Re: [Freesurfer] White matter and cp edits don't produce new results after reconall

Hi Annelinde the problem is that your original image only includes about half the cerebellum. We expect a full cerebellum and so the segmentation labels some of the cortex that is superior to cerebellum incorrectly as cerebellu, then removes it from the wm.mgz (since it isn't cerebral

Re: [Freesurfer] White matter and cp edits don't produce new results after reconall

glad to hear it's not all your subjects! Good luck Bruce On Wed, 2 Dec 2015, Annelinde Vandenbroucke wrote: Dear Bruce, Thank you very much for letting me know. Indeed, something went wrong with the slice prescription of that acquisition. I didn't know that would affect segmentation. Our

Re: [Freesurfer] White matter and cp edits don't produce new results after reconall

Dear Bruce, Thank you very much for letting me know. Indeed, something went wrong with the slice prescription of that acquisition. I didn't know that would affect segmentation. Our normal acquisition includes the whole brain. Thanks again for to you and your support team! Cheers, Annelinde

Re: [Freesurfer] White matter and cp edits don't produce new results after reconall

Dear Bruce, I was wondering whether you received my transfer well. If you sent me an email back already, my apologies. I accidentally switched of email service from the support list for a day. Thank you in advance, Annelinde 2015-11-24 10:29 GMT-08:00 Annelinde Vandenbroucke <

Re: [Freesurfer] White matter and cp edits don't produce new results after reconall

Dear Bruce, Thank you. I transferred via ftp, the entire Freesurfer subject folder (Sub5.zip). The most pronounced "miss" segmentation is around coordinate 169 158 91, but it extends from about 168 155 85 up until 168 164 106. Thank you very much for taking a look at it. Best, Annelinde

[Freesurfer] White matter and cp edits don't produce new results after reconall

Dear all, I have a faulty wm map (brainmask.mgz) where some regions are not labeled as white matter where they should. I tried to correct both the wm.mgz map and add control points (and saved these), afterwards running either -autorecon2-wm or autorecon2-cp, but neither of these work. I can see

Re: [Freesurfer] White matter and cp edits don't produce new results after reconall

Hi Bruce, Thank you very much for your quick response. Yes I mean that wm.mgz underestimates true white matter. Values are between 95 and 108 where it should be 110 or above. I will upload my subj dir tomorrow. Is there specific place I can upload to or shall attach it in I reply to you? Thank

Re: [Freesurfer] White matter and cp edits don't produce new results after reconall

Hi Annelinde when you say a fault wm map, do you mean that the wm.mgz underestimates the true white matter (that is, there are many voxels that are 0 in the wm.mgz that are in the white matter)? What is the intensity of the brain.mgz at those voxels? If you tar, gzip and upload a subject dir

Re: [Freesurfer] White matter and cp edits don't produce new results after reconall

P.s. You should use our filedrop which you can find on our website > On Nov 23, 2015, at 9:43 PM, Annelinde Vandenbroucke > wrote: > > Hi Bruce, > > Thank you very much for your quick response. > Yes I mean that wm.mgz underestimates true white matter. Values are

Re: [Freesurfer] White matter and cp edits don't produce new results after reconall

But is the wm.mgz 'off' (less than 5) there? If the wm.mgz is 95 or something it means we accurately segmented that voxel. If you upload we will take a look, but please include specific voxel coords Cheers Bruce > On Nov 23, 2015, at 9:43 PM, Annelinde Vandenbroucke >