Re: [Freesurfer] Troubles to determine the type of recon editing needed

[Bruce Fischl]

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  
a écrit :

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


  Bram 


From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on
behalf of Matthieu Vanhoutte 
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  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 :
  >       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
  :
  >                   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  
for your
  >             subject's id):
  >             recon-all -autorecon2-noaseg -autorecon3 -subjid 
  >
  >             I would try this before doing the wm.mgz edits I suggested 
in my
  previous
  >             email.
  >
  >             Best,
  >             Bram
  >
  
>___

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

Re: [Freesurfer] Troubles to determine the type of recon editing needed

[Matthieu Vanhoutte]

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 <
brdiam...@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-boun...@nmr.mgh.harvard.edu <
> freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Matthieu Vanhoutte <
> matthieuvanhou...@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 
> 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 :
> >   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 <
> brdiam...@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 
> for your
> > subject's id):
> > recon-all -autorecon2-noaseg -autorecon3 -subjid 
> >
> > I would try this before doing the wm.mgz edits I suggested
> in my previous
> > email.
> >
> > Best,
> > Bram
> >
> >
> ___
> > _
> > From: freesurfer-boun...@nmr.mgh.harvard.edu
> >  on
> > behalf of Diamond, Bram Ryder 
> > Sent: Friday, September 14, 2018 11:07:42 AM
> > To: matthieuvanhou...@gmail.com
> > Cc: freesurfer@nmr.mgh.harvard.edu;
> astev...@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 

Re: [Freesurfer] Troubles to determine the type of recon editing needed

[Diamond, Bram Ryder]

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


Bram


From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Matthieu Vanhoutte 

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 
mailto:fis...@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 
> mailto:fis...@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 
> mailto:brdiam...@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  for 
> your
> subject's id):
> recon-all -autorecon2-noaseg -autorecon3 -subjid 
>
> I would try this before doing the wm.mgz edits I suggested in my 
> previous
> email.
>
> Best,
> Bram
>
> ___
> _
> From: 
> freesurfer-boun...@nmr.mgh.harvard.edu
> 
> mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
>  on
> behalf of Diamond, Bram Ryder 
> mailto:brdiam...@mgh.harvard.edu>>
> Sent: Friday, September 14, 2018 11:07:42 AM
> To: 
> matthieuvanhou...@gmail.com
> Cc: 
> freesurfer@nmr.mgh.harvard.edu; 
> astev...@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 
> 
> for your
> subject's id):
>
>
> recon-all -autorecon2-wm -autorecon3 -subjid 
>
>
> The surface reconstruction may also benefit from labeling the 
> right lateral
> ventricle in the
>

Re: [Freesurfer] Troubles to determine the type of recon editing needed

[Matthieu Vanhoutte]

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  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 :
> >   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 <
> brdiam...@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 
> for your
> > subject's id):
> > recon-all -autorecon2-noaseg -autorecon3 -subjid 
> >
> > I would try this before doing the wm.mgz edits I suggested
> in my previous
> > email.
> >
> > Best,
> > Bram
> >
> >
> ___
> > _
> > From: freesurfer-boun...@nmr.mgh.harvard.edu
> >  on
> > behalf of Diamond, Bram Ryder 
> > Sent: Friday, September 14, 2018 11:07:42 AM
> > To: matthieuvanhou...@gmail.com
> > Cc: freesurfer@nmr.mgh.harvard.edu;
> astev...@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 
> > for your
> > subject's id):
> >
> >
> > recon-all -autorecon2-wm -autorecon3 -subjid 
> >
> >
> > 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 

Re: [Freesurfer] Troubles to determine the type of recon editing needed

[Bruce Fischl]

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 :
  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 
:
      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  for your
subject's id):
recon-all -autorecon2-noaseg -autorecon3 -subjid 

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

Best,
Bram

___
_
From: freesurfer-boun...@nmr.mgh.harvard.edu
 on
behalf of Diamond, Bram Ryder 
Sent: Friday, September 14, 2018 11:07:42 AM
To: matthieuvanhou...@gmail.com
Cc: freesurfer@nmr.mgh.harvard.edu; astev...@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 

for your
subject's id):


recon-all -autorecon2-wm -autorecon3 -subjid 


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 
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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 
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___
Freesurfer mailing list

Re: [Freesurfer] Troubles to determine the type of recon editing needed

[Matthieu Vanhoutte]

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 :

> 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 > >:
>>   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  for your
>> subject's id):
>> recon-all -autorecon2-noaseg -autorecon3 -subjid 
>>
>> I would try this before doing the wm.mgz edits I suggested in my previous
>> email.
>>
>> Best,
>> Bram
>>
>> 
>> 
>>
>> From: freesurfer-boun...@nmr.mgh.harvard.edu <
>> freesurfer-boun...@nmr.mgh.harvard.edu> on
>> behalf of Diamond, Bram Ryder 
>> Sent: Friday, September 14, 2018 11:07:42 AM
>> To: matthieuvanhou...@gmail.com
>> Cc: freesurfer@nmr.mgh.harvard.edu; astev...@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 
>> for your
>> subject's id):
>>
>>
>> recon-all -autorecon2-wm -autorecon3 -subjid 
>>
>>
>> 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
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> 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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contains patient 

Re: [Freesurfer] Troubles to determine the type of recon editing needed

[Bruce Fischl]

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 :
  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  for your subject's 
id):
recon-all -autorecon2-noaseg -autorecon3 -subjid 

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

Best,
Bram


From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on
behalf of Diamond, Bram Ryder 
Sent: Friday, September 14, 2018 11:07:42 AM
To: matthieuvanhou...@gmail.com
Cc: freesurfer@nmr.mgh.harvard.edu; astev...@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  for 
your
subject's id):


recon-all -autorecon2-wm -autorecon3 -subjid 


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.

Re: [Freesurfer] Troubles to determine the type of recon editing needed

[Matthieu Vanhoutte]

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 :

> 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  for your
> subject's id):
>
> recon-all -autorecon2-noaseg -autorecon3 -subjid 
>
> I would try this before doing the wm.mgz edits I suggested in my previous
> email.
>
> Best,
> Bram
> --
> *From:* freesurfer-boun...@nmr.mgh.harvard.edu <
> freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Diamond, Bram Ryder <
> brdiam...@mgh.harvard.edu>
> *Sent:* Friday, September 14, 2018 11:07:42 AM
> *To:* matthieuvanhou...@gmail.com
> *Cc:* freesurfer@nmr.mgh.harvard.edu; astev...@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
>  for your subject's id):
>
>
> recon-all -autorecon2-wm -autorecon3 -subjid 
>
>
> 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
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but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

Re: [Freesurfer] Troubles to determine the type of recon editing needed

[Bruce Fischl]

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  
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  for your subject's 
id):
recon-all -autorecon2-noaseg -autorecon3 -subjid 

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

Best,
Bram


From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on
behalf of Diamond, Bram Ryder 
Sent: Friday, September 14, 2018 11:07:42 AM
To: matthieuvanhou...@gmail.com
Cc: freesurfer@nmr.mgh.harvard.edu; astev...@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  for 
your
subject's id):


recon-all -autorecon2-wm -autorecon3 -subjid 


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.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.

Re: [Freesurfer] Troubles to determine the type of recon editing needed

[Diamond, Bram Ryder]

Hi Matthieu,


The initial estimate for surfaces is based off the wm.mgz. Since you're wm.mgz 
is incorrect (due to the large ventricles and wm abnormalities) the first pass 
at a surface reconstruction is way off. The wm.mgz is created in-part from the 
aseg.mgz, so it is important that you ensure your aseg.mgz is accurate. 
Additionally, it will be useful to have an accurate aseg.mgz for subcortical 
analyses.


I hope that answers your question.


Bram


From: Matthieu Vanhoutte 
Sent: Friday, September 14, 2018 4:48:36 PM
To: Diamond, Bram Ryder
Cc: Freesurfer support list
Subject: Re: Troubles to determine the type of recon editing needed


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 
mailto:brdiam...@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  for your 
subject's id):

recon-all -autorecon2-noaseg -autorecon3 -subjid 

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

Best,
Bram

From: 
freesurfer-boun...@nmr.mgh.harvard.edu
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 on behalf of Diamond, Bram Ryder 
mailto:brdiam...@mgh.harvard.edu>>
Sent: Friday, September 14, 2018 11:07:42 AM
To: matthieuvanhou...@gmail.com
Cc: freesurfer@nmr.mgh.harvard.edu; 
astev...@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 
 for your subject's id):


recon-all -autorecon2-wm -autorecon3 -subjid 


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.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.

Re: [Freesurfer] Troubles to determine the type of recon editing needed

[Matthieu Vanhoutte]

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 <
brdiam...@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  for your
> subject's id):
>
> recon-all -autorecon2-noaseg -autorecon3 -subjid 
>
> I would try this before doing the wm.mgz edits I suggested in my previous
> email.
>
> Best,
> Bram
> --
> *From:* freesurfer-boun...@nmr.mgh.harvard.edu <
> freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Diamond, Bram Ryder <
> brdiam...@mgh.harvard.edu>
> *Sent:* Friday, September 14, 2018 11:07:42 AM
> *To:* matthieuvanhou...@gmail.com
> *Cc:* freesurfer@nmr.mgh.harvard.edu; astev...@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
>  for your subject's id):
>
>
> recon-all -autorecon2-wm -autorecon3 -subjid 
>
>
> 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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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.

Re: [Freesurfer] Troubles to determine the type of recon editing needed

[Diamond, Bram Ryder]

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  for your 
subject's id):

recon-all -autorecon2-noaseg -autorecon3 -subjid 

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

Best,
Bram

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Diamond, Bram Ryder 

Sent: Friday, September 14, 2018 11:07:42 AM
To: matthieuvanhou...@gmail.com
Cc: freesurfer@nmr.mgh.harvard.edu; astev...@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 
 for your subject's id):


recon-all -autorecon2-wm -autorecon3 -subjid 


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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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] Troubles to determine the type of recon editing needed

[Diamond, Bram Ryder]

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 
 for your subject's id):


recon-all -autorecon2-wm -autorecon3 -subjid 


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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