[FIX] Add -cw256 flag for images with FoV > 256 voxels

[oesteban]

Close #29

[xj2019]

Thank both of you for the views!

Yes, after I cropped the images, it can work now. Because cropping is an easier way for me, I prefer using it to struggling with the code at this stage :)

In addition, since we used the short TR data, it seems a compatibility with some existing toolboxes, such as ICA-AROMA, is not so nice. Therefore, would you please tell me whether ICA-AROMA used in fmriprep is for denoising of short TR data or is based on the default version from FSL? It will help us to decide whether using ICA-AROMA in fmriprep or doing some changes.

Once again, thank you a lot.

[ins0mniac2]

I saw the last message at #52 which says the fix for this is now available in fmriprep. However, I just tried with 1.3.0.post3 I am still getting the error

ERROR! FOV=282.000 > 256
Include the flag -cw256 with recon-all!
Inspect orig.mgz to ensure the head is fully visible.

[ins0mniac2]

Just verified that 1.3.0.post3 still produces this error.

[ins0mniac2]

bump!

[effigies]

Hi @sandhitsu. Sorry for the delay; generally posting on a closed issue is going to be harder for us to notice. If this problem persists for you, please open a new issue.

I suspect that the issue is that you have sub-millimeter resolution, and FreeSurfer's -cw256 conformation is mutually exclusive with -hires. You can use --no-submm-recon to ensure that conformation takes place or manually crop to <(256mm)^3 to continue using sub-millimeter reconstruction.

For more information, see Neurostars #2171.

[ins0mniac2]

Thanks. I'll look in that thread. I don't think the data is sub-mm but will double check.