Re: [HCP-Users] Minimal Preprocessing Pipeline (on my own data): Flipped EPI (AP)

[Glasser, Matthew]

That’s not quite what I meant.  I was just saying more generally we cannot code things up for people to work with legacy data, they’re still welcome to post and we can point them to where they might focus their attention for hacking.  Put another way, failure to work with legacy data does not necessarily indicate an issue with the pipelines themselves (like a bug).   Peace, Matt. From: Julien Dubois <jcrdub...@gmail.com> Date: Tuesday, April 21, 2015 at 1:30 PM To: Matt Glasser <glass...@wusm.wustl.edu> Cc: "hcp-users@humanconnectome.org" <hcp-users@humanconnectome.org>, "tbbr...@wustl.edu" <tbbr...@wustl.edu> Subject: Re: [HCP-Users] Minimal Preprocessing Pipeline (on my own data): Flipped EPI (AP) I would focus your attention on the initial rigid alignment done in epi_reg (before BBR and the distortion correction).  This step we have found is sometimes not robust, particularly when acquisition protocols deviate from the recommended ones.  It isn’t BBR based and doesn’t yet have the data in rough alignment (generally pipeline failures occur at initial stages, if the initial stages work, generally everything else is more robust).   yes, this is where the problem occurs; more specifically, in the magnitude fieldmap to structural registration with flirt, line 346 of epi_reg (I realize now that "Scout_gdc_undistorted_" is the prefix for all files output by epi_reg [because Scout_gdc_undistorted.nii.gz is the final output of the epi_reg script], which is the info that I was missing to debug the alignment). I'm all set now. Thanks for your help. I understand you are working with legacy data, it’s just important to note that the amount of work required to make legacy data work with the HCP Pipelines is not indicative of the amount of work required when following the image acquisition guidelines.  We’re still willing to provide suggestions as to what to look at when getting the legacy data to work, but cannot fully support legacy data (e.g. you have to hack some on your own and figure it out).  Also, not all pipeline changes required when working with legacy data may be generally applicable to all data (so we’ll consider this when considering patches that come from trying to get legacy data to work).   Point taken, I will refrain from posting to this list about legacy data - unless I think it is a more generic issue.   - Julien   The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail. _______________________________________________ HCP-Users mailing list HCP-Users@humanconnectome.org http://lists.humanconnectome.org/mailman/listinfo/hcp-users