preprocessed-connectomes-project / abide

ABIDE Preprocessed Initiative

preprocessed-connectomes-project/abide ######################################

Contents

• download_abide_preproc.py - script to download ABIDE preprocessed data from S3, given phenotypic information
• map_rawout_to_organized_s3.py - script to organize the CPAC raw outputs from a pipeline run and organize them in the output format on S3

concordances

• abide_cc_plots.R - R script to plot the pairwise concordance values from an ABIDE concordance data frame
• abide_concordances.pdf - The pair-wise concordance plots (cross-strategy, cross-pipeline) for ABIDE preprocessed
• big_df.csv.gz - G-zipped csv dataframe of all the pairwise concordances; unzipping this and passing it to abide_cc_plots.R will generate the abide_concordances.pdf
• pairwise_concordance.py - a script to compute the pairwise concordances of the ABIDE preprocessed outputs and save to dataframe as a csv file
• query_download_abide.py - script to manually download and check the pairwise concordance between two images based on a data frame entry (for verification of entries produced by pairwise_concorfance.py)

preprocessing

realigned_inputs

• Anonymized anatomical scans from sites that we had registration problems with (so we realigned them and used the realigned versions as inputs)

resources

• abide_masks - nifti masked used in centrality calculation
• abide_rois - nifti roi files used in mean time series extraction
• abide_spatial_maps - nifti spatial maps file with 10 functional networks used for dual regression

scripts

• eigen_run.py - script to run eigenvector centrality in isolation by downloading the functional preprocessed data from the raw CPAC output of a separate pipeline run
• eigen_run.sge - the sge bash submission script to run eigen_run.py over an HPC
• run_cpac.py - script to run CPAC on one subject (input is index of a subject list)
• run_cpac.sge - the sge bash submission script to run run_cpac.py over an HPC

settings

• abide_rois.txt - text file with full paths to the ROI resources needed for timeseries extraction
• abide_spatial_maps.txt - text file with full paths to spatial maps used in dual regression
• centrality_mask.txt - text file with full paths to mask files used in centrality
• pipeline_config_abide_rerun.yml - CPAC configuration file for the CPAC ABIDE preprocessed outputs
• CPAC_subject_list_abide_rerun.yml - CPAC subject list for the CPAC ABIDE preprocessed inputs

yamls

• ccs_missing.yml - CCS outputs that weren't produced
• comparisons_list.yml - list of pairwise comparisons
• map_dict_rerun - the mapping dictionary from raw output files to the S3-organized structure
• rerun2_subs.yml - subject ids that needed to have raw outputs regenerated twice
• subs_list.yml - full SITE_SUBID list of ABIDE subjects

abide's Issues

Link to freesurfer data on S3

Hello,
I tried this link to get data from S3:
https://s3.amazonaws.com/fcp-indi/data/Projects/ABIDE_Initiative/Outputs/freesurfer/5.1/50002/surf/lh.pial
But I get an error. Am I doing something wrong?

Here's the error:

<Error>
<Code>NoSuchKey</Code>
<Message>The specified key does not exist.</Message>
<Key>data/Projects/ABIDE_Initiative/Outputs/freesurfer/5.1/50002/surf/lh.pial</Key>
<RequestId>809A3F0391F8BD8E</RequestId>
<HostId>fYcV661vrZd4jjhRa5Qo5bHLiTxww8+qsiBoe4t5CMyNFRCUzPT4in+QPSqS+CmhRRMphsUS6cQ=</HostId>
</Error>

Website for details about DKT labeling protocals is out of date.

Hi, the website you quoted to for more detail about the labeling protocals of the ROI-based morphology measuring is out of date. And this is the new website I found in the Mindboggle :DKT cortical labeling protocol (31 labels).

Error in downloading: " urlopen error [Errno 60] Operation timed out "

Hi,
I tried to run the "download_abide_preproc.py" script to download ABIDE preprocessed data from S3, but met the following error:
urllib.error.URLError: <urlopen error [Errno 60] Operation timed out>
I am wondering if the given url is still working? Or is there any update for that?

Any suggestion or comment is much appreciated!

Thank you!
Guixiang

Add documentation for structural scans

Currently, there's good documentation on downloading the different functional scans. Similar documentation should be completed for functional scans. Currently, the website is incomplete.

Extra ROI Variable in HO Atlas

According to the documentation, you should have 110 rois for this parcellation. However the actual dataset has an extra variable, I suspect variable 83 which does not seem to correspond to any legitimate cortical or subcortical region. The nifti atlas provided in the documentation suggests that 83 corresponds to two seemingly arbitrary voxels.

Also note that the documentation for many of the atlases do not provide ROI label files.

Harvard-Oxford (HO): The HO atlas distributed with FSL is split into cortical and subcortical probabilistic atlases. A 25% threshold was applied to each of these atlases and they were subsequently bisected into left and right hemispheres at the midline (x=0). ROIs representing left/right WM, left/right GM, left/right CSF and brainstem were removed from the subcortical atlas. The subcortical and cortical ROIs were combined and then fractionated into functional resolution using nearest-neighbor interpolation. [Atlas][Labels]

161 times series in ABIDE with derivatives rois_dosenbach160

Dosenbach atlas from
https://fcp-indi.s3.amazonaws.com/data/Projects/ABIDE_Initiative/Resources/dos160_roi_atlas.nii.gz

contains an extra label

>>> import nibabel
>>> import numpy as np
>>> img = nibabel.load('dos160_roi_atlas.nii.gz')
>>> print(np.unique(img.get_data()))

[  0   1   2   3   4   5   6   7   8   9  10  11  12  13  14  15  16  17
  18  19  20  21  22  23  24  25  26  27  28  29  30  31  32  33  34  35
  36  37  38  39  40  41  42  43  44  45  46  47  48  49  50  51  52  53
  54  55  56  57  58  59  60  61  62  63  64  65  66  67  68  69  70  71
  72  73  74  75  76  77  78  79  80  81  82  83  84  85  86  87  88  89
  90  91  92  93  94  95  96  97  98  99 100 101 102 103 104 105 106 107
 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125
 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143
 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 223]

>>> np.where(img.get_data()==223)

(array([33]), array([24]), array([30]))

The last region label 223 is not in the Dosenbach atlas but just an intersection between regions label 108/MNI (-5, -52, 17) and label 115/MNI (-11, -58, 17) which are too close.

Publication list for ABIDE is for ADHD200

The articles on the ABIDE preprocessed publication list seem to all be for the ADHD200 dataset.

Mean FD values not matching

Hi,

I am in the process of running subjects through the NIAK pipeline for ABIDE ; however, I am finding that the mean FD values I get do not match with what is in the existing ABIDE database I downloaded off of http://preprocessed-connectomes-project.org/abide/. Is there a repository or place I can view every step of the NIAK pipeline, so I can replicate the same results that was in the spreadsheet? Thank you!

Download structural T1 data with age parameters

Hello,

I'm trying to download T1w images for certain age groups. All the download pipelines seem to be centered around metrics functional imaging. I am able to download the functional nii's without issue, but I do not see a simple way to download the T1w. I've gone through the parameters/derivatives from the pulldown code and I simply do not see an option for pulling T1w's.

Any help would be appreciated.

Demographic (age) data missing

Hello,

Thanks for making these resources available, but I'm running into an issue. I downloaded the imaging data from XNAT nitrc server. I don't see any information about participant age anywhere. Could you please help out? The DOB is empty as you can see, I would need their age at scan. Thank you in advance

Data aquistion details

Where can I find the table describing the aquisition detail of ABIDE dataset? For eg. the MRI scanner used ,size and resolution of several images, time duration of each patient etc.

ABIDE preprocessed results don't match

Hi,

I downloaded the ABIDE raw and preprocessed data from the NITRC website. I have CPAC installed on my workstation and when I ran the pipeline, the preprocessed results (roi time series) for certain sites do not match the results posted in the website (with significant differences) . I used the same configuration pipeline provided on the website. Are there any other site-specific parameters while running the pipeline apart from slice timing pattern?

Thanks. Response is much appreciated!

Meenakshi

Registration of freesurfer files with preprocessed functional data?

Hi there!

We're working on surface-based analysis of resting-state data from ABIDE. So whttps://github.com/preprocessed-connectomes-project/abide/issues/18e're trying to use freesurfer's full output directory that we were able to download together with the preprocessed functional data in order to project the functional data onto freesurfer's meshes... (before doing whatever we'd like to do on the surface ;) )

However, the preprocessed functional data is in MNI space and it seems freesurfer's recon-all has been run in the subject's native space. So the two are not aligned and we cannot project directly the functional preprocessed data onto the surface...

So how would you do it? One of my ideas was to try to get the transformation "Anatomical2MNI" files that have been estimated to put the functional data into MNI space, to perform the inverse transformation in order to put the functional data back into native space (if possible), but I cannot find those transformation files... Are they available somewhere? If not, how would you do it?

Thanks for your help,

Sylvain

Extra ROI variable

I downloaded the CPAC preprocessed ABIDE data using the dosenbach atlas [1]. Although the atlas consists of 160 ROIs, the datasets contain 161 variables. Some documentation that explains the extra variable would be helpful. I suspect the 161st column is the global mean signal. Would be great if someone can confirm this.

[1] https://s3.amazonaws.com/fcp-indi/data/Projects/ABIDE_Initiative/Outputs/cpac/nofilt_noglobal/rois_dosenbach160/UCLA_1_0051201_rois_dosenbach160.1D

Freesurfer

Is there a script for running Freesurfer for all subjects? I would like to use the same Freesurfer pipeline for ABIDE 2

Dependencies version for this repo

Is it possible to get dependencies, especially C-PAC and other libraries version to reproduce the results and extend to ABIDE-II dataset?

There are different scan times in the KKI dataset

Hi

The scan time is different for some subjects in the KKI dataset. Does disappointment occur at the beginning or end of the scan?

the best,