oh, so it's already been run all the way through? Sorry, I didn't
understand that.
Bruce

On Wed, 19 Nov 2014, Douglas N Greve wrote:

>
> I think Michele only wants to regenerate the wmparc.mgz, so just running
> recon-all with --wmparc and the xopts should work
>
> On 11/19/2014 12:07 PM, Bruce Fischl wrote:
>> Hi Michele
>>
>> sorry, I don't think so. You need to run to the end. The good news is
>> that when we get V6 out you will find it is substantially faster (if
>> you have a multi-core machine)
>>
>> cheers
>> Bruce
>> On Wed, 19 Nov 2014, Michele Cavallari wrote:
>>
>>> Hi Douglas, thanks for your reply. Is there a way to rerun only WM
>>> segmentation with the threshold option, without going through the whole
>>> time-consuming FS pipeline?Thank you!
>>>
>>> On Tue, Nov 18, 2014 at 10:37 PM, Douglas Greve
>>> <greve@nmr.mgh.harvard.edu>
>>> wrote:
>>>
>>>       The unsegmented is all the WM that is further than 5mm from
>>>       cortex. You can change the threshold so that it labels all of WM
>>>       regardless of the distance. Other than that, I don't have much
>>>       to suggest.
>>>       doug
>>>
>>>       On 11/18/14 6:13 PM, Michele Cavallari wrote:
>>>       Hi, I am planning to perform some regional analysis of the
>>>       frontal white matter as a whole, and asking here for
>>>       suggestions/help. From the FS output wmparc.mgz I could
>>>       select and merge the following labels to define my ROI
>>>
>>> parsorbitalis [4019, 3019]
>>> parstriangularis [4020, 3020]
>>> lateralorbitofrontal [4012, 3012]
>>> medialorbitofrontal [4014, 3014]
>>> rostralmiddlefrontal [4027, 3027]
>>> frontalpole [4032, 3032]
>>> superiofrontal [4028, 3028]
>>> caudalmiddlefrontal [4003, 3003]
>>> paracentral [4017, 3017]
>>> parsopercularis [4018, 3018]
>>> postcentral [4022, 3022]
>>> precentral [4024, 3024]
>>> rostralantcingulate [4026, 3026]
>>>
>>> However, a non-negligible portion of the subcortical frontal WM
>>> is classified as unsegmented WM [5001, 5002] by FS. Would you
>>> recommend any other FS output or template/atlas that I could use
>>> for the purpose of measuring MRI signal in the frontal WM?
>>>
>>> Thanks
>>>
>>>
>>>
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