Closed sandrinebedard closed 3 years ago
It looks like the content hasn't been uploaded yet:
$ git clone --depth 1 git@data.neuro.polymtl.ca:datasets/uk-biobank
Cloning into 'uk-biobank'...
Enter passphrase for key '/home/kousu/.ssh/id_rsa.github':
remote: Enumerating objects: 1898, done.
remote: Counting objects: 100% (1898/1898), done.
remote: Compressing objects: 100% (1047/1047), done.
remote: Total 1898 (delta 506), reused 1877 (delta 503), pack-reused 0
Receiving objects: 100% (1898/1898), 407.50 KiB | 2.08 MiB/s, done.
Resolving deltas: 100% (506/506), done.
$ cd uk-biobank/
$ git annex init
init (scanning for unlocked files...)
Enter passphrase for key '/home/kousu/.ssh/id_rsa.github':
ok
(recording state in git...)
$ git annex whereis
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git-annex: whereis: 687 failed
This means that even doing get
will leave you with a pointer instead of the file:
$ git annex get sub-1000032/anat/sub-1000032_T1w.nii.gz
get sub-1000032/anat/sub-1000032_T1w.nii.gz (not available)
No other repository is known to contain the file.
failed
git-annex: get: 1 failed
(.venv) [kousu@requiem uk-biobank]$ cat sub-1000032/anat/sub-1000032_T1w.nii.gz
/annex/objects/SHA256E-s16686194--cdbd747c15c20c534857315b0d6cd4f64ebbd3fbea97ab6411da7c708ad8b92e.nii.gz
Thank you for looking into it @kousu . So the next question would be: would it be possible to upload it? Was @alexfoias on it?
Oh wait sorry that's a red-herring. The --depth 1
was a shortcut I shouldn't have taken here.
And my name is on the log. So either I messed up and didn't notice for weeks or it's something else.
Oh wait sorry that's a red-herring. The --depth 1 was a shortcut I shouldn't have taken here.
Been there done that 😅 https://github.com/neuropoly/data-management/issues/41#issuecomment-769235520
I've tried reproducing the error on my local station (took a few hours to get the 20GB 😅 ). Looks like I can get the data:
julien-macbook:~/data/uk-biobank $ git-annex get sub-1000032
(merging origin/git-annex into git-annex...)
(recording state in git...)
(scanning for unlocked files...)
get sub-1000032/anat/sub-1000032_T1w.nii.gz (from origin...)
(checksum...) ok
get sub-1000032/anat/sub-1000032_T2w.nii.gz (from origin...)
(checksum...) ok
(recording state in git...)
julien-macbook:~/data/uk-biobank $ ll sub-1000032/anat/sub-1000032_T1w.nii.gz
-rwxr-xr-x 1 julien staff 16686194 28 Jan 12:13 sub-1000032/anat/sub-1000032_T1w.nii.gz
So, @sandrinebedard the git clone didn't work properly on your end?
Ah yeah it's actually there, once I remembered to sync git-annex
$ git fetch origin git-annex
Enter passphrase for key '/home/kousu/.ssh/id_rsa.github':
From data.neuro.polymtl.ca:datasets/uk-biobank
* branch git-annex -> FETCH_HEAD
$ git checkout FETCH_HEAD
Note: switching to 'FETCH_HEAD'.
You are in 'detached HEAD' state. You can look around, make experimental
changes and commit them, and you can discard any commits you make in this
state without impacting any branches by switching back to a branch.
If you want to create a new branch to retain commits you create, you may
do so (now or later) by using -c with the switch command. Example:
git switch -c <new-branch-name>
Or undo this operation with:
git switch -
Turn off this advice by setting config variable advice.detachedHead to false
HEAD is now at 3ba1e85 update
$ git checkout -b git-annex
Switched to a new branch 'git-annex'
the files are there:
$ git annex get sub-1000032/anat/sub-1000032_T1w.nii.gz
get sub-1000032/anat/sub-1000032_T1w.nii.gz (from origin...)
You have enabled concurrency, but git-annex is not able to use ssh connection caching. This may result in multiple ssh processes prompting for passwords at the same time.
annex.sshcaching is not set to true
Enter passphrase for key '/home/kousu/.ssh/id_rsa.github':
(checksum...) ok
(recording state in git...)
$ git annex whereis sub-1000032/anat/sub-1000032_T1w.nii.gz
whereis sub-1000032/anat/sub-1000032_T1w.nii.gz (2 copies)
ea71146c-9360-4041-8378-87ab0dfff167 -- git@data.neuro.polymtl.ca:~/repositories/datasets/uk-biobank.git [origin]
fe74aae6-e1f5-4fd7-98ea-fd1905175a0c -- kousu@requiem:~/src/neuropoly/uk-biobank [here]
ok
I wonder if something disrupted @sandrinebedard's download halfway through.
I think there's something else off with this dataset btw. The af/add_subj
branch seems to have accidentally circumvented git-annex
, so git clone
wanted to download 18G. So maybe that's causing some problems.
Ahhh, I think I forgot to install v8 of git annex on joplin, I will try again after with the git clone!!!
Checking the header works now! 🎉
(base) sebeda@joplin:~/uk-biobank/sub-1007269/anat$ fslhd sub-1007269_T1w.nii.gz
filename sub-1007269_T1w.nii.gz
sizeof_hdr 348
data_type FLOAT32
dim0 3
dim1 208
dim2 256
dim3 256
dim4 1
dim5 1
dim6 1
dim7 1
vox_units mm
time_units s
datatype 16
nbyper 4
bitpix 32
pixdim0 0.000000
pixdim1 1.000002
pixdim2 1.000000
pixdim3 1.000000
pixdim4 1.000000
pixdim5 0.000000
pixdim6 0.000000
pixdim7 0.000000
vox_offset 352
cal_max 0.0000
cal_min 0.0000
scl_slope 1.000000
scl_inter 0.000000
phase_dim 0
freq_dim 0
slice_dim 0
slice_name Unknown
slice_code 0
slice_start 0
slice_end 0
slice_duration 0.000000
time_offset 0.000000
intent Unknown
intent_code 0
intent_name
intent_p1 0.000000
intent_p2 0.000000
intent_p3 0.000000
qform_name Scanner Anat
qform_code 1
qto_xyz:1 0.995400 -0.044741 0.084749 -108.668991
qto_xyz:2 0.048096 0.998121 -0.037955 -140.196686
qto_xyz:3 -0.082892 0.041856 0.995679 -169.504883
qto_xyz:4 0.000000 0.000000 0.000000 1.000000
qform_xorient Left-to-Right
qform_yorient Posterior-to-Anterior
qform_zorient Inferior-to-Superior
sform_name Scanner Anat
sform_code 1
sto_xyz:1 0.995400 -0.044741 0.084749 -108.668991
sto_xyz:2 0.048096 0.998121 -0.037955 -140.196686
sto_xyz:3 -0.082892 0.041856 0.995679 -169.504883
sto_xyz:4 0.000000 0.000000 0.000000 1.000000
sform_xorient Left-to-Right
sform_yorient Posterior-to-Anterior
sform_zorient Inferior-to-Superior
file_type NIFTI-1+
file_code 1
descrip FSL5.0
aux_file imgComments
(base) sebeda@joplin:~/uk-biobank/sub-1007269/anat$
I'm kind of unclear what happened here. I thought git-annex v7 could consume, just not contribute (easily) to v8 repos. Maybe #41 caused problems getting a clean download. :shrug:
Description
I git cloned the
uk-biobank
dataset on joplin to test preprocessing steps, it could'nt work because it was unable to open the nifti files. When I try to get the header of a nifti file from the dataset I get this:Can somebody check if they can reproduce this error? Maybe I downloaded the data the wrong way, I followed https://github.com/neuropoly/data-management/blob/master/internal-server.md#download