Search for MSMSulc here:

https://github.com/Washington-University/Pipelines/blob/master/PostFreeSurfer/scripts/FreeSurfer2CaretConvertAndRegisterNonlinear.sh

*refsulc* get copied to subject dir from here:

https://github.com/Washington-University/Pipelines/tree/7cc0bf1863cbc8a1a7ab9c6dd48a25de9be9bae7/global/templates/standard_mesh_atlases


> On Oct 12, 2016, at 10:53 AM, Jared P Zimmerman <jar...@mail.med.upenn.edu> 
> wrote:
>
> Thanks Michael, Donna, and Matt,
>
> RE: Michael, definitely aware this is an inferior approach to true 
> subject-specific parcellation but given that we don’t have the requisite data 
> to run the classifier this seems like an appropriate approach to use the 
> parcellation.
>
> RE: Donna and Matt, thanks for the advice, I think using an MSM sulc approach 
> is something we will definitely want to look into, but looking over the git 
> repo quickly I don’t see an MSM sulc script.  There’s the MSM all pipeline, 
> but that seems like it can only use myelin maps, RSNs or topography and 
> doesn’t have an option for sulcal depth.  Where might I find an MSM algorithm 
> that can use sulcal depth maps to register?
>
> Thanks,
> Jared
>
>
>> On Oct 12, 2016, at 9:48 AM, Dierker, Donna <do...@wustl.edu> wrote:
>>
>> If you can’t do MSMAll, then consider using just sulc, rather than sulc+curv.
>>
>> See figure 4, row B, in Emma Robinson’s paper:
>>
>> https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4190319/figure/F4/
>>
>> I have heard David describe curvature as capturing more local folding, sulc 
>> global folding.
>> In my experience, curvature varies too much across subjects, while sulc 
>> seems a more reasonable driver for intersubject registration.
>>
>> For intrasubject registration across timepoints, however, curvature is your 
>> friend.
>>
>>
>>> On Oct 11, 2016, at 6:54 PM, Glasser, Matthew <glass...@wustl.edu> wrote:
>>>
>>> Using folding-based alignment won’t be as good as areal-feature-based 
>>> alignment, but I wouldn’t worry about the alignment being any worse than 
>>> any other comparison of two studies driven by folding-based alignment.
>>>
>>> Peace,
>>>
>>> Matt.
>>>
>>> From: <hcp-users-boun...@humanconnectome.org> on behalf of Jared P 
>>> Zimmerman <jar...@mail.med.upenn.edu>
>>> Date: Tuesday, October 11, 2016 at 3:12 PM
>>> To: Timothy Coalson <tsc...@mst.edu>
>>> Cc: "hcp-users@humanconnectome.org" <hcp-users@humanconnectome.org>
>>> Subject: Re: [HCP-Users] Glasser nature atlas
>>>
>>> I have a related question to this.  I’d like to use the parcellation on 
>>> some more traditional volume data (i.e. 3x3x3mm voxels, 3s TR).  I have 
>>> made fs_LR surfaces from free surfer using the wb_command shortcuts for it, 
>>> as in here: 
>>> https://wiki.humanconnectome.org/download/attachments/63078513/Resampling-FreeSurfer-HCP.pdf?version=1&modificationDate=1472225460934&api=v2
>>>  but I am missing the registration from subject surface to group average.
>>>
>>> Is this registration, or the validity of the parcellation, dependent on 
>>> MSMAll or would an MSMSulc registration be effective (enough) here?  The 
>>> paper and parcellation are clearly based on MSMAll and this was essential 
>>> in generating parcellation, but since I don’t have the requisite rest data 
>>> to do an MSMAll register, would an MSMSulc registration be sufficient for 
>>> ultimately translating back to the subject volume?
>>>
>>> I read the above discussion about a month ago and didn’t see this covered, 
>>> but I don’t know if that was addressed in the discussion since.
>>>
>>>
>>> Tanks,
>>> Jared
>>>
>>>
>>>
>>>> On Oct 4, 2016, at 5:45 PM, Timothy Coalson <tsc...@mst.edu> wrote:
>>>>
>>>> Making a "nifti version" isn't a simple conversion, as some lengthy 
>>>> conversations on this list have elaborated on.
>>>>
>>>> The good news: if you want a single-subject-specific version, that is 
>>>> possible, using -cifti-separate and -label-to-volume-mapping, using the 
>>>> subject's own surfaces.
>>>>
>>>> The bad news: if you want it to be a group atlas, the currently popular 
>>>> volume registration methods aren't good enough at cortical area alignment 
>>>> to make our parcellation meaningful in a group-average volume space, and 
>>>> thus we do not recommend making a volumetric version in such a space.  In 
>>>> the meantime, surface registration avoids several difficulties inherent to 
>>>> volume registration, and was instrumental in being able to create the 
>>>> parcellation at all (via alignment of areal features).
>>>>
>>>> For more detailed discussion:
>>>>
>>>> https://www.mail-archive.com/hcp-users@humanconnectome.org/msg03078.html
>>>>
>>>> Tim
>>>>
>>>>
>>>> On Tue, Oct 4, 2016 at 9:47 AM, Elam, Jennifer <e...@wustl.edu> wrote:
>>>>> Hi Peter,
>>>>> The data for the new parcellation are available in the BALSA database, 
>>>>> see this thread: 
>>>>> http://www.mail-archive.com/hcp-users@humanconnectome.org/msg02876.html
>>>>>
>>>>> We recommend using the included Connectome Workbench scene file to 
>>>>> conveniently view the data in the wb_view part of the software platform. 
>>>>> Get Connectome Workbench here: 
>>>>> https://www.humanconnectome.org/software/get-connectome-workbench.html
>>>>>
>>>>> Many of the files are in the CIFTI data format, which has a lot of 
>>>>> advantages, but if you need NIFTI versions, you can use wb_command 
>>>>> (distributed as part of Connectome Workbench) to do the conversion.
>>>>>
>>>>> There's lots of help for using wb_command in the HCP-Users mail archive, 
>>>>> and/or you could post more questions to the list.
>>>>>
>>>>> Best,
>>>>> Jenn
>>>>>
>>>>>
>>>>> Jennifer Elam, Ph.D.
>>>>> Scientific Outreach, Human Connectome Project
>>>>> Washington University School of Medicine
>>>>> Department of Neuroscience, Box 8108
>>>>> 660 South Euclid Avenue
>>>>> St. Louis, MO 63110
>>>>> 314-362-9387
>>>>> e...@wustl.edu
>>>>> www.humanconnectome.org
>>>>>
>>>>>
>>>>> From:hcp-users-boun...@humanconnectome.org 
>>>>> <hcp-users-boun...@humanconnectome.org> on behalf of Peter McColgan 
>>>>> <pmccolga...@qub.ac.uk>
>>>>> Sent: Tuesday, October 4, 2016 9:29:30 AM
>>>>> To: hcp-users@humanconnectome.org
>>>>> Subject: [HCP-Users] Glasser nature atlas
>>>>>
>>>>>
>>>>> Dear HCP team,
>>>>>
>>>>> Is it possible to download a nifti version of the Glasser atlas featured 
>>>>> recently in nature?
>>>>>
>>>>> Thanks
>>>>>
>>>>> bw
>>>>>
>>>>> Peter
>>>>> _______________________________________________
>>>>> HCP-Users mailing list
>>>>> HCP-Users@humanconnectome.org
>>>>> http://lists.humanconnectome.org/mailman/listinfo/hcp-users
>>>>> _______________________________________________
>>>>> HCP-Users mailing list
>>>>> HCP-Users@humanconnectome.org
>>>>> http://lists.humanconnectome.org/mailman/listinfo/hcp-users
>>>>
>>>> _______________________________________________
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