thanks Dr. Fischl, Would there be a reason as to why recon-all crashed when doing the conformation then? I got the following error in my terminal:
Original Data has (0.5, 0.5, 0.5) mm size and (394, 466, 378) voxels. Data is conformed to 1 mm size and 256 voxels for all directions changing data type from short to uchar (noscale = 0)... MRIchangeType: Building histogram Reslicing using trilinear interpolation writing to /data-01/trisanna/freesurfer/MNI_average_2009b_asymm/mri/orig.mgz... mri_add_xform_to_header -c /data-01/trisanna/freesurfer/MNI_average_2009b_asymm/mri/transforms/talairach.xfm /data-01/trisanna/freesurfer/MNI_average_2009b_asymm/mri/orig.mgz /data-01/trisanna/freesurfer/MNI_average_2009b_asymm/mri/orig.mgz INFO: extension is mgz #-------------------------------------------- #@# Talairach Tue May 24 19:10:10 EDT 2016 /data-01/trisanna/freesurfer/MNI_average_2009b_asymm/mri mri_nu_correct.mni --n 1 --proto-iters 1000 --distance 50 --no-rescale --i orig.mgz --o orig_nu.mgz recon-all -s MNI_average_2009b_asymm exited with ERRORS at Tue May 24 19:11:34 EDT 2016 -- Ph.D. Candidate McGill University Integrated Program in Neuroscience Psychology On Wed, May 25, 2016 at 6:49 PM, Bruce Fischl <fis...@nmr.mgh.harvard.edu> wrote: > Hi Trisanna > > you can use the -cm flag, but typically what we do is let recon-all > "conform" the data to 1mm, then do a post-hoc surface deformation with > the original highres data using mris_make_surfaces > > cheers > Bruce > On Wed, 25 May 2016, Trisanna Sprung-Much wrote: > > > Hi there > > > > My initial email didn't seem to have sent and so I am re-sending it: > > > > I would like to know if it is possible to create surfaces from a scan > that > > is 0.5mm isotropic. I tried to run recon-all on our MNI 2009b atlas > which is > > 0.5mm cubed and it crashed quite quickly afterwards. I wonder if this > has to > > do with the fact that Freesurfer tried to conform it to 1mm isotropic? > > > > When I ran recon-all on the 1mm atlas it created some nice surfaces. > > > > Let me know if you would like the .log as I cannot seem to make much > sense > > of it. > > > > best wishes > > > > Trisanna > > -- > > Ph.D. CandidateMcGill University > > Integrated Program in Neuroscience > > Psychology > > > > > > > _______________________________________________ > 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. > >
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