Hi Doety, Consider these options for uploading data: https://surfer.nmr.mgh.harvard.edu/fswiki/FtpFileExchange https://www.nmr.mgh.harvard.edu/facility/filedrop/index.html
I think recon-all is expecting your wm.mgz to be conformed or 256^3. Something like: mri_convert wm.mgz wm.conform.mgz --conform You would need to rename wm.conform.mgz to wm.mgz, after renaming or saving a copy of the current non-conformed wm mask you got from FSL. -Louis 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
