ADNI to BIDS converter

[Maryam Hamzelu]

Hi,

I've downloaded all preprocessed ADNI Baseline dataset for MRI and PET modalities and when I tried to use ADNI-to-BIDS converter the result folder contains only 953Mb ...

I have 3 questions:

1- I have incomplete data issues in my thesis, some of samples don't have PET images. would it cause a problem for Clinica?

2- Why the result of converting more than 100 Gb of data is less than one Gb?

3- Some of the samples' MRI is like this:

they do not contain Gradwarp. Is this making problem?

4- I've downloaded only one session of each sample data. Is it making a problem?

Thank you for your time and effort.

[Maryam Hamzelu]

Hi,

I repeated the code for the converter, and, somehow, I don't understand; the BIDS folder contains 11 Gb, and for sure, it's more than 1 Gb. But still so much less than the original folder, which is about 150Gb of data. Anyway, I started preprocessing for T1 MRI, and I got an error. as you can see below, there is a T1 modality for the samples Clinica said there is not! please help me here :)

(clinicaEnv) maryam@maryam:~$ clinica run t1-volume /home/maryam/thesis/bids /home/maryam/thesis/caps ADvsCNvsMCIvsEMCIvsLMCI

The t1-volume pipeline is divided into 4 parts:

t1-volume-tissue-segmentation pipeline: Tissue segmentation, bias correction and spatial normalization to MNI space

t1-volume-create-dartel pipeline: Inter-subject registration with the creation of a new DARTEL template

t1-volume-dartel2mni pipeline: DARTEL template to MNI

t1-volume-parcellation pipeline: Atlas statistics

Part 1/4: Running t1-volume-segmentation pipeline

Clinica faced error(s) while trying to read files in your BIDS directory.

[Error] Clinica encountered 105 problem(s) while getting T1w MRI:

* (sub-ADNI006S0498 | ses-M00) : No file found

* (sub-ADNI006S0731 | ses-M00) : No file found

* (sub-ADNI007S0101 | ses-M00) : No file found

* (sub-ADNI007S1339 | ses-M00) : No file found

* (sub-ADNI007S2394 | ses-M00) : No file found

* (sub-ADNI009S0751 | ses-M00) : No file found

* (sub-ADNI009S0842 | ses-M00) : No file found

* (sub-ADNI009S2208 | ses-M00) : No file found

* (sub-ADNI009S2381 | ses-M00) : No file found

* (sub-ADNI010S0067 | ses-M00) : No file found

* (sub-ADNI010S0419 | ses-M00) : No file found

* (sub-ADNI011S0021 | ses-M00) : No file found

* (sub-ADNI011S0183 | ses-M00) : No file found

* (sub-ADNI012S0634 | ses-M00) : No file found

* (sub-ADNI012S0712 | ses-M00) : No file found

* (sub-ADNI012S0720 | ses-M00) : No file found

* (sub-ADNI012S0917 | ses-M00) : No file found

* (sub-ADNI014S2185 | ses-M00) : No file found

* (sub-ADNI014S2308 | ses-M00) : No file found

* (sub-ADNI016S2031 | ses-M00) : No file found

* (sub-ADNI018S0043 | ses-M00) : No file found

* (sub-ADNI018S0055 | ses-M00) : No file found

* (sub-ADNI018S0057 | ses-M00) : No file found

* (sub-ADNI018S0142 | ses-M00) : No file found

* (sub-ADNI018S0155 | ses-M00) : No file found

* (sub-ADNI018S0286 | ses-M00) : No file found

* (sub-ADNI018S0682 | ses-M00) : No file found

* (sub-ADNI018S2155 | ses-M00) : No file found

* (sub-ADNI018S2180 | ses-M00) : No file found

* (sub-ADNI021S0141 | ses-M00) : No file found

* (sub-ADNI021S0343 | ses-M00) : No file found

* (sub-ADNI021S0424 | ses-M00) : No file found

* (sub-ADNI021S0647 | ses-M00) : No file found

* (sub-ADNI021S1109 | ses-M00) : No file found

* (sub-ADNI021S2124 | ses-M00) : No file found

* (sub-ADNI021S2125 | ses-M00) : No file found

* (sub-ADNI021S2142 | ses-M00) : No file found

* (sub-ADNI021S2150 | ses-M00) : No file found

* (sub-ADNI022S2087 | ses-M00) : No file found

* (sub-ADNI022S2167 | ses-M00) : No file found

* (sub-ADNI022S2379 | ses-M00) : No file found

* (sub-ADNI024S0985 | ses-M00) : No file found

* (sub-ADNI024S1171 | ses-M00) : No file found

* (sub-ADNI024S2239 | ses-M00) : No file found

* (sub-ADNI027S0461 | ses-M00) : No file found

* (sub-ADNI027S2219 | ses-M00) : No file found

* (sub-ADNI027S2336 | ses-M00) : No file found

* (sub-ADNI029S0866 | ses-M00) : No file found

* (sub-ADNI029S1056 | ses-M00) : No file found

* (sub-ADNI029S2376 | ses-M00) : No file found

* (sub-ADNI029S2395 | ses-M00) : No file found

* (sub-ADNI031S0618 | ses-M00) : No file found

* (sub-ADNI031S2018 | ses-M00) : No file found

* (sub-ADNI031S2022 | ses-M00) : No file found

* (sub-ADNI032S0095 | ses-M00) : No file found

* (sub-ADNI032S0718 | ses-M00) : No file found

* (sub-ADNI032S2119 | ses-M00) : No file found

* (sub-ADNI032S2240 | ses-M00) : No file found

* (sub-ADNI035S2061 | ses-M00) : No file found

* (sub-ADNI052S2249 | ses-M00) : No file found

* (sub-ADNI053S2357 | ses-M00) : No file found

* (sub-ADNI053S2396 | ses-M00) : No file found

* (sub-ADNI057S2398 | ses-M00) : No file found

* (sub-ADNI067S2195 | ses-M00) : No file found

* (sub-ADNI067S2196 | ses-M00) : No file found

* (sub-ADNI068S2168 | ses-M00) : No file found

* (sub-ADNI068S2184 | ses-M00) : No file found

* (sub-ADNI068S2193 | ses-M00) : No file found

* (sub-ADNI068S2194 | ses-M00) : No file found

* (sub-ADNI068S2248 | ses-M00) : No file found

* (sub-ADNI068S2315 | ses-M00) : No file found

* (sub-ADNI068S2316 | ses-M00) : No file found

* (sub-ADNI072S2026 | ses-M00) : No file found

* (sub-ADNI072S2037 | ses-M00) : No file found

* (sub-ADNI072S2072 | ses-M00) : No file found

* (sub-ADNI072S2164 | ses-M00) : No file found

* (sub-ADNI073S2153 | ses-M00) : No file found

* (sub-ADNI073S2182 | ses-M00) : No file found

* (sub-ADNI073S2190 | ses-M00) : No file found

* (sub-ADNI073S2191 | ses-M00) : No file found

* (sub-ADNI073S2225 | ses-M00) : No file found

* (sub-ADNI073S2264 | ses-M00) : No file found

* (sub-ADNI082S2121 | ses-M00) : No file found

* (sub-ADNI082S2307 | ses-M00) : No file found

* (sub-ADNI094S2216 | ses-M00) : No file found

* (sub-ADNI094S2238 | ses-M00) : No file found

* (sub-ADNI094S2367 | ses-M00) : No file found

* (sub-ADNI098S2047 | ses-M00) : No file found

* (sub-ADNI098S2052 | ses-M00) : No file found

* (sub-ADNI123S2055 | ses-M00) : No file found

* (sub-ADNI126S1221 | ses-M00) : No file found

* (sub-ADNI126S2405 | ses-M00) : No file found

* (sub-ADNI126S2407 | ses-M00) : No file found

* (sub-ADNI127S2213 | ses-M00) : No file found

* (sub-ADNI128S2036 | ses-M00) : No file found

* (sub-ADNI128S2045 | ses-M00) : No file found

* (sub-ADNI129S2332 | ses-M00) : No file found

* (sub-ADNI129S2347 | ses-M00) : No file found

* (sub-ADNI130S2373 | ses-M00) : No file found

* (sub-ADNI130S2391 | ses-M00) : No file found

* (sub-ADNI130S2403 | ses-M00) : No file found

* (sub-ADNI141S2210 | ses-M00) : No file found

* (sub-ADNI141S2333 | ses-M00) : No file found

* (sub-ADNI153S2109 | ses-M00) : No file found

* (sub-ADNI153S2148 | ses-M00) : No file found

Documentation can be found here: http://www.clinica.run/doc/

If you need support, do not hesitate to ask: https://groups.google.com/forum/#!forum/clinica-user

Alternatively, you can also open an issue on GitHub: https://github.com/aramis-lab/clinica/issues

[Alexandre Routier]

Hello Myriam,

Sorry to hear you have issue with Clinica :(

Regarding your first post:

1) You can process T1w images which do not contain PET data

2) Can you confirm me that you followed instructions in guidelines written here : http://www.clinica.run/doc/Converters/ADNI2BIDS/#downloading-adni? Your BIDS dataset should be larger indeed.

3) I do not see the image attached to the first post. But in the second post, I can see GradWarp* folders. Images without Gradwarp* folders are likely to be discarded at the conversion. You may have warning messages but no issues at the execution.

4) No. But if you are flooded by warning messages for this situation, please let us now so we improve the behaviour of the converter.

Regarding your second message, can you show me what is the content of /home/maryam/thesis/bids/sub-ADNI006S0498? (BIDS identifier of 006_S_0498 should be ADNI006S0498). In the meantime, I propose you to investigate this issue as follows:

1) Create a file called 006_S_0498.txt containing the following line:

006_S_0498

2) Conversion to BIDS

    a) Run using this syntax:

clinica convert adni-2-bids <path_to_your_adni_dataset> <path_to_your_adni_clinica_directory> BIDS_006_S_0498 --subjects_list 006_S_0498.txt

    b) Tell me the content of BIDS_006_S_0498

3) T1-Volume:

    a) If BIDS_006_S_0498 contains T1w, then run part of T1-Volume pipeline:

clinica run t1-volume-tissue-segmentation BIDS_006_S_0498 BIDS_006_S_0498 --n_procs 1

    b) Tell me if it worked

On top of that, can you tell me which version of Clinica are you using?

Best,

Alexandre

[Maryam Hamzelu]

Hello Alexandre,

first of all thank you for your answers,

Yes, I've downloaded data as mentioned in the Clinica's documentation. I think this problem raised because PET data are for Session 0 for each sample, and I have another MRI session data :( I'm downloading MRI data again for session 0 for those samples. I though MRI data are needed for PET preprocessing only for alignments, and there is no need for PET data to be with the same MRI visit. Tell me if I'm right.

One thing I don't understand and can't figure out is volume decreasing of the converter. I've deleted the results of the converter folder, so I'll send the screenshot of what you asked soon after downloading missing data and rerunning the converter.

Thanks

 

[Maryam Hamzelu]

and sorry I missed your last question. I'm using the latest version (published 1st of Apr). I think the converter problem raised because I didn't download the whole of ADNI and I've downloaded only the ADNI baseline study. I'm working on it to know what is wrong. I'll let you know the result...

Bests,

Maryam

[Maryam Hamzelu]

Hi again, :)

I've figured why I got the error when I tried to run T1 preprocessing: because PET and MRI images should be from the same session.

The main issue that I can't figure out is why converter is decreasing data Volume this much. I've downloaded ADNI as said in documentation. The main folder contains about 200 Gb of data, but when I try to run the converter BIDS folder is about 15 Gb. the converter finishes its work without any error. I reinstalled Clinica and get the same error. When I try to run T1 preprocessing, CLI says the CAPS folder would be about 100 Gb, and I think I have PET and MRI data, so it's reasonable to have 100 Gb for the result of T1 MRI, CAPS folder. If I'm wrong, please let me know. So why BIDS folder is acting like this?

Thanks,

Maryam

[Polina Druzhinina]

Hello,

I faced the same problem, my data folder takes about 250GB, but after converting to BIDS format, the data takes about 15GB. Most of the objects are missing.

  Could this be due to the fact that subjects_list is not specified separately, but the standard ADNIMERGE file is used?

Have you solved this problem?

Thanks, Polina. 

[Alexandre Routier]

Hello Polina,

Sorry you are facing this issue.

We detailed recently what data to download on the ADNI website (http://www.clinica.run/doc/Converters/ADNI2BIDS/). Could you confirm that you followed the instructions?

On top of that, could you tell us which modalities you downloaded?

Best,

Alexandre

alexandre-routier.com

[Polina Druzhinina]

Hello, Alexander.

Yes, I followed all the instructions, as they said, I created a collection of images, which consisted of data from ADNI 1, 2 and GO for T1-weighted MRI modalities. I'm not sure how I should confirm this, but just in case, I am attaching a link to screen (https://drive.google.com/file/d/1To-lFpmivzRY-qJHxHjNNYffpEH9TYEB/view?usp=sharing) and csv file of data that I downloaded(https://drive.google.com/file/d/1jNITx8pidrSy3Lt_1bhtNx80mgnt07E-/view?usp=sharing).

Do you have any ideas?

Best wishes,
Polina.

[Polina Druzhinina]

Hello, Alexander.

I saw that in previous issues you advised to create a txt file with the list of subjects to convert using the optional parameter --subjects_list , so i did that. Since 793 files were skipped during the conversion, my txt file contained 793 files like:

002_S_0413

002_S_0559

002_S_0619

002_S_0685

002_S_0729

So i try to run "clinica convert adni-to-bids datasets/adni/ADNI1/ADNI/IMAGES datasets/adni/ADNI1/ADNI/CLINICAL_DATA datasets/adni/ADNI1/OUTPUT/ADNI/bids --subjects_list datasets/adni/ADNI1/list_to_bids.txt -m T1"
I saw such phrases as "More than 60 days for corresponding timepoint in ADNIMERGE for subject (for example) 014_S_0519 in visit ADNI2 Year 1 Visit on 2013-06-08".....
or "No corresponding timepoint in ADNIMERGE for subject (for example) 031_S_0773 in visit ADNI Screening" 
and then 
"No T1 image path found for subject (for example 073_S_0909) in visit m36 with image id 167021"
or "[T1] No path scpecified for 121_S_1350 in session m06 3286 / 4278"

I added links to the file with subjet_list (https://drive.google.com/file/d/1JWmD5kjr6XvImQxLLK0O38yUlsXjBhgS/view?usp=sharing) , as well as a record of the converter's work (https://drive.google.com/file/d/1fY2YImUUVJ6uVVvlmyZ88sOsG3ZXJK8a/view?usp=sharing), maybe it will tell you more.

I still have not received the conversion of the subjets that are in the subjet_list  , not even a folder is created, I don’t understand what is the difference between these subjets and those that are freely transformed (participation file (https://drive.google.com/file/d/1vToZ47IAqQvkiM-03lOf4OeJh3gmRstZ/view?usp=sharing)), so I don’t know what else can be done.

Best wishes,
Polina.

[Pallavi Saha]

Hello,

Can you please me to get the MPRAGEMETA.csv file in ADNI website.

[Elina Thibeau-Sutre]

Hello,

To get this file you have to log to your ADNI account at https://ida.loni.usc.edu/pages/access/studyData.jsp?categoryId=14&subCategoryId=45

Then choose Download --> Study Data --> Imaging --> MR Image Acquisition --> MP-RAGE Metadata Listing [ADNI1,GO,2] (see the image for more insight)

Best,

Elina