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

---

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-- Miguel Ángel Rivas Fernández

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



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        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 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 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

---

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*