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 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.

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