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Adds FreeSurfer labels and atrophy tables
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@bishesh
bishesh committed Jun 30, 2016
1 parent c2e16da commit 9b53772
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20 changes: 20 additions & 0 deletions ...les/atrophyTables/withFreesurferLabels/atrophyTableTemporalEntorhinalCorticesAndHipps.txt
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labels newValues
2035 0.5
2030 0.5
2034 0.5
2015 0.5
2009 0.5
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2006 0.5
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54 0.6
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18 0.6

3 changes: 3 additions & 0 deletions ...Files/freeSurferLabelsAndTables/freeSurferCsfRegionsExceptAllVentriclesLabelTableForModel
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labels newValues
24 1

49 changes: 49 additions & 0 deletions configFiles/freeSurferLabelsAndTables/freeSurferLabelsAseg.txt
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195 changes: 195 additions & 0 deletions configFiles/freeSurferLabelsAndTables/freeSurferLabelsWmparc.txt
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33 changes: 33 additions & 0 deletions configFiles/post_process/oasis_study.txt
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# data_base : Oasis
{
'patients' : ['Subject_0048'], #Either from command line or in a list here.
'sim_prefixes' : ['div12pt_atrophyMapR2_0_'], #Either from command line or in a list here.
'sim_cropped_img_suffices' : ['WarpedImageBsplineT1.nii.gz'], #As a list
'sim_full_img_suffices' : ['WarpedImageBsplineFullSizeT1.nii.gz'], #As a list
#'sim_resampled_img_suffices' : ['WarpedImageBsplineFullSizeT1Resampled.nii.gz'], #As a list
'sim_resampled_img_suffices' : ['WarpedImageBsplineFullSizeT1ResampledMinus.nii.gz'], #As a list
'sim_vel_suffices' : ['T1vel.nii.gz'], #As a list
'resampling_disp_suffices' : ['ResamplingDispFieldT1.nii.gz'], #As a list

'sim_base_dir' : '/epi/asclepios2/bkhanal/works/AdLemModel/results/patients',
'sim_crop_mask' : 'cropMaskD2_FS.nii.gz',

'data_base_dir' : '/epi/asclepios2/mhadjham/OASIS_full',
'in_img_dir' : 'Rigid_reg_intra',
'reg_dir' : 'Non_Rigid_reg_intra_robex_Mask',

'in_img_prefix' : 'Final_S0MNI_spline_',
'in_resample_img_prefix' : 'Final_S4MNI_spline_recall_S0_',
'in_img_to_resample_img_prefix' : 'Mask_Registered_output_S0MNI_to_S4MNI_', #This image is in reg_dir!!
'in_img_pid_skip' : 8, #num_of chars from start of patient id not used in real_img file names.
'in_img_suffix' : '.nii.gz',

'svf_prefix' : 'Mask_output_stationary_velocity_field_4_', #1, 2, 3 or 4 to choose tpt.
'svf_suffix' : '_2.0_0.15_3.0.mha',
'div_prefix' : 'Minus_Div_SVF_longi_native_',
#'disp_field_prefix' : 'output_displacement_field_',
'disp_field_prefix' : 'Minus_Mask_output_displacement_field_4_',

}


33 changes: 33 additions & 0 deletions configFiles/post_process/oasis_studyThreeTpts.txt
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# data_base : Oasis
{
'patients' : ['Subject_0048'], #Either from command line or in a list here.
'sim_prefixes' : ['div12pt_atrophyMapR2_0_'], #Either from command line or in a list here.
'sim_cropped_img_suffices' : ['WarpedImageBsplineT1.nii.gz', 'WarpedImageBsplineT2.nii.gz', 'WarpedImageBsplineT3.nii.gz'], #As a list
'sim_full_img_suffices' : ['WarpedImageBsplineFullSizeT1.nii.gz', 'WarpedImageBsplineFullSizeT2.nii.gz', 'WarpedImageBsplineFullSizeT3.nii.gz'], #As a list
#'sim_resampled_img_suffices' : ['WarpedImageBsplineFullSizeT1Resampled.nii.gz'], #As a list
'sim_resampled_img_suffices' : ['WarpedImageBsplineFullSizeT1ResampledMinus.nii.gz', 'WarpedImageBsplineFullSizeT2ResampledMinus.nii.gz', 'WarpedImageBsplineFullSizeT3ResampledMinus.nii.gz'], #As a list
'sim_vel_suffices' : ['T1vel.nii.gz', 'T2vel.nii.gz', 'T3vel.nii.gz'], #As a list
'resampling_disp_suffices' : ['ResamplingDispFieldT1.nii.gz', 'ResamplingDispFieldT2.nii.gz', 'ResamplingDispFieldT3.nii.gz'], #As a list

'sim_base_dir' : '/epi/asclepios2/bkhanal/works/AdLemModel/results/patients',
'sim_crop_mask' : 'cropMaskD2_FS.nii.gz',

'data_base_dir' : '/epi/asclepios2/mhadjham/OASIS_full',
'in_img_dir' : 'Rigid_reg_intra',
'reg_dir' : 'Non_Rigid_reg_intra_robex_Mask',

'in_img_prefix' : 'Final_S0MNI_spline_',
'in_resample_img_prefix' : 'Final_S4MNI_spline_recall_S0_',
'in_img_to_resample_img_prefix' : 'Mask_Registered_output_S0MNI_to_S4MNI_', #This image is in reg_dir!!
'in_img_pid_skip' : 8, #num_of chars from start of patient id not used in real_img file names.
'in_img_suffix' : '.nii.gz',

'svf_prefix' : 'Mask_output_stationary_velocity_field_4_', #1, 2, 3 or 4 to choose tpt.
'svf_suffix' : '_2.0_0.15_3.0.mha',
'div_prefix' : 'Minus_Div_SVF_longi_native_',
#'disp_field_prefix' : 'output_displacement_field_',
'disp_field_prefix' : 'Minus_Mask_output_displacement_field_4_',

}


33 changes: 33 additions & 0 deletions configFiles/post_process/oasis_studyTwoTpts.txt
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# data_base : Oasis
{
'patients' : ['Subject_0048'], #Either from command line or in a list here.
'sim_prefixes' : ['div12pt_atrophyMapR2_0_'], #Either from command line or in a list here.
'sim_cropped_img_suffices' : ['WarpedImageBsplineT1.nii.gz', 'WarpedImageBsplineT2.nii.gz'], #As a list
'sim_full_img_suffices' : ['WarpedImageBsplineFullSizeT1.nii.gz', 'WarpedImageBsplineFullSizeT2.nii.gz'], #As a list
#'sim_resampled_img_suffices' : ['WarpedImageBsplineFullSizeT1Resampled.nii.gz'], #As a list
'sim_resampled_img_suffices' : ['WarpedImageBsplineFullSizeT1ResampledMinus.nii.gz', 'WarpedImageBsplineFullSizeT2ResampledMinus.nii.gz'], #As a list
'sim_vel_suffices' : ['T1vel.nii.gz', 'T2vel.nii.gz'], #As a list
'resampling_disp_suffices' : ['ResamplingDispFieldT1.nii.gz', 'ResamplingDispFieldT2.nii.gz'], #As a list

'sim_base_dir' : '/epi/asclepios2/bkhanal/works/AdLemModel/results/patients',
'sim_crop_mask' : 'cropMaskD2_FS.nii.gz',

'data_base_dir' : '/epi/asclepios2/mhadjham/OASIS_full',
'in_img_dir' : 'Rigid_reg_intra',
'reg_dir' : 'Non_Rigid_reg_intra_robex_Mask',

'in_img_prefix' : 'Final_S0MNI_spline_',
'in_resample_img_prefix' : 'Final_S4MNI_spline_recall_S0_',
'in_img_to_resample_img_prefix' : 'Mask_Registered_output_S0MNI_to_S4MNI_', #This image is in reg_dir!!
'in_img_pid_skip' : 8, #num_of chars from start of patient id not used in real_img file names.
'in_img_suffix' : '.nii.gz',

'svf_prefix' : 'Mask_output_stationary_velocity_field_4_', #1, 2, 3 or 4 to choose tpt.
'svf_suffix' : '_2.0_0.15_3.0.mha',
'div_prefix' : 'Minus_Div_SVF_longi_native_',
#'disp_field_prefix' : 'output_displacement_field_',
'disp_field_prefix' : 'Minus_Mask_output_displacement_field_4_',

}


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