ok, so should I just re-run the recon-all with the wm option? i.e. recon-all -all --wmparc-dmax 100
On Wed, Nov 19, 2014 at 12:07 PM, Bruce Fischl fischl@nmr.mgh.harvard.edu 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 ROIparsorbitalis [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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