mri_vol2surf will produce an overlay, not a surface. If you want an overlay, use .nii or .mgh instead of .w or .gii (no need for --out_type) doug
On 02/03/2014 04:33 PM, Markus Gschwind wrote: > Hi Bruce, > > Thank you! The creation of register.data worked perfectly. > > Now in order to create the mesh file (I suppose .w) of the altered > brain with cut out temporal lobe (brain_T1fin), would this command be OK? > > mri_vol2surf --src FREESURFER/mri/brain_T1fin.nii.gz --srcreg > FREESURFER/mri/register2.dat --hemi lh --projfrac 0.5 --out > FREESURFER/mri/brain_T1fin_surf.w --out_type nifti > > ...however I get > ERROR: could not determine type of FREESURFER/mri/brain_T1fin_surf.w > > And when using output_type 'paint' or 'gii' (without the ' ' ) it is > calculating something, but freeview crashes when I try to look at > it... Actually I have no clue what the output_type should be... > > Thanks so much! > Markus > > > 2014-02-03 Bruce Fischl <fis...@nmr.mgh.harvard.edu > <mailto:fis...@nmr.mgh.harvard.edu>>: > > Hi Markus > > the --s option should be a subject name, not a path to a volume > > cheers > Bruce > > On Mon, 3 Feb 2014, Markus Gschwind wrote: > > Hi again, > It is certainly a beginners question, and probably the code > examples given > below are not right... > > Is there anyone that could advice me how to do this? > > Thanks so much! > Markus > > > 2014-02-01 Markus Gschwind <markus.gschw...@gmail.com > <mailto:markus.gschw...@gmail.com>>: > Dear all, > I want to create a surface of a partially altered brain T1 > (temporal > lobe cut away by hand). > > I figured out that this would be done with mri_vol2surf. > > This command asks for a register.dat file. > > I think that I can get it using this command: > > SUBJECT_DIR=/Users/FREESURFER > > bbregister --s /mri/brain_T1.mgz --mov > /Users/FREESURFER/mri/brain_T1_ins.mgz --reg > /FREESURFER/mri/register.dat --t1 --init-spm > > I well starts calculation, but suddenly stops and complains > that there > is no brainmask > /Users/FREESURFER/mri/brain_T1.mgz/mri/brainmask.mgz > > which makes somehow no sense as the brainmask is in > /Users/FREESURFER/mri/brainmask.mgz of course. > > But I don't find a option to specify the brainmask in bbregister. > > What am I doing wrong? > > Thanks for any help! > Markus > > > > > > > > > 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 -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
