Re: [HCP-Users] ERROR: surface exceeds the bounding box of the warpfield

Indeed the acpc registration is failing. He might check to be sure he is using the right templates (1mm, correct ones for original, down sampled, and brain mask). He could also try fiddling with the brain size parameter (trying values 10mm larger and smaller than 150mm). The acpc stage is

Re: [HCP-Users] ERROR: surface exceeds the bounding box of the warpfield

Thanks for the suggestions, Matt, which are excellent even though accidentally addressed to the wrong gender - said your mentor, (s)heepishly. David :<) > On Jan 12, 2016, at 10:23 PM, Glasser, Matthew wrote: > > Indeed the acpc registration is failing. He might check to

Re: [HCP-Users] Missing T1w_acpc_dc_restore files

Hello Matt, thanks for getting back to me. I have not downloaded all the structural files yet. I downloaded all the available files for a few subjects to test our software, but after testing I discovered that not all subjects have the same files available. Then I perused the files on the amazon

Re: [HCP-Users] Missing T1w_acpc_dc_restore files

Hi Greg, I believe the issue here is that some of the “MEG2” subjects that you’ve been looking at didn’t have their MRI structural packages released until the “S900” release, AND the Amazon S3 server is not yet synced with the S900 release.  We are currently working through some issues to

Re: [HCP-Users] Missing T1w_acpc_dc_restore files

Hooray, I think that resolves all the confusion then. Thank you for the clarification. On Tue, Jan 12, 2016 at 1:46 PM, Harms, Michael wrote: > > Hi Greg, > I believe the issue here is that some of the “MEG2” subjects that you’ve > been looking at didn’t have their MRI

Re: [HCP-Users] Missing T1w_acpc_dc_restore files

Hi Gregory, Although it is not clear to me why you would need the anatomical image when processing the MEG data - the coregistration information is provided in the MEG anatomy packages - the anatomicals you refer to (T1w_acpc_dc_restore.nii.gz) are available from the subjects’ MEG_anatomy

Re: [HCP-Users] Missing T1w_acpc_dc_restore files

Every subject that goes through the structural pipeline will have a T1w_acpc_dc_restore.nii.gz file.  Could you give some specific subject IDs for which that isn’t the case, so that our IT folks can look into what be going on with Amazon S3? cheers, -MH --  Michael Harms, Ph.D.

Re: [HCP-Users] Missing T1w_acpc_dc_restore files

Of course. The list below was generated by my python script, but I manually checked a few of the subjects as well to confirm that it was giving a true output. s3://hcp-openaccess/HCP/104012/ does not have T1w_acpc_dc_restore.nii.gz s3://hcp-openaccess/HCP/105923/ does not have

Re: [HCP-Users] Missing T1w_acpc_dc_restore files

Hi Jan-Mathijs, I've been pulling data from the Amazon S3 server (a valid option as explained here ) because aspera connect works very poorly with ubuntu (i.e. nobody seems to be able to get the aspera