View source for Mbirn: MBIRN XNAT MGH Details

''' PGP Data Modeling Working Page'''

''Sequence of Models''

* Structure

Start from WashU's [[Here%27s_a_schema|OASIS]] model

Structural analysis flow: DICOM off the scanner, DICOM tar-ball to CMA, extract structural-relavent scans, average together multiple structural runs, positionally normalize orientation, bias field correction, assign to segmenter, segmentation (creates outline dataset and summary volumetric metadata

* Structural DICOM tarball listing:

  1            localizer  ok  512 512   3   1 69268619
  2       gresuccflipAAS  ok  128 128 128   1 69268634
  3       gresuccflipAAS  ok  128 128 128   1 69267510
  4        tflmghautoSTD  ok  256 256 128   1 69266377
  5        tflmghautoSTD  ok  256 256 128   1 69265244
  6        tflmghautoSTD  ok  256 256 128   1 69261078
  7 FLASH30dgmultiechoauto  ok  256 256 128   8 69259945
  8 FLASH5dgmultiechoauto  ok  256 256 128   8 69244955
  9 FLASH3dgmultiechoauto  ok  256 256 128   8 69229965
 10        gresuccflipHE  ok  128 128 128   1 69211942
 11        gresuccflipHE  ok  128 128 128   1 69210809
 12    gresuccBCBODYCOIL  ok  128 128 128   1 69209676
 13    gresuccBCBODYCOIL  ok  128 128 128   1 69208543

<br /> Summary: In this case, scans 3, 4 & 5 are for CMA anatomic segmentation. These get assigned a CMA PID (patient identification number), and these are logged to the cma database, cmadb. CMA creates new scans for 1) motoion-corrected-averageing of these three scans (command = xxx, output = new scan and motion parameters), 2) positional normalization (command = norm, output = new scan, transformation parameters), and 3) biasfield correction (command = autoseg2, output = new scan, field correction parameters and intensity 'guesses' for anatomic structures'.

'''Details'''

* Create subject in cma_db

 Enter Command (a_,m_,l_,la,ld,f_,s_,d_,np,nx,p,pc,D,q,?) --> Lp 3352
 List Patients:
 pid   name                            dob            gender   study
 3352  PGP_ABY83                                               ONDCP
 (diagnostic= 1 printing=off)
 Enter Command (a_,m_,l_,la,ld,f_,s_,d_,np,nx,p,pc,D,q,?) -->

* Identify structural runs (from dicom listing shown above)

* Create raw structural scan runs in cma_db (scns 1, 2 and 3 below)

 Enter Command (a_,m_,l_,la,ld,f_,s_,d_,np,nx,p,pc,D,q,?) --> ls 3352
 List Scans:
 pid   scn   num_im   orient   param   stype   loc_perf   date       on_dsk   arch   pos_nrm   done   assign   o_on_dsk   o_arch
 3352  1     128      SAG      T13D    DCM     CMA        28-MAY-04  Y        N      N         N      N        N          N
 3352  2     128      SAG      T13D    DCM     CMA        28-MAY-04  Y        N      N         N      N        N          N
 3352  3     128      SAG      T13D    DCM     CMA        28-MAY-04  Y        N      N         N      N        N          N
 3352  4     140      COR      AVG-MC  IMG     CMA        25-AUG-04  Y        N      N         N      N        N          N
 3352  5     158      COR      T13DPN  IMG     CMA        20-SEP-04  Y        N      4         N      JCO      N
 3352  6     158      COR      BIASFX  IMG     CMA        20-SEP-04  Y        N      5         N      N        N          N

* motion correct - average the structural runs

 > mri_motion_correct PID.mnc ./data/69266377 ./data/69265244 ./data/69261078

A screen capture of this process follows:

 [cerebellum:structurals] (nmr-std-env) mri_motion_correct test.mnc ./data/3354275316  ./data/8881484223 ./data/2444689976
 /space/lyon/1/home/inverse/freesurfer_alpha/bin/Linux/mri_convert
 checking for mincresample...found
 checking for mincaverage...found
 checking for minctracc...found
 checking size of ./data/3354275316... done
 checking size of ./data/8881484223... done
 checking size of ./data/2444689976... done
 converting ./data/3354275316 to minc (volume 0)... done
 converting ./data/8881484223 to minc (volume 1)... done
 registering this volume (1) to volume 0... done
 reslicing registered volume... done
 removing unsliced minc data and transform file...done
 converting ./data/2444689976 to minc (volume 2)... done
 registering this volume (2) to volume 0... done
 reslicing registered volume... done
 removing unsliced minc data and transform file...done
 averaging volumes...done
 creating output volume...done
 cleaning up...

'''New ASSESSOR proposed: [[Oas:MGHRegAvgScns|oas:MGHRegAvgScns]]''' (stands for register and average scans)

* Create avg-mc entry in cma_db (scan 4 in listing above)

* Create CMA info file target location

 > mkdir /Data/PID/SN
 > mkdir /Data/PID/SN/otl

* Convert minc output of motion correct to CMA file (.img images, .info file)

 > mri_convert PID.mnc /Data/PID/SN/info.gdf -gis /Image/ONDCP/PID_SN -oid -1 0  0 -ojd  0 0 -1 -okd  0 1 0 -odt short -ois 1.0 -ojs 1.0 -oks 1.5 -oic 256 -ojc 256 -okc 140

* Run ''nmv'' to check result, if recentering is necessary, rerun mri_convert using -oc controls

* CMA manager updates study spreadsheet, assigns segmenter, monitors the study,etc.

* Positional Normalization

 > norm
 User enters in GUI: PID, SN
                     AC, PC, MSP
                     selects reslice orientation,
                     accepts the 1.5 slice thickness default

''norm'' inserts the following into the 'Native' scan info file:

 NORMALIZATION_ORIGIN 126.25 76.0 136.0
 NORMALIZATION_ANGLES -0.018516 0.073926 0.0
 
 ...
 
 START GDF HEADER
 ROW_NUM 3
 COL_NUM 4
 TYPE ascii table
 COLUMN_DATA_TYPES {35s,double,double,double}
 REFERENCE_FRAME nat_coord
 END GDF HEADER
 
 START POINTS
 AC_POINT                              126.500000    85.000000   135.000000
 PC_POINT                              126.000000    67.000000   137.000000
 MID_SAGITTAL_POINT                    126.000000    67.000000    70.000000
 END POINTS

This information includes the RAS index of the anterior commissure (AC), posterior commissure (PC) and a point on the mid-sagittal plant (at the level of the posterior commissure) (MSP). The ''norm'' procedure rotates and translates the scan to a standard location and orientation. The 'rotation' is listed as NORMALIZATION_ANGLES and prodived in radians for rotations about the x, y and z axes, respectively. The RAS of the 'origin' of the rotation (midpoint of the AC - PC linesegment) is provided in NORMALIZATION_ORIGIN; this is tanslated to the center of the output data matrix.

The following information is added to the info file of the newly created 'normalized' scan:

 NORMALIZATION_ORIGIN 126.25 76.0 136.0
 NORMALIZATION_ANGLES -0.018516 0.073926 0.0
 
 .
 
 START POINTS
 AC_POINT                              128.000005    88.026196   127.999994
 PC_POINT                              127.999995    69.973804   128.000006
 MID_SAGITTAL_POINT                    127.999995    73.272825    61.183001
 END POINTS

This is similar to what is added to the 'native' scan, except that the coordinates of the AC, PC and MSP are in the 'normalized' space.

'''New ASSESSOR proposed: [[Oas:MGHPosNorm|oas:MGHPosNorm]]'''

* cma_db auto updated for normed scan (scan 5 above).

* Set brain extents (crop)

 > cardviews PID SN
             user manually sets and check extens
             select crop data, save settings button

This updates the 'normalized' info file (in the POINTS section) with:

 MIN_CROP                               56.000000    18.000000    56.000000
 MAX_CROP                              198.000000   135.000000   197.000000

These RAS values indicate the MINimum and MAXimum indicies for the coordinates, respectively. Only this sub-portion of the datafile must be loaded in order to include the entire brain in the dataset.

* Run bias-field correction and intensity guesses

 > autoseg2 PID SN

This command automatically finds next available scan number from CMADB and creates entry (see scan 6 above), and enters a 'pile' of stuff into info file. Also creates file naut_variables.gdf in /Data/PID/SN

Sample entries to new scan info file:

 VERSION $Id: naut_rm_init_inhomo.c,v 1.11 1999/09/30 19:00:09 andy Exp $ (c) Copyright 1999 Neuromorphometrics
 PARAMETER_RI_threeDG_mult_fact_DEFAULT 1000.0
 PARAMETER_RI_threeDG_diam_DEFAULT 40.0
 PARAMETER_RI_bias_field_vox_size_DEFAULT 30.0
 PARAMETER_RI_bias_histo_sig_dig_DEFAULT 1000.0
 PARAMETER_RI_rm_bias_frac_DEFAULT 1.0
 VERSION $Id: naut_global_context.c,v 1.9 2000/04/05 13:43:23 andy Exp $ (c) Copyright 1999 Neuromorphometrics
 PARAMETER_GC1_set_smooth_using_cumu_DEFAULT 1
 PARAMETER_GC1_RIR_loval_frac_DEFAULT 0.1
 PARAMETER_GC1_RIR_hival_frac_DEFAULT 0.9
 PARAMETER_GC1_aarea_frac_DEFAULT 0.0333333333333
 PARAMETER_GC1_acceptable_residual_DEFAULT 0.08
 PARAMETER_GC1_smoo_DEFAULT 0.05
 PARAMETER_GC1_mult_factor_DEFAULT 10000.0
 PARAMETER_GC1_edge_thresh_frac_DEFAULT 0.5
 PARAMETER_GC1_zero_bg_thresh_DEFAULT 0.00
 PARAMETER_GC1_brain_thresh_frac_DEFAULT 0.85
 PARAMETER_GC2_aarea_frac_DEFAULT 0.01
 PARAMETER_GC2_acceptable_residual_DEFAULT 0.08
 PARAMETER_GC2_smoo_DEFAULT 0.05
 PARAMETER_GC2_mult_factor_DEFAULT 10000.0
 VERSION $Id: naut_GC3.c,v 1.10 2001/07/26 21:19:20 andy Exp $ (c) Copyright 1999 Neuromorphometrics
 PARAMETER_GC3_set_smooth_using_cumu_DEFAULT 1
 PARAMETER_GC3_RIR_loval_frac_DEFAULT 0.1
 PARAMETER_GC3_RIR_hival_frac_DEFAULT 0.9
 PARAMETER_GC3_aarea_frac_DEFAULT 0.01
 PARAMETER_GC3_acceptable_residual_DEFAULT 0.08
 PARAMETER_GC3_smoo_DEFAULT 0.03
 PARAMETER_GC3_mult_factor_DEFAULT 10000.00
 PARAMETER_GC3_peak_conf_sdevs_DEFAULT 2.00
 PARAMETER_GC3_peak_loc_factor_DEFAULT 1.00
 PARAMETER_GC3_width_factor_DEFAULT 3.00
 PARAMETER_GC3_minusG_factor_DEFAULT 0.50
 PARAMETER_GC3_peak_aprox_factor_DEFAULT 0.95

Sample naut_variables.gdf file:

 GDF FILE VERSION3
 START MAIN HEADER
 ONUM 120
 END MAIN HEADER
 
 START GDF HEADER
 ROW_NUM 0
 COL_NUM 1
 TYPE char
 NAUTILOS_BLOCK Parameters
 pid 3352
 scn 5
 Tal_acpc 23.2
 Tal_wdth 137.0
 Tal_actop 74.0
 X_AC 128.000005
 Y_AC 88.026196
 Z_AC 127.999994
 X_PC 127.999995
 Y_PC 69.973804
 Z_PC 128.000006
 X_MID_SAG 127.999995
 Y_MID_SAG 73.272825
 Z_MID_SAG 61.183001
 X_MIN_CROP 56.0
 Y_MIN_CROP 18.0
 Z_MIN_CROP 56.0
 X_MAX_CROP 198.0
 Y_MAX_CROP 135.0
 Z_MAX_CROP 197.0
 VERSION $Id: naut_rm_init_inhomo.c,v 1.11 1999/09/30 19:00:09 andy Exp $ (c) Copyright 1999  Neuromorphometrics
 PARAMETER_RI_threeDG_mult_fact_DEFAULT 1000.0
 PARAMETER_RI_threeDG_diam_DEFAULT 40.0
 PARAMETER_RI_bias_field_vox_size_DEFAULT 30.0
 PARAMETER_RI_bias_histo_sig_dig_DEFAULT 1000.0
 PARAMETER_RI_rm_bias_frac_DEFAULT 1.0
 GC_MIN_INTEN 0.0
 GC_B_PEAK 33.635502
 GC_B_SDEV 19.69475
 GC_B_HEIGHT 62407.0
 GC_CSF_PEAK 76.5
 GC_CSF_SDEV 0.5
 GC_CSF_HEIGHT 567.0
 GC_CP_PEAK 110.791489
 GC_CP_SDEV 0.46798
 GC_CP_HEIGHT 2270.0
 GC_G_PEAK 211.441177
 GC_G_SDEV 41.835285
 GC_G_HEIGHT 1170.0
 GC_W_PEAK 396.368805
 GC_W_SDEV 22.731707
 GC_W_HEIGHT 2270.0
 GC_MAX_INTEN 956.0
 GC_B_CSF_THRESH 73.0
 GC_CSF_W_THRESH 236.0
 GC_CSF_G_THRESH 128.0
 GC_EXT_THRESH 111.0
 GC_G_W_THRESH 328.0
 GC_W_NB_THRESH 956.0
 NAUT_CODE_VERSION GC1 $Id: naut_global_context.c,v 1.9 2000/04/05 13:43:23 andy Exp $ (c) Copyright 1999 Neuromorphometrics
 NAUT_CODE_VERSION GC2 $Id: naut_global_context.c,v 1.9 2000/04/05 13:43:23 andy Exp $ (c)  Copyright 1999 Neuromorphometrics
 PARAMETER_GC2_aarea_frac_DEFAULT 0.01
 PARAMETER_GC2_acceptable_residual_DEFAULT 0.08
 PARAMETER_GC2_smoo_DEFAULT 0.05
 PARAMETER_GC2_mult_factor_DEFAULT 10000.0
 NAUT_CODE_VERSION GC3 $Id: naut_GC3.c,v 1.10 2001/07/26 21:19:20 andy Exp $ (c) Copyright 1999 Neuromorphometrics
 PARAMETER_GC3_set_smooth_using_cumu_DEFAULT 1
 PARAMETER_GC3_RIR_loval_frac_DEFAULT 0.1
 PARAMETER_GC3_RIR_hival_frac_DEFAULT 0.9
 PARAMETER_GC3_aarea_frac_DEFAULT 0.01
 PARAMETER_GC3_acceptable_residual_DEFAULT 0.08
 PARAMETER_GC3_smoo_DEFAULT 0.03
 PARAMETER_GC3_mult_factor_DEFAULT 10000.00
 PARAMETER_GC3_peak_conf_sdevs_DEFAULT 2.00
 PARAMETER_GC3_peak_loc_factor_DEFAULT 1.00
 PARAMETER_GC3_width_factor_DEFAULT 3.00
 PARAMETER_GC3_minusG_factor_DEFAULT 0.50
 PARAMETER_GC3_peak_aprox_factor_DEFAULT 0.95
 END GDF HEADER

'''New ASSESSOR proposed: [[Oas:MGHBiasFx|oas:MGHBiasFx]]'''

* Segmenter performs the segmentation

 > cardviews PID SN
       segmenter enter prefix: jdh (for outline files)

* Initial segmentation file check

 > xvol
   User enters PID, SN, prfx

to check volumes are reasonable size, errors (bad extraction, missing labels)

* Second segmentation file check

 > check_otls xvol/vol/otl_list

checks for same size structures (slice-by-slice) (double labelers) regions excluded from exterior, etc.)

* Final data 'conditioning' and check

 > extract_I PID SN jdh fst lst

This catches errors, right/left labeling problems, etc.)

* Final volume generation

 > xvol
   User enters PID, SN, prfx

<br /> Example metadata for the volumetric result of the segmentation analysis of this resultant scan follows:

 TOTALS: /Data/3352/6/otl/jkcI*.otl, slices 20 to 131
 pix dim(x,y,sl)= 0.500000 0.500000 1.500000 mm

 Right Cerebral Exterior        total volume   =  503.082 cm3
 Left Cerebral Exterior         total volume   =  504.948 cm3
 Right Cerebral White Matter    total volume   =  199.677 cm3
 Left Cerebral White Matter     total volume   =  201.125 cm3
 Right Cerebral Cortex          total volume   =  271.826 cm3
 Left Cerebral Cortex           total volume   =  272.218 cm3
 Right Lateral Ventricle        total volume   =    5.092 cm3
 Left Lateral Ventricle         total volume   =    5.544 cm3
 Right Inf Lat Vent             total volume   =    0.216 cm3
 Left Inf Lat Vent              total volume   =    0.153 cm3
 Right Cerebellum Exterior      total volume   =   67.454 cm3
 Left Cerebellum Exterior       total volume   =   67.377 cm3
 Right Cerebellum White Matter  total volume   =   12.637 cm3
 Left Cerebellum White Matter   total volume   =   13.007 cm3
 Right Cerebellum Cortex        total volume   =   54.827 cm3
 Left Cerebellum Cortex         total volume   =   54.378 cm3
 Right Thalamus Proper          total volume   =    5.884 cm3
 Left Thalamus Proper           total volume   =    5.714 cm3
 Right Caudate                  total volume   =    4.153 cm3
 Left Caudate                   total volume   =    4.288 cm3
 Right Putamen                  total volume   =    4.635 cm3
 Left Putamen                   total volume   =    4.691 cm3
 Right Pallidum                 total volume   =    1.449 cm3
 Left Pallidum                  total volume   =    1.376 cm3
 3rd Ventricle                  total volume   =    2.535 cm3
 4th Ventricle                  total volume   =    1.375 cm3
 Optic Chiasm                   total volume   =    0.307 cm3
 Brain Stem                     total volume   =   18.643 cm3
 Right Hippocampus              total volume   =    3.453 cm3
 Left Hippocampus               total volume   =    3.110 cm3
 Right Amygdala                 total volume   =    1.580 cm3
 Left Amygdala                  total volume   =    1.564 cm3
 Right Accumbens area           total volume   =    0.404 cm3
 Left Accumbens area            total volume   =    0.461 cm3
 Right VentralDC                total volume   =    4.712 cm3
 Left VentralDC                 total volume   =    4.588 cm3
 Right vessel                   total volume   =    0.037 cm3
 Left vessel                    total volume   =    0.159 cm3

'''New ASSESSOR proposed: [[Oas:MGHcmaGSegmentation|oas:MGHcmaGSegmentation]]'''

'''Structural Data Model Summary:''' So, to first approximation, for the PGP structural analysis, we need to get XDAT to track the subjects, the raw volumetric scans, the derived scans, the derived segmentation, and the volumetric results metadata. The majority of this mateches the OASIS schema, and we will next make this explicit.

* Function

Start from fBIRN XML Schema

* Behavioral

----

[[Beta_Testing_%40_MGH|Beta_Testing_@_MGH]]