On Tue, Oct 31, 2017 at 11:27 AM, Bruce Fischl <fischl@nmr.mgh.harvard.edu> wrote:

Hi Nicholas

can you tell us exactly what you did. What volume did you edit? What command did you run? That kind of thing

cheers
Bruce

On Tue, 31 Oct 2017, Nicholas Goh wrote:

Hello,
I tried to correct a topological defect as described on the wiki but it did not produce the proper value. Because
the wiki said to use recon-edit, any additions made were given a value of 255 and not seen as possible white
matter. Would it cause a problem if I were to use free editing and changing the brush value to the correct one?
or is there another way to address this issue?
Thanks,

Nicholas Goh

On Wed, Oct 25, 2017 at 9:32 AM, Nicholas Goh <ngoh95@gmail.com> wrote:
Hello,
I have tried fixing the image using the topical defects page. However, because it uses recon-edit the
affected area does not seem to be recognized as white matter. Is it okay to do free editing for the same
results, or is there something else that I should try for implementation?
Thank you for the help,

Nicholas Goh

On Mon, Oct 23, 2017 at 4:10 PM, Douglas N Greve <greve@nmr.mgh.harvard.edu> wrote:
I think you have an incorrectly fixed defect at that location. Follow
the instructions on fixing defects on our wiki.
https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/TopologicalDefect_freeview

On 10/23/2017 09:18 AM, Nicholas Goh wrote:
> Sorry for the delay, I was hoping to get some input from another on
> why my numbers seemed off.
> I have attached a screenshot which I believe has an image of an
> example which needs to be fixed, along with the coordinates.
> Please let me know if you need anything else,
>
> Nicholas Goh
>
> On Mon, Oct 16, 2017 at 1:08 PM, Douglas Greve
> <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> wrote:
>
> I don't know what coordinates those are. Can you give indices?
> indices are non-neg
>
>
> On 10/16/17 12:59 PM, Nicholas Goh wrote:
>> An example of the aparc+aseg not covering all that it needs to
>> can be found around [-7, 114, 133]
>>
>> On Mon, Oct 16, 2017 at 12:47 PM, Douglas Greve
>> <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> wrote:
>>
>> what is the index (ie, col, row, slice) where you are seeing
>> a problem?
>>
>>
>> On 10/16/17 11:44 AM, Nicholas Goh wrote:
>>> Hi,
>>>
>>> I am not sure if this email got lost in the process or is
>>> still awaiting approval, but I was asked to tar and gzip the
>>> images that I was having no luck with fixing the white
>>> matter for.
>>> Any help would be appreciated.
>>> Thank you,
>>>
>>> Nicholas Goh
>>> ---------- Forwarded message ----------
>>> From: *Nicholas Goh* <ngoh95@gmail.com
>>> <mailto:ngoh95@gmail.com>>
>>> Date: Mon, Oct 2, 2017 at 12:33 PM
>>> Subject: Re: [Freesurfer] Adding control points to aparc+aseg
>>> To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu
>>> <mailto:freesurfer@nmr.mgh.harvard.edu>>
>>>
>>>
>>> I have still been having trouble with fixing the white
>>> matter of the aparc+aseg.mgz file for a subject.
>>> I have tried using
>>>
>>> recon-all -autorecon2-cp -autorecon3 -subjid XXXX
>>> recon-all -autorecon2-wm -subjid XXXX
>>> recon-all -autorecon2-wm -autorecon3 -subjid XXXX
>>>
>>> None of these have solved the issue, and I was hoping for
>>> help in finding a way to fix this? There are other more
>>> extreme examples, but this one seems to have an error at
>>> [-7, 114, 133]
>>> Thank you for the help,
>>>
>>> Nicholas Goh
>>>
>>> On Thu, Sep 28, 2017 at 5:34 PM, Nicholas Goh
>>> <ngoh95@gmail.com <mailto:ngoh95@gmail.com>> wrote:
>>>
>>> Ping, is this okay to do? I Think it is but wanted to
>>> check before sending
>>> ---------- Forwarded message ----------
>>> From: *Bruce Fischl* <fischl@nmr.mgh.harvard.edu
>>> <mailto:fischl@nmr.mgh.harvard.edu>>
>>> Date: Thu, Sep 28, 2017 at 5:23 PM
>>> Subject: Re: [Freesurfer] Adding control points to
>>> aparc+aseg
>>> To: Freesurfer support list
>>> <freesurfer@nmr.mgh.harvard.edu
>>> <mailto:freesurfer@nmr.mgh.harvard.edu>>
>>>
>>>
>>> Hi Nicholas
>>>
>>> why don't you tar, gzip and upload your subject and we
>>> will take a look. Make sure to tell us the coordinates
>>> of where you are trying to fix things
>>>
>>> cheers
>>> Bruce
>>>
>>>
>>> On Thu, 28 Sep 2017, Nicholas Goh wrote:
>>>
>>> I am still having trouble with getting the
>>> aparc+aseg to recognize sections
>>> that should be white matter as such. Using the
>>> control points paired
>>> withrecon-all -autorecon2-cp -autorecon3 -subjid XXXX
>>>
>>> did not work, after 4 or 5 attempts with different
>>> control points, and using
>>> recon-all -autorecon2-wm -s XXXX
>>> also did not yield appreciable results. Is there
>>> anything else that I might
>>> be able to try to fix this?
>>> Thank you for all the help,
>>>
>>> Nicholas Goh
>>>
>>> On Wed, Sep 27, 2017 at 12:49 PM, Elijah Mak
>>> <fkm24@medschl.cam.ac.uk
>>> <mailto:fkm24@medschl.cam.ac.uk>>
>>> wrote:
>>>    Hi Nicholas,
>>>
>>> In such situations, I have learned that
>>> autorecon2-wm after adding WM
>>> voxels seems to work pretty well. Hope that helps.
>>>
>>> Best Wishes,
>>> Elijah
>>>
>>> On 27 September 2017 at 16:46:43, Nicholas Goh
>>> (ngoh95@gmail.com <mailto:ngoh95@gmail.com>)
>>> wrote:
>>>
>>> Bruce,
>>> Thank you for the response. Attempting to use this
>>> method has
>>> not produced results, and I am unsure how to proceed
>>> or if I had
>>> performed it improperly. I have attached an example
>>> of the
>>> control points being placed, if that helps any.
>>> Thank you,
>>>
>>> Nicholas Goh
>>>
>>> On Wed, Sep 27, 2017 at 11:04 AM, Bruce Fischl
>>> <fischl@nmr.mgh.harvard.edu
>>> <mailto:fischl@nmr.mgh.harvard.edu>> wrote:
>>>    Hi Nicholas
>>>
>>>    yes, possibly, depending on why you are missing
>>>    chunks. If the white matter in the regions you are
>>>    missing has intensity values significantly < 110
>>>    then what you are doing should help. The
>>> control.dat
>>>    file must be place in the subject/tmp dir for
>>> us to
>>>    find it.
>>>
>>>    cheers
>>>    Bruce
>>>    On Wed, 27 Sep 2017, Nicholas Goh wrote:
>>>
>>>    I am attempting to fix the
>>> aparc+aseg.mgz file for an image, and
>>> wanted to check to see if I am
>>> doing it correctly.What I was doing
>>> which seemed to be ineffective was
>>> 1)create a new point set of control
>>> points labelled control.dat
>>> 2)place control points along what should
>>>    be white matter
>>> 3)save point set
>>> 4)run recon-all -autorecon2-cp
>>> -autorecon3 -subjid XXXX
>>>
>>>    Is this the correct way to go about
>>> fixing aparc+aseg files that are missing
>>> chunks of the brain? Is
>>> there a better way to go about this?
>>> Thanks for the help,
>>>
>>> Nicholas Goh
>>>
>>>
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