Unfortunately, the HCP Pipelines do not currently support rerunning FreeSurfer after editing. It is on our list of “things to do” to add that functionality.
cheers, -MH -- Michael Harms, Ph.D. ----------------------------------------------------------- Conte Center for the Neuroscience of Mental Disorders Washington University School of Medicine Department of Psychiatry, Box 8134 660 South Euclid Ave. Tel: 314-747-6173 St. Louis, MO 63110 Email: mha...@wustl.edu From: <hcp-users-boun...@humanconnectome.org<mailto:hcp-users-boun...@humanconnectome.org>> on behalf of Lisa Kramarenko <lisa.kramare...@gmail.com<mailto:lisa.kramare...@gmail.com>> Date: Wednesday, June 7, 2017 at 11:00 AM To: "Glasser, Matthew" <glass...@wustl.edu<mailto:glass...@wustl.edu>>, "hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>" <hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>> Subject: Re: [HCP-Users] values in myelin maps Dear Matthew, I have now manually edited brainmask.gmz ans wm.gmz to remove dura that was still mistaken for a surface. Now I am not sure from which step to re-run these participants. 1. Do I understand it correctly that after replacing brainmask.gmz and wm.gmz in the <subjid>/mri I need to start the FreeSurfer Pipeline after the step "# Generate brain mask" (meaning starting with the step "# Call recon-all to run most of the "-autorecon2" stages, but turning off smooth2, inflate2, curvstats, and segstats stages")? 2. Do I need to use any additional flags in the autorecon after my intervention? 3. I also created some control points to fix missing white matter. Should I put the control.dat file in the <subjid>/tmp folder? Will FreeSurfer see the file automatically or should I add some flag for it? thanks a lot for your help! Lisa On 30 May 2017 at 16:38, Lisa Kramarenko <lisa.kramare...@gmail.com<mailto:lisa.kramare...@gmail.com>> wrote: thanks best, Lisa On 30 May 2017 at 16:37, Glasser, Matthew <glass...@wustl.edu<mailto:glass...@wustl.edu>> wrote: Yes. Peace, Matt. From: Lisa Kramarenko <lisa.kramare...@gmail.com<mailto:lisa.kramare...@gmail.com>> Date: Tuesday, May 30, 2017 at 9:31 AM To: Matt Glasser <glass...@wustl.edu<mailto:glass...@wustl.edu>> Cc: "hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>" <hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>> Subject: Re: [HCP-Users] values in myelin maps do I find the files I should inspect in the {subject_id}/T1w/{subject_id}/mri/ folder? On 30 May 2017 at 16:28, Lisa Kramarenko <lisa.kramare...@gmail.com<mailto:lisa.kramare...@gmail.com>> wrote: ok. so basically just go through recon-all output and manually correct whatever might have gone wrong? best, Lisa On 30 May 2017 at 16:13, Glasser, Matthew <glass...@wustl.edu<mailto:glass...@wustl.edu>> wrote: I would look for locations in which the FreeSurfer aseg is clearly labeling things outside of the brain as grey or white matter. Peace, Matt. From: Lisa Kramarenko <lisa.kramare...@gmail.com<mailto:lisa.kramare...@gmail.com>> Date: Tuesday, May 30, 2017 at 8:59 AM To: Matt Glasser <glass...@wustl.edu<mailto:glass...@wustl.edu>> Cc: "hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>" <hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>> Subject: Re: [HCP-Users] values in myelin maps Alright, thanks for the quick reply! Should I look for some specific problem with the surfaces which is to be fixed? I mean I imagine a lot of things can go wrong with a surface, so that I need to know what exactly to fix? Or is it something more general like this: http://sites.bu.edu/cnrlab/lab-resources/freesurfer-quality-control-guide/freesurfer-quality-control-step-1-fix-pial-surface/ ? And does it look like it affect both pial and white matter surfaces, so that both need to be fixed? Sorry for the naive questions and thanks again. On 30 May 2017 at 15:51, Glasser, Matthew <glass...@wustl.edu<mailto:glass...@wustl.edu>> wrote: Fat saturation reduces the intensity of the fat within the bone marrow, which reduces the chance that FreeSurfer will mistake this fat for white matter. You would need to have this on during acquisition. As for how to fix the surfaces after the fact, I would look at FreeSurfer’s documentation. Peace, Matt. From: Lisa Kramarenko <lisa.kramare...@gmail.com<mailto:lisa.kramare...@gmail.com>> Date: Tuesday, May 30, 2017 at 8:49 AM To: Matt Glasser <glass...@wustl.edu<mailto:glass...@wustl.edu>> Cc: "hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>" <hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>> Subject: Re: [HCP-Users] values in myelin maps Yes, this is data of the lab I am in. I assume that I don't have fat saturation as I have never heard about it before... If I understand correctly it can't be done post-hoc after acquisition and should have been done during scanning? Other patients from the same batch (acquired the same way) don't have this problem. What would be the way to fix the surfaces manually? Thanks a lot! On 30 May 2017 at 15:42, Glasser, Matthew <glass...@wustl.edu<mailto:glass...@wustl.edu>> wrote: Are these of your own data? Do you have fat sat on in your T1w? This looks like most likely surface errors because of not using fat sat and you would need to exclude these subjects or fix the surfaces manually. Peace, Matt. From: Lisa Kramarenko <lisa.kramare...@gmail.com<mailto:lisa.kramare...@gmail.com>> Date: Tuesday, May 30, 2017 at 7:53 AM To: Matt Glasser <glass...@wustl.edu<mailto:glass...@wustl.edu>> Cc: "hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>" <hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>> Subject: Re: [HCP-Users] values in myelin maps Thanks! Another question I have concerning myelin maps is the following: when I was doing quality control I noticed that some of them look rather weird (see screenshot). Why are some areas grey? And I presume the fact that the values in this grey area are negative, indicates that something is wrong... And are the black parts normal (they still have positive values)? Do you have an idea of what to do? Thanks a lot! Lisa On 29 May 2017 at 15:55, Glasser, Matthew <glass...@wustl.edu<mailto:glass...@wustl.edu>> wrote: They are the ratio of the T1w/T2w images and are a relative measure of myelin content. See this publication for more details: http://www.jneurosci.org/content/31/32/11597.short Peace, Matt. From: <hcp-users-boun...@humanconnectome.org<mailto:hcp-users-boun...@humanconnectome.org>> on behalf of Lisa Kramarenko <lisa.kramare...@gmail.com<mailto:lisa.kramare...@gmail.com>> Date: Monday, May 29, 2017 at 5:29 AM To: "hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>" <hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>> Subject: [HCP-Users] values in myelin maps Hello, I am not sure what exactly are the values shown for the myelin maps. E.g. on the screenshot the values are 0.998 to 1.771. I understand that higher values mean higher myelination and vice versa, but what do they mean exactly? Thanks! 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