Paul,
This got rejected because of the attached data set. Please download that from
http://www.umich.edu/~bennet/test_data.tar.gz
If you would, let me know once you've fetched it, so I can delete it.
Thank you, -- bennet
---------- Forwarded message ---------
From: Bennet Fauber <[log in to unmask]>
Date: Fri, Jan 31, 2020 at 3:55 PM
Subject: Re: [FSL] FSLeyes 0.32.0 Mac shows BIDS error when opening brain mask
To: FSL - FMRIB's Software Library <[log in to unmask]>
Paul,
Confirmed no error message written to the console when started using
$ /Users/bennet/Downloads/FSLeyes-32.app/Contents/MacOS/fsleyes
I attach test_data.tar.gz, which is the JSON files from the root of
the ds102_R2.0.0 and just that anatomical data from sub-08.
I get the error message by loading the
FSLdata/sub-08/anat/sub-08_T1w.nii.gz image, then trying to add
FSLdata/sub-08/anat/sub-08_T1w_brain.nii.gz as an overlay. That
should cause the pop-up with version 32.0. If you move the *.json
files from FSLdata to FSLdata/jsons and then attempt to load
FSLdata/sub-08/anat/sub-08_T1w_brain.nii.gz, no error dialog should
appear.
This is using
MD5 (FSLeyes-latest-macos.zip) = 612d677c282f7db8925d86e9ab956a71
On
MacOS High Sierra
version 10.13.6
iMac 27-inch, mid 2011
2.7 GHz Intel Core i5
8 GB 1333 MHz DDR3
AMD Radeon HD 6770M 512 MB
but also exercised on a MacBook for which I do not have the specs.
Let me know if you need anything else.
-- bennet
On Fri, Jan 31, 2020 at 7:17 AM paul mccarthy <[log in to unmask]> wrote:
>
> Hi Bennet,
>
> That may help, if possible. What would also help is if you could prepare and send to me a minimal data set which I can use to reproduce the problem. I've not been able to reproduce it yet.
>
> Thanks,
>
> Paul
>
> On Jan 31 2020, at 12:07 pm, Bennet Fauber <[log in to unmask]> wrote:
>
> 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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