On Wed, Nov 19, 2014 at 11:43 AM, Douglas N Greve <greve@nmr.mgh.harvard.edu> wrote:

There are two ways you can do this.

1. Make an expert options file with the contents
mri_aparc2aseg --wmparc-dmax 100
Run run recon-all like
recon-all -s subject -wmparc -expert YourXOptsFile

2. Look in recon-all.log for the mri_aparc2aseg command, cut and paste
it into the terminal, add
--wmparc-dmax 100, and run

On 11/19/2014 11:34 AM, 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 <mailto: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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--
Douglas N. Greve, Ph.D.
MGH-NMR Center
greve@nmr.mgh.harvard.edu
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