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-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 <[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
