Fmriprep 1.0.6-2 issues: semi-random brain mask failure and super bright areas in epi

5

Its up in the same link!

I gave the last test described (i.e. 7 runs, without fieldmaps).

I will rerun the case with all runs --ignore fieldmaps slicetiming and upload those files as well if its helpful! Thanks for looking into it!

6

Thanks this is very useful. It seems that the BOLD brainmasks was estimated correctly (judging from the ROIs reportlets). The BOLD/T1w coregistration also looks ok, but indeed the BOLD volumes in those reportlets look weird. I wonder if this is just a vizualization issue. Could you open the BOLD brainmask nifti files and check if the look ok?

7

I should have mentioned!
The brainmask nii file look like the EPI-T1 registration issue (not like the brainmask in the compcorr outline figure… (uploaded nii to same dropbox, fetch automaticlaly unzipped the image hence the different filename, but its …ses-1_task-rest_run-03_bold_space-T1w_brainamask.nii.gz)

8

I see. Sorry for that. We can look deeper into this if you could share the raw data with us (a single problematic EPI should suffice to start with).

9

I opened two issues based on your reports: https://github.com/poldracklab/fmriprep/issues/964 and https://github.com/poldracklab/fmriprep/issues/963

Let us know if you still have issues with suppressing slicetiming correction.

10

BTW could you also try to run this with FreeSurfer?

11

thanks for getting at it!

@slicetiming: ran it with “–ignore fieldmaps slicetiming” and not applied this time. I’ll keep having an extra eye on it for future subjects.
@freesurfer: The midline pial estimation and parcellation is not satisfactory because of the agenisis of the corpus callosum, so we’re running it outside of fmriprep and have not fed it back into it (probably wouldnt’ because we’re trying to stay in subject space, given the large ventricles).
If you just want to see if it improves the skullstripping, happy to run it and see what happens.

I can send an EPI run over. Do you have a direct upload option?

12

Maybe you can upload the minimal dataset on http://OpenNeuro.org and share it with krzysztof.gorgolewski@gmail.com

13

Done.

You still think its useful to run with FS?

14

Hi @dorit, I don’t think it is necessary to run FS (https://github.com/poldracklab/fmriprep/issues/963#issuecomment-364252548)

15

@oesteban ok thanks!

16

@dorit: one minor check. Could you please see if the data type of the original functional series is int16?

e.g. (using nibabel)

$ nib-ls myfile.nii.gz 
myfile.nii.gz uint16 [ 64,  64,  48, 484] 3.00x3.00x3.00x0.00   sform

This example would confirm that this image is uint16.

17

Having never used nibabel directly I made it up to this output (following http://nipy.org/nibabel/gettingstarted.html) , which is I think what you wanted to know?

img.get_data_dtype() == np.dtype(np.int16)
True

here “img” is the nifti file from the run that prodced the funky output.

18

just checking in about this.
I saw you guys jumped right at it and already closed one issue a couple of days ago (awesome).
I’m trying to decide whether to move forward with an older version of fmriprep or wait for the new release. Any input you can give on the timeline here?

19

We are working to release ASAP. In fact, I’d like to release today.

I would totally recommend waiting for that new release as it should fix your issue (I looked through 2000 masks to make sure it does…). Any feedback on this new release will be very very much appreciated.

20

sure thing! I’m more than happy to test it!

21

It happened, 1.0.7 is out!

1 Like
22

Fantastic! Will test and report back!

23

All worked fine now (tested the originally problematic subject, another lesion brain and some normal brains).
Sorry for the slow response!

Thanks for getting at this so quickly!

3 Likes
24

Dear fMRIprep experts:

I’m currently preprocessing data with frmiprep and would like to ignore both: fieldmaps and slicetiming. To do that I’ve specified, as suggested in this thread, --ignore fieldmaps slicetiming.

I’m running fmriprep-v20.2.0 via singularity.

When I do that I get the following error:

fmriprep: error: argument --ignore: invalid choice: ' ' (choose from 'fieldmaps', 'slicetiming', 'sbref', 't2w', 'flair')
./run_fmriprep_seb_noST.sh: line 23: --use-syn-sdc: command not found

I’ve tried most other conceivable permutations of adding both, i.e. --ignore fieldmaps, slicetiming, --ignore [fieldmaps slicetiming] etc and also adding ignore twice.

Could you help me with this issue?

Thanks,

Sebastian