External Email - Use Caution

Dear Bram,

Thank you for your answer. As soon as possible I will run recon-all with the -bigventricles flag.

Concerning the manual editing I don't understand well the aim of editing aseg.mgz since it seems to most concern subcortical structures and statistics and not have an impact on surfaces computed ?

Best, Matthieu

Le ven. 14 sept. 2018 à 17:35, Diamond, Bram Ryder < BRDIAMOND@mgh.harvard.edu> a écrit :

If you haven't already, you may want to run the subject through recon-all with the -bigventricles flag since it looks like the lateral ventricle was significantly mislabeled in the aseg. If using the -bigventricles flag doesn't fix your problem, you can edit the aseg.mgz manually by following the directions in this tutorial https://surfer.nmr.mgh.harvard.edu/fswiki/TkMeditGuide/TkMeditWorkingWithData/FreeviewSegmentations. Then run the following command (again, substituting <subj_id> for your subject's id):

recon-all -autorecon2-noaseg -autorecon3 -subjid <subj_id>

I would try this before doing the wm.mgz edits I suggested in my previous email.

Best, Bram

---

*From:* freesurfer-bounces@nmr.mgh.harvard.edu < freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Diamond, Bram Ryder < BRDIAMOND@mgh.harvard.edu> *Sent:* Friday, September 14, 2018 11:07:42 AM *To:* matthieuvanhoutte@gmail.com *Cc:* freesurfer@nmr.mgh.harvard.edu; astevens@nmr.mgh.harvard.edu *Subject:* [Freesurfer] Troubles to determine the type of recon editing needed

Hi Matthieu,

I've taken a look through the files you shared with us and I see the poor surfaces in the posterior right hemisphere you were referring to in your message. It looks like your subject has a combination of abnormally large ventricles and significant wm abnormalities, so I'm surprised FreeSurfer did as well as it did.

As for the recon editing - I would recommend editing the wm.mgz to more accurately represent the wm from slice 84 to 39. You can take a look at the white matter edits tutorial https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/WhiteMatterEditsV6.0 for details on how to do that. Then run the following command (substituting <subj_id> for your subject's id):

recon-all -autorecon2-wm -autorecon3 -subjid <subj_id>

The surface reconstruction may also benefit from labeling the right lateral ventricle in the wm.mgz (as an intensity of 250) - but I'm not certain since you didn't send us the surfaces for the left hemisphere. Before you do that, edit the wm.mgz as explained in the tutorial and tell us how that goes.

All the best,

Bram

*Bram R. Diamond, BSc* Research Technician II Laboratory for Computational Neuroimaging Martinos Center for Biomedical Imaging Massachusetts General Hospital 149 13th Street Charlestown, MA 02129 (p): 617-726-6598

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.

Hi Matthieu

the aseg is used to automatically edit the wm.mgz, which helps the creation of cortical surfaces. For example, the ventricles are filled using the aseg. I think in your case with greatly expanded ventricles, some of the ventricular voxels were incorrectly labeled in the aseg and hence resulted in incorrect surfaces.

cheers Bruce

On Fri, 14 Sep 2018, Matthieu Vanhoutte wrote:

External Email - Use Caution

Dear Bram, Thank you for your answer. As soon as possible I will run recon-all with the -bigventricles flag.

Concerning the manual editing I don't understand well the aim of editing aseg.mgz since it seems to most concern subcortical structures and statistics and not have an impact on surfaces computed ?

Best, Matthieu

Le ven. 14 sept. 2018 à 17:35, Diamond, Bram Ryder BRDIAMOND@mgh.harvard.edu a écrit : If you haven't already, you may want to run the subject through recon-all with the -bigventricles flag since it looks like the lateral ventricle was significantly mislabeled in the aseg. If using the -bigventricles flag doesn't fix your problem, you can edit the aseg.mgz manually by following the directions in this tutorial. Then run the following command (again, substituting <subj_id> for your subject's id): recon-all -autorecon2-noaseg -autorecon3 -subjid <subj_id>

I would try this before doing the wm.mgz edits I suggested in my previous email.

Best, Bram

---

From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Diamond, Bram Ryder BRDIAMOND@mgh.harvard.edu Sent: Friday, September 14, 2018 11:07:42 AM To: matthieuvanhoutte@gmail.com Cc: freesurfer@nmr.mgh.harvard.edu; astevens@nmr.mgh.harvard.edu Subject: [Freesurfer] Troubles to determine the type of recon editing needed

Hi Matthieu,

I've taken a look through the files you shared with us and I see the poor surfaces in the posterior right hemisphere you were referring to in your message. It looks like your subject has a combination of abnormally large ventricles and significant wm abnormalities, so I'm surprised FreeSurfer did as well as it did.

As for the recon editing - I would recommend editing the wm.mgz to more accurately represent the wm from slice 84 to 39. You can take a look at the white matter edits tutorial for details on how to do that. Then run the following command (substituting <subj_id> for your subject's id):

recon-all -autorecon2-wm -autorecon3 -subjid <subj_id>

The surface reconstruction may also benefit from labeling the right lateral ventricle in the wm.mgz (as an intensity of 250) - but I'm not certain since you didn't send us the surfaces for the left hemisphere. Before you do that, edit the wm.mgz as explained in the tutorial and tell us how that goes.

All the best,

Bram

Bram R. Diamond, BSc Research Technician II Laboratory for Computational Neuroimaging Martinos Center for Biomedical Imaging Massachusetts General Hospital 149 13th Street  Charlestown, MA 02129 (p): 617-726-6598

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.

Hi Matthieu

yes, you will want to run all of your subjects with it

cheers Bruce On Tue, 18 Sep 2018, Matthieu Vanhoutte wrote:

External Email - Use Caution

Dear Bram,

It looks like the -bigventricles flag fixed my problem with my specific subject. Not only, this took into account large ventricles but also corrected grey matter segmentation from extra Dura tissue that was erroneously segmented in GM.

I understand the first point of amelioration allowed by the flag but don't understand where the second point come from ?

If I used the -bigventricles flag for all my atrophied and large ventricles patients and not for my healthy patients, wouldn't it introduce a bias when further statistically comparing groups between them ?

Best, Matthieu

2018-09-14 15:35 GMT+00:00 Diamond, Bram Ryder BRDIAMOND@mgh.harvard.edu: If you haven't already, you may want to run the subject through recon-all with the -bigventricles flag since it looks like the lateral ventricle was significantly mislabeled in the aseg. If using the -bigventricles flag doesn't fix your problem, you can edit the aseg.mgz manually by following the directions in this tutorial. Then run the following command (again, substituting <subj_id> for your subject's id): recon-all -autorecon2-noaseg -autorecon3 -subjid <subj_id>

I would try this before doing the wm.mgz edits I suggested in my previous email.

Best, Bram

---

From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Diamond, Bram Ryder BRDIAMOND@mgh.harvard.edu Sent: Friday, September 14, 2018 11:07:42 AM To: matthieuvanhoutte@gmail.com Cc: freesurfer@nmr.mgh.harvard.edu; astevens@nmr.mgh.harvard.edu Subject: [Freesurfer] Troubles to determine the type of recon editing needed

Hi Matthieu,

I've taken a look through the files you shared with us and I see the poor surfaces in the posterior right hemisphere you were referring to in your message. It looks like your subject has a combination of abnormally large ventricles and significant wm abnormalities, so I'm surprised FreeSurfer did as well as it did.

As for the recon editing - I would recommend editing the wm.mgz to more accurately represent the wm from slice 84 to 39. You can take a look at the white matter edits tutorial for details on how to do that. Then run the following command (substituting <subj_id> for your subject's id):

recon-all -autorecon2-wm -autorecon3 -subjid <subj_id>

The surface reconstruction may also benefit from labeling the right lateral ventricle in the wm.mgz (as an intensity of 250) - but I'm not certain since you didn't send us the surfaces for the left hemisphere. Before you do that, edit the wm.mgz as explained in the tutorial and tell us how that goes.

All the best,

Bram

Bram R. Diamond, BSc Research Technician II Laboratory for Computational Neuroimaging Martinos Center for Biomedical Imaging Massachusetts General Hospital 149 13th Street  Charlestown, MA 02129 (p): 617-726-6598

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.

I think it should be ok. It will be a bit slower, but shouldn't reduce accuracy I don't think. Try it and see Bruce On Tue, 18 Sep 2018, Matthieu Vanhoutte wrote:

External Email - Use Caution

Hi Bruce,

Thanks, but in this case will recon-all with -bigventricles flag work well on normal patients without big ventricles ?

Best, Matthieu

2018-09-18 15:56 GMT+00:00 Bruce Fischl fischl@nmr.mgh.harvard.edu: Hi Matthieu

  yes, you will want to run all of your subjects with it

  cheers
  Bruce
  On Tue, 18 Sep 2018, Matthieu Vanhoutte wrote:


                External Email - Use Caution        

        Dear Bram,

        It looks like the -bigventricles flag fixed my problem with my specific
        subject. Not only, this took
        into account large ventricles but also corrected grey matter segmentation
        from extra Dura tissue
        that was erroneously segmented in GM.

        I understand the first point of amelioration allowed by the flag but don't
        understand where the
        second point come from ?

        If I used the -bigventricles flag for all my atrophied and large ventricles
        patients and not for my
        healthy patients, wouldn't it introduce a bias when further statistically
        comparing groups between
        them ?

        Best,
        Matthieu

        2018-09-14 15:35 GMT+00:00 Diamond, Bram Ryder <BRDIAMOND@mgh.harvard.edu>:
              If you haven't already, you may want to run the subject through
        recon-all with the
              -bigventricles flag since it looks like the lateral ventricle was
        significantly
              mislabeled in the aseg. If using the -bigventricles flag doesn't fix
        your problem, you
              can edit the aseg.mgz manually by following the directions in this
        tutorial. Then run
              the following command (again, substituting <subj_id> for your
        subject's id):
        recon-all -autorecon2-noaseg -autorecon3 -subjid <subj_id>

        I would try this before doing the wm.mgz edits I suggested in my previous
        email.

        Best,
        Bram

---

        _
        From: freesurfer-bounces@nmr.mgh.harvard.edu
        <freesurfer-bounces@nmr.mgh.harvard.edu> on
        behalf of Diamond, Bram Ryder <BRDIAMOND@mgh.harvard.edu>
        Sent: Friday, September 14, 2018 11:07:42 AM
        To: matthieuvanhoutte@gmail.com
        Cc: freesurfer@nmr.mgh.harvard.edu; astevens@nmr.mgh.harvard.edu
        Subject: [Freesurfer] Troubles to determine the type of recon editing needed
         

        Hi Matthieu,


        I've taken a look through the files you shared with us and I see the poor
        surfaces in the
        posterior right hemisphere you were referring to in your message. It looks
        like your subject
        has a combination of abnormally large ventricles and significant wm
        abnormalities, so I'm
        surprised FreeSurfer did as well as it did.


        As for the recon editing - I would recommend editing the wm.mgz to more
        accurately represent
        the wm from slice 84 to 39. You can take a look at the white matter edits
        tutorial for details
        on how to do that. Then run the following command (substituting <subj_id>
        for your
        subject's id):


        recon-all -autorecon2-wm -autorecon3 -subjid <subj_id>


        The surface reconstruction may also benefit from labeling the right lateral
        ventricle in the
        wm.mgz (as an intensity of 250) - but I'm not certain since you didn't send
        us the surfaces
        for the left hemisphere. Before you do that, edit the wm.mgz as explained in
        the tutorial and
        tell us how that goes.


        All the best,

        Bram


        Bram R. Diamond, BSc
        Research Technician II
        Laboratory for Computational Neuroimaging
        Martinos Center for Biomedical Imaging
        Massachusetts General Hospital
        149 13th Street 
        Charlestown, MA 02129
        (p): 617-726-6598

        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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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.

Yes - if you've used the -bigventricles flag, you should always include it with the recon-all command.

Bram

________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Matthieu Vanhoutte matthieuvanhoutte@gmail.com Sent: Tuesday, September 18, 2018 12:45:23 PM To: Freesurfer support list Subject: Re: [Freesurfer] Troubles to determine the type of recon editing needed

External Email - Use Caution

Ok I will test it on normal subjects.

Do I have to put this -bigventricles flag on all recon-all commands following manual editing of brainmask, white matter,...etc or just once at the first recon-all -all command ?

Best, Matthieu

Le mar. 18 sept. 2018 à 18:03, Bruce Fischl <fischl@nmr.mgh.harvard.edumailto:fischl@nmr.mgh.harvard.edu> a écrit : I think it should be ok. It will be a bit slower, but shouldn't reduce accuracy I don't think. Try it and see Bruce On Tue, 18 Sep 2018, Matthieu Vanhoutte wrote:

    External Email - Use Caution

Hi Bruce,

Thanks, but in this case will recon-all with -bigventricles flag work well on normal patients without big ventricles ?

Best, Matthieu

2018-09-18 15:56 GMT+00:00 Bruce Fischl <fischl@nmr.mgh.harvard.edumailto:fischl@nmr.mgh.harvard.edu>: Hi Matthieu

  yes, you will want to run all of your subjects with it

  cheers
  Bruce
  On Tue, 18 Sep 2018, Matthieu Vanhoutte wrote:


                External Email - Use Caution

        Dear Bram,

        It looks like the -bigventricles flag fixed my problem with my specific
        subject. Not only, this took
        into account large ventricles but also corrected grey matter segmentation
        from extra Dura tissue
        that was erroneously segmented in GM.

        I understand the first point of amelioration allowed by the flag but don't
        understand where the
        second point come from ?

        If I used the -bigventricles flag for all my atrophied and large ventricles
        patients and not for my
        healthy patients, wouldn't it introduce a bias when further statistically
        comparing groups between
        them ?

        Best,
        Matthieu

        2018-09-14 15:35 GMT+00:00 Diamond, Bram Ryder <BRDIAMOND@mgh.harvard.edu<mailto:BRDIAMOND@mgh.harvard.edu>>:
              If you haven't already, you may want to run the subject through
        recon-all with the
              -bigventricles flag since it looks like the lateral ventricle was
        significantly
              mislabeled in the aseg. If using the -bigventricles flag doesn't fix
        your problem, you
              can edit the aseg.mgz manually by following the directions in this
        tutorial. Then run
              the following command (again, substituting <subj_id> for your
        subject's id):
        recon-all -autorecon2-noaseg -autorecon3 -subjid <subj_id>

        I would try this before doing the wm.mgz edits I suggested in my previous
        email.

        Best,
        Bram

---

        _
        From: freesurfer-bounces@nmr.mgh.harvard.edu<mailto:freesurfer-bounces@nmr.mgh.harvard.edu>
        <freesurfer-bounces@nmr.mgh.harvard.edu<mailto:freesurfer-bounces@nmr.mgh.harvard.edu>> on
        behalf of Diamond, Bram Ryder <BRDIAMOND@mgh.harvard.edu<mailto:BRDIAMOND@mgh.harvard.edu>>
        Sent: Friday, September 14, 2018 11:07:42 AM
        To: matthieuvanhoutte@gmail.com<mailto:matthieuvanhoutte@gmail.com>
        Cc: freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>; astevens@nmr.mgh.harvard.edu<mailto:astevens@nmr.mgh.harvard.edu>
        Subject: [Freesurfer] Troubles to determine the type of recon editing needed


        Hi Matthieu,


        I've taken a look through the files you shared with us and I see the poor
        surfaces in the
        posterior right hemisphere you were referring to in your message. It looks
        like your subject
        has a combination of abnormally large ventricles and significant wm
        abnormalities, so I'm
        surprised FreeSurfer did as well as it did.


        As for the recon editing - I would recommend editing the wm.mgz to more
        accurately represent
        the wm from slice 84 to 39. You can take a look at the white matter edits
        tutorial for details
        on how to do that. Then run the following command (substituting <subj_id>
        for your
        subject's id):


        recon-all -autorecon2-wm -autorecon3 -subjid <subj_id>


        The surface reconstruction may also benefit from labeling the right lateral
        ventricle in the
        wm.mgz (as an intensity of 250) - but I'm not certain since you didn't send
        us the surfaces
        for the left hemisphere. Before you do that, edit the wm.mgz as explained in
        the tutorial and
        tell us how that goes.


        All the best,

        Bram


        Bram R. Diamond, BSc
        Research Technician II
        Laboratory for Computational Neuroimaging
        Martinos Center for Biomedical Imaging
        Massachusetts General Hospital
        149 13th Street
        Charlestown, MA 02129
        (p): 617-726-6598

        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.edumailto: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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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.

Hi Matthieu

only recon2 will use it, but you can specify it for all of them cheers Bruce

On Wed, 19 Sep 2018, Matthieu Vanhoutte wrote:

External Email - Use Caution

Dear Bram, According recon-all help "If a subject has enlarged ventricles due to atrophy, include the -bigventricles flag with the -autorecon2 stage in order to prevent surfaces extending into the ventricle regions. The flag directly affects the binary mri_ca_register, and mris_make_surfaces indirectly via aseg.presurf.mgz.

So doesn't this mean that we should only out the -bigventricles flag for the -autorecon2 stage of recon-all ?

Best, Matthieu

Le mer. 19 sept. 2018 à 15:17, Diamond, Bram Ryder BRDIAMOND@mgh.harvard.edu a écrit :

  Yes - if you've used the -bigventricles flag, you should always include it with the
  recon-all command.


  Bram 

---

From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Matthieu Vanhoutte matthieuvanhoutte@gmail.com Sent: Tuesday, September 18, 2018 12:45:23 PM To: Freesurfer support list Subject: Re: [Freesurfer] Troubles to determine the type of recon editing needed

External Email - Use Caution

Ok I will test it on normal subjects. Do I have to put this -bigventricles flag on all recon-all commands following manual editing of brainmask, white matter,...etc or just once at the first recon-all -all command ?

Best, Matthieu

Le mar. 18 sept. 2018 à 18:03, Bruce Fischl fischl@nmr.mgh.harvard.edu a écrit : I think it should be ok. It will be a bit slower, but shouldn't reduce accuracy I don't think. Try it and see Bruce On Tue, 18 Sep 2018, Matthieu Vanhoutte wrote:

  >
  >         External Email - Use Caution        
  >
  > Hi Bruce,
  >
  > Thanks, but in this case will recon-all with -bigventricles flag work well on
  normal patients
  > without big ventricles ?
  >
  > Best,
  > Matthieu
  >
  > 2018-09-18 15:56 GMT+00:00 Bruce Fischl <fischl@nmr.mgh.harvard.edu>:
  >       Hi Matthieu
  >
  >       yes, you will want to run all of your subjects with it
  >
  >       cheers
  >       Bruce
  >       On Tue, 18 Sep 2018, Matthieu Vanhoutte wrote:
  >
  >
  >                     External Email - Use Caution        
  >
  >             Dear Bram,
  >
  >             It looks like the -bigventricles flag fixed my problem with my
  specific
  >             subject. Not only, this took
  >             into account large ventricles but also corrected grey matter
  segmentation
  >             from extra Dura tissue
  >             that was erroneously segmented in GM.
  >
  >             I understand the first point of amelioration allowed by the flag but
  don't
  >             understand where the
  >             second point come from ?
  >
  >             If I used the -bigventricles flag for all my atrophied and large
  ventricles
  >             patients and not for my
  >             healthy patients, wouldn't it introduce a bias when further
  statistically
  >             comparing groups between
  >             them ?
  >
  >             Best,
  >             Matthieu
  >
  >             2018-09-14 15:35 GMT+00:00 Diamond, Bram Ryder
  <BRDIAMOND@mgh.harvard.edu>:
  >                   If you haven't already, you may want to run the subject
  through
  >             recon-all with the
  >                   -bigventricles flag since it looks like the lateral ventricle
  was
  >             significantly
  >                   mislabeled in the aseg. If using the -bigventricles flag
  doesn't fix
  >             your problem, you
  >                   can edit the aseg.mgz manually by following the directions
  in this
  >             tutorial. Then run
  >                   the following command (again, substituting <subj_id> for your
  >             subject's id):
  >             recon-all -autorecon2-noaseg -autorecon3 -subjid <subj_id>
  >
  >             I would try this before doing the wm.mgz edits I suggested in my
  previous
  >             email.
  >
  >             Best,
  >             Bram
  >
  >___________________________________________________________________________________________________

  >             _
  >             From: freesurfer-bounces@nmr.mgh.harvard.edu
  >             <freesurfer-bounces@nmr.mgh.harvard.edu> on
  >             behalf of Diamond, Bram Ryder <BRDIAMOND@mgh.harvard.edu>
  >             Sent: Friday, September 14, 2018 11:07:42 AM
  >             To: matthieuvanhoutte@gmail.com
  >             Cc: freesurfer@nmr.mgh.harvard.edu; astevens@nmr.mgh.harvard.edu
  >             Subject: [Freesurfer] Troubles to determine the type of recon
  editing needed
  >              
  >
  >             Hi Matthieu,
  >
  >
  >             I've taken a look through the files you shared with us and I see the
  poor
  >             surfaces in the
  >             posterior right hemisphere you were referring to in your message. It
  looks
  >             like your subject
  >             has a combination of abnormally large ventricles and significant wm
  >             abnormalities, so I'm
  >             surprised FreeSurfer did as well as it did.
  >
  >
  >             As for the recon editing - I would recommend editing the wm.mgz to
  more
  >             accurately represent
  >             the wm from slice 84 to 39. You can take a look at the white matter
  edits
  >             tutorial for details
  >             on how to do that. Then run the following command (substituting
  <subj_id>
  >             for your
  >             subject's id):
  >
  >
  >             recon-all -autorecon2-wm -autorecon3 -subjid <subj_id>
  >
  >
  >             The surface reconstruction may also benefit from labeling the right
  lateral
  >             ventricle in the
  >             wm.mgz (as an intensity of 250) - but I'm not certain since you
  didn't send
  >             us the surfaces
  >             for the left hemisphere. Before you do that, edit the wm.mgz as
  explained in
  >             the tutorial and
  >             tell us how that goes.
  >
  >
  >             All the best,
  >
  >             Bram
  >
  >
  >             Bram R. Diamond, BSc
  >             Research Technician II
  >             Laboratory for Computational Neuroimaging
  >             Martinos Center for Biomedical Imaging
  >             Massachusetts General Hospital
  >             149 13th Street 
  >             Charlestown, MA 02129
  >             (p): 617-726-6598
  >
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