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KristinBH
April 19, 2015 08:55AM
Hi,

I am interested in using the Juelich probabilistic atlas of the subnuclei of the amygdala from FSL as seed regions in GroupInCorr.

I created binarized masks of each subnucleus in FSL (and also added them together to create binarized whole amygdala masks), used 3dwarp to transform from MNI to Talairach space, used 3dresample to resample to 3x3x3mm resolution and RAI orientation, but now I'm stuck on different size matrices (or at least I think that's the problem). When I run 3dGroupInCorr using these warped and resampled masks, I get an error that the masks are the wrong size. 3dinfo seems to confirm this (comparing the Juelich masks I've made, first, to an amygdala mask from TT Daemon in AFNI that I made with the whereami command, second):

-------------

kristin% 3dinfo bilat_amygdala_Juelich50_resam_recalc+tlrc
++ 3dinfo: AFNI version=AFNI_2011_12_21_1014 (Nov 21 2014) [64-bit]

Dataset File: bilat_amygdala_Juelich50_resam_recalc+tlrc
Identifier Code: AFN_pdvoGIAUJjK6JmnndVS5Ew Creation Date: Fri Apr 17 00:48:26 2015
Template Space: TLRC
Dataset Type: Echo Planar (-epan)
Byte Order: LSB_FIRST [this CPU native = LSB_FIRST]
Storage Mode: BRIK
Storage Space: 271,633 (272 thousand [kilo]) bytes
Geometry String: "MATRIX(3,0,0,-89.5,0,3,0,-90.5,0,0,3,-71.5):61,73,61"
Data Axes Tilt: Plumb
Data Axes Orientation:
first (x) = Right-to-Left
second (y) = Anterior-to-Posterior
third (z) = Inferior-to-Superior [-orient RAI]
R-to-L extent: -89.500 [R] -to- 90.500 [L] -step- 3.000 mm [ 61 voxels]
A-to-P extent: -90.500 [A] -to- 125.500 [P] -step- 3.000 mm [ 73 voxels]
I-to-S extent: -71.500 -to- 108.500 [S] -step- 3.000 mm [ 61 voxels]
Number of values stored at each pixel = 1
-- At sub-brick #0 '#0' datum type is byte: 0 to 1

----- HISTORY -----
[kristin@Kristins-MacBook-Pro.local: Thu Apr 16 19:24:13 2015] 3dWarp -prefix bilat_amygdala_Juelich50 -mni2tta bilat_amygdala_Juelich50.nii.gz
[kristin@Kristins-MacBook-Pro.local: Thu Apr 16 22:20:59 2015] 3dresample -dxyz 3.0 3.0 3.0 -orient RAI -prefix bilat_amygdala_Juelich50_resam+tlrc -inset bilat_amygdala_Juelich50+tlrc
[kristin@Kristins-MacBook-Pro.local: Fri Apr 17 00:48:26 2015] 3dcalc -a bilat_amygdala_Juelich50_resam+tlrc -expr 'ispositive(a-0.5)' -datum byte -prefix bilat_amygdala_Juelich50_resam_recalc+tlrc

-------------

kristin% 3dinfo bilateral_amygdala_mask_resam+tlrc
++ 3dinfo: AFNI version=AFNI_2011_12_21_1014 (Nov 21 2014) [64-bit]

Dataset File: bilateral_amygdala_mask_resam+tlrc
Identifier Code: AFN_G4hnwb0-1g1_bM5D7j8oqA Creation Date: Tue Apr 14 16:11:07 2015
Template Space: TLRC
Dataset Type: Intensity (-fim)
Byte Order: LSB_FIRST [this CPU native = LSB_FIRST]
Storage Mode: BRIK
Storage Space: 172,800 (173 thousand [kilo]) bytes
Geometry String: "MATRIX(3,0,0,-79.5,0,3,0,-79.5,0,0,3,-63.5):54,64,50"
Data Axes Tilt: Plumb
Data Axes Orientation:
first (x) = Right-to-Left
second (y) = Anterior-to-Posterior
third (z) = Inferior-to-Superior [-orient RAI]
R-to-L extent: -79.500 [R] -to- 79.500 [L] -step- 3.000 mm [ 54 voxels]
A-to-P extent: -79.500 [A] -to- 109.500 [P] -step- 3.000 mm [ 64 voxels]
I-to-S extent: -63.500 -to- 83.500 [S] -step- 3.000 mm [ 50 voxels]
Number of values stored at each pixel = 1
-- At sub-brick #0 'amygdala' datum type is byte: 0 to 1

----- HISTORY -----
[kristin@Kristins-MacBook-Pro.local: Tue Apr 14 16:09:23 2015] whereami -mask_atlas_region TT_Daemon::amygdala -prefix bilateral_amygdala_mask
[kristin@Kristins-MacBook-Pro.local: Tue Apr 14 16:11:07 2015] 3dresample -dxyz 3.0 3.0 3.0 -prefix bilateral_amygdala_mask_resam+tlrc -inset bilateral_amygdala_mask+tlrc

-------------

I tried to run align_epi_anat.py to align the Juelich mask to the errts data of a subject but that failed to change the matrix (and 3dGroupInCorr still fails):

align_epi_anat.py -dset1_strip None -dset2_strip None -dset1 bilat_amygdala_Juelich50_resam_recalc+tlrc -dset2 errts.anaticor.DS201+tlrc -dset1to2

3dinfo output:

kristin% 3dinfo bilat_amygdala_Juelich50_resam_recalc_al+tlrc
++ 3dinfo: AFNI version=AFNI_2011_12_21_1014 (Nov 21 2014) [64-bit]

Dataset File: bilat_amygdala_Juelich50_resam_recalc_al+tlrc
Identifier Code: AFN_IrsucrX1Xo1FFCKgcEbzrg Creation Date: Sun Apr 19 08:48:28 2015
Template Space: TLRC
Dataset Type: Anat Bucket (-abuc)
Byte Order: LSB_FIRST [this CPU native = LSB_FIRST]
Storage Mode: BRIK
Storage Space: 271,633 (272 thousand [kilo]) bytes
Geometry String: "MATRIX(3,0,0,-89.5,0,3,0,-90.5,0,0,3,-71.5):61,73,61"
Data Axes Tilt: Plumb
Data Axes Orientation:
first (x) = Right-to-Left
second (y) = Anterior-to-Posterior
third (z) = Inferior-to-Superior [-orient RAI]
R-to-L extent: -89.500 [R] -to- 90.500 [L] -step- 3.000 mm [ 61 voxels]
A-to-P extent: -90.500 [A] -to- 125.500 [P] -step- 3.000 mm [ 73 voxels]
I-to-S extent: -71.500 -to- 108.500 [S] -step- 3.000 mm [ 61 voxels]
Number of values stored at each pixel = 1
-- At sub-brick #0 '#0' datum type is byte: 0 to 1

----- HISTORY -----
[kristin@Kristins-MacBook-Pro.local: Thu Apr 16 19:24:13 2015] 3dWarp -prefix bilat_amygdala_Juelich50 -mni2tta bilat_amygdala_Juelich50.nii.gz
[kristin@Kristins-MacBook-Pro.local: Thu Apr 16 22:20:59 2015] 3dresample -dxyz 3.0 3.0 3.0 -orient RAI -prefix bilat_amygdala_Juelich50_resam+tlrc -inset bilat_amygdala_Juelich50+tlrc
[kristin@Kristins-MacBook-Pro.local: Fri Apr 17 00:48:26 2015] 3dcalc -a bilat_amygdala_Juelich50_resam+tlrc -expr 'ispositive(a-0.5)' -datum byte -prefix bilat_amygdala_Juelich50_resam_recalc+tlrc
[kristin@Kristins-MacBook-Pro.local: Sun Apr 19 08:48:25 2015] 3dcopy ./bilat_amygdala_Juelich50_resam_recalc+tlrc ./__tt_bilat_amygdala_Juelich50_resam_recalc+tlrc
[kristin@Kristins-MacBook-Pro.local: Sun Apr 19 08:48:28 2015] 3dAllineate -lpa -wtprefix ./__tt_bilat_amygdala_Juelich50_resam_recalc_al_wtal -weight ./__tt_errts.anaticor.DS201_ts_wt+tlrc -source ./__tt_bilat_amygdala_Juelich50_resam_recalc+tlrc -prefix ./bilat_amygdala_Juelich50_resam_recalc_al -base ./__tt_errts.anaticor.DS201_ts+tlrc -nocmass -1Dmatrix_save ./bilat_amygdala_Juelich50_resam_recalc_al_mat.aff12.1D -master SOURCE -weight_frac 1.0 -maxrot 6 -maxshf 10 -VERB -warp aff -source_automask+4 -onepass
[kristin@Kristins-MacBook-Pro.local: Sun Apr 19 08:48:28 2015] align_epi_anat.py -dset1_strip None -dset2_strip None -dset1 bilat_amygdala_Juelich50_resam_recalc+tlrc -dset2 errts.anaticor.DS201+tlrc -dset1to2

-------------

How can I get the mask to be the same size as the data?

Any suggestions would be greatly appreciated.

Thank you!
Kristin
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Subject Author Posted

getting FSL atlas mask into groupincorr

KristinBH April 19, 2015 08:55AM

Re: getting FSL atlas mask into groupincorr

Daniel Glen April 19, 2015 05:29PM