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AshsAtlasesConfig.json
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{
"Atlas": "ASHS-PMC-T1",
"Directory": "/app/atlas/data/ashsT1_atlas_upennpmc_07202018",
"Inputs": {
"T1" : "testdata/124822x20210126x3TxABC/T1_3D_0.8x0.8x0.8_ND.nii.gz"
},
"md5Url": "https://upenn.box.com/shared/static/602oyyvkiyukeqwej6444vklwvyydhkz.md5sum",
"QaFileRegEx": [
"qa/.*qa_seg_bootstrap_heur_(left|right)_qa.png"
],
"OutputDir": [
{
"FileRegEx": "tse.nii.gz$",
"MapTo": "higresmri.nii.gz",
"Tags": "HighResMri",
"Modality": "MR",
"ExpectedCount": 1
},
{
"FileRegEx": "mprage.nii.gz$",
"MapTo": "t1.nii.gz",
"ExpectedCount": 1
},
{
"FileRegEx": "final/.*(left|right)_lfseg.*.nii.gz$",
"Modality": "SEG",
"Classification": "$SegmentationJson",
"Tags": [ "$Handedness", "$Atlas" ],
"ExpectedCount": 6
},
{
"FileRegEx": "final/.*bootstrap.*txt$",
"ExpectedCount": 8
}
],
"Url": "https://upenn.box.com/shared/static/9q9q9e5d58mg9f0aurcjkdx1bt3anvp7.tgz"
}
{
"Atlas": "ASHS-PMC-T2",
"Directory": "/app/atlas/data/ashs_atlas_upennpmc_20170810",
"Inputs": {
"T1" : "testdata/124822x20210126x3TxABC/T1_3D_0.8x0.8x0.8_ND.nii.gz",
"T2" : "testdata/124822x20210126x3TxABC/T2_2D_0.4x0.4x1.2mm_180flip_ND.nii.gz"
},
"md5Url": "https://upenn.box.com/shared/static/tu2sjoy0omq5vgrcg2od7fccqfcixt61.md5sum",
"QaFileRegEx": [
"qa/.*qa_seg_bootstrap_heur_(left|right)_qa.png"
],
"OutputDir": [
{
"FileRegEx": "tse.nii.gz$",
"MapTo": "higresmri.nii.gz",
"Tags": "HighResMri",
"Modality": "MR",
"ExpectedCount": 1
},
{
"FileRegEx": "mprage.nii.gz$",
"MapTo": "t1.nii.gz",
"ExpectedCount": 1
},
{
"FileRegEx": "final/.*(left|right)_lfseg.*.nii.gz$",
"Modality": "SEG",
"Classification": "$SegmentationJson",
"Tags": [ "$Handedness", "$Atlas" ],
"ExpectedCount": 6
},
{
"FileRegEx": "final/.*bootstrap.*txt$",
"ExpectedCount": 8
},
{
"FileRegEx": "affine_t1_to_template/greedy_t1_to_template.mat$",
"MapTo": "greedy.mat",
"ExpectedCount": 1
},
{
"FileRegEx": "flirt.*/flirt.*.mat$",
"ExpectedCount": 2
}
],
"Url": "https://upenn.box.com/shared/static/zdikuhgwc67tp3d85bml36n6asbm92yy.tgz"
}
{
"Atlas": "ASHS-ABC-3T",
"Directory": "/app/atlas/data/ashs_atlas_abc_prisma_20200406",
"Inputs": {
"T1" : "testdata/124822x20210126x3TxABC/T1_3D_0.8x0.8x0.8_ND.nii.gz",
"T2" : "testdata/124822x20210126x3TxABC/T2_2D_0.4x0.4x1.2mm_180flip_ND.nii.gz"
},
"md5Url": "https://upenn.box.com/shared/static/fvl2977kvx1a5hk62xlp75l66aef5f34.md5sum",
"QaFileRegEx": [
"_(left|right)_lfseg_corr_usegray.nii.gz",
"qa_seg_bootstrap_corr_usegray_(left|right)_qa.png"
],
"Url": "https://upenn.box.com/shared/static/907f7xl7z4mukwvvdzpdlduq3lxkd2xc.tgz"
}
{
"Atlas": "ASHS-ABC-7T",
"Directory": "/app/atlas/data/ashs_atlas_abc_7t_20230511",
"Inputs": {
"T1" : "testdata/124822x20210126x7TxABC/T2_Coronal_p2_0.4x0.4x1.0mm_ND.nii.gz"
},
"md5Url": "https://upenn.box.com/shared/static/gh7kajy3yw3udk48oa996adykrgtqnn4.md5sum",
"QaFileRegEx": [
"_(left|right)_lfseg_corr_usegray.nii.gz",
"qa_seg_bootstrap_heur_(left|right)_qa.png"
],
"Url": "https://upenn.box.com/shared/static/v2sxlxannw31h54vwybo0mpt85vkoyaj.tgz"
}
{
"Atlas": "ASHS-Magdeburg",
"Directory": "/app/atlas/data/ashs_atlas_dzne7t",
"Inputs": {
"T1" : "testdata/125590x20221020x7TxYMTL/memp2rage_700um_TI700_2700_TR5000_p3_PF0.75_BW800Hz_INV2_ND_RMS.nii.gz",
"T2" : "testdata/125590x20221020x7TxYMTL/T2_Coronal_p2_0.4x0.4x1.0mm_ND.nii.gz"
},
"md5Url": "https://upenn.box.com/shared/static/ant1wdbdnpkky7hfirya83v4w9xe1kag.md5sum",
"Url": "https://upenn.box.com/shared/static/hb7u370gy1djpz2lqlp17533buu209qk.tgz"
}
{
"Atlas": "ASHS-HarP",
"Directory": "/app/atlas/data/ashs_atlas_harp30/final",
"Inputs": {
"T1" : "testdata/124822x20210126x3TxABC/T1_3D_0.8x0.8x0.8_ND.nii.gz"
},
"md5Url": "https://upenn.box.com/shared/static/i5k4gkm93v6lx7ylsq0n03m4nc4wbwig.md5sum",
"QaFileRegEx": [
"qa/qa_seg_bootstrap_corr_nogray_(left|right)_qa.png"
],
"OutputDir": [
{
"FileRegEx": "tse.nii.gz$",
"MapTo": "higresmri.nii.gz",
"Tags": "HighResMri",
"Modality": "MR",
"ExpectedCount": 1
},
{
"FileRegEx": "final/.*(left|right)_lfseg.*.nii.gz$",
"Modality": "SEG",
"Classification": "$SegmentationJson",
"Tags": [ "$Handedness", "$Atlas" ],
"ExpectedCount": 6
}
],
"SubAtlas": "ASHS-ICV",
"Url": "https://upenn.box.com/shared/static/uijwemiz4rvp5kbtqoat8c8g4c8kgw1h.tgz"
}
{
"Atlas": "ASHS-ICV",
"Directory": "/app/atlas/data/ashs_atlas_icv/final",
"Inputs": {
"T1" : "testdata/124822x20210126x3TxABC/T1_3D_0.8x0.8x0.8_ND.nii.gz"
},
"md5Url": "https://upenn.box.com/shared/static/z0nh75zpit2ll2c2by1zwvyiqrubjbvk.md5sum",
"QaFileRegEx": [
"qa/qa_seg_multiatlas_corr_nogray_left_qa.png"
],
"OutputDir": [
{
"FileRegEx": "tse.nii.gz$",
"MapTo": "higresmri.nii.gz",
"Tags": "HighResMri",
"Modality": "MR",
"ExpectedCount": 1
},
{
"FileRegEx": "final/.*_left_lfseg_corr_nogray.nii.gz",
"Modality": "SEG",
"Classification": "$SegmentationJson",
"Tags": [ "$Handedness", "$Atlas" ],
"ExpectedCount": 6
}
],
"Url": "https://upenn.box.com/shared/static/1yy653yuy2zcd2rots1eaftg7theyyoq.tgz"
}
{
"Atlas": "ASHS-Princeton",
"Directory": "/app/atlas/data/ashs_atlas_princeton",
"Inputs": {
"T1" : "testdata/126954x20230413x3TxYMTL/T1_3D_0.8x0.8x0.8_ND.nii.gz",
"T2" : "testdata/126954x20230413x3TxYMTL/T2_2D_0.4x0.4x1.2mm_180flip_ND.nii.gz"
},
"md5Url": "https://upenn.box.com/shared/static/j1irtnl990r8pxh1pn5jvfc3b5f7m4kt.md5sum",
"Url": "https://upenn.box.com/shared/static/g2zu3x7yg0x7phryynqcucfmxj3oibdr.tgz"
}
{
"Atlas": "ASHS-Utrecht",
"Directory": "/app/atlas/data/ashs_atlas_umcutrecht_7t_20170810",
"Inputs": {
"T1" : "testdata/124822x20210126x3TxABC/T1_3D_0.8x0.8x0.8_ND.nii.gz",
"T2" : "testdatatestdata//124822x20210126x3TxABC/T2_2D_0.4x0.4x1.2mm_180flip_ND.nii.gz"
},
"md5Url": "https://upenn.box.com/shared/static/l38ziflahabhmkepmfvfuwj23lje8t4x.md5sum",
"Url": "https://upenn.box.com/shared/static/36ojbo2u51bc215twzch6ym2bszaehw8.tgz"
}