Clinica

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Welcome to the Clinica users' group!

AVERTISSEMENT triangle | Vecteurs publiques New ADNI download interface The LONI Image and Data Archive is currently refactoring the ADNI data download interface. Because of the ongoing modifications, both the documentation and the code of this converter are not up-to-date. The Clinica team will work on updating the converter once the interface stabilizes. In the mean-time, we recommend using previous versions of the downloaded clinical data (before Sept. 2024).

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Shilei Wang, Alice Joubert5

Dec 20

[Error] Killed when run petpvc during the pipeline of pet-surface

Glad to hear that ! Le ven. 20 déc. 2024 à 10:37, Shilei Wang <wangshi...@gmail.com> a

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[Error] Killed when run petpvc during the pipeline of pet-surface

Glad to hear that ! Le ven. 20 déc. 2024 à 10:37, Shilei Wang <wangshi...@gmail.com> a

Dec 20

Rommy Elyan, ninon....@gmail.com3

Dec 18

Averaging PET projection data

Hi Ninon, I kinda figured it out a while ago. I ended up using nibabel and numpy in python to average

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Averaging PET projection data

Hi Ninon, I kinda figured it out a while ago. I ended up using nibabel and numpy in python to average

Dec 18

Mathilde Bateson, ninon....@gmail.com2

Dec 17

Using Clinica on "raw" MRI data (original scans) or need for preprocessing before ?

Hi Mathilde, The pre-processing pipelines available in Clinica include correction of some acquisition

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Using Clinica on "raw" MRI data (original scans) or need for preprocessing before ?

Hi Mathilde, The pre-processing pipelines available in Clinica include correction of some acquisition

Dec 17

Dec 17

Can anyone find where MPRAGEMETA file is ?

I encouter OSError: Expecting to find exactly one file in folder /mnt/e/workplace/clinical_data

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Can anyone find where MPRAGEMETA file is ?

I encouter OSError: Expecting to find exactly one file in folder /mnt/e/workplace/clinical_data

Dec 17

Yibing Fu, Alice Joubert2

Dec 16

where to find the clinical data of OASIS3

Hello, I am currently investigating this and will be back in touch as soon as possible. Best, Alice

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where to find the clinical data of OASIS3

Hello, I am currently investigating this and will be back in touch as soon as possible. Best, Alice

Dec 16

Mathilde Bateson, Nicolas Gensollen3

Nov 26

t1-freesurfer running but no outputs

Hello Mathilde, Looking at the logs you provided, you have a problem with your installation of

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t1-freesurfer running but no outputs

Hello Mathilde, Looking at the logs you provided, you have a problem with your installation of

Nov 26

Aya Rabea, Alice Joubert2

Nov 19

ADNI to BIDS Keyerror

Hello Aya, I will try to reproduce. Can you tell me : the version of clinica you're using, which

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ADNI to BIDS Keyerror

Hello Aya, I will try to reproduce. Can you tell me : the version of clinica you're using, which

Nov 19

S. Steffen, Mathilde Bateson2

Nov 19

MPRAGEMETA.csv missing in ADNI

Hello there, I am running into the exact same issues as Steffen. I was able to find the ADNIMERGE.csv

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MPRAGEMETA.csv missing in ADNI

Hello there, I am running into the exact same issues as Steffen. I was able to find the ADNIMERGE.csv

Nov 19

Unai Torres, Nicolas Gensollen4

Nov 15

Error transforming OASIS DATA to BIDS

Thank you Nicolas! El viernes, 15 de noviembre de 2024 a las 11:46:23 UTC+1, Nicolas Gensollen

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Error transforming OASIS DATA to BIDS

Thank you Nicolas! El viernes, 15 de noviembre de 2024 a las 11:46:23 UTC+1, Nicolas Gensollen

Nov 15

JI FA, … Aya Rabea5

Nov 14

Unable to find the required csv file

Hi All, I found only ADNIMERGE csv file how can I find the remains csv files? On Tuesday 12 November

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Unable to find the required csv file

Hi All, I found only ADNIMERGE csv file how can I find the remains csv files? On Tuesday 12 November

Nov 14

Shahzad ALi, Alice Joubert5

Nov 4

Dear Ali, Thanks for your answer. From the beginning when downloading the images for these two

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Dear Ali, Thanks for your answer. From the beginning when downloading the images for these two

Nov 4

朱德新, … Nicolas Gensollen4

Nov 4

Request for Update to ADNI BIDS Conversion Software Tutorial

Hello, Thanks for reporting. We are indeed aware of the very recent and significant modifications

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Request for Update to ADNI BIDS Conversion Software Tutorial

Hello, Thanks for reporting. We are indeed aware of the very recent and significant modifications

Nov 4

Oct 24

Need previous version of ADNI1 Clinical Data

Hello, I noticed that the ADNI platform has been updated recently. However, it seems to be unstable

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Need previous version of ADNI1 Clinical Data

Hello, I noticed that the ADNI platform has been updated recently. However, it seems to be unstable

Oct 24

Shahzad ALi, Alice Joubert6

Oct 22

Issues Encountered During ADNI-to-BIDS Conversion

Hello Ali ! Thank you very much for the file, that is very helpful. Best, Alice Le lundi 21 octobre

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Issues Encountered During ADNI-to-BIDS Conversion

Hello Ali ! Thank you very much for the file, that is very helpful. Best, Alice Le lundi 21 octobre

Oct 22

Thomas Andrews, … Alice Joubert7

Oct 21

ADNI-to-BIDS no Clinical Data

Hi Tom, Great for the converter :). For dwi-preprocessing-using-t1 as of now, the T1 is also used for

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ADNI-to-BIDS no Clinical Data

Hi Tom, Great for the converter :). For dwi-preprocessing-using-t1 as of now, the T1 is also used for

Oct 21

oumayma soula, … Alice Joubert27

Sep 17

Assistance with NIFD to BIDS Conversion

Hello ! Thanks for reporting. This issue has been relayed to us several times these past days but we

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Assistance with NIFD to BIDS Conversion

Hello ! Thanks for reporting. This issue has been relayed to us several times these past days but we

Sep 17

Thomas Andrews, Nicolas Gensollen2

Aug 1

Node Labels Connectivity Matrix

Hi Tom, The connectivity matrices depend on the Desikan and Destrieux parcellations and these should

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Node Labels Connectivity Matrix

Hi Tom, The connectivity matrices depend on the Desikan and Destrieux parcellations and these should

Aug 1

Remi Silva, Nicolas Gensollen4

Jul 19

Hi Renata, I'm replying on the group such that everyone can benefit from these interactions. I am

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Hi Renata, I'm replying on the group such that everyone can benefit from these interactions. I am

Jul 19

Remi Silva, Nicolas Gensollen2

Jul 16

Hi, This error has been reported before (see https://github.com/aramis-lab/clinica/issues/890 and

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Hi, This error has been reported before (see https://github.com/aramis-lab/clinica/issues/890 and

Jul 16

Remi Silva, Nicolas Gensollen2

Jul 10

Hi, What is the command line you used to run the pet-surface pipeline ? I don't see anything

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Hi, What is the command line you used to run the pet-surface pipeline ? I don't see anything

Jul 10

Remi Silva, Alice Joubert2

Jul 9

Machine learning with MRI and PET

Hello Renata, To answer your questions : - The ML pipeline from Clinica supports classification for

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Machine learning with MRI and PET

Hello Renata, To answer your questions : - The ML pipeline from Clinica supports classification for

Jul 9

Remi Silva, Nicolas Gensollen4

Jul 8

T1-volume atlas error

Hi, Were you able to run the pet-volume pipeline since then ? If not, could you give more details

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T1-volume atlas error

Hi, Were you able to run the pet-volume pipeline since then ? If not, could you give more details

Jul 8

Remi Silva, Alice Joubert2

Jul 3

Hello Renata, That .tsv file is supposed to be generated by the user based on the .json files

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Hello Renata, That .tsv file is supposed to be generated by the user based on the .json files

Jul 3

Remi Silva, Nicolas Gensollen5

Jun 27

adni-to-bids converter

Hmm, looks like everything is fine. I don't see why you get this FileNotFoundError... 🤔 Could you

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adni-to-bids converter

Hmm, looks like everything is fine. I don't see why you get this FileNotFoundError... 🤔 Could you

Jun 27

Remi Silva, Nicolas Gensollen2

Jun 25

adni-to-bids PET

Hi, It is difficult to answer your question without a bit more context: - What version of clinica are

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adni-to-bids PET

Hi, It is difficult to answer your question without a bit more context: - What version of clinica are

Jun 25

Remi Silva, Nicolas Gensollen2

Jun 24

adni-to-bids error

Hi, What version of clinica are you using ? This has been fixed in version 0.8.1 (April 2024). Best,

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adni-to-bids error

Hi, What version of clinica are you using ? This has been fixed in version 0.8.1 (April 2024). Best,

Jun 24

Ethan Harvey, ninon....@gmail.com4

May 17

Creating Custom Reference Template

Hello Ethan, Yes, this is exactly that. If you have issues registering your T2w images, you might

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Creating Custom Reference Template

Hello Ethan, Yes, this is exactly that. If you have issues registering your T2w images, you might

May 17

Scott Gurney, Nicolas Gensollen3

Apr 25

adni-to-bids Field Mapping output?

Hi Nicolas Thank you for getting back to me. I doubt it will be soonish enough for my needs, but I

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adni-to-bids Field Mapping output?

Hi Nicolas Thank you for getting back to me. I doubt it will be soonish enough for my needs, but I

Apr 25

Nicolas Gensollen

Apr 23

Re: [clinica-forum] ImportError: cannot import name 'ImageFileError' from 'nibabel.spatialimages'

Hi Scott, From a quick look at the error message you provided, I think you have a mismatch in your

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Re: [clinica-forum] ImportError: cannot import name 'ImageFileError' from 'nibabel.spatialimages'

Hi Scott, From a quick look at the error message you provided, I think you have a mismatch in your

Apr 23

Apr 7

According to clinica's data selection instructions, how should I select the correct data in advanced search, and what are the options that I need to check off?

Dear Clinica According to clinica's data selection instructions, how should I select the correct

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According to clinica's data selection instructions, how should I select the correct data in advanced search, and what are the options that I need to check off?

Dear Clinica According to clinica's data selection instructions, how should I select the correct

Apr 7

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