ADNI-to-BIDS no Clinical Data

[Thomas Andrews]

Hello,

I am currently using Clinica 091. I have downloaded the ADNI dataset, the majority of which are from ADNI3. I am dealing with a substantial amount of warnings at the start of the ADNI2BIDS conversion, noting that clinical data is not present. My understanding is this is because the participants are not present in the ADNIMERGE.csv. 

I wanted to ask how this effects the conversion?

Best,

Tom

[Alice Joubert]

Hello Tom,

Thanks for using Clinica ! Yes, these lines appear when a subject is not in the ADNIMERGE file. Currently, clinica does not convert these subjects at all.

Best,

Alice

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[wusat ulh]

thank you for reply. so what can i do?

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[Thomas Andrews]

Thank you Alice.

Further to this, when using the --xml_path option, should this be to the metadata folder downloaded with ADNI? The format of this folder is an ADNI folder, with multiple xml files in the root directory and a subdirectory for each patient with multiple subdirectories here with xml files. Should any part of this folder be merged with the ADNI images prior to the adni_to_bids conversion, or can I use the root directory of this metadata as the xml_path? Or should I flatten this folder entirely into a single directory for the --xml_path?

You can get an idea for the directory structure below.

This is in the root directory:

This is the strcuture for the folder 082_S_4244

├── 3_Plane_Localizer

│   ├── 2018-03-14_13_09_43.0

│   │   ├── I974157

│   │   │   └── S667374I974157.xml

│   │   ├── I974158

│   │   │   └── S667374I974158.xml

│   │   ├── I974159

│   │   │   └── S667374I974159.xml

│   │   ├── I974160

│   │   │   └── S667375I974160.xml

│   │   ├── I974161

│   │   │   └── S667375I974161.xml

│   │   └── I974162

│   │       └── S667375I974162.xml

│   ├── 2019-06-12_13_40_47.0

│   │   ├── I1175744

│   │   │   └── S832446I1175744.xml

│   │   ├── I1175745

│   │   │   └── S832446I1175745.xml

│   │   └── I1175746

│   │       └── S832446I1175746.xml

│   └── 2022-06-30_10_32_26.0

│       ├── I1603777

│       │   └── S1146175I1603777.xml

│       ├── I1603780

│       │   └── S1146175I1603780.xml

│       └── I1603791

│           └── S1146175I1603791.xml

├── Accelerated_Sagittal_MPRAGE

│   ├── 2018-03-14_13_09_43.0

│   │   └── I974164

│   │       └── S667377I974164.xml

│   ├── 2019-06-12_13_40_47.0

│   │   └── I1175747

│   │       └── S832447I1175747.xml

│   └── 2022-06-30_10_32_26.0

│       └── I1603787

│           └── S1146184I1603787.xml

├── Accelerated_Sagittal_MPRAGE_ND

│   ├── 2018-03-14_13_09_43.0

│   │   └── I974163

│   │       └── S667376I974163.xml

│   ├── 2019-06-12_13_40_47.0

│   │   └── I1175748

│   │       └── S832448I1175748.xml

│   └── 2022-06-30_10_32_26.0

│       └── I1603792

│           └── S1146187I1603792.xml

├── Axial_2D_PASL__EYES_OPEN_

│   ├── 2018-03-14_13_09_43.0

│   │   └── I974154

│   │       └── S667371I974154.xml

│   ├── 2019-06-12_13_40_47.0

│   │   └── I1175741

│   │       └── S832443I1175741.xml

│   └── 2022-06-30_10_32_26.0

│       └── I1603779

│           └── S1146177I1603779.xml

├── Axial_DTI_SEE_NOTE_

│   ├── 2018-03-14_13_49_15.0

│   │   └── I974172

│   │       └── S667384I974172.xml

│   ├── 2019-06-12_14_19_17.0

│   │   └── I1175756

│   │       └── S832455I1175756.xml

│   └── 2022-06-30_11_06_48.0

│       └── I1603786

│           └── S1146183I1603786.xml

├── Axial_T2_Star__NO_ANGLE_

│   ├── 2018-03-14_13_09_43.0

│   │   └── I974165

│   │       └── S667378I974165.xml

│   ├── 2019-06-12_13_40_47.0

│   │   └── I1175749

│   │       └── S832449I1175749.xml

│   └── 2022-06-30_10_32_26.0

│       └── I1603785

│           └── S1146182I1603785.xml

├── Field_Mapping

│   ├── 2018-03-14_13_09_43.0

│   │   ├── I974167

│   │   │   └── S667380I974167.xml

│   │   ├── I974170

│   │   │   └── S667380I974170.xml

│   │   └── I974171

│   │       └── S667383I974171.xml

│   ├── 2019-06-12_13_40_47.0

│   │   ├── I1175751

│   │   │   └── S832451I1175751.xml

│   │   ├── I1175754

│   │   │   └── S832451I1175754.xml

│   │   └── I1175755

│   │       └── S832454I1175755.xml

│   └── 2022-06-30_10_32_26.0

│       ├── I1603776

│       │   └── S1146174I1603776.xml

│       ├── I1603782

│       │   └── S1146179I1603782.xml

│       └── I1603790

│           └── S1146174I1603790.xml

├── HighResHippocampus

│   ├── 2018-03-14_13_09_43.0

│   │   └── I974169

│   │       └── S667382I974169.xml

│   ├── 2019-06-12_13_40_47.0

│   │   └── I1175753

│   │       └── S832453I1175753.xml

│   └── 2022-06-30_10_32_26.0

│       └── I1603789

│           └── S1146186I1603789.xml

└── Sagittal_3D_FLAIR

    ├── 2018-03-14_13_09_43.0

    │   └── I974168

    │       └── S667381I974168.xml

    ├── 2019-06-12_13_40_47.0

    │   └── I1175752

    │       └── S832452I1175752.xml

    └── 2022-06-30_10_32_26.0

        └── I1603778

            └── S1146176I1603778.xml

Thanks,

Tom

[Alice Joubert]

Hello Thomas, 

You can use the ADNI folder path (the root of the metadata) directly for the --xml_path option. Please note that there was a bug recently reported for this parameter which has yet to be fixed (cf the issue on github), so I do not expect it to work right now.

Sorry for the inconvenience,

Best,

Alice

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[Thomas Andrews]

Thank you Alice, that's not a problem. The adni2bids converter seems to work well as it is for me :)

One more question if that's OK, for the dwi-processing-using-t1,  are the DWI registered to the T1, or is the T1 only used to correct for magnetic susceptibility distortions,. The reason I ask, is that for my analysis, it is preferred that my DWI remain in the DWI native space.

Best,

Tom

[Alice Joubert]

Hi Tom, 

Great for the converter :).

For dwi-preprocessing-using-t1 as of now, the T1 is also used for the registration so you do not stay in the DWI space.

Best,

Alice

To view this discussion on the web visit https://groups.google.com/d/msgid/clinica-user/f2e48393-e0e7-4f0a-817b-e88730c46d4bn%40googlegroups.com.