[Freesurfer] orientation problem resulting in talairach failure
Dear Freesurfer developers, I have a few analyse images which are oriented incorrectly that are part of a larger dataset. When viewed in tkmedit, what is supposed to be coronal is actually displayed as axial and the sagittal is flipped. In these cases the Talairach transform fails spectacularly. To try and fix the problem I used mri_info to determine the orientation information of my good files (LSA) and of the ones that aren't working (LAS), then used mri_convert with the --in_orientation and out_orientation flags to change the dimensions in analyse format. The analyze images look fine in MRIcro and the orig.mgz looks fine in tkmedit, but yet again the Talairach fails in the same way. I've also tried this by reorienting the images using MRIcro but this has the same result. When you view the analyze images using GWRaw MRI viewer http://www.wideman-one.com/gw/brain/orientation/orientterms.htm (supposed to read the image file without header information), they look the same, but I'm a bit unsure of this program. I'm really at a bit of a loss to try and fix this problem now so any help or suggestions would be really appreciated! Many thanks, Dominic Melbourne Neuropsychiatry Centre ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] orientation problem resulting in talairach failure
Hi Bruce, Thanks for your quick reply. Unfortunately the images are more than 10 years old and have only been stored on our systems in analyze format. I'm trying to source the original DAT tapes, but thought I'd try to fix the problem without them. In the main I was puzzled that tkmedit reads the converted image ok, but the talairach fails as if the orientation information was still wrong. If there are other things I could try it would be great to know, otherwise I'll just cross my fingers and hope for the tapes. Thanks very much. Dominic -Original Message- From: Bruce Fischl [mailto:fis...@nmr.mgh.harvard.edu] Sent: Monday, 2 November 2009 11:20 PM To: Dominic Brendon Dwyer Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] orientation problem resulting in talairach failure Hi Dominic, do you have access to any format previous to the analyze one? It doesn't preserve orientation info, and all bets are off once you go through it. cheers Bruce On Mon, 2 Nov 2009, Dominic Brendon Dwyer wrote: > Dear Freesurfer developers, > > > > I have a few analyse images which are oriented incorrectly that are part > of a larger dataset. When viewed in tkmedit, what is supposed to be > coronal is actually displayed as axial and the sagittal is flipped. In > these cases the Talairach transform fails spectacularly. > > > > To try and fix the problem I used mri_info to determine the orientation > information of my good files (LSA) and of the ones that aren't working > (LAS), then used mri_convert with the --in_orientation and > out_orientation flags to change the dimensions in analyse format. The > analyze images look fine in MRIcro and the orig.mgz looks fine in > tkmedit, but yet again the Talairach fails in the same way. I've also > tried this by reorienting the images using MRIcro but this has the same > result. > > > > When you view the analyze images using GWRaw MRI viewer > http://www.wideman-one.com/gw/brain/orientation/orientterms.htm > (supposed to read the image file without header information), they look > the same, but I'm a bit unsure of this program. > > > > I'm really at a bit of a loss to try and fix this problem now so any > help or suggestions would be really appreciated! > > > > Many thanks, > > > > Dominic > > Melbourne Neuropsychiatry Centre > > > > > > > > > > ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] QDEC discrete covariate question
Hi all, We're using QDEC DODS to compare the average thickness maps of patients V. controls using sex and age as covariates. The results are identical for "Does the average thickness differ between patientsVscontrols with sex and age as covariates" and "Does the average thickness differ between sex with patientsVscontrols and age as covariates". This doesn't seem to make sense (with my limited statistical knowledge) because the criterion variable has changed. Also it is not the case that the groups contain only one sex. Could anyone shed light on this? Also, we tried to check the contrasts but weren't able to find the categories for each of the columns in the vector. Where can this be found? Thanks very much in advance, Dominic Melbourne Neuropsychiatry Centre ___ 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.
[Freesurfer] re-calculating stats based on an updated ?h.pial surface
Hi all, We're using a tool which allows direct alteration of the pial surface (http://sites.google.com/site/vxxsoftware/) resulting in another ?h.pial file being created. We've found that it is a good way to both decrease and increase the pial boundary where there are errors. The current procedure is to use mris_fill once the surfaces are created and then apply this to the brainmask.mgz before re-running recon2. I was wondering if it was possible to recalculate the surface stats based on an altered ?h.pial file without running recon2 again? The reason being is that if the surface is extended rather than reduced then it will not necessarily appear in the updated pial surface. Any help would be greatly appreciated. Many thanks, Dominic Melbourne Neuropsychiatry Centre ___ 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.
