dHCP infant data downloading issue

42

Hi Arash

The dHCP volumetric atlas which includes the 40wk template can be downloaded here:

Cheers, Sean

43

Thank you very much.

44

Hello Jianliang,
I did that but I still I can not see anything when I choose Manage files. (see print screen atteched)

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image.jpg3840Ɨ1080 596 KB

I can download a single MR session at a time.
Again the question is how do I download multiple sessions and not one at a time?
regards
Michal

45

Hi Michal,

Sorry for the inconvenience. The files size is so huge that we canā€™t afford bandwidth for downloading multiple subjects/sessions over HTTPS link. Alternatively, we offer academic torrent download. All torrent seeds can be found at https://academictorrents.com/browse.php?search=dHCP you can download a spreadsheet about the subjects from dHCP XNAT website and choose your interest sujbects/sessions by torrent download client tools.

Best regards,
Jianliang

46

Hi Jianliang,
I am having issues with the torrent links. I have tried multiple clients on both Windows (transmission, picotorrent), Linux (transmission) and on our cluster (aria2) directly. Iā€™ve tried both magnet links and the torrent files.
I have also tried locally with a mobile connection in case torrents are being blocked by our IT providers (which they have instructed that they are not blocking).
Sometimes there are errors connecting to all trackers, and no peers are found. Other times, peers are found, but none ever seem to connect. I have never successfully downloaded any data.

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image.png1473Ɨ596 39 KB

Any advice is much appreciated.
Thanks,
Ash

47

Hi Ash,

Thank you for your interest in dHCP project. Can you please try deluge for downloading the data. A quick tutorial can be found at https://www.youtube.com/watch?v=lz3TPYQLD7M

Best regards,
Jianliang

48

Hi all,

Would surface templates and registered surfaces also be included with the 2nd release?

Best,

Arash

49

Hi Arash

The dHCP surface templates can be downloaded here:

https://brain-development.org/brain-atlases/atlases-from-the-dhcp-project/cortical-surface-atlas-bozek/

The surface registrations are not part of release 2. They will be released but a date has not yet been decided.

Cheers, Sean

50

The scripts to run template alignment are here

51

Hi Jianliang,

Thanks for your super helpful reply here!
BTW, I am trying to download the raw anatomical images but it looks I have to download all source data including fmri and dwi images (takes foreverā€¦). Could you also upload a torrent seed only including anatomical raw data?
Appreciate your help.

Yun

52

I used the warp field (*from-T2w_to-template40wk_mode-image.nii.gz) to register the images using FSLā€™s applywarp to the 40 wk [template_t2.nii.gz] file and I get the following that donā€™t seem quite right:

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image.png1849Ɨ698 105 KB

Are these the correct warp field and template for applywarp?

53

Hi Yun,

Youā€™re welcome. That will take a while for me to create such a torrent file. Can you please try Deluge? A quick tutorial can be found at https://www.youtube.com/watch?v=lz3TPYQLD7M If Deluge can improve download speed, maybe its better.
Please let me know if that helps.

Best regards,
Jianliang

54

Hi Arash

Could you please post the full applywarp command?

Also, could you please start a new question (with developing-hcp tag) as this thread is getting quite long and this question if off-topic for this thread.

Cheers, Sean

55

Hi, I am having trouble accessing the second data release in the Developing Connectome project.
I am already registered on the connectome website, as I signed up previously to download the first data release. When I follow the link to register for the second data release, the website says that my email is not currently enabled, and gives a link to send an activation email. I have received this email and clicked to verify. However, at this point it says that I need to wait for an invitation to the dataset.
I completed this verification last week, and am not sure how long this invitation normally takes, or if something has gone wrong?
Has anyone else encountered this issue?
Thanks

56

Hi Jianliang,
Iā€™ve tried with Deluge, but no different results to any other BitTorrent clients. I am following up with our IT department. They have a preference for direct download, is this an option?
Cheers,
Ash

57

Hi Ash,

If you want to download directly, you can only download sourcedata and only download one session a time via dHCP XNAT. Furthermore, the speed will be terribly slow.

The entire data set size is about 2TB. Torrent will be the only option if you want to download entire dataset. If you tried the method in https://www.youtube.com/watch?v=lz3TPYQLD7M , and you canā€™t download anything at your institute, please try with networks outside of your institute.

Best regards,
Jianliang

58

Hi Jianliang,

I have trouble to connect to the dHCP website as well. Could you please look into my registeration?
username: benjamindeleener

Thank you very much,

Benjamin

59

Hi there,

we downloaded t1/t2 data of release 2.0 today, but found 80/1118 files (e.g., 900_0) missing. Are these not all t1/t2 for all subjects available?

Thanks and best wishes, Frithjof

60

Hi Frithjof,

No. There are 558 T2 files and 492 T1 files. Some sessions have T1 files missing.

Best wishes,
Jianliang

61

Just to add to this: In most cases where the T1 scan is missing this is due to motion artefacts which caused the scan not to pass the QC step.

Best wishes, Daniel