so that means if something went wrong with the skull strip and surfaces during the FreeSurfer Pipeline there is no other alternative than to exclude these subjects?
On 7 June 2017 at 18:04, Harms, Michael <[email protected]> wrote: > > 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 <(314)%20747-6173> > St. Louis, MO 63110 Email: [email protected] > > From: <[email protected]> on behalf of Lisa > Kramarenko <[email protected]> > Date: Wednesday, June 7, 2017 at 11:00 AM > To: "Glasser, Matthew" <[email protected]>, " > [email protected]" <[email protected]> > > 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 <[email protected]> > wrote: > >> thanks >> >> best, >> Lisa >> >> On 30 May 2017 at 16:37, Glasser, Matthew <[email protected]> wrote: >> >>> Yes. >>> >>> Peace, >>> >>> Matt. >>> >>> From: Lisa Kramarenko <[email protected]> >>> Date: Tuesday, May 30, 2017 at 9:31 AM >>> >>> To: Matt Glasser <[email protected]> >>> Cc: "[email protected]" <[email protected]> >>> 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 <[email protected]> >>> 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 <[email protected]> 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 <[email protected]> >>>>> Date: Tuesday, May 30, 2017 at 8:59 AM >>>>> >>>>> To: Matt Glasser <[email protected]> >>>>> Cc: "[email protected]" <[email protected]> >>>>> 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-qu >>>>> ality-control-guide/freesurfer-quality-control-step-1-fix-pi >>>>> al-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 <[email protected]> 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 <[email protected]> >>>>>> Date: Tuesday, May 30, 2017 at 8:49 AM >>>>>> >>>>>> To: Matt Glasser <[email protected]> >>>>>> Cc: "[email protected]" <[email protected]> >>>>>> 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 <[email protected]> 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 <[email protected]> >>>>>>> Date: Tuesday, May 30, 2017 at 7:53 AM >>>>>>> To: Matt Glasser <[email protected]> >>>>>>> Cc: "[email protected]" <[email protected]> >>>>>>> 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 <[email protected]> >>>>>>> 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: <[email protected]> on behalf of Lisa >>>>>>>> Kramarenko <[email protected]> >>>>>>>> Date: Monday, May 29, 2017 at 5:29 AM >>>>>>>> To: "[email protected]" <[email protected]> >>>>>>>> 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! >>>>>>>> >>>>>>>> Lisa >>>>>>>> >>>>>>>> _______________________________________________ >>>>>>>> HCP-Users mailing list >>>>>>>> [email protected] >>>>>>>> http://lists.humanconnectome.org/mailman/listinfo/hcp-users >>>>>>>> >>>>>>> >>>>>>> >>>>>> >>>>> >>>> >>> >> > _______________________________________________ > HCP-Users mailing list > [email protected] > http://lists.humanconnectome.org/mailman/listinfo/hcp-users > > > ------------------------------ > > 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. 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