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 >> >>
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