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 the control points and wm edits in my maps, but the wm segmentation is still the same. I have not found a solution on the mailing list yet and was wondering whether anybody had a similar problem or could help.
Thank you in advance, Annelinde
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 and send us specific voxel coords where you think this is happening (of a control point that should be wm and doesn't recover it after reprocessing with autorecon2-cp), one of us will take a look.
cheers Bruce
On Mon, 23 Nov 2015, Annelinde Vandenbroucke wrote:
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 the control points and wm edits in my maps, but the wm segmentation is still the same. I have not found a solution on the mailing list yet and was wondering whether anybody had a similar problem or could help.
Thank you in advance, Annelinde
-- Annelinde R. E. Vandenbroucke, PhD University of California, Berkeley || Helen Wills Neuroscience Institute 10 Giannini Hall Berkeley, CA 94720
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 you, Annelinde
2015-11-23 17:54 GMT-08:00 Bruce Fischl fischl@nmr.mgh.harvard.edu:
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 and send us specific voxel coords where you think this is happening (of a control point that should be wm and doesn't recover it after reprocessing with autorecon2-cp), one of us will take a look.
cheers Bruce
On Mon, 23 Nov 2015, Annelinde Vandenbroucke wrote:
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 the control points and wm edits in my maps, but the wm segmentation is still
the
same. I have not found a solution on the mailing list yet and was
wondering
whether anybody had a similar problem or could help.
Thank you in advance, Annelinde
-- Annelinde R. E. Vandenbroucke, PhD University of California, Berkeley || Helen Wills Neuroscience Institute 10 Giannini Hall Berkeley, CA 94720
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.
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 vandenbroucke.work@gmail.com wrote:
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 you, Annelinde
2015-11-23 17:54 GMT-08:00 Bruce Fischl fischl@nmr.mgh.harvard.edu:
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 and send us specific voxel coords where you think this is happening (of a control point that should be wm and doesn't recover it after reprocessing with autorecon2-cp), one of us will take a look.
cheers Bruce
On Mon, 23 Nov 2015, Annelinde Vandenbroucke wrote:
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 the control points and wm edits in my maps, but the wm segmentation is still the same. I have not found a solution on the mailing list yet and was wondering whether anybody had a similar problem or could help.
Thank you in advance, Annelinde
-- Annelinde R. E. Vandenbroucke, PhD University of California, Berkeley || Helen Wills Neuroscience Institute 10 Giannini Hall Berkeley, CA 94720
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.
-- Annelinde R. E. Vandenbroucke, PhD University of California, Berkeley || Helen Wills Neuroscience Institute 10 Giannini Hall Berkeley, CA 94720 _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
P.s. You should use our filedrop which you can find on our website
On Nov 23, 2015, at 9:43 PM, Annelinde Vandenbroucke vandenbroucke.work@gmail.com wrote:
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 you, Annelinde
2015-11-23 17:54 GMT-08:00 Bruce Fischl fischl@nmr.mgh.harvard.edu:
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 and send us specific voxel coords where you think this is happening (of a control point that should be wm and doesn't recover it after reprocessing with autorecon2-cp), one of us will take a look.
cheers Bruce
On Mon, 23 Nov 2015, Annelinde Vandenbroucke wrote:
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 the control points and wm edits in my maps, but the wm segmentation is still the same. I have not found a solution on the mailing list yet and was wondering whether anybody had a similar problem or could help.
Thank you in advance, Annelinde
-- Annelinde R. E. Vandenbroucke, PhD University of California, Berkeley || Helen Wills Neuroscience Institute 10 Giannini Hall Berkeley, CA 94720
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.
-- Annelinde R. E. Vandenbroucke, PhD University of California, Berkeley || Helen Wills Neuroscience Institute 10 Giannini Hall Berkeley, CA 94720 _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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
2015-11-23 18:59 GMT-08:00 Bruce Fischl fischl@nmr.mgh.harvard.edu:
P.s. You should use our filedrop which you can find on our website
On Nov 23, 2015, at 9:43 PM, Annelinde Vandenbroucke < vandenbroucke.work@gmail.com> wrote:
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 you, Annelinde
2015-11-23 17:54 GMT-08:00 Bruce Fischl fischl@nmr.mgh.harvard.edu:
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 and send us specific voxel coords where you think this is happening (of a control point that should be wm and doesn't recover it after reprocessing with autorecon2-cp), one of us will take a look.
cheers Bruce
On Mon, 23 Nov 2015, Annelinde Vandenbroucke wrote:
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
the
control points and wm edits in my maps, but the wm segmentation is
still the
same. I have not found a solution on the mailing list yet and was
wondering
whether anybody had a similar problem or could help.
Thank you in advance, Annelinde
-- Annelinde R. E. Vandenbroucke, PhD University of California, Berkeley || Helen Wills Neuroscience Institute 10 Giannini Hall Berkeley, CA 94720
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.
-- Annelinde R. E. Vandenbroucke, PhD University of California, Berkeley || Helen Wills Neuroscience Institute 10 Giannini Hall Berkeley, CA 94720
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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.
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 < vandenbroucke.work@gmail.com>:
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
2015-11-23 18:59 GMT-08:00 Bruce Fischl fischl@nmr.mgh.harvard.edu:
P.s. You should use our filedrop which you can find on our website
On Nov 23, 2015, at 9:43 PM, Annelinde Vandenbroucke < vandenbroucke.work@gmail.com> wrote:
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 you, Annelinde
2015-11-23 17:54 GMT-08:00 Bruce Fischl fischl@nmr.mgh.harvard.edu:
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 and send us specific voxel coords where you think this is happening (of a control point that should be wm and doesn't recover it after reprocessing with autorecon2-cp), one of us will take a look.
cheers Bruce
On Mon, 23 Nov 2015, Annelinde Vandenbroucke wrote:
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
the
control points and wm edits in my maps, but the wm segmentation is
still the
same. I have not found a solution on the mailing list yet and was
wondering
whether anybody had a similar problem or could help.
Thank you in advance, Annelinde
-- Annelinde R. E. Vandenbroucke, PhD University of California, Berkeley || Helen Wills Neuroscience
Institute
10 Giannini Hall Berkeley, CA 94720
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.
-- Annelinde R. E. Vandenbroucke, PhD University of California, Berkeley || Helen Wills Neuroscience Institute 10 Giannini Hall Berkeley, CA 94720
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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.
-- Annelinde R. E. Vandenbroucke, PhD University of California, Berkeley || Helen Wills Neuroscience Institute 10 Giannini Hall Berkeley, CA 94720
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 cortex). You need to change your acquisitions to include the full cerebellum
cheers Bruce
On Mon, 30 Nov 2015, Annelinde Vandenbroucke wrote:
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 vandenbroucke.work@gmail.com: 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
2015-11-23 18:59 GMT-08:00 Bruce Fischl fischl@nmr.mgh.harvard.edu: P.s. You should use our filedrop which you can find on our website
On Nov 23, 2015, at 9:43 PM, Annelinde Vandenbroucke vandenbroucke.work@gmail.com wrote:
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 you, Annelinde
2015-11-23 17:54 GMT-08:00 Bruce Fischl fischl@nmr.mgh.harvard.edu: 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 and send us specific voxel coords where you think this is happening (of a control point that should be wm and doesn't recover it after reprocessing with autorecon2-cp), one of us will take a look. cheers Bruce On Mon, 23 Nov 2015, Annelinde Vandenbroucke wrote: > 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 the > control points and wm edits in my maps, but the wm segmentation is still the > same. I have not found a solution on the mailing list yet and was wondering > whether anybody had a similar problem or could help. > > Thank you in advance, > Annelinde > > -- > Annelinde R. E. Vandenbroucke, PhD > University of California, Berkeley || Helen Wills Neuroscience Institute > 10 Giannini Hall > Berkeley, CA 94720 > >
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.
-- Annelinde R. E. Vandenbroucke, PhD University of California, Berkeley || Helen Wills Neuroscience Institute 10 Giannini Hall Berkeley, CA 94720
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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.
-- Annelinde R. E. Vandenbroucke, PhD University of California, Berkeley || Helen Wills Neuroscience Institute 10 Giannini Hall Berkeley, CA 94720
-- Annelinde R. E. Vandenbroucke, PhD University of California, Berkeley || Helen Wills Neuroscience Institute 10 Giannini Hall Berkeley, CA 94720
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
2015-12-02 7:12 GMT-08:00 Bruce Fischl fischl@nmr.mgh.harvard.edu:
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 cortex). You need to change your acquisitions to include the full cerebellum
cheers Bruce
On Mon, 30 Nov 2015, Annelinde Vandenbroucke wrote:
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 < vandenbroucke.work@gmail.com>: 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
2015-11-23 18:59 GMT-08:00 Bruce Fischl fischl@nmr.mgh.harvard.edu: P.s. You should use our filedrop which you can find on our website
On Nov 23, 2015, at 9:43 PM, Annelinde Vandenbroucke < vandenbroucke.work@gmail.com> wrote:
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 you, Annelinde
2015-11-23 17:54 GMT-08:00 Bruce Fischl fischl@nmr.mgh.harvard.edu: Hi Annelinde
when you say a fault wm map, do you mean that the wm.mgzunderestimates 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 and send us specificvoxel coords where you think this is happening (of a control point that should be wm and doesn't recover it after reprocessing with autorecon2-cp), one of us will take a look.
cheers Bruce On Mon, 23 Nov 2015, Annelinde Vandenbroucke wrote: > Dear all, > > I have a faulty wm map (brainmask.mgz) where some regions are notlabeled 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 the > control points and wm edits in my maps, but the wm segmentation is still the > same. I have not found a solution on the mailing list yet and was wondering > whether anybody had a similar problem or could help. > > Thank you in advance, > Annelinde > > -- > Annelinde R. E. Vandenbroucke, PhD > University of California, Berkeley || Helen Wills Neuroscience Institute > 10 Giannini Hall > Berkeley, CA 94720 > > _______________________________________________ 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.
-- Annelinde R. E. Vandenbroucke, PhD University of California, Berkeley || Helen Wills Neuroscience Institute 10 Giannini Hall Berkeley, CA 94720
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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.
-- Annelinde R. E. Vandenbroucke, PhD University of California, Berkeley || Helen Wills Neuroscience Institute 10 Giannini Hall Berkeley, CA 94720
-- Annelinde R. E. Vandenbroucke, PhD University of California, Berkeley || Helen Wills Neuroscience Institute 10 Giannini Hall Berkeley, CA 94720
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.
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 normal acquisition includes the whole brain.
Thanks again for to you and your support team! Cheers, Annelinde
2015-12-02 7:12 GMT-08:00 Bruce Fischl fischl@nmr.mgh.harvard.edu: 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 cortex). You need to change your acquisitions to include the full cerebellum cheers Bruce On Mon, 30 Nov 2015, Annelinde Vandenbroucke wrote: 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 <vandenbroucke.work@gmail.com>: 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 2015-11-23 18:59 GMT-08:00 Bruce Fischl <fischl@nmr.mgh.harvard.edu>: P.s. You should use our filedrop which you can find on our website On Nov 23, 2015, at 9:43 PM, Annelinde Vandenbroucke <vandenbroucke.work@gmail.com> wrote: 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 you, Annelinde 2015-11-23 17:54 GMT-08:00 Bruce Fischl <fischl@nmr.mgh.harvard.edu>: 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 and send us specific voxel coords where you think this is happening (of a control point that should be wm and doesn't recover it after reprocessing with autorecon2-cp), one of us will take a look. cheers Bruce On Mon, 23 Nov 2015, Annelinde Vandenbroucke wrote: > 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 the > control points and wm edits in my maps, but the wm segmentation is still the > same. I have not found a solution on the mailing list yet and was wondering > whether anybody had a similar problem or could help. > > Thank you in advance, > Annelinde > > -- > Annelinde R. E. Vandenbroucke, PhD > University of California, Berkeley || Helen Wills Neuroscience Institute > 10 Giannini Hall > Berkeley, CA 94720 > > _______________________________________________ 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. -- Annelinde R. E. Vandenbroucke, PhD University of California, Berkeley || Helen Wills Neuroscience Institute 10 Giannini Hall Berkeley, CA 94720 _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer _______________________________________________ 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. -- Annelinde R. E. Vandenbroucke, PhD University of California, Berkeley || Helen Wills Neuroscience Institute 10 Giannini Hall Berkeley, CA 94720 -- Annelinde R. E. Vandenbroucke, PhD University of California, Berkeley || Helen Wills Neuroscience Institute 10 Giannini Hall Berkeley, CA 94720
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.
-- Annelinde R. E. Vandenbroucke, PhD University of California, Berkeley || Helen Wills Neuroscience Institute 10 Giannini Hall Berkeley, CA 94720
freesurfer@nmr.mgh.harvard.edu
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Annelinde Vandenbroucke -
Bruce Fischl