Hi Michael, I took a look at your data and it seems that you paired a T2 image with a T1 image when you submitted to recon all. Recon-all will try to average these together, and since they have such different contrasts, you will end up with a poor template for surfaces later on.
Try running recon-all again without the T2 and see if that helps. -Ani On Wed, 2014-10-08 at 17:21 +0000, Smith, Michael wrote: > Ah, sorry for some reason it just wasn’t clicking before. I was able to > upload a dataset. Thanks! > > On 10/8/14, 10:59 AM, "Bruce Fischl" <fis...@nmr.mgh.harvard.edu> wrote: > > >Hi Michael > > > >you need to follow the directions on this page: > > > >http://surfer.nmr.mgh.harvard.edu/fswiki/FtpFileExchange > > > >in particular, make sure you change directories before trying to put > > > >cheers > >Bruce > > > >On Wed, > >8 Oct 2014, > >Smith, > >Michael wrote: > > > >> See attached > >> > >> On 10/8/14, 10:46 AM, "Bruce Fischl" <fis...@nmr.mgh.harvard.edu> wrote: > >> > >>> can you send us the details of your ftp command? > >>> On Wed, 8 Oct 2014, Smith, > >>> Michael wrote: > >>> > >>>> Hi Bruce, > >>>> > >>>> Do I not have permission to transfer files to the remote machine? I > >>>>can > >>>> login fine as an anonymous user but when I attempt to use the put > >>>> command > >>>> it says it could not create the file. > >>>> > >>>> On 10/7/14, 7:33 PM, "Bruce Fischl" <fis...@nmr.mgh.harvard.edu> > >>>>wrote: > >>>> > >>>>> Hi Michael > >>>>> > >>>>> sure, the T2 can help if you have it (although you'll need to > >>>>>download > >>>>> some > >>>>> updated binaries), but it is impossible to tell from these images > >>>>>what > >>>>> is > >>>>> going on. Looks either the intensity normalization, mri_segment or > >>>>> mris_make_surfaces failed. You can try the expert options for each > >>>>>one > >>>>> to > >>>>> prespecify the range of allowable intensities for gray and white > >>>>> matter. > >>>>> If > >>>>> you upload the subject to our ftp site (the whole subject directory > >>>>> tarred > >>>>> and gzipped) we will take a look > >>>>> > >>>>> cheers > >>>>> Bruce > >>>>> > >>>>> On Mon, 6 Oct 2014, Smith, Michael wrote: > >>>>> > >>>>>> Hi, > >>>>>> > >>>>>> I¹ve been having trouble on a few of our subjects with getting the > >>>>>> white > >>>>>> matter and pial surface files to ³line up² correctly with the volume > >>>>>> files. > >>>>>> I¹ve attached a screenshot of what is happening: the pial surface > >>>>>>is > >>>>>> in red > >>>>>> and the white matter surface file is in yellow. I have also attached > >>>>>> an > >>>>>> example of a ³good² subject for comparison. > >>>>>> > >>>>>> I¹ve tried looking through the tutorials online but didn¹t see > >>>>>> anything > >>>>>> that > >>>>>> was really related to my issue and I was wondering what the best way > >>>>>> to > >>>>>> correct this. We have T2 weighted images for several subjects is > >>>>>>well > >>>>>> if > >>>>>> that helps. Not sure if Freesurfer can use T2 images instead of T1 > >>>>>>in > >>>>>> the > >>>>>> reconall script but I thought I would mention it. Thank you very > >>>>>> much > >>>>>> in > >>>>>> advance! > >>>>>> > >>>>>> Best, > >>>>>> > >>>>>> Michael S. > >>>>>> > >>>> > >>>> > >>>> > >>>> _______________________________________________ > >>>> 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 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.
