Hi Bruce,

When I have a look in the recon-all script I see that it is tested if there are voxels present in wm.mgz with value 1 or 255. Both indicate wm editing. The comment in recon-all says that 1 means remove and 255 means add. And concerning my second question: are these edited voxels correcly processed with the option autorecon2-wm and subsequently with longitudinal processing?

Cheers, ed

On 4 Feb 2014, at 14:27, Bruce Fischl wrote:

Hi Ed,

yes, although we reserve the values under 5 I think for editing changes, I believe we only use 1 at the moment.

cheers Bruce On Tue, 4 Feb 2014, Ed Gronenschild wrote:

...

Hi,

From what I can read in the wiki about wm editing, I understand that edited wm voxels have values of either 255 (added) or 1 (removed) and no other values. These are stored in the file wm.mgz. Is that correct? Before processing a lot of data I want to be sure that running recon-all with the option autorecon2-wm will recognize these voxels, also during longitudinal processing. Can you confirm this.

FreeSurfer v5.3.0 Mac OSX10.6

Kind regards, Ed

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Hi Ed,

take a look at this wiki page about edits in the long stream: https://surfer.nmr.mgh.harvard.edu/fswiki/LongitudinalEdits

everything should work. for long, you'd edit the base. If that is not sufficient, you can edit the cross or the long. Edits from the cross should be transferred to the long, except if the long already contain manual edits.

Best, Martin

On Feb 4, 2014, at 9:06 AM, Ed Gronenschild ed.gronenschild@maastrichtuniversity.nl wrote:

Hi Bruce,

When I have a look in the recon-all script I see that it is tested if there are voxels present in wm.mgz with value 1 or 255. Both indicate wm editing. The comment in recon-all says that 1 means remove and 255 means add. And concerning my second question: are these edited voxels correcly processed with the option autorecon2-wm and subsequently with longitudinal processing?

Cheers, ed

On 4 Feb 2014, at 14:27, Bruce Fischl wrote:

...

Hi Ed,

yes, although we reserve the values under 5 I think for editing changes, I believe we only use 1 at the moment.

cheers Bruce On Tue, 4 Feb 2014, Ed Gronenschild wrote:

...

Hi,

From what I can read in the wiki about wm editing, I understand that edited wm voxels have values of either 255 (added) or 1 (removed) and no other values. These are stored in the file wm.mgz. Is that correct? Before processing a lot of data I want to be sure that running recon-all with the option autorecon2-wm will recognize these voxels, also during longitudinal processing. Can you confirm this.

FreeSurfer v5.3.0 Mac OSX10.6

Kind regards, Ed

---

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--------------------------------- Dr. Martin Reuter Assistant in Neuroscience - Massachusetts General Hospital Instructor in Neurology - Harvard Medical School MGH / HMS / MIT

A.A.Martinos Center for Biomedical Imaging 149 Thirteenth Street, Suite 2301 Charlestown, MA 02129

Phone: +1-617-724-5652 Email: mreuter@nmr.mgh.harvard.edu reuter@mit.edu Web : http://reuter.mit.edu

Hi Ed

it was never the case that an edited on wm.mgz voxel had the value of 110. It was always 255. 110 is the value that locations have when they are either an automatically or manually added control point

cheers Bruce On Tue, 4 Feb 2014, Ed Gronenschild wrote:

Hi Martin, One thing I want to be sure of: should the edited wm voxels really have a value of either 1 or 255. In previous versions an added wm voxel had a value of about 110, this is not anymore the case? I'm asking this because I want to edit wm by using results from another application that segments wm, so not by means of manually editing with freeview.

Cheers, Ed

On 4 Feb 2014, at 17:00, Martin Reuter wrote:

  Hi Ed,

take a look at this wiki page about edits in the long stream: https://surfer.nmr.mgh.harvard.edu/fswiki/LongitudinalEdits

everything should work. for long, you'd edit the base. If that is not sufficient, you can edit the cross or the long. Edits from the cross should be transferred to the long, except if the long already contain manual edits.

Best, Martin

On Feb 4, 2014, at 9:06 AM, Ed Gronenschild ed.gronenschild@maastrichtuniversity.nl wrote:

  Hi Bruce,

  When I have a look in the recon-all script I see that it
  is tested if  
  there
  are voxels present in wm.mgz with value 1 or 255. Both
  indicate
  wm editing. The comment in recon-all says that 1 means
  remove
  and 255 means add.
  And concerning my second question: are these edited voxels
  correcly processed with the option autorecon2-wm and
  subsequently
  with longitudinal processing?

  Cheers,
  ed

  On 4 Feb 2014, at 14:27, Bruce Fischl wrote:

        Hi Ed,

        yes, although we reserve the values under 5 I
        think for editing  
        changes,
        I believe we only use 1 at the moment.

        cheers
        Bruce
        On Tue, 4 Feb 2014, Ed Gronenschild
        wrote:

              Hi,

              From what I can read in the wiki
              about wm editing, I understand
              that edited wm voxels have values
              of either 255 (added) or
              1 (removed) and no other values.
              These are stored in the file
              wm.mgz. Is that correct?
              Before processing a lot of data I
              want to be sure that running
              recon-all with the option
              autorecon2-wm will recognize these
              voxels, also during longitudinal
              processing. Can you confirm
              this.

              FreeSurfer v5.3.0 Mac OSX10.6

              Kind regards,
              Ed

              _______________________________________________
              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.


  _______________________________________________
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  Freesurfer@nmr.mgh.harvard.edu
  https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

---

Dr. Martin Reuter Assistant in Neuroscience - Massachusetts General Hospital Instructor in Neurology   - Harvard Medical School MGH / HMS / MIT

A.A.Martinos Center for Biomedical Imaging 149 Thirteenth Street, Suite 2301 Charlestown, MA 02129

Phone: +1-617-724-5652 Email:     mreuter@nmr.mgh.harvard.edu    reuter@mit.edu Web  : http://reuter.mit.edu

Hi Derin

we replace all 255s with 254 I think and 1 with 5 or something like that. I'd have to go dig up the code. If you add 110 it will work, but if you rerun it will not be retained.

cheers Bruce

On Wed, 5 Feb 2014, Derin J Cobia wrote:

Could you clarify this a little more Bruce? I was under the same impression as Ed that 110s could be used in editing the wm volume (but cannot recall why/how I know that). We've edited using 110s and 255s with some limited success for both (rerunning occasionally deletes these manual edits or surface does not follow them) - maybe it is related to the mixing of intensities? In a sense does using 110s trigger the stream to think a control point was placed there (absent the Voronoi diagram, etc)?

So, if manual 255s are always used, how are they differentiated from ventricle or internal capsule ones? Does this even matter? Broadly, does using a variety of intensity values affect other volumes (e.g. aseg, brainfinalsurfs, etc)?

Thanks, Derin

On Feb 4, 2014, at 11:25 AM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:

...

Hi Ed

it was never the case that an edited on wm.mgz voxel had the value of 110. It was always 255. 110 is the value that locations have when they are either an automatically or manually added control point

cheers Bruce On Tue, 4 Feb 2014, Ed Gronenschild wrote:

...

Hi Martin, One thing I want to be sure of: should the edited wm voxels really have a value of either 1 or 255. In previous versions an added wm voxel had a value of about 110, this is not anymore the case? I'm asking this because I want to edit wm by using results from another application that segments wm, so not by means of manually editing with freeview. Cheers, Ed On 4 Feb 2014, at 17:00, Martin Reuter wrote:

 Hi Ed,

take a look at this wiki page about edits in the long stream: https://surfer.nmr.mgh.harvard.edu/fswiki/LongitudinalEdits everything should work. for long, you'd edit the base. If that is not sufficient, you can edit the cross or the long. Edits from the cross should be transferred to the long, except if the long already contain manual edits. Best, Martin On Feb 4, 2014, at 9:06 AM, Ed Gronenschild ed.gronenschild@maastrichtuniversity.nl wrote:

 Hi Bruce,

 When I have a look in the recon-all script I see that it
 is tested if
 there
 are voxels present in wm.mgz with value 1 or 255. Both
 indicate
 wm editing. The comment in recon-all says that 1 means
 remove
 and 255 means add.
 And concerning my second question: are these edited voxels
 correcly processed with the option autorecon2-wm and
 subsequently
 with longitudinal processing?

 Cheers,
 ed

 On 4 Feb 2014, at 14:27, Bruce Fischl wrote:

       Hi Ed,

       yes, although we reserve the values under 5 I
       think for editing
       changes,
       I believe we only use 1 at the moment.

       cheers
       Bruce
       On Tue, 4 Feb 2014, Ed Gronenschild
       wrote:

             Hi,

             From what I can read in the wiki
             about wm editing, I understand
             that edited wm voxels have values
             of either 255 (added) or
             1 (removed) and no other values.
             These are stored in the file
             wm.mgz. Is that correct?
             Before processing a lot of data I
             want to be sure that running
             recon-all with the option
             autorecon2-wm will recognize these
             voxels, also during longitudinal
             processing. Can you confirm
             this.

             FreeSurfer v5.3.0 Mac OSX10.6

             Kind regards,
             Ed

             _______________________________________________
             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.

 _______________________________________________
 Freesurfer mailing list
 Freesurfer@nmr.mgh.harvard.edu
 https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

---

Dr. Martin Reuter Assistant in Neuroscience - Massachusetts General Hospital Instructor in Neurology - Harvard Medical School MGH / HMS / MIT A.A.Martinos Center for Biomedical Imaging 149 Thirteenth Street, Suite 2301 Charlestown, MA 02129 Phone: +1-617-724-5652 Email: mreuter@nmr.mgh.harvard.edu reuter@mit.edu Web : http://reuter.mit.edu

---

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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.