Plotting the Optic Radiations#

pyAFQ is designed to be customizable. This example shows how you can customize it to define a new bundle based on both waypoint ROIs of your design, as well as endpoint ROIs of your design.

In these example, we run pyAFQ with both the custom ROIs and the default waypoint ROIs.

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Downloading https://templateflow.s3.amazonaws.com/tpl-MNI152NLin2009cAsym/tpl-MNI152NLin2009cAsym_res-01_T2w.nii.gz

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100%|##########| 127466/127466.0 [00:35<00:00, 3639.84it/s]
Optimizing level 2 [max iter: 10000]
Optimizing level 1 [max iter: 1000]
Optimizing level 0 [max iter: 100]
Optimizing level 2 [max iter: 10000]
Optimizing level 1 [max iter: 1000]
Optimizing level 0 [max iter: 100]
Optimizing level 2 [max iter: 10000]
Optimizing level 1 [max iter: 1000]
Optimizing level 0 [max iter: 100]

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 41%|####1     | 114684/277588 [00:06<00:08, 19040.80it/s]
 43%|####2     | 118780/277588 [00:07<00:08, 19630.23it/s]
 44%|####4     | 122876/277588 [00:07<00:08, 18947.95it/s]
 46%|####5     | 126972/277588 [00:07<00:07, 20042.82it/s]
 47%|####7     | 131068/277588 [00:07<00:08, 18111.50it/s]
 49%|####8     | 135164/277588 [00:07<00:07, 19259.52it/s]
 50%|#####     | 139260/277588 [00:08<00:06, 20937.12it/s]
 52%|#####1    | 143356/277588 [00:08<00:06, 19457.67it/s]
 53%|#####3    | 147452/277588 [00:08<00:06, 19516.07it/s]
 55%|#####4    | 151548/277588 [00:08<00:06, 18714.36it/s]
 56%|#####6    | 155644/277588 [00:08<00:06, 19192.01it/s]
 58%|#####7    | 159740/277588 [00:09<00:06, 19184.27it/s]
 59%|#####9    | 163836/277588 [00:09<00:06, 18910.64it/s]
 60%|######    | 167932/277588 [00:09<00:06, 17337.86it/s]
 62%|######1   | 172028/277588 [00:09<00:05, 17902.49it/s]
 63%|######3   | 176124/277588 [00:10<00:05, 17253.36it/s]
 65%|######4   | 180220/277588 [00:10<00:05, 16748.40it/s]
 66%|######6   | 184316/277588 [00:10<00:05, 17656.63it/s]
 68%|######7   | 188412/277588 [00:10<00:05, 16891.76it/s]
 69%|######9   | 192508/277588 [00:11<00:05, 16150.22it/s]
 71%|#######   | 196604/277588 [00:11<00:05, 15811.94it/s]
 72%|#######2  | 200700/277588 [00:11<00:04, 15890.33it/s]
 74%|#######3  | 204796/277588 [00:11<00:04, 15103.90it/s]
 75%|#######5  | 208892/277588 [00:12<00:05, 13727.09it/s]
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 78%|#######8  | 217084/277588 [00:12<00:04, 13647.45it/s]
 80%|#######9  | 221180/277588 [00:13<00:04, 11465.52it/s]
 81%|########1 | 225276/277588 [00:13<00:04, 11898.21it/s]
 83%|########2 | 229372/277588 [00:14<00:04, 11436.80it/s]
 84%|########4 | 233468/277588 [00:14<00:03, 11121.85it/s]
 86%|########5 | 237564/277588 [00:14<00:03, 11424.61it/s]
 87%|########7 | 241660/277588 [00:15<00:03, 9986.77it/s]
 89%|########8 | 245756/277588 [00:15<00:02, 11866.45it/s]
 90%|######### | 249852/277588 [00:15<00:02, 12316.34it/s]
 91%|#########1| 253948/277588 [00:16<00:02, 10823.80it/s]
 93%|#########2| 258044/277588 [00:16<00:01, 11838.23it/s]
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 99%|#########8| 274428/277588 [00:17<00:00, 13686.24it/s]
100%|##########| 277588/277588 [00:17<00:00, 15599.26it/s]

  0%|          | 0/81196 [00:00<?, ?it/s]
  0%|          | 380/81196 [00:00<00:22, 3666.80it/s]
  4%|3         | 3068/81196 [00:00<00:05, 14267.29it/s]
  8%|7         | 6140/81196 [00:00<00:04, 17834.70it/s]
 10%|#         | 8188/81196 [00:00<00:04, 15697.76it/s]
 13%|#2        | 10236/81196 [00:00<00:04, 15165.13it/s]
 15%|#5        | 12284/81196 [00:00<00:04, 14956.44it/s]
 18%|#7        | 14332/81196 [00:00<00:04, 15130.25it/s]
 20%|##        | 16380/81196 [00:01<00:04, 14615.41it/s]
 23%|##2       | 18428/81196 [00:01<00:04, 12878.18it/s]
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 30%|###       | 24572/81196 [00:01<00:04, 14154.31it/s]
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 38%|###7      | 30716/81196 [00:02<00:03, 14116.18it/s]
 40%|####      | 32764/81196 [00:02<00:03, 13262.57it/s]
 43%|####2     | 34812/81196 [00:02<00:03, 13719.03it/s]
 45%|####5     | 36860/81196 [00:02<00:03, 13755.86it/s]
 48%|####7     | 38908/81196 [00:02<00:02, 14713.80it/s]
 50%|#####     | 40956/81196 [00:02<00:02, 14713.53it/s]
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 55%|#####5    | 45052/81196 [00:03<00:02, 14704.01it/s]
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 61%|######    | 49148/81196 [00:03<00:02, 14218.20it/s]
 63%|######3   | 51196/81196 [00:03<00:02, 11973.02it/s]
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 71%|#######   | 57340/81196 [00:04<00:01, 14784.97it/s]
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 81%|########  | 65532/81196 [00:04<00:01, 14467.41it/s]
 83%|########3 | 67580/81196 [00:04<00:00, 14603.39it/s]
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 98%|#########8| 79868/81196 [00:05<00:00, 15894.18it/s]
100%|##########| 81196/81196 [00:05<00:00, 14717.90it/s]

  0%|          | 0/82696 [00:00<?, ?it/s]
  1%|          | 508/82696 [00:00<00:17, 4623.65it/s]
  5%|4         | 4092/82696 [00:00<00:04, 17118.27it/s]
 10%|9         | 8188/82696 [00:00<00:03, 19663.93it/s]
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 99%|#########9| 81916/82696 [00:05<00:00, 14611.25it/s]
100%|##########| 82696/82696 [00:05<00:00, 15340.35it/s]

  0%|          | 0/22564 [00:00<?, ?it/s]
  1%|          | 188/22564 [00:00<00:12, 1852.32it/s]
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 18%|#8        | 4092/22564 [00:00<00:02, 8231.27it/s]
 23%|##2       | 5116/22564 [00:00<00:02, 8300.79it/s]
 27%|##7       | 6140/22564 [00:00<00:02, 5871.52it/s]
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100%|#########9| 22524/22564 [00:02<00:00, 8692.37it/s]
100%|##########| 22564/22564 [00:02<00:00, 7886.07it/s]

  0%|          | 0/40517 [00:00<?, ?it/s]
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100%|##########| 40517/40517 [00:05<00:00, 8034.10it/s]

  0%|          | 0/39195 [00:00<?, ?it/s]
  1%|1         | 508/39195 [00:00<00:08, 4693.22it/s]
 10%|#         | 4092/39195 [00:00<00:02, 16897.07it/s]
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 84%|########3 | 32764/39195 [00:01<00:00, 20645.16it/s]
 94%|#########4| 36860/39195 [00:01<00:00, 21001.04it/s]
100%|##########| 39195/39195 [00:01<00:00, 22279.37it/s]

  0%|          | 0/34257 [00:00<?, ?it/s]
  1%|1         | 508/34257 [00:00<00:06, 4981.14it/s]
 12%|#1        | 4092/34257 [00:00<00:01, 21434.66it/s]
 24%|##3       | 8188/34257 [00:00<00:00, 28986.80it/s]
 48%|####7     | 16380/34257 [00:00<00:00, 33961.03it/s]
 60%|#####9    | 20476/34257 [00:00<00:00, 30816.15it/s]
 72%|#######1  | 24572/34257 [00:00<00:00, 29450.29it/s]
 84%|########3 | 28668/34257 [00:01<00:00, 28204.85it/s]
 96%|#########5| 32764/34257 [00:01<00:00, 26035.45it/s]
100%|##########| 34257/34257 [00:01<00:00, 28611.47it/s]

  0%|          | 0/73788 [00:00<?, ?it/s]
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  6%|5         | 4092/73788 [00:00<00:09, 7001.85it/s]
  7%|6         | 5116/73788 [00:00<00:09, 7016.15it/s]
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 10%|9         | 7164/73788 [00:01<00:10, 6446.63it/s]
 11%|#1        | 8188/73788 [00:01<00:11, 5594.89it/s]
 12%|#2        | 9212/73788 [00:01<00:12, 5380.73it/s]
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 21%|##        | 15356/73788 [00:02<00:12, 4555.22it/s]
 22%|##2       | 16380/73788 [00:03<00:14, 4045.50it/s]
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 33%|###3      | 24572/73788 [00:05<00:12, 4084.29it/s]
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 51%|#####1    | 37884/73788 [00:07<00:06, 5235.87it/s]
 53%|#####2    | 38908/73788 [00:07<00:06, 5565.48it/s]
 54%|#####4    | 39932/73788 [00:08<00:05, 5811.26it/s]
 56%|#####5    | 40956/73788 [00:08<00:05, 5521.66it/s]
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 79%|#######9  | 58364/73788 [00:11<00:03, 4954.08it/s]
 80%|########  | 59388/73788 [00:11<00:02, 5024.14it/s]
 82%|########1 | 60412/73788 [00:12<00:02, 5368.76it/s]
 83%|########3 | 61436/73788 [00:12<00:02, 4752.35it/s]
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 87%|########7 | 64508/73788 [00:12<00:01, 5416.00it/s]
 89%|########8 | 65532/73788 [00:13<00:01, 5399.94it/s]
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 92%|#########1| 67580/73788 [00:13<00:01, 5469.50it/s]
 93%|#########2| 68604/73788 [00:13<00:00, 6113.56it/s]
 94%|#########4| 69628/73788 [00:13<00:00, 6761.01it/s]
 96%|#########5| 70652/73788 [00:13<00:00, 5792.31it/s]
 99%|#########8| 72700/73788 [00:14<00:00, 6385.33it/s]
100%|#########9| 73724/73788 [00:14<00:00, 6934.46it/s]
100%|##########| 73788/73788 [00:14<00:00, 5169.80it/s]

  0%|          | 0/76608 [00:00<?, ?it/s]
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  1%|1         | 1020/76608 [00:00<00:14, 5095.20it/s]
  3%|2         | 2044/76608 [00:00<00:10, 6906.55it/s]
  5%|5         | 4092/76608 [00:00<00:09, 7769.63it/s]
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 11%|#         | 8188/76608 [00:01<00:14, 4835.38it/s]
 12%|#2        | 9212/76608 [00:01<00:13, 4940.34it/s]
 13%|#3        | 10236/76608 [00:01<00:12, 5238.14it/s]
 15%|#4        | 11260/76608 [00:01<00:10, 6022.52it/s]
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 20%|##        | 15356/76608 [00:02<00:10, 5973.16it/s]
 23%|##2       | 17404/76608 [00:02<00:08, 7034.74it/s]
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100%|##########| 76608/76608 [00:12<00:00, 5936.20it/s]

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 97%|#########6| 53756/55575 [00:20<00:00, 2541.40it/s]
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 99%|#########9| 55292/55575 [00:20<00:00, 2585.95it/s]
100%|##########| 55575/55575 [00:20<00:00, 2664.31it/s]

  0%|          | 0/96886 [00:00<?, ?it/s]
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  2%|1         | 1532/96886 [00:00<00:14, 6666.04it/s]
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  4%|4         | 4092/96886 [00:00<00:15, 5985.45it/s]
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 10%|9         | 9212/96886 [00:01<00:19, 4439.65it/s]
 11%|#         | 10236/96886 [00:02<00:18, 4704.02it/s]
 12%|#1        | 11260/96886 [00:02<00:18, 4601.42it/s]
 13%|#2        | 12284/96886 [00:02<00:20, 4185.05it/s]
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 19%|#9        | 18428/96886 [00:03<00:16, 4826.21it/s]
 20%|##        | 19452/96886 [00:04<00:18, 4297.13it/s]
 21%|##1       | 20476/96886 [00:04<00:18, 4170.65it/s]
 22%|##2       | 21500/96886 [00:04<00:16, 4563.88it/s]
 23%|##3       | 22524/96886 [00:04<00:17, 4181.39it/s]
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 30%|##9       | 28668/96886 [00:06<00:18, 3610.22it/s]
 31%|###       | 29692/96886 [00:06<00:16, 4155.92it/s]
 32%|###1      | 30716/96886 [00:07<00:16, 4009.07it/s]
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 34%|###3      | 32764/96886 [00:07<00:18, 3532.57it/s]
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 39%|###9      | 37884/96886 [00:08<00:15, 3879.88it/s]
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 50%|####9     | 48124/96886 [00:11<00:14, 3449.82it/s]
 51%|#####     | 49148/96886 [00:11<00:12, 3960.07it/s]
 52%|#####1    | 50172/96886 [00:12<00:12, 3612.95it/s]
 53%|#####2    | 51196/96886 [00:12<00:12, 3617.50it/s]
 54%|#####3    | 52220/96886 [00:12<00:13, 3247.13it/s]
 55%|#####4    | 53244/96886 [00:13<00:12, 3589.54it/s]
 56%|#####6    | 54268/96886 [00:13<00:11, 3819.31it/s]
 57%|#####7    | 55292/96886 [00:13<00:10, 4002.07it/s]
 58%|#####8    | 56316/96886 [00:13<00:10, 3862.04it/s]
 59%|#####9    | 57340/96886 [00:14<00:11, 3563.53it/s]
 60%|######    | 58364/96886 [00:14<00:12, 3184.13it/s]
 61%|######1   | 59388/96886 [00:14<00:10, 3410.66it/s]
 62%|######2   | 60412/96886 [00:15<00:09, 3974.34it/s]
 63%|######3   | 61436/96886 [00:15<00:09, 3863.14it/s]
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 79%|#######9  | 76796/96886 [00:19<00:04, 4609.76it/s]
 80%|########  | 77820/96886 [00:19<00:03, 4855.22it/s]
 81%|########1 | 78844/96886 [00:19<00:03, 4909.22it/s]
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 83%|########3 | 80892/96886 [00:19<00:02, 5656.67it/s]
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100%|##########| 96886/96886 [00:22<00:00, 4251.69it/s]

  0%|          | 0/81085 [00:00<?, ?it/s]
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 10%|#         | 8188/81085 [00:02<00:23, 3162.36it/s]
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100%|#########9| 80892/81085 [00:23<00:00, 4877.25it/s]
100%|##########| 81085/81085 [00:23<00:00, 3514.50it/s]

  0%|          | 0/73937 [00:00<?, ?it/s]
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100%|##########| 73937/73937 [00:14<00:00, 5157.36it/s]

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import os.path as op
from AFQ.api.group import GroupAFQ
import AFQ.api.bundle_dict as abd
import AFQ.data.fetch as afd
from AFQ.definitions.image import LabelledImageFile, RoiImage

afd.organize_stanford_data(clear_previous_afq=True)

or_rois = afd.read_or_templates()

bundles = abd.BundleDict({
    "L_OR": {
        "include": [
            or_rois["left_OR_1"],
            or_rois["left_OR_2"]],
        "exclude": [
            or_rois["left_OP_MNI"],
            or_rois["left_TP_MNI"],
            or_rois["left_pos_thal_MNI"]],
        "start": or_rois['left_thal_MNI'],
        "end": or_rois['left_V1_MNI'],
        "cross_midline": False,
    },
    "R_OR": {
        "include": [
            or_rois["right_OR_1"],
            or_rois["right_OR_2"]],
        "exclude": [
            or_rois["right_OP_MNI"],
            or_rois["right_TP_MNI"],
            or_rois["right_pos_thal_MNI"]],
        "start": or_rois['right_thal_MNI'],
        "end": or_rois['right_V1_MNI'],
        "cross_midline": False
    }
})

# combine custom ROIs with default BundleDict ROIs
bundles = bundles + abd.BundleDict()

brain_mask_definition = LabelledImageFile(
    suffix="seg",
    filters={"scope": "freesurfer"},
    exclusive_labels=[0])

my_afq = GroupAFQ(
    bids_path=op.join(
        afd.afq_home,
        'stanford_hardi'),
    brain_mask_definition=brain_mask_definition,
    tracking_params={"n_seeds": 3,
                     "directions": "prob",
                     "odf_model": "CSD",
                     "seed_mask": RoiImage()},
    bundle_info=bundles)

my_afq.export_all()

Total running time of the script: ( 56 minutes 26.350 seconds)

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