Hi All,
We have run recon-all on T1 FLASH images have identified regions where the sulci were included inside the white matter boundary. We added controls points around the sulci (please see attached pic) and reran recon-all as follows
recon-all -autorecon2-cp -autorecon3 -subjid <subject>
but on a lot of instances, the specified control points were not incorporated (please see attached image). How do we fix this, now that we have already run the recon-all with -autorecon2-cp and the error persists ?
Can someone please suggest ?
Thank you,
Rito and Jack
Hi Rito,
I just read this today myself "Select a few control points around your trouble areas, space them out throughout the brain and on different slices. You want to pick points in a region where the wm intensity is lower than it should be (that is, having a voxel value less than 110)." from https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/ControlPoints_freeview
Could it be that those control points grasp voxels that already have an intensity of at least 110?
Best wishes,
Barbara
On 06/07/2016 17:25, Ritobrato Datta wrote:
Hi All,
We have run recon-all on T1 FLASH images have identified regions where the sulci were included inside the white matter boundary. We added controls points around the sulci (please see attached pic) and reran recon-all as follows
recon-all -autorecon2-cp -autorecon3 -subjid <subject>
but on a lot of instances, the specified control points were not incorporated (please see attached image). How do we fix this, now that we have already run the recon-all with -autorecon2-cp and the error persists ?
Can someone please suggest ?
Thank you,
Rito and Jack
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Hi Rito
the control points you have look like they are in voxels that contain some gray matter, which will probably make things worse. YOu need to identify why you are missing that part of the surface. Is the dark stuff there labeled as white? Maybe it's a topological defect that gets filled incorrectly?
cheers Bruce
On Wed, 6 Jul 2016, Ritobrato Datta wrote:
Hi All,
We have run recon-all on T1 FLASH images have identified regions where the sulci were included inside the white matter boundary. We added controls points around the sulci (please see attached pic) and reran recon-all as follows
recon-all -autorecon2-cp -autorecon3 -subjid <subject>
but on a lot of instances, the specified control points were not incorporated (please see attached image). How do we fix this, now that we have already run the recon-all with -autorecon2-cp and the error persists ?
Can someone please suggest ?
Thank you,
Rito and Jack
Dear All,
I few days back I posted a question regarding a sulcus being included inside the white matter region. Please see attached pic. When I look at the wm.mgz, the sulcus has been excluded correctly (red crosshair) out of white matter but when I look at the output of mris_fix_topology, I find that the region has been included inside white matter. Adding the control points (as in the pic) didn't change anything. So are there some flags in the mris_fix_topology that I can play with that can recognize that sulcus as non white matter ? Another suggestion was to edit the wm.mgz itself but here the wm.mgz is correctly excluding the sulci (around the red cross hairs). Can someone share their experience and suggest how to fix this ?
Much appreciated,
Best
Rito
----- Original Message ----- From: Bruce Fischl fischl@nmr.mgh.harvard.edu To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Cc: SOLLEEJ@EMAIL.CHOP.EDU Sent: Wed, 06 Jul 2016 15:45:25 -0400 (EDT) Subject: Re: [Freesurfer] question about white matter edits
Hi Rito
the control points you have look like they are in voxels that contain some gray matter, which will probably make things worse. YOu need to identify why you are missing that part of the surface. Is the dark stuff there labeled as white? Maybe it's a topological defect that gets filled incorrectly?
cheers Bruce
On Wed, 6 Jul 2016, Ritobrato Datta wrote:
Hi All,
We have run recon-all on T1 FLASH images have identified regions where the sulci were included inside the white matter boundary. We added controls points around the sulci (please see attached pic) and reran recon-all as follows
recon-all -autorecon2-cp -autorecon3 -subjid <subject>
but on a lot of instances, the specified control points were not incorporated (please see attached image). How do we fix this, now that we have already run the recon-all with -autorecon2-cp and the error persists ?
Can someone please suggest ?
Thank you,
Rito and Jack
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
freesurfer@nmr.mgh.harvard.edu
-
Barbara Kreilkamp -
Bruce Fischl -
Harms, Michael -
Ritobrato Datta