axes realigned to RAS with mri_convert in FreeSurfer prior to running -init-fsl? If that is the case, FLIRT should work well enough assuming the input orientation information in the T2w and T1w NIFTI headers was accurate. I suppose you could also restrict the -searchxyz angles to +/-30 degrees to keep FLIRT from making large (and incorrect if the axes are aligned) image rotations.
Peace,
Matt.
On 11/14/13 9:52 AM, "Bruce Fischl" fischl@nmr.mgh.harvard.edu wrote:
Hi Matt
hopefully Doug will chime in, but I don't see why that is the case. We preserve all the RAS information when we "conform", so the info should be there for flirt
cheers Bruce
On Thu, 14 Nov 2013, Matt Glasser wrote:
I think you can do it with mri_convert ?rl. I don't think it makes sense to expect FLIRT to get the registration right reliably if the axes are off (in the HCP Pipelines we definitely don't expect this and make sure all images are RPI before processing them).
Peace,
Matt.
From: Martijn Steenwijk martijnsteenwijk@gmail.com Date: Thursday, November 14, 2013 9:27 AM To: Bruce Fischl fischl@nmr.mgh.harvard.edu Cc: Veronica Popescu v.popescu@vumc.nl, Hugo Vrenken h.vrenken@vumc.nl, freesurfer freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] T2pial/FLAIRpial processing issues
Hi Matt, Bruce, The problems are indeed a flirt issue, but given that it's programmed with --init-fsl there is not much flexibility.
However, from a FS point of view, it might be a better and more robust approach to first register FLAIRraw.mgz to raw.mgz, and then concatenate the resulting registration with the (header based) registration from raw.mgz to orig.mgz - instead of trusting the robustness of either registration algorithms.
... or, as Matt suggests, fix the image axes appropriately after converting the FLAIR to mgz, and then run the registration. But I'm not sure how to do that.
Best, Martijn
On Thu, Nov 14, 2013 at 5:53 PM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote: Hi Martijn
we can print warning and errors if FSLDIR is not set, but the registration errros seem to be mostly a flirt issue, no? Have you posted on the FSL list? Bruce On Thu, 14 Nov 2013, Martijn Steenwijk wrote: Dear all, There seem to be some serious issues with the T2pial / FLAIRpial processing options provided in the latest versions of FreeSurfer. First of all, although not clearly documented, T2pial / FLAIRpial processing does require the FSLDIR to be set (in order to use bbregister with --init-fsl). If not set, recon-all will finish just without using the T2 or FLAIR information. Importantly, no clear warning about this is given although the user expects that T2/FLAIR has been used for pial surface refinement. I think this is a very easy source of errors, so it might be a good idea to just throw an error when FSLDIR is missing and T2pial/FLAIRpial processing is requested. Second, if FSLDIR has been set. T2pial/FLAIRpial uses bbregister with FLIRT initialisation to align the T2 or FLAIR image to orig.mgz. However, we have some high-res 3DFLAIR data in which this registration (more specifially, the FLIRT initialisation step of bbregister) seems to fail in more than half of the cases. Apparently, the FSL initialisation is not capable to change the orientation such that it fits to the coordinate system used for orig.mgz. Again, no warning or error is thrown, but the processing just continues with the wrong registration and without noticing the results will get worse compared to not using T2 or FLAIR. Although I know its essential to look at the output data; would it be possible to put some effort in letting the user know that things got wrong? As a sidenote; I tried to fix this registration issue, but it seems to be very complicated using bbregister (other than just inserting my own registration obtained by using FLIRT to register native FLAIR to native T1, and subsequently transform the result to Freesurfer space in order to obtain FLAIR.mgz). Best, MartijnThe 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.
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