Dear freesurfer users community,
I need your help concerning manual segmentation issues.
Dear freesurfer users,
I need your help concerning manual segmentation issues.
In fact I used the editing tool with an intensity of 250 to add some missing part on the wm.mgz file but some of the added areas were not considered for the creation of the surface.
Some of the added parts were only connected through one voxel to the existing parts and I guess that it might have prevented the surface to include these areas but in some other cases the supplementary parts were clear and connected by two or more voxels but were not added.
Do you know what are the criteria used by recon-all to determine the surface ? Do you have advices about how to add voxels and be sure that they will be included in the surface?
Best regards, Antoine
On Mon, May 9, 2016 at 3:25 PM, Saturne Fox saturne.fox@gmail.com wrote:
Dear freesurfer users community,
I need your help concerning manual segmentation issues.
Hi Antoine
if you upload the entire subject dir we will take a look. It sounds like it might be a topological defect. You can check this by seeing if the orig.nofix contains the voxels that you added, but the orig does not.
cheers Bruce
On Mon, 9 May 2016, Saturne Fox wrote:
Dear freesurfer users,
I need your help concerning manual segmentation issues.
In fact I used the editing tool with an intensity of 250 to add some missing part on the wm.mgz file but some of the added areas were not considered for the creation of the surface.
Some of the added parts were only connected through one voxel to the existing parts and I guess that it might have prevented the surface to include these areas but in some other cases the supplementary parts were clear and connected by two or more voxels but were not added.
Do you know what are the criteria used by recon-all to determine the surface ? Do you have advices about how to add voxels and be sure that they will be included in the surface?
Best regards, Antoine
On Mon, May 9, 2016 at 3:25 PM, Saturne Fox saturne.fox@gmail.com wrote: Dear freesurfer users community,
I need your help concerning manual segmentation issues.
sanlm_IRC04H_00M034_P_1_WIP_T1W_3D_IRCstandard3... https://drive.google.com/file/d/0BzdSon_87KLzYl9SMGJIcGcxakE/view?usp=drive_web Dear Bruce,
Most of the time the added voxels are included in the orig file but are lost in the ?h.white one.
Here is the subject file.
Thanks a lot for your help
Antoine
On Mon, May 9, 2016 at 3:42 PM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:
Hi Antoine
if you upload the entire subject dir we will take a look. It sounds like it might be a topological defect. You can check this by seeing if the orig.nofix contains the voxels that you added, but the orig does not.
cheers Bruce
On Mon, 9 May 2016, Saturne Fox wrote:
Dear freesurfer users,
I need your help concerning manual segmentation issues. In fact I used the editing tool with an intensity of 250 to addsome missing part on the wm.mgz file but some of the added areas were not considered for the creation of the surface.
Some of the added parts were only connected through one voxel tothe existing parts and I guess that it might have prevented the surface to include these areas but in some other cases the supplementary parts were clear and connected by two or more voxels but were not added.
Do you know what are the criteria used by recon-all to determinethe surface ? Do you have advices about how to add voxels and be sure that they will be included in the surface?
Best regards, Antoine
On Mon, May 9, 2016 at 3:25 PM, Saturne Fox saturne.fox@gmail.com wrote: Dear freesurfer users community,
I need your help concerning manual segmentation issues.
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.
Hi Antoine
we need the entire subject directory tarred and gzipped if you want us to look. And please upload it to our ftp site
thanks Bruce
On Mon, 9 May 2016, Saturne Fox wrote:
[icon_10_generic_list.png] sanlm_IRC04H_00M034_P_1_WIP_T1W_3D_IRCstandard3...[x_8px.png] Dear Bruce,
Most of the time the added voxels are included in the orig file but are lost in the ?h.white one. Here is the subject file.
Thanks a lot for your help
Antoine
On Mon, May 9, 2016 at 3:42 PM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote: Hi Antoine
if you upload the entire subject dir we will take a look. It sounds like it might be a topological defect. You can check this by seeing if the orig.nofix contains the voxels that you added, but the orig does not. cheers Bruce On Mon, 9 May 2016, Saturne Fox wrote: Dear freesurfer users, I need your help concerning manual segmentation issues. In fact I used the editing tool with an intensity of 250 to add some missing part on the wm.mgz file but some of the added areas were not considered for the creation of the surface. Some of the added parts were only connected through one voxel to the existing parts and I guess that it might have prevented the surface to include these areas but in some other cases the supplementary parts were clear and connected by two or more voxels but were not added. Do you know what are the criteria used by recon-all to determine the surface ? Do you have advices about how to add voxels and be sure that they will be included in the surface? Best regards, Antoine On Mon, May 9, 2016 at 3:25 PM, Saturne Fox <saturne.fox@gmail.com> wrote: Dear freesurfer users community, I need your help concerning manual segmentation issues.
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.
Bruce,
I just uploaded the directory through the FTP server, the name of the archive is 00M034.tar.gz .
Concerning our issue we tried to identify the problem in the light of your advices and we observed that the *orig *file contains most of the manual modifications, which are then lost in *?h.white*. We spotted some topological errors but since the *orig *file is created after the topological corrections and that this file mainly suits us, we don't think that it is the main source of error.
Thus, we would like to know what is the influence of the variables used during the creation of the* ?h.white* surface and how we can increase the consideration brought to the added voxels. More precisely, when using the* aseg.presurf* file must the added voxels be part of the segmented white matter to be taken into account in the *?h.white* surface ? As well, we would like to know if 250 is an appropriate intensity to manually add voxels.
Best regards, Antoine
On Mon, May 9, 2016 at 6:06 PM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:
Hi Antoine
we need the entire subject directory tarred and gzipped if you want us to look. And please upload it to our ftp site
thanks Bruce
On Mon, 9 May 2016, Saturne Fox wrote:
[icon_10_generic_list.png]
sanlm_IRC04H_00M034_P_1_WIP_T1W_3D_IRCstandard3...[x_8px.png]
Dear Bruce,
Most of the time the added voxels are included in the orig filebut are lost in the ?h.white one.
Here is the subject file.Thanks a lot for your help
Antoine
On Mon, May 9, 2016 at 3:42 PM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote: Hi Antoine
if you upload the entire subject dir we will take a look. It soundslike it might be a topological defect. You can check this by seeing if the orig.nofix contains the voxels that you added, but the orig does not.
cheers Bruce On Mon, 9 May 2016, Saturne Fox wrote: Dear freesurfer users, I need your help concerning manual segmentationissues.
In fact I used the editing tool with an intensity of250 to add some missing part on the wm.mgz file but some of the added areas were not considered for the creation of the surface.
Some of the added parts were only connected throughone voxel to the existing parts and I guess that it might have prevented the surface to include these areas but in some other cases the supplementary parts were clear and connected by two or more voxels but were not added.
Do you know what are the criteria used byrecon-all to determine the surface ? Do you have advices about how to add voxels and be sure that they will be included in the surface?
Best regards, Antoine On Mon, May 9, 2016 at 3:25 PM, Saturne Fox <saturne.fox@gmail.com> wrote: Dear freesurfer users community,
I need your help concerning manual segmentationissues.
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 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.
PS: For instance you can notice that the added voxels in the axial slice, coordinates * -39.69, 10.78, 11.54*were not included in the surface. By the way, the subject is 13 months old.
On Tue, May 10, 2016 at 5:06 PM, Saturne Fox saturne.fox@gmail.com wrote:
Bruce,
I just uploaded the directory through the FTP server, the name of thearchive is 00M034.tar.gz .
Concerning our issue we tried to identify the problem in the lightof your advices and we observed that the *orig *file contains most of the manual modifications, which are then lost in *?h.white*. We spotted some topological errors but since the *orig *file is created after the topological corrections and that this file mainly suits us, we don't think that it is the main source of error.
Thus, we would like to know what is the influence of the variablesused during the creation of the* ?h.white* surface and how we can increase the consideration brought to the added voxels. More precisely, when using the* aseg.presurf* file must the added voxels be part of the segmented white matter to be taken into account in the *?h.white* surface ? As well, we would like to know if 250 is an appropriate intensity to manually add voxels.
Best regards, Antoine
On Mon, May 9, 2016 at 6:06 PM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:
Hi Antoine
we need the entire subject directory tarred and gzipped if you want us to look. And please upload it to our ftp site
thanks Bruce
On Mon, 9 May 2016, Saturne Fox wrote:
[icon_10_generic_list.png]
sanlm_IRC04H_00M034_P_1_WIP_T1W_3D_IRCstandard3...[x_8px.png]
Dear Bruce,
Most of the time the added voxels are included in the orig filebut are lost in the ?h.white one.
Here is the subject file.Thanks a lot for your help
Antoine
On Mon, May 9, 2016 at 3:42 PM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote: Hi Antoine
if you upload the entire subject dir we will take a look. Itsounds like it might be a topological defect. You can check this by seeing if the orig.nofix contains the voxels that you added, but the orig does not.
cheers Bruce On Mon, 9 May 2016, Saturne Fox wrote: Dear freesurfer users, I need your help concerning manual segmentationissues.
In fact I used the editing tool with an intensity of250 to add some missing part on the wm.mgz file but some of the added areas were not considered for the creation of the surface.
Some of the added parts were only connected throughone voxel to the existing parts and I guess that it might have prevented the surface to include these areas but in some other cases the supplementary parts were clear and connected by two or more voxels but were not added.
Do you know what are the criteria used byrecon-all to determine the surface ? Do you have advices about how to add voxels and be sure that they will be included in the surface?
Best regards, Antoine On Mon, May 9, 2016 at 3:25 PM, Saturne Fox <saturne.fox@gmail.com> wrote: Dear freesurfer users community,
I need your help concerning manual segmentationissues.
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 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
-
Bruce Fischl -
Saturne Fox