External Email - Use Caution
Hi guys,
I'm having some trouble extending the pial surface of my bm volume. I am aware that the general procedure for extending the pial is to extend the wm first and the pial will follow. However, is it possible to extend the pial surface without affecting the wm boundary?
Thanks,
Saum
Hi Saum
it is, but you need to figure out why it isn't getting out far enough. The easiest way is to override the intensity statistics that are computed automatically in mris_make_surfaces. You can see them if you look in your recon-all.log. For example if the lowest value gm is allowed to be at the pial surface is too high, then it will settle too far in
cheers Bruce
On Fri, 27 Apr 2018, Saum Naderi wrote:
External Email - Use Caution
Hi guys,
I'm having some trouble extending the pial surface of my bm volume. I am aware that the general procedure for extending the pial is to extend the wm first and the pial will follow. However, is it possible to extend the pial surface without affecting the wm boundary?
Thanks,
Saum
External Email - Use Caution
Hi guys,
I have the same problem as Saum, I executed the recon-all in several subjects and I did not obtain a completely correct segmentation of the pial surface. To solve this error could I use the control points? When I use the control points, will I also be able to correct the white matter segmentation?
I send you a image if you want to check it.
Thank you very much!
Cheers,
2018-04-27 21:28 GMT+02:00 Bruce Fischl fischl@nmr.mgh.harvard.edu:
Hi Saum
it is, but you need to figure out why it isn't getting out far enough. The easiest way is to override the intensity statistics that are computed automatically in mris_make_surfaces. You can see them if you look in your recon-all.log. For example if the lowest value gm is allowed to be at the pial surface is too high, then it will settle too far in
cheers Bruce
On Fri, 27 Apr 2018, Saum Naderi wrote:
External Email - Use CautionHi guys,
I'm having some trouble extending the pial surface of my bm volume. I am aware that the general procedure for extending the pial is to extend the wm first and the pial will follow. However, is it possible to extend the pial surface without affecting the wm boundary?
Thanks,
Saum
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.
that looks like a big temporal lobe bias field to me. Is the WM in the temporal lobes significantly darker than 110? I can't tell if some of the stuff in e.g. the left medial temporal lobe is WM or GM. Try putting some control points in regions where the intensity is in say [95, 110) and see if that helps
cheers Bruce
On Sat, 28 Apr 2018, Miguel Ángel Rivas Fernández wrote:
External Email - Use Caution
Hi guys,
I have the same problem as Saum, I executed the recon-all in several subjects and I did not obtain a completely correct segmentation of the pial surface. To solve this error could I use the control points? When I use the control points, will I also be able to correct the white matter segmentation?
I send you a image if you want to check it.
Thank you very much!
Cheers,
[IMAGE]
2018-04-27 21:28 GMT+02:00 Bruce Fischl fischl@nmr.mgh.harvard.edu: Hi Saum
it is, but you need to figure out why it isn't getting out far enough. The easiest way is to override the intensity statistics that are computed automatically in mris_make_surfaces. You can see them if you look in your recon-all.log. For example if the lowest value gm is allowed to be at the pial surface is too high, then it will settle too far in cheers Bruce On Fri, 27 Apr 2018, Saum Naderi wrote: External Email - Use Caution Hi guys, I'm having some trouble extending the pial surface of my bm volume. I am aware that the general procedure for extending the pial is to extend the wm first and the pial will follow. However, is it possible to extend the pial surface without affecting the wm boundary? Thanks, Saum
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.
-- Miguel Ángel Rivas Fernández
External Email - Use Caution
Hi Bruce,
The problem is that the reconstruction of the pial surface is incorrect. I tried to put control points on some voxels but did a wrong reconstruction because in this region there is no voxel with an intensity between 95-110. How can I improve the reconstruction of the pial surface (in this case extend) without modifying the boundaries of wm? . Sorry, I read the answer you gave to Saum but I could not understand very well how to modify the statistics that FreeSurfer does in the mri_make_surfaces.
*Hi Saum it is, but you need to figure out why it isn't getting out far enough. The easiest way is to override the intensity statistics that are computed automatically in mris_make_surfaces. You can see them if you look in your recon-all.log. For example if the lowest value gm is allowed to be at the pial surface is too high, then it will settle too far in *
Thanks,
Cheers,
2018-04-29 17:33 GMT+02:00 Bruce Fischl fischl@nmr.mgh.harvard.edu:
that looks like a big temporal lobe bias field to me. Is the WM in the temporal lobes significantly darker than 110? I can't tell if some of the stuff in e.g. the left medial temporal lobe is WM or GM. Try putting some control points in regions where the intensity is in say [95, 110) and see if that helps
cheers Bruce
On Sat, 28 Apr 2018, Miguel Ángel Rivas Fernández wrote:
External Email - Use CautionHi guys,
I have the same problem as Saum, I executed the recon-all in several subjects and I did not obtain a completely correct segmentation of the pial surface. To solve this error could I use the control points? When I use the control points, will I also be able to correct the white matter segmentation?
I send you a image if you want to check it.
Thank you very much!
Cheers,
[IMAGE]
2018-04-27 21:28 GMT+02:00 Bruce Fischl fischl@nmr.mgh.harvard.edu: Hi Saum
it is, but you need to figure out why it isn't getting out farenough. The easiest way is to override the intensity statistics that are computed automatically in mris_make_surfaces. You can see them if you look in your recon-all.log. For example if the lowest value gm is allowed to be at the pial surface is too high, then it will settle too far in
cheers Bruce On Fri, 27 Apr 2018, Saum Naderi wrote: External Email - Use Caution Hi guys, I'm having some trouble extending the pial surface of my bmvolume. I am aware that the general procedure for extending the pial is to extend the wm first and the pial will follow. However, is it possible to extend the pial surface without affecting the wm boundary?
Thanks, Saum
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.
-- Miguel Ángel Rivas Fernández
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.
why don't you tar and gzip the whole subject dir and upload it to our ftp site and we will take a look cheers Bruce On Tue, 1 May 2018, Miguel Ángel Rivas Fernández wrote:
External Email - Use Caution
Hi Bruce,
The problem is that the reconstruction of the pial surface is incorrect. I tried to put control points on some voxels but did a wrong reconstruction because in this region there is no voxel with an intensity between 95-110. How can I improve the reconstruction of the pial surface (in this case extend) without modifying the boundaries of wm? . Sorry, I read the answer you gave to Saum but I could not understand very well how to modify the statistics that FreeSurfer does in the mri_make_surfaces.
Hi Saum
it is, but you need to figure out why it isn't getting out far enough. The easiest way is to override the intensity statistics that are computed automatically in mris_make_surfaces. You can see them if you look in your recon-all.log. For example if the lowest value gm is allowed to be at the pial surface is too high, then it will settle too far in
Thanks,
Cheers,
2018-04-29 17:33 GMT+02:00 Bruce Fischl fischl@nmr.mgh.harvard.edu: that looks like a big temporal lobe bias field to me. Is the WM in the temporal lobes significantly darker than 110? I can't tell if some of the stuff in e.g. the left medial temporal lobe is WM or GM. Try putting some control points in regions where the intensity is in say [95, 110) and see if that helps
cheers Bruce On Sat, 28 Apr 2018, Miguel Ángel Rivas Fernández wrote: External Email - Use Caution Hi guys, I have the same problem as Saum, I executed the recon-all in several subjects and I did not obtain a completely correct segmentation of the pial surface. To solve this error could I use the control points? When I use the control points, will I also be able to correct the white matter segmentation? I send you a image if you want to check it. Thank you very much! Cheers, [IMAGE] 2018-04-27 21:28 GMT+02:00 Bruce Fischl <fischl@nmr.mgh.harvard.edu>: Hi Saum it is, but you need to figure out why it isn't getting out far enough. The easiest way is to override the intensity statistics that are computed automatically in mris_make_surfaces. You can see them if you look in your recon-all.log. For example if the lowest value gm is allowed to be at the pial surface is too high, then it will settle too far in cheers Bruce On Fri, 27 Apr 2018, Saum Naderi wrote: External Email - Use Caution Hi guys, I'm having some trouble extending the pial surface of my bm volume. I am aware that the general procedure for extending the pial is to extend the wm first and the pial will follow. However, is it possible to extend the pial surface without affecting the wm boundary? Thanks, Saum _______________________________________________ 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. -- Miguel Ángel Rivas Fernández
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.
-- Miguel Ángel Rivas Fernández
External Email - Use Caution
Hi Bruce,
I tried to upload the whole subject dir in the ftp site but i didn´t works. I send you the file in 7zip format trough a google drive link . I would know how can i extend the pial surface without affect the wm boundaries because the pial surface segmentation in some subjects (as this that i send to you) was incorrect.
https://drive.google.com/open?id=11xcWuDlWzGeLLV4MvW-bJK3-rrlsIA8Q
Thaks in advance
Cheers,
2018-05-01 16:26 GMT+02:00 Bruce Fischl fischl@nmr.mgh.harvard.edu:
why don't you tar and gzip the whole subject dir and upload it to our ftp site and we will take a look cheers Bruce
On Tue, 1 May 2018, Miguel Ángel Rivas Fernández wrote:
External Email - Use CautionHi Bruce,
The problem is that the reconstruction of the pial surface is incorrect. I tried to put control points on some voxels but did a wrong reconstruction because in this region there is no voxel with an intensity between 95-110. How can I improve the reconstruction of the pial surface (in this case extend) without modifying the boundaries of wm? . Sorry, I read the answer you gave to Saum but I could not understand very well how to modify the statistics that FreeSurfer does in the mri_make_surfaces.
Hi Saum
it is, but you need to figure out why it isn't getting out far enough. The easiest way is to override the intensity statistics that are computed automatically in mris_make_surfaces. You can see them if you look in your recon-all.log. For example if the lowest value gm is allowed to be at the pial surface is too high, then it will settle too far in
Thanks,
Cheers,
2018-04-29 17:33 GMT+02:00 Bruce Fischl fischl@nmr.mgh.harvard.edu: that looks like a big temporal lobe bias field to me. Is the WM in the temporal lobes significantly darker than 110? I can't tell if some of the stuff in e.g. the left medial temporal lobe is WM or GM. Try putting some control points in regions where the intensity is in say [95, 110) and see if that helps
cheers Bruce On Sat, 28 Apr 2018, Miguel Ángel Rivas Fernández wrote: External Email - Use Caution Hi guys, I have the same problem as Saum, I executed the recon-all inseveral subjects and I did not obtain a completely correct segmentation of the pial surface. To solve this error could I use the control points? When I use the control points, will I also be able to correct the white matter segmentation?
I send you a image if you want to check it. Thank you very much! Cheers, [IMAGE] 2018-04-27 21:28 GMT+02:00 Bruce Fischl <fischl@nmr.mgh.harvard.edu>: Hi Saum
it is, but you need to figure out why it isn't gettingout far enough. The easiest way is to override the intensity statistics that are computed automatically in mris_make_surfaces. You can see them if you look in your recon-all.log. For example if the lowest value gm is allowed to be at the pial surface is too high, then it will settle too far in
cheers Bruce On Fri, 27 Apr 2018, Saum Naderi wrote: External Email - Use Caution Hi guys, I'm having some trouble extending the pialsurface of my bm volume. I am aware that the general procedure for extending the pial is to extend the wm first and the pial will follow. However, is it possible to extend the pial surface without affecting the wm boundary?
Thanks, Saum _______________________________________________ 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 theperson 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.
-- Miguel Ángel Rivas Fernández
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.
-- Miguel Ángel Rivas Fernández
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.
External Email - Use Caution
Hi Bruce,
I sent you the whole directory if one subject un which we had some problems extending the pial surface. Se would like extend the pial surface without affect the wm boundary.
Did you have a chance to review It?
Thanks in advance,
Cheers,
El vie., 4 may. 2018 1:02, Miguel Ángel Rivas Fernández < miguelrivasfdez@gmail.com> escribió:
Hi Bruce,
I tried to upload the whole subject dir in the ftp site but i didn´t works. I send you the file in 7zip format trough a google drive link . I would know how can i extend the pial surface without affect the wm boundaries because the pial surface segmentation in some subjects (as this that i send to you) was incorrect.
https://drive.google.com/open?id=11xcWuDlWzGeLLV4MvW-bJK3-rrlsIA8Q
Thaks in advance
Cheers,
2018-05-01 16:26 GMT+02:00 Bruce Fischl fischl@nmr.mgh.harvard.edu:
why don't you tar and gzip the whole subject dir and upload it to our ftp site and we will take a look cheers Bruce
On Tue, 1 May 2018, Miguel Ángel Rivas Fernández wrote:
External Email - Use CautionHi Bruce,
The problem is that the reconstruction of the pial surface is incorrect. I tried to put control points on some voxels but did a wrong reconstruction because in this region there is no voxel with an intensity between 95-110. How can I improve the reconstruction of the pial surface (in this case extend) without modifying the boundaries of wm? . Sorry, I read the answer you gave to Saum but I could not understand very well how to modify the statistics that FreeSurfer does in the mri_make_surfaces.
Hi Saum
it is, but you need to figure out why it isn't getting out far enough. The easiest way is to override the intensity statistics that are computed automatically in mris_make_surfaces. You can see them if you look in your recon-all.log. For example if the lowest value gm is allowed to be at the pial surface is too high, then it will settle too far in
Thanks,
Cheers,
2018-04-29 17:33 GMT+02:00 Bruce Fischl fischl@nmr.mgh.harvard.edu: that looks like a big temporal lobe bias field to me. Is the WM in the temporal lobes significantly darker than 110? I can't tell if some of the stuff in e.g. the left medial temporal lobe is WM or GM. Try putting some control points in regions where the intensity is in say [95, 110) and see if that helps
cheers Bruce On Sat, 28 Apr 2018, Miguel Ángel Rivas Fernández wrote: External Email - Use Caution Hi guys, I have the same problem as Saum, I executed the recon-all inseveral subjects and I did not obtain a completely correct segmentation of the pial surface. To solve this error could I use the control points? When I use the control points, will I also be able to correct the white matter segmentation?
I send you a image if you want to check it. Thank you very much! Cheers, [IMAGE] 2018-04-27 21:28 GMT+02:00 Bruce Fischl <fischl@nmr.mgh.harvard.edu>: Hi Saum
it is, but you need to figure out why it isn't gettingout far enough. The easiest way is to override the intensity statistics that are computed automatically in mris_make_surfaces. You can see them if you look in your recon-all.log. For example if the lowest value gm is allowed to be at the pial surface is too high, then it will settle too far in
cheers Bruce On Fri, 27 Apr 2018, Saum Naderi wrote: External Email - Use Caution Hi guys, I'm having some trouble extending the pialsurface of my bm volume. I am aware that the general procedure for extending the pial is to extend the wm first and the pial will follow. However, is it possible to extend the pial surface without affecting the wm boundary?
Thanks, Saum _______________________________________________ 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 theperson 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.
-- Miguel Ángel Rivas Fernández
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.
-- Miguel Ángel Rivas Fernández
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.
-- *Miguel Ángel Rivas Fernández*
freesurfer@nmr.mgh.harvard.edu