T1w
UCLA Consortium for Neuropsychiatric Phenomics LA5c Study

BIDS Validation

2 Warnings Valid

We found 2 Warnings in your dataset. You are not required to fix warnings, but doing so will make your dataset more BIDS compliant.

view 2 warnings in 748 files

Warning: 1626 files

Not all subjects contain the same files. Each subject should contain the same number of files with the same naming unless some files are known to be missing.

Location:

/sub-10159/func/sub-10159_task-bht_bold.json

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This file is missing for subject sub-10159, but is present for at least one other subject.

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/sub-10159/func/sub-10159_task-bht_bold.nii.gz

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This file is missing for subject sub-10159, but is present for at least one other subject.

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/sub-10159/func/sub-10159_task-bht_events.tsv

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This file is missing for subject sub-10159, but is present for at least one other subject.

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/sub-10159/func/sub-10159_task-bht_physio.json

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This file is missing for subject sub-10159, but is present for at least one other subject.

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/sub-10159/func/sub-10159_task-bht_physio.tsv.gz

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This file is missing for subject sub-10159, but is present for at least one other subject.

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/sub-10159/func/sub-10159_task-pamenc_bold.json

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This file is missing for subject sub-10159, but is present for at least one other subject.

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/sub-10159/func/sub-10159_task-pamenc_bold.nii.gz

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This file is missing for subject sub-10159, but is present for at least one other subject.

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/sub-10159/func/sub-10159_task-pamenc_events.tsv

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This file is missing for subject sub-10159, but is present for at least one other subject.

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/sub-10159/func/sub-10159_task-pamret_bold.json

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This file is missing for subject sub-10159, but is present for at least one other subject.

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/sub-10159/func/sub-10159_task-pamret_bold.nii.gz

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This file is missing for subject sub-10159, but is present for at least one other subject.

and 616 more files

Warning: 2122 files

Not all subjects/sessions/runs have the same scanning parameters.

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/sub-10159/dwi/sub-10159_dwi.nii.gz

Reason:

The most common set of dimensions is: 96,96,60,65 (voxels), This file has the dimensions: 96,96,50,65 (voxels). The most common resolution is: 1.98mm x 1.98mm x 2.00mm x 8.40s, This file has the resolution: 1.98mm x 1.98mm x 2.00mm x 7.00s.

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/sub-10171/dwi/sub-10171_dwi.nii.gz

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/sub-10171/func/sub-10171_task-bht_bold.nii.gz

Reason:

The most common set of dimensions is: 64,64,34,79 (voxels), This file has the dimensions: 64,64,34,80 (voxels).

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/sub-10189/dwi/sub-10189_dwi.nii.gz

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/sub-10193/dwi/sub-10193_dwi.nii.gz

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/sub-10206/dwi/sub-10206_dwi.nii.gz

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/sub-10217/dwi/sub-10217_dwi.nii.gz

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/sub-10225/dwi/sub-10225_dwi.nii.gz

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/sub-10227/dwi/sub-10227_dwi.nii.gz

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/sub-10228/dwi/sub-10228_dwi.nii.gz

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FilesDownloadDerivativesMetadata

README

N/A

UCLA Consortium for Neuropsychiatric Phenomics LA5c Study

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Files: 29703 Size: 5.2GB

UCLA Consortium for Neuropsychiatric Phenomics LA5c Study

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Comments

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By arianavajdi@gmail.com - almost 4 years ago

Hi, I have downloaded the T1 images and am having a difficult time locating the "derivatives" folder - was looking for the QC results to know which subjects to remove from my analyses. Would appreciate any help!

By krzysztof.gorgolewski@gmail.com - almost 4 years ago

Derivatives are available at https://legacy.openfmri.org/dataset/ds000030/ and via Amazon Web Services S3 protocol at: s3://openneuro/ds000030/ds000030_R1.0.5/uncompressed/derivatives/ 

By yarkinslav@gmail.com - almost 4 years ago

Dear Openneuro team, thank you for sharing the data! Could I get this data in raw .dcm, .ima? any help would be very appreciated.

By huashuai.xu@foxmail.com - almost 3 years ago

I want to use the the pro-processed 1st-level data from the 'switch-noswitch' contrast, as used in Gopi's paper(10.1016/j.neuroimage.2018.09.078). However, I download all the data, but the data set do not include them, only raw data available.

By lindenparkes@gmail.com - about 4 years ago

Hi,

re: the included physiological signals, were there any processing done to these prior to upload? or are they straight off the recording equipment?

Cheers,
Linden

By franklin.feingold@gmail.com - about 4 years ago

Hello, Thank you for your question. The physiological signals appear to be the raw signal from the recording equipment. 

By huashuai.xu@foxmail.com - almost 3 years ago

I want to use the the pro-processed 1st-level data from the 'switch-noswitch' contrast, as used in  Tamas's paper(10.1016/j.neuroimage.2018.09.078). However, I download all the data, but the data set do not include them, only raw data available.

By joenecus@gmail.com - over 4 years ago

Hello,

I can't seem to locate the Freesurfer derivative folders which are described as being included in this dataset. Are they located in another place?

Thanks,
Joe

By krzysztof.gorgolewski@gmail.com - over 4 years ago

This are available via Amazon Web Services S3 protocol at: s3://openneuro/ds000030/ds000030_R1.0.5/uncompressed/derivatives/ 

By matthewlondon101@gmail.com - about 4 years ago

I'm sorry if I'm missing it, but where can I find DSM diagnoses associated to each subject?

By franklin.feingold@gmail.com - about 4 years ago

Hello, Thank you for your question. To confirm, are you interested in determining the diagnosis group (Control, Schizophrenia, ADHD, or Bipolar) for each subject? This information can be found in the participants.tsv file. 

By matthewlondon101@gmail.com - about 4 years ago

Yes, thank you.

By brochard.jules@gmail.com - over 3 years ago

Hello and thank you for sharing this data set. 
It is truly amazing and prone to a lot of great research :)
Is it possible to share some data on the evolution and potential remission of the pathology ? Any kind of longitudinal data could be fascinating, for example to try to differentiate patients :)

By brochard.jules@gmail.com - over 3 years ago

Also are there diagnosis information available ? Beside from the group ADHD, Bipolar and Schizophrenia ? 
Like the DSM code for each patient as well as the comorbid conditions ?

By liuliang198325@gmail.com - almost 3 years ago

I can not download this dataset. There is no download speed during the download process. I do not know why?

By xuan.gu@liu.se - almost 3 years ago

By lindenparkes@gmail.com - about 4 years ago

Hey all,
I'm trying to use the Chapman scales (chapphy, chapper, and chapsoc) and I have a query about the item level coding.

The item level data are True/False responses. In most cases, 1 = True and 0 = False. But, in each of the different scales there are meant to be a proportion of items for which this is reversed; 0 = True, 1 = False.
Looking at the .json files, all the item "Levels" are listed as 1 = True and 0 = False.

For example, in the chapsoc scale:
Item 20 reads "When I move to a new city, I feel a strong need to make new friends."
This item should be coded at 0 = True and 1 = False, but according to the .json file it isn't.

Is this just a problem in the .json files? (i.e., were all item "Levels" generically defined as 1=True and 0=False). In which case, the .json files can be safely ignored.

Or is the item level data incorrectly scored? In which case, items will need to be recoded.

Also, each scale has a *_total variable in the .tsv file. How were these calculated? There isn't any description in the corresponding .json files and it doesn't appear as though these total scores are the sum of the item level data.

Cheers,
Linden

By poldrack@gmail.com - about 4 years ago

hi - I will have to dig into the code used to create these files, but I'm on vacation for the month of July so it won't happen until next month, sorry about that.

By lindenparkes@gmail.com - about 4 years ago

Hi Russ, just following up on this. Have you had a chance to check the code? Cheers

By lindenparkes@gmail.com - about 4 years ago

Hi Russ, thanks for responding. Okay, no worries, in the mean time I'll assume that the item data are correctly coded and sum them to create scale scores. Let me know when you've had a chance to check it out. Cheers.

By xzeng0512@gmail.com - about 4 years ago

Thanks for sharing the data. When doing analysis on task fmri, did you subtract each dataset with the resting state mean value of individual subject, or the resting state mean value of healthy control group? 

By wasanamadushanka@yahoo.com - almost 4 years ago

Hello, Thank you for sharing this data set. How to find clinical characteristics (ex-PANSS, age of onset, duration, antiphychotics) and some demographic data such as education in years? 

By lastrlfak@gmail.com - over 3 years ago

Hi, Thank you for the dataset. I want to know about the stimulus information (what colors and what words) in the paired associates memory task. I only get the trial type information in pamenc.events.tsv files. Could I get that information?

By meighen.roes@gmail.com - about 1 year ago

Hi, I am wondering the same. I would like any information that can be provided on the stimulus information. I see on the LA5C's Wiki page http://lcni-3.uoregon.edu/phenowiki/index.php/PAM that "files were created by Theo to show the stimuli pairing and presentation order. ..
Media:PAMenc_stims.xlsx‎
Media:PAMret_stims.xlsx"
It would be fantastic to be able to view these (not downloadable through the wiki page).
Thank you!

By matthewlondon101@gmail.com - about 4 years ago

Is there a "Download All" option for this dataset? What would data storage size be to download all? If this information is typically found for datasets on OpenNEURO, where is it listed? Thank you.

By krzysztof.gorgolewski@gmail.com - almost 4 years ago

There is a download button in the upper left corner of the page. If I remember correctly the whole dataset is ~300Gb

By yukiso0017@gmail.com - about 4 years ago

Hi, thank you very much for making the data available. I wish to know why subjects' brain sizes are still different in preprocessed data after coregistration to a same ICBM template? 

By krzysztof.gorgolewski@gmail.com - almost 4 years ago

The physical (in mm) size of each brain after normalization is the same. They might differ in terms of number of voxels (and thus voxel size - resolution) because FMRIPREP by default maintains the same voxel size of the outputs as the inputs and there were slight differences in scanning protocol between participants.

By camthieba@gmail.com - about 4 years ago

Hi, I was wondering if you accounted for commodities in the patients group ? If yes is the information available ?

By xuan.gu@liu.se - almost 3 years ago

Hi, thanks for the data sharing. Could you tell where I can find the raw diffusion MRI data (without preprocessing)? Thank you.

By arianavajdi@gmail.com - almost 4 years ago

Hi, I've downloaded the T1 images and am having a hard time finding the "derivatives" folder - I wanted to get a hold of the QC results to know which subjects to remove from my analyses. Would appreciate any help!

By stevennz@g.ucla.edu - about 4 years ago

Hi, for task dataset, does the first scan/volume take place at the first onset time provided in .tsv file, or when time was 0 second?

By krzysztof.gorgolewski@gmail.com - almost 4 years ago

Yes. This is true for all BIDS compliant datasets since such interpretation of timing is part of the standard.

By ylliu2003@gmail.com - almost 4 years ago

Thank you for sharing the data! I was wondering which version of the TCI was administered and how were the items selected (not all items from TCI are included judging from the .tsv and .json files AFAIK). 

Also, could someone give info/references on the "Scale for Traits that Increase Risk for Bipolar II Disorder"? Can't seem to find relevant information about this scale. Really appreciated!

By mohammadhadiarabi@gmail.com - about 4 years ago

Hi, Thank you so much for sharing this valuable database. I couldn't find the " Impulsiveness, Venturesomeness and Empathy Scale (IVE)"that you mentioned in the https://www.nature.com/articles/sdata2016110/tables/3.Is possible to share this test? 

 

By franklin.feingold@gmail.com - about 4 years ago

Hi, Thank you for your question. I believe the information for the IVE Scale can be found within phenotype/eysenck.tsv for the scores and the phenotype/eysenck.json for the different questions that were asked and possible answers. 

By liuliang198325@gmail.com - almost 3 years ago

I can not download this dataset. There is no download speed during the download process. I do not know why?

By davidyoungisok@gmail.com - about 4 years ago

Hello, I have checked the participants.tsv and  I couldn't find the information about disease duration

By ebru.ztrk3@gmail.com - almost 4 years ago

 Hello,
Thanks for sharing this amazing data set.  My question is that is there any inconvenience in publishing the results of our analysis with this data set?

By camthieba@gmail.com - over 4 years ago

 Hi, Thank you for making this dataset available. Could you tell me where I can find the phenotypic information for each participants including the neuro-psychological testing results ? Are there available ? 

By krzysztof.gorgolewski@gmail.com - about 4 years ago

The missing phenotypic data has been added in v3.

By camthieba@gmail.com - about 4 years ago

Thank you