Hi Bruce, Thanks for your reply. In my previous e-mail I already tried to attach one of my subjects, but got the response that the message was too big, and therefore it was rejected. So how should I upload the image? The images are T1-weighted, 3D, acquired with a 3T scanner, resolution 256 256.
I discovered that FSL does a proper segmentation on this subjects, so I was looking for a way to import these segments from FSL into the Freesurfer pipeline, but I didn't succeed so far. I used the white matter segment from FSL as wm.mgz (in a subject in which I already ran recon-all), I used mri_vol2vol to get this segment in the right space, and normalized with mri_normalize. Then I rerun recon-all with -autorecon2-wm. But it gives me the error message: 'ERROR: mri_segment-MRIcheckVolDims: volume1 depth=160 != volume2 depth=256.' So apparently, the wm.mgz still doesn't have the right size. Do you have any experience with this? Or any ideas about this? Best regards, Doety On 9 jul. 2014, at 15:00, Bruce Fischl <fis...@nmr.mgh.harvard.edu> wrote: > Hi Doety > > yes, that looks pretty bad. Can you tell us about the acquisition? What > resolution/field strength/scan type was it? > > If you upload the subject we will take a look > > cheers > Bruce > On Wed, 9 Jul 2014, Doety > Prins > wrote: > >>> Dear freesurfer experts, >>> >>> I experienced some problems with the segmentation of my T1 scans, as both >>> the white surface and the pial surface are placed incorrectly (see attached >>> images). This seems to me to be a too big difference with what it should >>> look like, that I think could not be fixed with the standard >>> troubleshooting strategies. >>> >>> Do you have any solutions for this? Is it for instance possible to make >>> changes to the recon-all script to shift the surfaces? >>> >>> Thanks in advance, >>> >>> Doety >> >> > _______________________________________________ > 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 mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
