brain-life/encode

dtiImportFibersMrtrix fails to parse track.tck header

Closed this issue · 8 comments

soichih commented

I am trying to run app-life on output track.tck generated by brain-life/app-dipy-tracking (multishell tractograph with CSA) app.

When I run LiFE, I get following error message.

{�Error using dtiImportFibersMrtrix (line 76)
Unable to parse header for file ../59a09712682fb20024ca9af8/track.tck


Error in fgRead (line 39)
        fg = dtiImportFibersMrtrix(fgFile);

Error in feConnectomeInit (line 49)
  fg = fgRead(fgFileName);

Error in life (line 10)
fe = feConnectomeInit(config.dwi, ...

Here is the header contained inside the output track.tck.

$ head ../59a09712682fb20024ca9af8/track.tck
mrtrix tracks
count: 0000272259
datatype: Float32LE
file: . 67

It's short, but the structure looks OK? It could be missing some parameters that LiFE needs?

The brain-life/app-dipy-tracking creates track.tck by doing following.

https://github.com/brain-life/app-dipy-tracking/blob/master/main.py#L108

    tractogram = Tractogram(streamlines, affine_to_rasmm=affine)
    save(tractogram, 'track.tck')

It am not sure if this issue needs to be fixed by the tractography app, or the .tck file header parser used by LiFE.

soichih commented

@ccaiafa @Garyfallidis Please comment.

ccaiafa commented

Not clear idea what is happening. dtiImportFibersMrtrix is a VISTASOFT function, not part of LiFE.

francopestilli commented

@soichih This is actually a trick question. I do not think Dipy can save .tck files. @Garyfallidis (I just realized this is all within Python/Dipy, so it is relevant to you.)

soichih commented

@francopestilli Here is the nibabel method that app-dipy-tracking is using to save the .tck file

http://nipy.org/nibabel/reference/nibabel.streamlines.html

app-life app then tries to load the .tck using Vistasoft dtiImportFiberMrtrix() and it fails with the error message.

My hunch is that, dtiImportFiberMrtrix() is having trouble parsing the count

count: 0000272259

I think nibabel should output this in following format instead.

count: 272259

So I think this could be nibabel issue. OR.. vistasoft can be updated to trim the leading 0000 and be able to handle such format.

soichih commented

Actually, I was wrong about the count format. vistasoft can parse it just fine.

The real issue is that dtiImportFiberMrtrix() requires step_size field to be present in the header, but nibabel is not outputting this field (and it looks like that's the only field that's missing)

I will open an issue with nibabel to see if they can add this field.

nipy/nibabel#553

soichih commented

Marc from nibabel says that step_size is an optional field, and I saw this issue was already addressed by Vistasoft (vistalab/vistasoft#164). They made it so that it assumes step_size to be 1 if it's not set, although I am not sure how safe that is..

Anyway, I just pulled the latest master branch of vistasoft, and tested it. I also just realized that, app-life needs dtiInit output (single shell) and app-dipy-tracking needs multi-shell dwi input.. So I can no longer run app-life against app-dipy-tracking output.

francopestilli commented

Do we need to make any in the code here?

soichih commented

No, I think everything should work fine as far as encode/app-life goes. I am recompiling the msa binary and docker container for app-life.