1. CIVET stage 47. thickness_tlink_20mm_right
49.resample_left_mean_curvature
Ku Yoon Jeong

2. Stages nuc_t1_native skull_masking_native stx_register stx_tal_to_7
nuc_inorm_t1
skull_removal
nlfit
mask_classify
pve_curvature
pve
reclassify
segment
cls_volumes
cortical_masking
segment_volumes
surface_classify
artefact
create_wm_hemispheres
segment_mask
expand_from_white_left
expand_from_white_right
slide_left_hemi_obj_back
flip_right_hemi_obj_back
slide_right_hemi_obj_back
calibrate_left_white
calibrate_right_white
laplace_field
gray_surface_left
gray_surface_right
mid_surface_left
mid_surface_right
surface_fit_error
verify_image_nlfit
gyrification_index_left
verify_brain_mask
classify_qc
dataterm_left_surface
brain_mask_qc
gyrification_index_right
dataterm_right_surface
surface_registration_left
surface_registration_right
mean_curvature_20mm_left
mean_curvature_20mm_right
thickness_tlink_20mm_right
thickness_tlink_20mm_left
resample_left_mean_curvature
resample_right_mean_curvature
resample_right_thickness
resample_left_thickness
lobe_area_right
lobe_area_left
verify_clasp
verify_image

3. 47. thickness_tlink_20mm_right
-모듈: Cortical_Measurements.pm -Label: “native thickness” -실행명령: bin/cortical_thickness(s) bin/xfminvert bin/transform_objects bin/average_surfaces bin/dump_rms bin/diffuse -입력: /surfaces/ mni_icbm_00340_white_surface_right_calibrated_81920.obj /surfaces/ mni_icbm_00340_gray_surface_right_81920.obj -출력: native_rms_tlink_20mm_right.txt -의존성: surface_registration_left(stage 43), surface_registration_right(stage 44)
xfminvert ../transforms/linear/mni_icbm_00340_t1_tal.xfm /usr/tmp/cortical_thickness_16712//inv_trans.xfm
transform_objects ./surfaces/mni_icbm_00340_white_surface_right_calibrated_81920.obj /usr/tmp/cortical_thickness_16712//inv_trans.xfm /usr/tmp/cortical_thickness_16712//white_trans.obj
xfminvert ../transforms/linear/mni_icbm_00340_t1_tal.xfm /usr/tmp/cortical_thickness_16718//inv_trans.xfm
transform_objects ../surfaces/mni_icbm_00340_white_surface_right_calibrated_81920.obj /usr/tmp/cortical_thickness_16718//inv_trans.xfm /usr/tmp/cortical_thickness_16718//white_trans.obj
transform_objects ../surfaces/mni_icbm_00340_gray_surface_right_81920.obj /usr/tmp/cortical_thickness_16718//inv_trans.xfm /usr/tmp/cortical_thickness_16718//gray_trans.obj
average_surfaces /usr/tmp/cortical_thickness_16718//midSurface.obj none none 1 /usr/tmp/cortical_thickness_16718//white_trans.obj /usr/tmp/cortical_thickness_16718//gray_trans.obj
1: /usr/tmp/cortical_thickness_16718//white_trans.obj
2: /usr/tmp/cortical_thickness_16718//gray_trans.obj
Objects output.
dump_rms /usr/tmp/cortical_thickness_16718//white_trans.obj /usr/tmp/cortical_thickness_16718//gray_trans.obj ./native_rms_tlink_20mm_right.txt
Rms over the points:
Average dist:
Std dev dist:
Min dist:
Max dist:
Elapsed time in cortical_thickness (16718) and children:
2.57 sec (user) sec (system) = 2.64 sec (total)

4. ##### Calculation of the cortical thickness in native space #####
##### Right hemisphere #####
${$pipeline_ref}->addStage(
{ name => "thickness_${tmethod}_${tkernel}mm_right",
label => "native thickness",
inputs => [$white_right, $gray_right, $t1_tal_xfm],
outputs => [$native_rms_right],
args => ["cortical_thickness", "-${tmethod}", "-fwhm", ${tkernel},
"-transform", $t1_tal_xfm, $white_right, $gray_right, $native_rms_right],
prereqs => $Prereqs });
[Command line]
cortical_thickness -transform ../transforms/linear/mni_icbm_00340_t1_tal.xfm -tlink -keeptmp -noclobber ../surfaces/mni_icbm_00340_white_surface_right_calibrated_81920.obj
../surfaces/mni_icbm_00340_gray_surface_right_81920.obj ./native_rms_tlink_20mm_right.txt
[Option]
-transform : transformation from native to stereotaxic (if surfaces in stx space)
-tlink: use t-link method for thickness
-tnear: use t-near method for thickness
-tnormal : use t-normal method for thickness
-tlaplace: use t-Laplace method for thickness
-tnear use t-near method for thickness
-notnear opposite of -tnear [default]
-tnormal use t-normal method for thickness
-notnormal opposite of -tnormal [default]
-tlaplace use t-Laplace method for thickness

5. Cortical Thickness measurements
Reference

6. cortical_thickness source & logs
if( defined $transform_xfm ) {
my $white_trans = "${TmpDir}/white_trans.obj";
my $gray_trans = "${TmpDir}/gray_trans.obj";
my $inv_trans = "${TmpDir}/inv_trans.xfm";
&run( "xfminvert", $transform_xfm, $inv_trans );
&run( "transform_objects", $white, $inv_trans, $white_trans );
&run( "transform_objects", $gray, $inv_trans, $gray_trans );
$white = $white_trans;
$gray = $gray_trans; }
[Command line]
xfminvert ../transforms/linear/mni_icbm_00340_t1_tal.xfm inv_trans.xfm
transform_objects :[Transforms the input objects by the input transform]
mni_icbm_00340_white_surface_right_calibrated_81920.obj ./inv_trans.xfm ./white_trans.obj
(3) transform_objects
mni_icbm_00340_gray_surface_right_81920.obj ./inv_trans.xfm ./gray_trans.obj
(4) average_surfaces
average_surfaces midsurface.obj none none 1 ./white_trans.obj ./gray_trans.obj
Usage: average_surfaces output.obj none|rms_file none|variance_file n_groups
[input1.obj] [input2.obj] ...

7. Native Space
White
Matter
Gray
Matter
Mid-Surface

8. cortical thickness measurement
if( $tlink ) {
# also: &run( "diff_surfaces", $white, $gray, "link", $output );
&run( "dump_rms", $white, $gray, $output ); }
if( $tnear ) {
&run( "diff_surfaces", $white, $gray, "near", $output ); }
if( $tnormal ) {
&run( "diff_surfaces", $white, $gray, "normal", $output ); }
# Blur the cortical thickness on the mid-surface in new space.
if( $fwhm gt 0 ) {
my $output_blurred = "${TmpDir}/thickness_blurred.mnc";
&run( "diffuse", "-kernel", $fwhm, "-iterations", 1000, "-parametric", 1,
$midSurface, $output, $output_blurred );
&run( "mv", "-f", $output_blurred, $output ); }
[Command line]
dump_rms white_trans.obj gray_trans.obj ./native_rms_tlink_20mm_right.txt
[cf. diff_surfaces white_trans.obj gray_trans.obj link link_test.txt] ->dump_rms와 동일
Rms over the points:
Average dist:
Std dev dist:
Min dist:
Max dist:
cortical thickness measurement
Blur
diffuse -kernel 20 -iterations parametric 1 ../midsurface.obj ../link_test.txt ../diffuse_cth_blur.mnc >> ../blur.txt

9. [Command line]
(2) diffuse -kernel 20 -iterations parametric 1 ../midsurface.obj ../link_test.txt ../diffuse_cth_blur.mnc
Usage: diffuse [-kernel FWHM] [-iterations n] [-parametric p]
file.obj input_signal.txt output_signal.txt
Values: FWHM > 0 (in mm, default 20mm)
n > 0 (default 100)
p = 0 (linear) or 1 (quadratic, default) or 2 (heat kernel)
(3) mv diffuse_cth_blur.mnc ./diffuse_cth_blur.txt
Iter 0 #clipped = 6287
Iter 50 #clipped = 89492
Iter 100 #clipped = 46709
Iter 150 #clipped = 32698
Iter 200 #clipped = 25875
Iter 250 #clipped = 22523
Iter 300 #clipped = 19436
Iter 350 #clipped = 18069
Iter 400 #clipped = 16261
Iter 450 #clipped = 14269
Iter 500 #clipped = 13199
Iter 550 #clipped = 12385
Iter 600 #clipped = 11386
Iter 650 #clipped = 11110
Iter 700 #clipped = 10318
Iter 750 #clipped = 9366
Iter 800 #clipped = 9008
Iter 850 #clipped = 8553
Iter 900 #clipped = 8226
Iter 950 #clipped = 7899
cortical thickness 명령어를 사용할 때 –fwhm 옵션을 주어야 이 명령어가 작동한다.

10. if( $tlaplace ) { if( defined $transform_xfm ) { #when transformation is given, transform both surfaces(done above) and icbm model to native space (ugly!) my $icbmModel = "0.50"; my $ModelDir = "$FindBin::Bin/../share/ICBM/"; = ("icbm_template_${icbmModel}mm.mnc"); MNI::DataDir::check_data($ModelDir, &run( "mincresample", "-quiet", "$ModelDir/icbm_template_${icbmModel}mm.mnc", "-transform", $transform_xfm, "-invert", "-tfm_input_sampling", "-step", "0.5", "0.5", "0.5", "-clobber", "${TmpDir}/laplace_like_file.mnc" ); &run( "laplacian_initialisation", "-like", "${TmpDir}/laplace_like_file.mnc", $gray, $white, "${TmpDir}/laplace_initial.mnc" ); unlink( "${TmpDir}/laplace_like_file.mnc" ); } else { # assume transformation is identity, so surfaces are already in icbm space &run( "laplacian_initialisation", "-icbm_model", "0.50", $gray, $white, "${TmpDir}/laplace_initial.mnc" ); } &run( "laplacian_thickness", "-h", "0.1", "-convergence", " ", "-2nd_rk", "-max_iterations", "300", "-object_eval", $midSurface, "-from_grid", "${TmpDir}/laplace_initial.mnc", "${TmpDir}/thickness_uncleaned.txt" ); &run( "vertex_stats", "-replace_nans", "${TmpDir}/thickness_uncleaned.txt", $output ); }
diffuse -kernel 20 -iterations parametric 1 ../midsurface.obj ../link_test.txt ../diffuse_cth_blur.mnc >> ../blur.txt

11. -like: Specifies a model file for the resampling.
[Command line]
mincresample -quiet icbm_template_0.50mm.mnc -transform mni_icbm_00340_t1_tal.xfm -invert -tfm_input_sampling -step clobber laplace_like_file.mnc
[Usage]
-tfm_input_sampling: Transform the input sampling with the transform (default).
-transformation: File giving world transformation. (Default = identity).
-like: Specifies a model file for the resampling.
-step: Step size along each dimension (X, Y, Z) Default value: 0 0 0
laplacian_initialisation -clobber -like laplace_like_file.mnc ../gray_trans.obj
../white_trans.obj laplace_initial.mnc
-like : Volume to base grid on. Can optionally be resampled using the -step option. This argument is required unless -icbm_model is specified.
laplacian_thickness -h 0.1 -convergence nd_rk -max_iterations 300 -object_eval ../midsurface.obj -from_grid laplace_initial.mnc ./thickness_uncleaned.txt
Usage: laplacian_thickness [options] -like sample.mnc grey_surface.obj
white_surface.obj output_thickness.mnc or
Usage: laplacian_thickness [options] -like sample.mnc -object_eval surface.obj
grey_surface.obj white_surface.obj output_thickness.txt
-like: MINC file whose shape the cortical mantle will take
-h: H value to use for Eulerian integration
-convergence: Stop criteria for equation relaxation.
-2nd_rk: Use second order Runge-Kutta integration
-object_eval: Evaluate thickness only at vertices of the obj file. Output text rather than minc.
-from_grid: Use a prepared grid.
-tfm_input_sampling: Transform the input sampling with the transform (default).
-transformation: File giving world transformation. (Default = identity).
-like: Specifies a model file for the resampling.
-step: Step size along each dimension (X, Y, Z)
Default value: 0 0 0

12. thickness_uncleaned.txt
vertex_stats -replace_nans thickness_uncleaned.txt vertex_la.txt
STATS:
# points = 40962
# used = 40962
# NaN = 0
# inval = 448
mean =
std =
[options]
-replace_nans: Replace NaNs with mean.
-replace_outliers: Replace outliers with mean.
-std_constant: Define outlier as this constant times the standard deviation
Default value: 3

15. 49. Resample_left_mean_curvature
모듈: Cortical_Measurements.pm
Label: "nonlinear resample left mean curvature“
실행명령: bin/surface-resample
입력:
../surfaces/mni_icbm_00340_mid_surface_left_81920.obj
../thickness/mni_icbm_00340_native_mc_20mm_left.txt
../transforms/surfreg/mni_icbm_00340_left_surfmap.sm
/models/surf_reg_model_left.obj => Oliver_template
출력: ./mni_native_mc_rsl_20mm_left.txt
의존성: mean_curvature_20mm_left (stage 45)

16. [Command line] ##### Resampling of the mean curvature #####
my $left_surfmap = ${$image}->{surface_map}{left};
my $right_surfmap = ${$image}->{surface_map}{right};
my $rsl_left_mc = ${$image}->{mc_rsl}{left};
my $rsl_right_mc = ${$image}->{mc_rsl}{right};
${$pipeline_ref}->addStage( {
name => "resample_left_mean_curvature",
label => "nonlinear resample left mean curvature",
inputs => [$native_mc_left, $left_surfmap, $left_mid_surface],
outputs => [$rsl_left_mc],
args => ["surface-resample", $surfreg_model, $left_mid_surface,
$native_mc_left, $left_surfmap, $rsl_left_mc],
prereqs => ["mean_curvature_${tkernel}mm_left"] });
[Command line]
surface-resample /usr/local/mni/Dec /CIVET-1.1.9/models/surf_reg_model_left.obj
../surfaces/mni_icbm_00340_mid_surface_left_81920.obj ../thickness/mni_icbm_00340_native_mc_20mm_left.txt ../transforms/surfreg/mni_icbm_00340_left_surfmap.sm ./mni_native_mc_rsl_20mm_left.txt
Usage: surface-resample [options] source_geom target_geom target_attr mapfile resampled_attr
Command-specific options:
-nearest: nearest-neighbour interpolation (default: linear)
xfminvert mni_icbm_00340_t1_tal.xfm mni_icbm_00340_t1_tal_inv.xfm
test]$ transform_objects mni_icbm_00340_white_surface_left_calibrated_81920.obj mni_icbm_
mni_icbm_00340_gray_surface_left_81920.obj mni_icbm_00340_t1_tal.xfm
mni_icbm_00340_native_mc_20mm_left.txt mni_icbm_00340_white_surface_left_calibrated_81920.obj
mni_icbm_00340_t1_tal_inv.xfm mni_icbm_native_mc_rsl_20mm_left.txt
test]$ transform_objects mni_icbm_00340_white_surface_left_calibrated_81920.obj mni_icbm_00340_t1_tal_inv.xfm mni_icbm_00340_white_surface_left_native.obj
test]$ transform_objects mni_icbm_00340_gray_surface_left_81920.obj mni_icbm_00340_t1_tal_inv.xfm mni_icbm_00340_gray_surface_left_81920_native.obj
test]$ average_surfaces mni_icbm_00340_mid_surface_left_native.obj none none 1 ./mni_icbm_00340_white_surface_left_native.obj mni_icbm_00340_gray_surface_left_81920_native.obj
1: ./mni_icbm_00340_white_surface_left_native.obj
2: mni_icbm_00340_gray_surface_left_81920_native.obj
Objects output.
surface-resample /usr/local/mni/Dec /CIVET-1.1.9/models/surf_reg_model_left.obj ../../surfaces/mni_icbm_00340_mid_surface_left_81920.obj ../../thickness/mni_icbm_00340_native_mc_20mm_left.txt ../../transforms/surfreg/mni_icbm_00340_left_surfmap.sm ./mni_icbm_00340_native_mc_rsl_20mm_left.txt
colour_object mni_icbm_00340_mid_surface_left_native.obj mni_icbm_00340_native_mc_20mm_left.txt mni_icbm_00340_native_mc_20mm_left.obj spectral
Value range:

17. surf_reg_model_left.obj
surf_reg_model_right.obj

18. colour_object [obj file] [txt file] [output obj file] …
mni_icbm_00340_native_mc_20mm_left.obj

19. Resampling meancurvature
mni_icbm_00340_native_mc_rsl_20mm_left.obj