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hth d On Thu, Jul 2, 2015 at 8:57 AM, Mojdeh Zamyadi <mojde...@gmail.com> wrote: > Could someone please tell me how to unsubscribe from this list? I couldn't > find it on the website. > Thanks > > On Jul 2, 2015 4:56 AM, "Milde, Christopher" > <christopher.mi...@zi-mannheim.de> wrote: >> >> Dear Freesurfers, >> >> I have problems converting .nii.gz files into .mgh files needed e.g. for >> performing ROI analysis. >> >> I used mri_vol2surf and mri_vol2vol to produce .mgh files either to >> visualize contrast estimates and significance maps on volumes or surfaces >> >> I think the problem is due to voxel resolution mismatches between source >> and registration files but I don't know how to solve this problem. >> >> I worked with different registration files: the register.dof6.dat >> (originally outpu from the preproc-sess) as well as register.dat and >> register.lta by running bbregister for the template.nii.gz >> >> >> >> --------------------------------------------------------------------------------------------------------------------------- >> here is an example command: >> >> # resample to surface >> >> mri_vol2surf --mov $sub/bold/EX.sm5.lh/EX/sig.nii.gz --reg >> $sub/bold/register.lta --projfrac 0.5 \ >> --interp nearest --hemi lh --o $sub/bold/lh.sig.mgh >> >> >> mri_vol2surf --mov $sub/bold/EX.sm5.lh/EX/sig.nii.gz --reg >> $sub/bold/register.lta --projfrac 0.5 \ >> > --interp nearest --hemi lh --o $sub/bold/lh.sig.mgh >> srcvol = PM_04001/bold/EX.sm5.lh/EX/sig.nii.gz >> srcreg = PM_04001/bold/register.lta >> srcregold = 0 >> srcwarp unspecified >> surf = white >> hemi = lh >> ProjFrac = 0.5 >> thickness = thickness >> reshape = 0 >> interp = nearest >> float2int = round >> GetProjMax = 0 >> INFO: float2int code = 0 >> Done loading volume >> regio_read_register: loading lta >> reading extra input line subject PM_04001 >> reading extra input line fscale 0.150000 >> WARNING: the voxel resolution in the source volume (1,1,1) differs >> from that listed in the registration file (2.29167,2.29167,2.99) >> Reading surface /home/christopher/subjects/PM_04001/surf/lh.white >> Done reading source surface >> Reading thickness /home/christopher/subjects/PM_04001/surf/lh.thickness >> Done >> Mapping Source Volume onto Source Subject Surface >> 1 0.5 0.5 0.5 >> using old >> Done mapping volume to surface >> Number of source voxels hit = 5 >> Writing to PM_04001/bold/lh.sig.mgh >> Dim: 126553 1 1 >> >> >> ---------------------------------------------------------------------------------------------------------------------------- >> >> Thanks, >> >> Christopher >> >> _______________________________________________ >> 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 > > > 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
