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Paul,

No, not that I noticed. We're starting it by double-clicking the

FSLeyes.app folder. Do you want us to try to start it from a

Terminal?

-- bennet

On Thu, Jan 30, 2020 at 5:46 AM paul mccarthy <[log in to unmask]> wrote:

Hi Bennet,

This is a bug - is anything printed to the terminal when the error occurs?

Paul

On Jan 29 2020, at 11:42 pm, Bennet Fauber <[log in to unmask]> wrote:

I have a user who downloaded and installed FSLeyes 0.32.0 for Mac,

.zip file. She is in a workshop, and they are working with the

standard ds102 dataset from OpenfMRI.org (OpenNeuro).

She uses FSL to create from sub-08_T1w.nii.gz using bet the mask file,

sub-08_T1w_brain.nii.gz.

When she uses FSLeyes 0.32.0 to open first the T1w file, that works,

but when she tries to add the mask as an overlay she gets the error

window attached, which says, basically, that the mask file isn't

proper BIDS. In case the screen shot does not pass the listserver,

the text is roughly,

Error loading overlay

An error occurred loading the image /path/to/sub-08_T1w_brain.nii.gz

Details: Does not look like a BIDS file: /path/to/mask

This error does not occur with FSLeyes 0.31.2+build0. Can checking

BIDS format be suppressed via an option? I looked, as did several

others here, and we aren't finding this settable.

It doesn't seem like an image viewer/manipulator should really care

what the format of the image filenames is.

This situation surprised many of us here, and I am able to replicate easily.

We can make the error stop by removing all .json files from the root

of the BIDS directory, and effectively de-BIDSifying it.

It also appears to work if the image is removed entirely from the BIDS

directory, but I think that would not be obvious, nor in agreement

with current, standard practice according to FSL tutorials, which I

think suggest creating the mask in the same directory.

Assuming that the directory that contains the subject's anatomical

image is username/ds102/sub-08/anat, then what directory location and

filename will FSLeyes accept according to its BIDS validation rules?

I tried creating inside the derivatives directory a directory for FSL,

adding a dataset_description.json per the description at

https://bids-specification.readthedocs.io/en/derivatives/05-derivatives/01-introduction.html

and putting the mask file into

derivatives/fsl/sub-08/anat/sub-08_T1w_brain.nii.gz and that did not

help.

I see from the Changelog at

https://github.com/pauldmccarthy/fsleyes/blob/master/CHANGELOG.rst

that

Metadata from JSON sidecar files (e.g. in BIDS data sets) is now

displayed in the overlay information panel.

Anyway, if you would, please let us know where FSLeyes expects to see

the brain masks generated by bet/bet2, which JSON files might need to

be written, and what information might be required in them.

Presumably, this will also be a problem when using FSLeyes to look at

images directories created by feat, if they are in the same BIDS

folder?

Thanks in advance for your guidance, -- bennet

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