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Repo that deals with datalad aspects for internal use
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Bad header info for nifti files in uk-biobank dataset #39

Closed sandrinebedard closed 3 years ago

sandrinebedard commented 3 years ago

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:

(base) sebeda@joplin:~/uk-biobank/sub-1000032/anat$ fslhd sub-1000032_T1w.nii.gz
** ERROR (nifti_image_read): bad binary header read for file 'sub-1000032_T1w.nii.gz'
  - read 106 of 348 bytes
** ERROR: nifti_image_open(sub-1000032_T1w): bad header info
ERROR: failed to open file sub-1000032_T1w
ERROR: Could not open file

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

kousu commented 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
jcohenadad commented 3 years ago

Thank you for looking into it @kousu . So the next question would be: would it be possible to upload it? Was @alexfoias on it?

kousu commented 3 years ago

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.

jcohenadad commented 3 years ago

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

jcohenadad commented 3 years ago

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
checking the image header (success 🎉 ) ```console julien-macbook:~/data/uk-biobank $ fslhd sub-1000032/anat/sub-1000032_T1w.nii.gz filename sub-1000032/anat/sub-1000032_T1w.nii.gz size of header 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 1.000000 pixdim1 0.999996 pixdim2 1.000000 pixdim3 1.000000 pixdim4 1.000000 pixdim5 0.000000 pixdim6 0.000000 pixdim7 0.000000 vox_offset 352 cal_max 0.000000 cal_min 0.000000 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 toffset 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 0.998528 -0.008565 -0.053496 -94.543823 qto_xyz:2 0.003043 0.994731 -0.102473 -128.339478 qto_xyz:3 0.054091 0.102160 0.993296 -204.920868 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 0.998528 -0.008565 -0.053496 -94.543823 sto_xyz:2 0.003043 0.994731 -0.102473 -128.339478 sto_xyz:3 0.054091 0.102160 0.993296 -204.920868 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 ```

So, @sandrinebedard the git clone didn't work properly on your end?

kousu commented 3 years ago

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.

kousu commented 3 years ago

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.

sandrinebedard commented 3 years ago

Ahhh, I think I forgot to install v8 of git annex on joplin, I will try again after with the git clone!!!

sandrinebedard commented 3 years ago

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$
kousu commented 3 years ago

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: