A quick look at the source shows that the same error text is used when the mask volume doesn't have the same dimensions as the cortical ribbon volume, please check that file also.
Tim On Thu, Jul 31, 2014 at 1:31 PM, <sha...@nmr.mgh.harvard.edu> wrote: > Matt, > The output of fslhd when i apply it to my T1 and T2 files are as below: > > For T2: > > filename T2w.nii.gz > > > sizeof_hdr 348 > data_type INT16 > dim0 3 > dim1 256 > dim2 256 > dim3 256 > dim4 1 > dim5 1 > dim6 1 > dim7 1 > vox_units mm > time_units s > datatype 4 > nbyper 2 > bitpix 16 > pixdim0 0.0000000000 > pixdim1 1.0000000000 > pixdim2 1.0000000000 > pixdim3 1.0000000000 > pixdim4 3.2000000477 > pixdim5 0.0000000000 > pixdim6 0.0000000000 > pixdim7 0.0000000000 > vox_offset 352 > cal_max 0.0000 > cal_min 0.0000 > scl_slope 1.000000 > scl_inter 0.000000 > phase_dim 0 > freq_dim 0 > slice_dim 0 > slice_name Unknown > slice_code 0 > slice_start 0 > slice_end 0 > slice_duration 0.000000 > time_offset 0.000000 > intent Unknown > intent_code 0 > intent_name > intent_p1 0.000000 > intent_p2 0.000000 > intent_p3 0.000000 > qform_name Scanner Anat > qform_code 1 > qto_xyz:1 -1.000000 -0.000000 -0.000000 123.848427 > qto_xyz:2 -0.000000 -0.000000 1.000000 -86.819458 > qto_xyz:3 0.000000 -1.000000 0.000000 136.943146 > qto_xyz:4 0.000000 0.000000 0.000000 1.000000 > qform_xorient Right-to-Left > qform_yorient Superior-to-Inferior > qform_zorient Posterior-to-Anterior > sform_name Scanner Anat > sform_code 1 > sto_xyz:1 -1.000000 -0.000000 0.000000 123.848427 > sto_xyz:2 0.000000 -0.000000 1.000000 -86.819458 > sto_xyz:3 -0.000000 -1.000000 0.000000 136.943146 > sto_xyz:4 0.000000 0.000000 0.000000 1.000000 > sform_xorient Right-to-Left > sform_yorient Superior-to-Inferior > sform_zorient Posterior-to-Anterior > file_type NIFTI-1+ > file_code 1 > descrip FSL5.0 > aux_file > > > For T1: > > filename OrigT1.nii.gz > > sizeof_hdr 348 > data_type UINT8 > dim0 3 > dim1 256 > dim2 256 > dim3 256 > dim4 1 > dim5 1 > dim6 1 > dim7 1 > vox_units mm > time_units s > datatype 2 > nbyper 1 > bitpix 8 > pixdim0 0.0000000000 > pixdim1 1.0000000000 > pixdim2 1.0000000000 > pixdim3 1.0000000000 > pixdim4 2.5299999714 > pixdim5 1.0000000000 > pixdim6 1.0000000000 > pixdim7 1.0000000000 > vox_offset 352 > cal_max 0.0000 > cal_min 0.0000 > scl_slope 0.000000 > scl_inter 0.000000 > phase_dim 0 > freq_dim 0 > slice_dim 0 > slice_name Unknown > slice_code 0 > slice_start 0 > slice_end 0 > slice_duration 0.000000 > time_offset 0.000000 > intent Unknown > intent_code 0 > intent_name > intent_p1 0.000000 > intent_p2 0.000000 > intent_p3 0.000000 > qform_name Scanner Anat > qform_code 1 > qto_xyz:1 -1.000000 -0.000000 -0.000000 123.848427 > qto_xyz:2 -0.000000 -0.000000 1.000000 -86.819458 > qto_xyz:3 0.000000 -1.000000 0.000000 136.943146 > qto_xyz:4 0.000000 0.000000 0.000000 1.000000 > qform_xorient Right-to-Left > qform_yorient Superior-to-Inferior > qform_zorient Posterior-to-Anterior > sform_name Scanner Anat > sform_code 1 > sto_xyz:1 -1.000000 -0.000000 0.000000 123.848427 > sto_xyz:2 0.000000 -0.000000 1.000000 -86.819458 > sto_xyz:3 -0.000000 -1.000000 0.000000 136.943146 > sto_xyz:4 0.000000 0.000000 0.000000 1.000000 > sform_xorient Right-to-Left > sform_yorient Superior-to-Inferior > sform_zorient Posterior-to-Anterior > file_type NIFTI-1+ > file_code 1 > descrip FreeSurfer May 14 2013 > aux_file > > > > Please paste the output of fslhd on both files. > > > > Peace, > > > > Matt. > > > > From: SHAHIN NASR <sha...@nmr.mgh.harvard.edu> > > Reply-To: "Caret, SureFit, and SuMS software users" > > <caret-users@brainvis.wustl.edu> > > Date: Thursday, July 31, 2014 at 11:18 AM > > To: "Caret, SureFit, and SuMS software users" > > <caret-users@brainvis.wustl.edu> > > Subject: [caret-users] Myelin Mapping > > > > Hi, > > I am trying to do myelin mapping. I am following your instructions on > > this website: > > > > http://brainvis.wustl.edu/wiki/index.php/Caret:Operations/MyelinMapping > > > > and I don't get any error till the last command which says: > > > > MYELIN MAPPING ERROR: t1 Dimensions do not match t2 dimensions > > > > But when I check the my T1 and T2 files (using mri_info), I do not see > > any difference: > > > > For T1: > > type: nii > > dimensions: 256 x 256 x 256 > > voxel sizes: 1.0000, 1.0000, 1.0000 > > type: UCHAR (0) > > fov: 256.000 > > dof: 0 > > xstart: -128.0, xend: 128.0 > > ystart: -128.0, yend: 128.0 > > zstart: -128.0, zend: 128.0 > > > > > > > > For T2: > > type: nii > > dimensions: 256 x 256 x 256 > > voxel sizes: 1.0000, 1.0000, 1.0000 > > type: FLOAT (3) > > fov: 256.000 > > dof: 0 > > xstart: -128.0, xend: 128.0 > > ystart: -128.0, yend: 128.0 > > zstart: -128.0, zend: 128.0 > > > > Would you tell me what is the problem. > > > > P.S.: I have already checked the Registration and it looks very OK. > > > > Regards > > - > > Shahin Nasr > > > > PhD in Cognitive Neuroscience > > Martinos Imaging Center, MGH > > Harvard Medical School > > > > _______________________________________________ caret-users mailing list > > caret-users@brainvis.wustl.edu > > http://brainvis.wustl.edu/mailman/listinfo/caret-users > > > > _______________________________________________ > > caret-users mailing list > > caret-users@brainvis.wustl.edu > > http://brainvis.wustl.edu/mailman/listinfo/caret-users > > > > > > 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. > > > _______________________________________________ > caret-users mailing list > caret-users@brainvis.wustl.edu > http://brainvis.wustl.edu/mailman/listinfo/caret-users >
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