That file has multiple problems, the first being that it isn't plumb, the sform/qform have some rotation in them. Caret5 won't read those kinds of volumes correctly, and it is nontrivial to try to reverse-generate the equivalent in the volume space you need it in. The easiest way to get something that works may be to first remove obliques from your original T1 volume, and then rerun freesurfer, so that this file is no longer oblique.
However, I'm not clear on why the third volume dimension has a different number of voxels - you might need to pad your original input volume or something. I haven't had to deal with these things in freesurfer, so someone else should probably give you some guidance. Tim On Thu, Jul 31, 2014 at 3:11 PM, SHAHIN NASR <sha...@nmr.mgh.harvard.edu> wrote: > Hi Timothy, > That may be the problem. When the output is like this: > > ribbon.nii.gz > > sizeof_hdr 348 > data_type INT16 > dim0 3 > dim1 256 > dim2 256 > dim3 176 > 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 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 0.009315 -0.034602 -0.999358 87.028618 > qto_xyz:2 -0.998443 0.054645 -0.011198 162.972198 > qto_xyz:3 -0.054997 -0.997906 0.034039 140.719284 > qto_xyz:4 0.000000 0.000000 0.000000 1.000000 > qform_xorient Anterior-to-Posterior > qform_yorient Superior-to-Inferior > qform_zorient Right-to-Left > sform_name Scanner Anat > sform_code 1 > sto_xyz:1 0.009315 -0.034602 -0.999358 87.028618 > sto_xyz:2 -0.998443 0.054645 -0.011199 162.972198 > sto_xyz:3 -0.054997 -0.997906 0.034039 140.719284 > sto_xyz:4 0.000000 0.000000 0.000000 1.000000 > sform_xorient Anterior-to-Posterior > sform_yorient Superior-to-Inferior > sform_zorient Right-to-Left > file_type NIFTI-1+ > file_code 1 > descrip FreeSurfer May 14 2013 > aux_file > > > As you see, dim3 is different than the T1 and T2. But I used the command > the command that was mentioned in the instruction to generate ribbon (i.e. > mri_convert > -rl mri/rawavg.mgz mri/ribbon.mgz ribbon.nii.gz). > > Any suggestion how to correct this problem? > > > > > On Thu, Jul 31, 2014 at 3:08 PM, Timothy Coalson <tsc...@mst.edu> wrote: > >> 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 >>> >> >> >> _______________________________________________ >> caret-users mailing list >> caret-users@brainvis.wustl.edu >> http://brainvis.wustl.edu/mailman/listinfo/caret-users >> >> > > > -- > 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 > >
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