the 2mm slice thickness is going to be problematic and is probably why you lose so much cortical constrast. Typically we don't recommend using anything more than 1.5 and really no reason these days not to get closer to 1mm (for example, you can get a very nice 1.25mmx1.25x1mm mprage in a bit over 2 minutes)
cheers Bruce On Fri, 11 Jul 2014, Doety Prins wrote: > slice thickness: 2 mm > Repetition time: 25 ms (I think this might have caused the low contrast) > flip angle: 30 degrees > I'm sorry, can't find any data on acceleration > > Doety > > On 11 jul. 2014, at 15:10, Bruce Fischl <fis...@nmr.mgh.harvard.edu> wrote: > >> Hi Doety >> >> that is a very low contrast-to-noise image. Can you give us more details >> on the acquisition? The matrix was 256x256, what is the slice thickness? >> And the other parameter (sequence name? TR/TR/flip angle? acceleration?) >> >> cheers >> Bruce >> >> >> On >> Thu, 10 Jul 2014, Doety Prins wrote: >> >>> 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 >>> >>> >>> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
