Freesurfers --
This morning, I was trying to convert a 4 frame MPRAGE scan into a 1 frame RMS image. I wrote my own matlab code to do it ...
function err = rms_mprage(old,new) %convert 4-frame mprage into 1 frame mprage by taking RMS of voxels
old_hdr = load_nifti(old); new_hdr = old_hdr; new_hdr.vol = sqrt((old_hdr.vol(:,:,:,1).^2+old_hdr.vol(:,:,:,2).^2+old_hdr.vol(:,:,:,3).^2+old_hdr.vol(:,:,:,4).^2)/4); err = save_nifti(new_hdr,new);
So I ran >>> rms_mprage('MPRAGE1.nii','MPRAGE_new.nii')
Also, Bruce said I could do this ...
mri_average -noconform -sqr MPRAGE1.nii#0 MPRAGE1.nii#1 MPRAGE1.nii#2 MPRAGE1.nii#3 MPRAGE_rms.nii
However... kerryave:002 $ ls -l -rw-rw-r-- 1 sburns lingua 92275040 Dec 21 12:27 MPRAGE1.nii -rw-rw-r-- 1 sburns lingua 24340 Dec 20 15:17 MPRAGE1.nii-infodump.dat -rw-rw-r-- 1 sburns lingua 23069024 Apr 12 13:29 MPRAGE_new.nii -rw-rw-r-- 1 sburns lingua 46137696 Apr 12 13:35 MPRAGE_rms.nii
So I was curious why the _rms.nii was twice as big. Probably a datatype issue, right?
kerryave:002 $ mri_info MPRAGE_new.nii Volume information for MPRAGE_new.nii type: nii dimensions: 256 x 256 x 176 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: -88.0, zend: 88.0 TR: 2530.00 msec, TE: 0.00 msec, TI: 0.00 msec, flip angle: 0.00 degrees nframes: 1 PhEncDir: UNKNOWN ras xform present xform info: x_r = 0.0055, y_r = 0.0068, z_r = -1.0000, c_r = -0.9523 : x_a = -0.9719, y_a = 0.2354, z_a = -0.0037, c_a = 2.8859 : x_s = -0.2354, y_s = -0.9719, z_s = -0.0079, c_s = 0.8822 Orientation : PIL Primary Slice Direction: sagittal
voxel to ras transform: 0.0055 0.0068 -1.0000 85.4734 -0.9719 0.2354 -0.0037 97.4806 -0.2354 -0.9719 -0.0079 156.1061 0.0000 0.0000 0.0000 1.0000
voxel-to-ras determinant -1
ras to voxel transform: 0.0055 -0.9719 -0.2354 131.0176 0.0068 0.2354 -0.9719 128.1845 -1.0000 -0.0037 -0.0079 87.0654 0.0000 0.0000 0.0000 1.0000
And...
kerryave:002 $ mri_info MPRAGE_rms.nii Volume information for MPRAGE_rms.nii type: nii dimensions: 256 x 256 x 176 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: -88.0, zend: 88.0 TR: 2530.00 msec, TE: 0.00 msec, TI: 0.00 msec, flip angle: 0.00 degrees nframes: 1 PhEncDir: UNKNOWN ras xform present xform info: x_r = 0.0055, y_r = 0.0068, z_r = -1.0000, c_r = -0.9523 : x_a = -0.9719, y_a = 0.2354, z_a = -0.0037, c_a = 2.8859 : x_s = -0.2354, y_s = -0.9719, z_s = -0.0079, c_s = 0.8822 Orientation : PIL Primary Slice Direction: sagittal
voxel to ras transform: 0.0055 0.0068 -1.0000 85.4734 -0.9719 0.2354 -0.0037 97.4806 -0.2354 -0.9719 -0.0079 156.1061 0.0000 0.0000 0.0000 1.0000
voxel-to-ras determinant -1
ras to voxel transform: 0.0055 -0.9719 -0.2354 131.0176 0.0068 0.2354 -0.9719 128.1845 -1.0000 -0.0037 -0.0079 87.0654 0.0000 0.0000 0.0000 1.0000
Weird that mri_info shows the datatype for both images as float. fslhd shows different things...
kerryave:002 $ fslhd MPRAGE_new.nii filename MPRAGE_new.nii
sizeof_hdr 348 data_type INT16 dim0 4 dim1 256 dim2 256 dim3 176 dim4 1 dim5 1 dim6 1 dim7 1 vox_units mm time_units ms datatype 4 nbyper 2 bitpix 16 pixdim0 0.0000000000 pixdim1 1.0000000000 pixdim2 1.0000000000 pixdim3 1.0000000000 pixdim4 2530.0000000000 pixdim5 1.0000000000 pixdim6 1.0000000000 pixdim7 1.0000000000 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 0.000000 0.000000 -1.000000 87.473366 qto_xyz:2 -0.976296 0.216439 -0.000000 100.261627 qto_xyz:3 -0.216439 -0.976296 -0.000000 153.275482 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 Aligned Anat sform_code 2 sto_xyz:1 0.005469 0.006804 -0.999962 85.473358 sto_xyz:2 -0.971887 0.235419 -0.003714 97.480621 sto_xyz:3 -0.235385 -0.971870 -0.007900 156.106079 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 Dec 18 2010 aux_file
kerryave:002 $ fslhd MPRAGE_rms.nii filename MPRAGE_rms.nii
sizeof_hdr 348 data_type FLOAT32 dim0 3 dim1 256 dim2 256 dim3 176 dim4 1 dim5 1 dim6 1 dim7 1 vox_units mm time_units s datatype 16 nbyper 4 bitpix 32 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 0.005469 0.006804 -0.999962 85.473358 qto_xyz:2 -0.971887 0.235419 -0.003714 97.480621 qto_xyz:3 -0.235385 -0.971870 -0.007900 156.106079 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 0.005469 0.006804 -0.999962 85.473358 sto_xyz:2 -0.971887 0.235419 -0.003714 97.480621 sto_xyz:3 -0.235385 -0.971870 -0.007900 156.106079 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 Mar 19 2011 aux_file
fslhd shows different data types, which explains the difference in size. I think there's a bug in mri_info that is incorrectly reading MPRAGE_new.nii as float data. Not an earth shattering bug by any means, but I thought I'd let you know anyways.
Scott Burns Kuperberg Lab Martinos Center for Biomedical Imaging sburns@nmr.mgh.harvard.edu
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