Morphologist UI "some input files do not exist"

[tjneuro47]

Hi all,

when I try to run Morphologist UI using a brainvisa database containing T1w images in nii.gz it displays the above mentioned error "Run analysis error: Some input files do not exist". It does not matter if I use the database as source directory or if I select the nii.gz files manually.

I can load the files into morphologist UI without any problems, and the RAW T1 Images gets displayed as ususal.

Thanks in advance :)

[denisri]

Hi,
Sorry, I can't see the attached image you are talking about, which apparently shows the error you get, so I am guessing...
If I understand your use case, you have a database where BrainVisa/Morphologist has already run, and you want to reuse it using Morpholiogist-UI, is that right ?
I have spotted a couple of bugs in the import procedure in Morphologist-UI so I understand it doesn't work for you, but the issues I have seem not correspond to your description, so I'll ask you a few more details:

• which exact version of BrainVisa / Morphologist are you using ? (first is it a pixi-based version 6 or an earlier ? Then the complete version number would help, you can get them using pixi ls brainvisa and pixi ls morphologist in a pixi install)
• What's the ontology of your BrainVisa database ? brainvisa-3.2, morphologist-bids-2.0 ?
• How have you proceeded ? Normally you start morphologist, then in the Study menu you select Import..., choose the BrainVisa directory, and select the matching directory organization (morphologist-bids-2.0 or brainvisa classic depending on the ontology of the BrainVisa database). It should parse the database, and show you the list of subjects to be imported. You should ensure the same Study directory organization is used (one of the bugs I found was that it was not following your first choice), then click Apply. You should now have in the GUI the same subjects list as in BrainVisa - if everything works correctly, but as I said I have found bugs here. I have just fixed them but you'll have to wait for us to publish an update. I don't promise anything but I hope I can do that during this week.
• In the terminal displaying the error messages, did you see a message starting with MISSING INPUTS IN NODES: ?

Well I have tried some fixes but as I cannot reproduce the same error as you had, I don't know if it will fix it for you, so I am expecting some precisions from you.

Denis

[tjneuro47]

Hi Denis,

thanks for the quick answer.

1. Im using pixi-based version 6.0.39 and morphologist 6.0.18
2. the ontology of my database is braivisa-3.2.0
3. My Procedure: I started the morphologist UI, then I selected "New" to create a new study and study directory. I think I did not (or could not) change the "Study directory oragnizaztion" to anything other than "morphologist-bids-2.0). Then I Added subject via "organized files" and select "brainvisa classic as the database organization. But I also tried to Add subjects "from files" and it didnt make a difference. The subjects are correctly imported and after clicking apply they appear in the Morphologist GUI and the T1 image gets displayed correctly in the RAW MRI window. The error only occurs when I click "Run". All the error message says is: "Run analysis error: Some input files do not exist" (see screenshot)
4. I am using the software on a shared network system at a research center. I tried the same steps with the same data at my PC at home and it worked so it might have something to do with morphologist not accessing the data the right way? at home I am using pixi-based Brainvisa 6.0.28 and morphologist 6.0.5.

Thanks
Tom

[denisri]

OK. I now have tested the same use case as you describe, and I can reproduce the same error using brainvisa 6.0.39 / morphologist 6.0.18 (even on a local filesystem so it's not related to that). And I don't have it any longer when using the modified version with recent fixes. So I guess the fixes have actually solved the problem.
I'll try to publish a new update very soon so that you will be able to test.

[tjneuro47]

Thank you for the help and the quick answers. Do you have any estimate how long it will take for the new version to be published because I am using the software for my masters thesis and have the deadline in November. This way I could plan it a little better :).

Thanks again and kind regards,
Tom

[denisri]

This week if no more urgent job pops out (or if I don't remember one that I had forgotten...)

[denisri]

It's done. Can you update (pixi update brainvisa, then restart the pixi environment) and try again please ?