Comments (11)
from abide.
Hi,
I used the "download_abide_preproc.py" script to download ABIDE preprocessed, as following, for CMU site: python download_abide_preproc_up.py -d func_preproc -p cpac -s filt_global -o /path for data -t CMU
However the resulting files are not for all the subjects in the site and there are several error messages:"Error extracting info from phenotypic file, skipping..."
I tried for other sites also and the number of downloaded files always less than the number of subjects.
I used also the fetch_abide_pcp function in nilearn and I did not get all the subjects for each site.
Could you please provide me a script to download all the subjects for each site.
Thank you in advance.
from abide.
from abide.
Just found out that they already have the site filter, but it is not clear on the documentation.
For example, this python command will download your data into "/tmp":
nilearn.datasets.fetch_abide_pcp('/tmp',
derivatives=['func_preproc'],
pipeline='cpac',
band_pass_filtering=True,
global_signal_regression=True,
SITE_ID=['NYU'])
from abide.
Hi Anibal,
Thank you for your replies. Yes I used at the end the fetch_abide_pcp function from nilearn to download the preprocessed data of Abide I according to each site but always the number of downloaded data (preprocessed by capc) for the subjects is less than the number of subjects presented in this link:
http://fcon_1000.projects.nitrc.org/indi/abide/abide_I.html
for instance, I got 871 preprocessed data for all the subjects however the number of subjects for all the sites is more than 1000 subjects.
from abide.
It is probably because of the quality control.
You can disable the quality control with the option quality_checked=False
.
from abide.
@Jeansma @anibalsolon @AbdelbassetBrahim @czarrar @pbellec
Recently I have downloaded ABIDE 1 Preprocessed dataset by fetching it from “Nilearn”.
pipeline: cpac
derivatives: func_preproc
The code is here
abide_dataset = nilearn.datasets.fetch_abide_pcp(data_dir=’/content/ABIDE’, n_subjects=None, pipeline=‘cpac’, band_pass_filtering=True, global_signal_regression=True, derivatives=[‘func_preproc’], quality_checked=False, verbose=1)
By disabling the quality control parameter I was able to download fMRI images of only 1035 subjects… In the phenotype information (CSV file) remaining 77 subjects file_name was mentioned as no_filename…
Does these subjects have only phenotype information (no fMRI images)?
Does the number of subject’s (fMRI images) depends on the choice of pipeline and derivative?
Is it possible to download fMRI images of 1112 subjects using nilearn?
It will be of great help if any one can give a clarification
from abide.
from abide.
@AbdelbassetBrahim
Thanks for your reply..
Is it possible to download fMRI images of 1112 subjects other than using nilearn?
from abide.
You can try this python script and see: download_abide_preproc.py
from abide.
hi, while downloading abide dataset using fetch_abide_pcp , I am getting connection error in between .
after PITT, in OLIN id I am getting error.
I tried 3 times but every time I got connection error from host.
can anybody please help me ?
from abide.
Related Issues (17)
- Add documentation for structural scans HOT 6
- Link to freesurfer data on S3 HOT 3
- Publication list for ABIDE is for ADHD200
- 161 times series in ABIDE with derivatives rois_dosenbach160
- Mean FD values not matching
- ABIDE preprocessed results don't match
- Data aquistion details HOT 2
- Dependencies version for this repo HOT 1
- Registration of freesurfer files with preprocessed functional data?
- Freesurfer
- Extra ROI variable
- There are different scan times in the KKI dataset
- Download structural T1 data with age parameters HOT 3
- Website for details about DKT labeling protocals is out of date.
- Demographic (age) data missing
- Extra ROI Variable in HO Atlas HOT 4
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from abide.