# Retiring midas.kitware.com data repository

**URL:** <https://discourse.slicer.org/t/retiring-midas-kitware-com-data-repository/2243>\
**Category:** Uncategorized\
**Created:** [March 5, 2018, 7:45pm UTC](https://discourse.slicer.org/t/retiring-midas-kitware-com-data-repository/2243 "2018-03-05T19:45:01Z")\
**Posts on this page:** 5\
**Page:** 1

<div class="post-metadata">

**Author:** ![jcfr](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/jcfr/32/17825_2.png) [@jcfr](https://discourse.slicer.org/u/jcfr)\
**Post date:** [March 5, 2018, 7:45pm UTC](https://discourse.slicer.org/t/retiring-midas-kitware-com-data-repository/2243/1 "2018-03-05T19:45:01Z")

</div>

Hi Slicers,

Slicer4 community that was hosted on that server has been removed.

For now, associated datasets have been moved to [http://slicer.kitware.com/midas3/folder/4539](http://slicer.kitware.com/midas3/folder/4539)

These includes:

- [blocks-fruit-phones.tar.gz](http://slicer.kitware.com/midas3/item/347107)
- [CTHeadAxialDicom](http://slicer.kitware.com/midas3/folder/5038)
- [DicomToNrrdTestBaselineData](http://slicer.kitware.com/midas3/folder/5037)
- [DWIDicom](http://slicer.kitware.com/midas3/folder/5039)
- [EMSegmentTestData](http://slicer.kitware.com/midas3/folder/5044)
- [Miscellaneous](http://slicer.kitware.com/midas3/folder/5040)
- [vhp2](http://slicer.kitware.com/midas3/folder/5042)
- [WMQL Testing Dataset](http://slicer.kitware.com/midas3/folder/5043)

### Questions

Does anyone have more information or details about the following ones ? And if there are currently used in any tests ?

- `vhp2`

- `blocks-fruit-phones.tar.gz`

- `DWIDicom`

- `DicomToNrrdTestBaselineData`

### Detailed list of files

#### CTHeadAxialDicom

```nohighlight
CTHead1.dcm
[...]
CTHead93.dcm

```

#### DWIDicom

```nohighlight
MR_0004_0028.dcm
[...]
MR_0004_1800.dcm

```

#### DicomToNrrdTestBaselineData

```nohighlight
219d9bd6d755fab0acf2a908db496cde
GeSignaHDx.bval
GeSignaHDx.nii.gz
GeSignaHDx.nrrd
GeSignaHDxTest.bvec
PhilipsAchieva1.nrrd
PhilipsAchieva2.nrrd
PhilipsAchieva3.nrrd
PhilipsAchieva4.nrrd
PhilipsAchieva5.nrrd
PhilipsAchieva6.nrrd
PhilipsAchieva7.nrrd
SiemensTrio-Syngo2004A-1.nrrd
SiemensTrio-Syngo2004A-2.nrrd
SiemensTrioTim1.nrrd
SiemensTrioTim2.nrrd
SiemensTrioTim3.nrrd
SiemensVerio.nrrd

```

#### EMSegmentTestData

_Datasets related to Primal are missing from this list. These will be uploaded shortly_

```nohighlight
./CT_Hand_Bone/CT_Hand_Bone_Subject_2.nrrd
./CT_Hand_Bone/CT_Hand_Bone_Subject_1.nrrd
./CT_Hand_Bone/CT_Hand_Bone_Subject_3.nrrd

./MRI-Human-Brain-Parcellation /RESULT_very_small_MRIHumanBrainParcellation_T1.nrrd
./MRI-Human-Brain-Parcellation /RESULT_small_MRIHumanBrainParcellation_T1.nrrd

./MRI-Human-Brain-Full-Parcellation/RESULT_small_MRIHumanBrainFullParcellation_T1.nrrd
./MRI-Human-Brain-Full-Parcellation/RESULT_very_small_MRIHumanBrainFullParcellation_T1.nrrd

./MRI-Human-Brain/atlas_greymatter.nrrd
./MRI-Human-Brain/atlas_csf.nrrd
./MRI-Human-Brain/atlas_skulneck.nrrd
./MRI-Human-Brain/atlas_air.nrrd
./MRI-Human-Brain/atlas_t1.nrrd

```

#### Miscellaneous

_Some of these data are already associated with module specific folder found in [Public/Slicer/Data/Modules](http://slicer.kitware.com/midas3/folder/298) directory. We will consolidate and remove duplicated entries found in this folder at a later time._

```auto
ACPC.fcsv
ACPCTest.mrml
brainSliceCHAR.mha
brainSliceDOUBLE.mha
brainSliceFLOAT.mha
brainSliceINT.mha
brainSliceLONG.mha
brainSliceSHORT.mha
brainSliceUCHAR.mha
brainSliceUINT.mha
brainSliceULONG.mha
brainSliceUSHORT.mha
BSplineDisplacements3D_00.txt
CastTest.nrrd
CTHeadAxialDoubled.nhdr
CTHeadAxialDoubled.raw.gz
CTHeadAxialMask.nrrd
CTHeadAxial.nhdr
CTHeadAxial.raw.gz
CTHeadResampled.nhdr
CTHeadResampledOtsuSegmented.nhdr
CTHeadResampledOtsuSegmented.raw.gz
CTHeadResampled.raw.gz
ExecutionModelTourTest.mrml
he3mask.nii.gz
he3volume.nii.gz
itkAffineTransform00.txt
itkAffineTransform01.txt
itkAffineTransform02.txt
itkAffineTransform03.txt
itkAffineTransform04.txt
itkQuaternionRigidTransform00.txt
itkQuaternionRigidTransform01.txt
itkQuaternionRigidTransform02.txt
itkQuaternionRigidTransform03.txt
itkQuaternionRigidTransform04.txt
midsag.fcsv
ModelMakerTest.mrml
MRHeadResampledBSplineInterpolationTest.nrrd
MRHeadResampledBSplineTransform.tfm
MRHeadResampledBSplineWSInterpolationTest.nrrd
MRHeadResampledHField.nrrd
MRHeadResampledHFieldTest.nrrd
MRHeadResampled.nhdr
MRHeadResampled.raw.gz
MRHeadResampledRotationAndAffine.nrrd
MRHeadResampledRotationNN.nrrd
MRMeningioma01segmented.nrrd
MRMeningioma01.tfm
MRMeningioma0.nrrd
MRMeningioma1.nrrd
SparseFieldLevelSetContourTest.vtp

```

#### vhp2

```auto
0070.jpeg
[...]
0079.jpeg

```

#### WMQL Testing Dataset

```auto
IIT3mean_desikan_2009.nii.gz
IIT3mean_left_hemisphere_small.trk
IIT3mean_left_hemisphere_small.vtp
IIT3mean_left_hemisphere.vtp
IIT3mean.vtp
wmql_1_cst.qry
wmql_2_uf.qry
wmql_3_commissural.qry
WMQL_Testing_Dataset.tgz
wmql_testing.qry

```

---

<div class="post-metadata">

**Author:** ![pieper](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/pieper/32/8_2.png) [@pieper](https://discourse.slicer.org/u/pieper)\
**Post date:** [March 5, 2018, 8:14pm UTC](https://discourse.slicer.org/t/retiring-midas-kitware-com-data-repository/2243/2 "2018-03-05T20:14:02Z")

</div>

> [@jcfr](#):
>
> blocks-fruit-phones.tar.gz

This is a freely sharable CT scan of a collection of objects that can be used for segmentation or visualization experiments. I do not believe any tests currently use it.

> [@jcfr](#):
>
> WMQL Testing Dataset

I believe this is for the [White Matter Query Language](https://www.ncbi.nlm.nih.gov/pubmed/26754839). Maybe @ihnorton knows if any SlicerDMRI work depends on it.

---

<div class="post-metadata">

**Author:** ![ihnorton](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/ihnorton/32/9_2.png) [@ihnorton](https://discourse.slicer.org/u/ihnorton)\
**Post date:** [March 5, 2018, 9:06pm UTC](https://discourse.slicer.org/t/retiring-midas-kitware-com-data-repository/2243/3 "2018-03-05T21:06:12Z")

</div>

Yes, some of these files are used in the tests:

> <https://github.com/demianw/tract_querier/blob/master/tract_querier/tests/datasets.py#L10-L26>

I just posted an issue to let Demian know:

> <https://github.com/demianw/tract_querier/issues/42>
>
> Steve just asked the following on the Slicer forum (coincidentally, 10 minutes a…fter you were in the office) -- whether WMQL is still using the test data on \`midas.kitware.com\`, because the server is being retired:
> 
> https://discourse.slicer.org/t/retiring-midas-kitware-com-data-repository/2243/2
> 
> ~~The server is still up, currently~~. The data was backed up at slicer.kitware.com.
> 
> (although it looks like the \[tests are disabled\](https://github.com/demianw/tract\_querier/blob/master/tract\_querier/tests/datasets.py#L10-L31) right now)

---

<div class="post-metadata">

**Author:** ![jcfr](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/jcfr/32/17825_2.png) [@jcfr](https://discourse.slicer.org/u/jcfr)\
**Post date:** [March 5, 2018, 9:08pm UTC](https://discourse.slicer.org/t/retiring-midas-kitware-com-data-repository/2243/4 "2018-03-05T21:08:15Z")

</div>

> [@ihnorton](#):
>
> Yes, some of these files are used in the tests:

**EDITED:** ~~I will ask our sysadmins to setup redirects so that these tests still work as expected.~~ Following, @ihnorton comment below, the test are updated and there is no need to set the redirects.

For reference, the new download URLs are the following:

_Note that while we could have an equivalent URL associated with the `bitstream` endpoint, I suggest to use the `item` endpoint._

- IIT3mean\_left\_hemisphere\_small.trk  
`http://midas.kitware.com/bitstream/view/17631`  
 → [http://slicer.kitware.com/midas3/download/item/347269/IIT3mean\_left\_hemisphere\_small.trk](http://slicer.kitware.com/midas3/download/item/347269/IIT3mean_left_hemisphere_small.trk)

- IIT3mean\_desikan\_2009.nii.gz  
`http://midas.kitware.com/bitstream/view/17622`  
 → [http://slicer.kitware.com/midas3/download/item/347267/IIT3mean\_desikan\_2009.nii.gz](http://slicer.kitware.com/midas3/download/item/347267/IIT3mean_desikan_2009.nii.gz)

- wmql\_2\_uf.qry  
`http://midas.kitware.com/bitstream/view/17627`  
 → [http://slicer.kitware.com/midas3/download/item/347272/wmql\_2\_uf.qry](http://slicer.kitware.com/midas3/download/item/347272/wmql_2_uf.qry)

---

<div class="post-metadata">

**Author:** ![ihnorton](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/ihnorton/32/9_2.png) [@ihnorton](https://discourse.slicer.org/u/ihnorton)\
**Post date:** [March 5, 2018, 9:17pm UTC](https://discourse.slicer.org/t/retiring-midas-kitware-com-data-repository/2243/5 "2018-03-05T21:17:45Z")

</div>

> [@jcfr](#):
>
> I will ask our sysadmins to setup redirects so that these tests still work as expected.

For simplicity, just made a [PR](https://github.com/demianw/tract_querier/pull/43) to update (though I think the test might actually be disabled).