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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