T1-volume atlas error

[Remi Silva]

Hi

I am running the T1-volume pipeline and from the logs it appears to have worked fine for the first 3 steps but i got his error message for the 4th step.

ERROR:Unable to download atlas-Hammers_dseg.nii.gz from https://aramislab.paris.inria.fr/files/software/cat12/CAT12-Atlases/: /users/rs2472/.cache/clinica/data/atlas-Hammers_dseg.nii.gz has an SHA256 checksum (e3b0c44298fc1c149afbf4c8996fb92427ae41e4649b934ca495991b7852b855) from expected (c034a7bce2dcab390a0b72f4e7d04769eb3fe5b990d0e18d89b0ce73339a5376), file may be corrupted. [0m

I also got this warning message in the error log:

UserWarning: SPM standalone is not available on this system. The pipeline will try to use SPM and Matlab instead. If you want to rely on spm standalone, please make sure to set the following environment variables: $SPMSTANDALONE_HOME, and $MCR_HOME
  warnings.warn(

stty: 'standard input': Inappropriate ioctl for device

note. i have set up environmental variables as follows:

export FREESURFER_HOME=$EBROOTFREESURFER
export SPM_HOME=$EBROOTSPM
export MATLAB_HOME=$EBROOTMATLAB/bin
export MATLABCMD=$MATLAB_HOME/matlab

[Nicolas Gensollen]

Hi,

I don't know why but it looks like the download of the Hammers atlas went wrong because the hash of the downloaded file doesn't match the expected checksum.

You can verify by manually downloading the atlas file from https://aramislab.paris.inria.fr/files/software/cat12/CAT12-Atlases/ and computing the hash of the downloaded file:

```python

>>> from clinica.utils.inputs import compute_sha256_hash

>>> from pathlib import Path
>>> compute_sha256_hash(Path.cwd() / "atlas-Hammers_dseg.nii.gz")
'c034a7bce2dcab390a0b72f4e7d04769eb3fe5b990d0e18d89b0ce73339a5376'

```

If this works, you can put this image into the cache folder "$HOME/.cache/clinica/data/". This way, clinica won't download the atlas every time but will use the cached image instead. 

Alternatively, you can try re-runing the pipeline as the error might just be due to data corruption during download. 

If you have SPM12 et Matlab installed on your system and if you prefer to use this instead of SPM standalone, then you can ignore the warning.

Hope this helps!

Best,

Nicolas

[Remi Silva]

Hi

Thank you I reran the pipeline and it works. However, I am now having issues running the pet-volume pipeline. 

Using the CAPS directory with the t1-volume output I keep getting this error message: 

ERROR:Clinica faced error(s) while trying to read files in your CAPS/BIDS directories.

Clinica encountered 102 problem(s) while getting PET data with 18FAV45 tracer:
* (016_S_6790 | ses-M000): No file found

.... 

However, this is the structure for the CAPS Directory:

And this is the BIDS directory:

I have set these as the file paths:

export ADNI_PATH="/mnt/scratch/users/rs2472"
export OUT_PATH="/mnt/scratch/users/rs2472/OUTPUT"
export WORKING_DIR="/users/rs2472/scratch"

adni_bids_path="$OUT_PATH/BIDS"
adni_caps_dir="$OUT_PATH/CAPS" 

Thank you again for your help

Renata

[Nicolas Gensollen]

Hi,

Were you able to run the pet-volume pipeline since then ?

If not, could you give more details about the input folders (caps and bids) ? The screenshots of your last message don't tell us much as we don't see the files in the different folders (they could very well be empty...). The output of a `tree` command would be much more explicit and useful.

Could you also give the command you used to run the pet-volume pipeline ? Did you provide a list of subjects ?

Best,

Nicolas