ADNI to BIDS conversion Error

[김승규]

Hi I am trying to convert ANDI to BIDS.

I have some issues in conversion.

So , I register PATH of dcm2nii and I also tried dcm2niix. But both of them are not working.

the PATH that I registered as bellow.

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export LC_ALL=en_US.UTF-8

export LANG=en_US.UTF-8

# ANTs

export ANTSPATH="/Users/imac_icml/ants"

export PATH=${ANTSPATH}:${PATH}

# FreeSurfer

export FREESURFER_HOME="/Applications/freesurfer"

source ${FREESURFER_HOME}/SetUpFreeSurfer.sh &> /dev/null

# dcm2nii

export PATH="/Users/imac_icml/MRIcron/dcm2nii:$PATH"

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(Version of dcm2nii was 2016  and also tried dcm2niix)

and tried as bellow

clinica convert adni-to-bids ./test_paper_clinical_ad ./test_paper_ad_5_25_2021.csv ./

and then the error was coming out.

[Error] Clinica could not find dcm2nii tool from MRIcron in your PATH environment: this can be downloaded from https://www.nitrc.org/frs/?group_id=152 (choose the 2016 version).

my environment : MAC / zsh

I would be really grateful to know what can I try to do.

Thanks

[Omar Rifai]

Hello,

It looks like the path you specified might not complete. Have you tried verifying that you can  run "dcm2nii" in the terminal directly ? In my case the complete path to the binary file is the following:

/../MRIcron-1.0.20160502/dcm2nii/dcm2nii.app/Contents/MacO/

There I can find the executable file. At any rate, you'll need to install both dcm2niix (which can be installed through conda forge) and dcm2nii (which is used as a fallback in case dcm2niix fails on some images).

Regards,

[SeungKyu Kim]

Thank you Omar.

Thanks to your advice, I can fix the problem.

Can you let me know about exact path of "dcm2niix"?

Also, Is it right that just adding the path of "dcm2niix" like this?

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# dcm2niix

export PATH="/Users/imac_icml/dcm2niix:$PATH"

# dcm2nii

export PATH="/Users/imac_icml/MRIcron/dcm2nii/dcm2nii.app/Contents/MacOS/:$PATH"

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2021년 5월 25일 화요일 오후 11시 43분 11초 UTC+9에 omar...@gmail.com님이 작성:

[SeungKyu Kim]

And I only 2 subjects of 93 subjects was converted.

I got a numerous error like this

[T1] No path specified for 022_S_5004 in session m12 8685/10333

[T1] No path specified for 067_S_2301 in session m72 8686/10333

[T1] No path specified for 109_S_4499 in session m48 8687/10333

[T1] No path specified for 127_S_4210 in session m96 8688/10333

[T1] No path specified for 011_S_0326 in session m24 8689/10333

[T1] No path specified for 941_S_6017 in session bl 8690/10333

[T1] Processing subject 116_S_1083 - session bl, 8691/10333

[T1] No path specified for 022_S_5004 in session m24 8692/10333

[T1] No path specified for 067_S_2301 in session m96 8693/10333

[T1] No path specified for 033_S_4505 in session bl 8694/10333

[T1] No path specified for 031_S_4218 in session bl 8695/10333

I would be really grateful to know what can I try to do

Thanks,

2021년 5월 26일 수요일 오전 12시 41분 29초 UTC+9에 SeungKyu Kim님이 작성:

[Omar Rifai]

For dcm2niix you might want to follow the instructions on the github  in the README.md document: https://github.com/rordenlab/dcm2niix

or install via the conda forge https://anaconda.org/conda-forge/dcm2niix

Normally, in both cases you normally don't have to set the PATH manually. You can also test the installation typing (dcm2niix) in the terminal.

For the output, you can specify which subjects you want to run adni-to-bids on using the --subject-like command line argument (https://aramislab.paris.inria.fr/clinica/docs/public/PR-221/Converters/ADNI2BIDS/#optional-parameters).

The output is particularly verbose but only the subjects you specified in the file should be handled.

Regards,

[SeungKyu Kim]

Thanks for your quick response.

I make the subject file and Tried.

It doesn't work.(It can't change the results)

It looks like the program can't find the path.
Very few subjects are converted. (only 2 scan of 2 subjects)

I also tried another dataset. It is also 4 scans of 4 subjects.

(total number of subjects are 309)

Best Regards,

2021년 5월 26일 수요일 오전 12시 56분 4초 UTC+9에 omar...@gmail.com님이 작성: