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
>> >
>>
>>
>>
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>
>
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>
--
Shahin Nasr
PhD in Cognitive Neuroscience
Martinos Imaging Center, MGH
Harvard Medical School
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