Re: [Freesurfer] Odd Extremely High/Low Banding of Functional Values in Volume

[Dowling, Kevin Francis]

Hi Doug,

Thank you for your note and my apologies for a delayed response. To create the 
sig.mgh file we used a volume specific mri_glmfit analysis, omitting the --surf 
flag and using our volume specific input (ces.nii.gz in 
SIRP_LoadRegression_Stable5.3_012616_sm5_mni305). I don't know if this 
information is helpful but when we've run a nearly identical analysis using 
almost all of the same participants and a different blood folate marker (serum 
folate) the volumes came out completely fine. I've tried de-meaning the RBC 
folate values and re-running the mri_glmfit, but the odd activation persists.

This is our mri_glmfit command:
mri_glmfit --y 
/cluster/roffman/users/Stable5_PerRun/Analyses_GDD/GDD_Adults/137_GDD_RBC_Folate_Cond2vfix_KD/SIRP_LoadRegression_Stable5.3_012616_sm5_mni305/Cond2vFix/ces.nii.gz
--fsgd 
/cluster/roffman/users/fsgd/GDD/137_GDD_Cond2vFix_Covary_RBC_Folate_linear_KDcorrect.fsgd
--C /cluster/roffman/users/fsgd/TwoGroups1CovariateRegressOut1Covariate_KD
--glmdir 
/cluster/roffman/users/Stable5_PerRun/Analyses_GDD/GDD_Adults/137_GDD_RBC_Folate_Cond2vfix_KD/SIRP_LoadRegression_Stable5.3_012616_sm5_mni305/Cond2vFix/2vFix_ClassUsed_Covary_RBCFOLATE_Nuis_Age_Gender
--fwhm 6 --no-prune

Thank you very much, I am most appreciative of your help!

Kind regards,
Kevin

Kevin F. Dowling
Clinical Research Coordinator
Brain Genomics Laboratory
Division of Psychiatric Neuroimaging
Martinos Center for Biomedical Imaging
Massachusetts General Hospital
149 13th Street
Charlestown, MA, 02129
(p) 617.643.2479
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[Freesurfer] (no subject)

[Abigail Noyce]

Hi Doug et al,

I would like to get a different cluster summary stat out of mri_glmfit-sim.
Rather than size, I'd like to use the "sum of t-scores" (after Maris &
Oostenwald 2007, for example). That is, set a cluster inclusion threshold,
and then for each cluster of adjacent vertices that clear the threshold,
sum their t-scores. For the permutation significance testing, then, the
largest such clusterwise sum would be the statistic used to generate the
null distribution... I'm happy to write my own scripts, but can't figure
out where to try to pull this number out.

Thanks!

Abby Noyce
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Re: [Freesurfer] MS Lesions effects on cortical thickness in FS 6.0

[Ismail Koubiyr]

Alright, thanks a lot for your help Bruce.

Best,

Ismail

PhD candidate
Neurocentre Magendie, INSERM
Bordeaux, France

2016-12-12 17:33 GMT+01:00 Bruce Fischl :

> because filling in the T1 may cause artifacts
>
> On Mon, 12 Dec 2016, Ismail Koubiyr wrote:
>
> Would you please give me the reasons why the former would be better ?
>> Ismail
>>
>> PhD candidate
>> Neurocentre Magendie, INSERM
>> Bordeaux, France
>>
>>
>> 2016-12-12 15:47 GMT+01:00 Bruce Fischl :
>>   the former I think, but it's an empirical question
>>   Bruce
>>   On Mon, 12 Dec 2016, Ismail Koubiyr wrote:
>>
>>   > Hi Bruce,
>>   > Thanks for your answer.
>>   > What do you think would be better, run recon-all on the original
>> data (with
>>   > lesions) then edit the aseg for the juxtacortical lesions or use
>> a lesion
>>   > filling on the T1 and then run recon-all on it.
>>   > Thanks again.
>>   >
>>   > Cheers,
>>   >
>>   > Ismail
>>   >
>>   > PhD candidate
>>   > Neurocentre Magendie, INSERM
>>   > Bordeaux, France
>>   >
>>   > 2016-12-09 22:58 GMT+01:00 Bruce Fischl <
>> fis...@nmr.mgh.harvard.edu>:
>>   >   I Ismail
>>   >
>>   >   yes, if you have juxtacortical lesions you should label
>> them as
>>   >   such in
>>   >   the aseg, then I think it should work
>>   >
>>   >   cheers
>>   >   Bruce
>>   >   On Fri, 9 Dec 2016, Ismail Koubiyr
>>   >   wrote:
>>   >
>>   >   > Dear Freesurfer experts,
>>   >   > We are facing a problem in our study and would need your
>>   >   advice on it.
>>   >   > We want to get an accurate measurement for the cortical
>>   >   thickness from our
>>   >   > MS patients data. For that we are using 3D T1 and FLAIR
>>   >   (recon-all will be
>>   >   > used with the FLAIR option so that we can a more accurate
>> pial
>>   >   surface).
>>   >   > However, we were wondering if running recon-all on the raw
>>   >   data would lead
>>   >   > to some errors specially because of the juxtacortical
>> lesions
>>   >   or not. Or, is
>>   >   > it better to first apply a lesion filling using our lesion
>>   >   mask ?
>>   >   > I should specify that we will use the longitudinal
>> pipeline if
>>   >   it is of any
>>   >   > use.
>>   >   >
>>   >   > Thank you all.
>>   >   >
>>   >   > Ismail
>>   >   >
>>   >   > PhD candidate
>>   >   > Neurocentre Magendie, INSERM
>>   >   > Bordeaux, France
>>   >   >
>>   >   >
>>   > ___
>>   > 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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Re: [Freesurfer] white matter segmentation incorrect after intensity change

[Rizvi, Batool]

Hi Bruce,
I noticed I did it incorrectly, so I started running an hour ago just recon-all 
-autorecon2-cp -autorecon2 without the -all, about an hour ago. It's starting 
to generate output now, not sure why it didn't at all last time (may have to do 
with our new cluster). Will let you know if anything goes wrong with the output 
this time..

Thanks!
Batool 


From: freesurfer-boun...@nmr.mgh.harvard.edu 
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Bruce Fischl 
[fis...@nmr.mgh.harvard.edu]
Sent: Monday, December 12, 2016 11:34 AM
To: Freesurfer support list
Subject: Re: [Freesurfer] white matter segmentation incorrect after intensity 
change

Hi Batool

you don't need -all and -autorecon2-cp -aurorecon3 (-all is both of those
and more). It must have generated some output. Is there a recon-all.log in
the freesurferfolder/scripts dir?

cheers
Bruce

On Mon, 12 Dec 2016,
Rizvi, Batool wrote:

>
> Hi Bruce,
> We re-ran these subjects using recon-all -all -autorecon2-cp -aurorecon3 
> -subjid freesurferfolder.
> We got no output files from that, but I'm wondering if freesurfer didn't run 
> only because we incorrectly ran this command with the '-all', or do you think 
> there was some other reason? We ran this on the cluster, and it generated no 
> error logs.
>
> Thanks again for your help!
>
> Batool___
> From: freesurfer-boun...@nmr.mgh.harvard.edu 
> [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Bruce Fischl 
> [fis...@nmr.mgh.harvard.edu]
> Sent: Thursday, December 01, 2016 5:21 PM
> To: Freesurfer support list
> Subject: Re: [Freesurfer] white matter segmentation incorrect after intensity 
> change
>
> sure, good luck
> Bruce
> On Thu, 1 Dec 2016, Rizvi, Batool wrote:
>
>> Sounds great, thanks again for your help and will try out your 
>> recommendations.
>> Have a great day!
>>
>> B
>>
>> 
>> From: freesurfer-boun...@nmr.mgh.harvard.edu 
>> [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Bruce Fischl 
>> [fis...@nmr.mgh.harvard.edu]
>> Sent: Thursday, December 01, 2016 4:27 PM
>> To: Freesurfer support list
>> Subject: Re: [Freesurfer] white matter segmentation incorrect after 
>> intensity change
>>
>> yes, you can remove the control.dat file and run autorecon2-cp and
>> autorecon3. Should only take a couple of hours depending on your
>> processor
>> On Thu, 1 Dec 2016, Rizvi, Batool wrote:
>>
>>>
>>> Hi Bruce,
>>> Thanks so much for the feedback, that is very helpful. We'll try deleting 
>>> the control points then. Is there a quick way to rerun recon-all without 
>>> having it take up to 5-8 hours?
>>>
>>> Also, a separate question, when running autorecon, after edits to the white 
>>> matter and pial surfaces, should we run the command -autorecon2 
>>> -autorecon3, or would that include too many steps? I read that it's 
>>> recommended to run from -autorecon2-cp instead?
>>>
>>>
>>> Thanks so much for your help,
>>> B
>>>
>>> 
>>> From: freesurfer-boun...@nmr.mgh.harvard.edu 
>>> [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Bruce Fischl 
>>> [fis...@nmr.mgh.harvard.edu]
>>> Sent: Thursday, December 01, 2016 4:04 PM
>>> To: Freesurfer support list
>>> Subject: Re: [Freesurfer] white matter segmentation incorrect after 
>>> intensity change
>>>
>>> the problme is that you have several control points in voxels that aren't
>>> entirely wm. For example, 129, 134, 173 is a control point and it has no wm
>>> in it. This causes the intensity in that region to go up way too high, as
>>> we will normalize the control points to the desired wm intensity (110). I
>>> ran it without any control points and it worked pretty well. You should
>>> probably get rid of your control.dat. If you think that those thin frontal
>>> strands should go out a bit further, since some voxels that are entirely
>>> white matter (e.g. 134, 135, 162) but have an intensity that is less than
>>> 110 (this one is 103 after normalizating) and it will bring the intensity
>>> up a bit in that entire region (by the ratio of 110/103).
>>>
>>> On Thu, 1 Dec 2016, Rizvi, Batool wrote:
>>>
 Hi Bruce,
 Thanks for your reply. It is actually brighter on the brainmask.mgz than 
 the orig.mgz when I checked. I'm uploading the freesurfer subject here.

 Thanks!
 BR

 
 From: freesurfer-boun...@nmr.mgh.harvard.edu 
 [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Bruce Fischl 
 [fis...@nmr.mgh.harvard.edu]
 Sent: Thursday, December 01, 2016 2:31 PM
 To: Freesurfer support list
 Subject: Re: [Freesurfer] white matter segmentation incorrect after 
 intensity change

 hmmm, that's awfully bright. Is it also bright on the orig.mgz? It's not
 really possible to diagnose from a single slice from a single subject. If
 you tar, gzip and upload the subject 

Re: [Freesurfer] white matter segmentation incorrect after intensity change

[Bruce Fischl]

Hi Batool

you don't need -all and -autorecon2-cp -aurorecon3 (-all is both of those 
and more). It must have generated some output. Is there a recon-all.log in 
the freesurferfolder/scripts dir?

cheers
Bruce

On Mon, 12 Dec 2016, 
Rizvi, Batool wrote:

>
> Hi Bruce,
> We re-ran these subjects using recon-all -all -autorecon2-cp -aurorecon3 
> -subjid freesurferfolder.
> We got no output files from that, but I'm wondering if freesurfer didn't run 
> only because we incorrectly ran this command with the '-all', or do you think 
> there was some other reason? We ran this on the cluster, and it generated no 
> error logs.
>
> Thanks again for your help!
>
> Batool___
> From: freesurfer-boun...@nmr.mgh.harvard.edu 
> [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Bruce Fischl 
> [fis...@nmr.mgh.harvard.edu]
> Sent: Thursday, December 01, 2016 5:21 PM
> To: Freesurfer support list
> Subject: Re: [Freesurfer] white matter segmentation incorrect after intensity 
> change
>
> sure, good luck
> Bruce
> On Thu, 1 Dec 2016, Rizvi, Batool wrote:
>
>> Sounds great, thanks again for your help and will try out your 
>> recommendations.
>> Have a great day!
>>
>> B
>>
>> 
>> From: freesurfer-boun...@nmr.mgh.harvard.edu 
>> [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Bruce Fischl 
>> [fis...@nmr.mgh.harvard.edu]
>> Sent: Thursday, December 01, 2016 4:27 PM
>> To: Freesurfer support list
>> Subject: Re: [Freesurfer] white matter segmentation incorrect after 
>> intensity change
>>
>> yes, you can remove the control.dat file and run autorecon2-cp and
>> autorecon3. Should only take a couple of hours depending on your
>> processor
>> On Thu, 1 Dec 2016, Rizvi, Batool wrote:
>>
>>>
>>> Hi Bruce,
>>> Thanks so much for the feedback, that is very helpful. We'll try deleting 
>>> the control points then. Is there a quick way to rerun recon-all without 
>>> having it take up to 5-8 hours?
>>>
>>> Also, a separate question, when running autorecon, after edits to the white 
>>> matter and pial surfaces, should we run the command -autorecon2 
>>> -autorecon3, or would that include too many steps? I read that it's 
>>> recommended to run from -autorecon2-cp instead?
>>>
>>>
>>> Thanks so much for your help,
>>> B
>>>
>>> 
>>> From: freesurfer-boun...@nmr.mgh.harvard.edu 
>>> [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Bruce Fischl 
>>> [fis...@nmr.mgh.harvard.edu]
>>> Sent: Thursday, December 01, 2016 4:04 PM
>>> To: Freesurfer support list
>>> Subject: Re: [Freesurfer] white matter segmentation incorrect after 
>>> intensity change
>>>
>>> the problme is that you have several control points in voxels that aren't
>>> entirely wm. For example, 129, 134, 173 is a control point and it has no wm
>>> in it. This causes the intensity in that region to go up way too high, as
>>> we will normalize the control points to the desired wm intensity (110). I
>>> ran it without any control points and it worked pretty well. You should
>>> probably get rid of your control.dat. If you think that those thin frontal
>>> strands should go out a bit further, since some voxels that are entirely
>>> white matter (e.g. 134, 135, 162) but have an intensity that is less than
>>> 110 (this one is 103 after normalizating) and it will bring the intensity
>>> up a bit in that entire region (by the ratio of 110/103).
>>>
>>> On Thu, 1 Dec 2016, Rizvi, Batool wrote:
>>>
 Hi Bruce,
 Thanks for your reply. It is actually brighter on the brainmask.mgz than 
 the orig.mgz when I checked. I'm uploading the freesurfer subject here.

 Thanks!
 BR

 
 From: freesurfer-boun...@nmr.mgh.harvard.edu 
 [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Bruce Fischl 
 [fis...@nmr.mgh.harvard.edu]
 Sent: Thursday, December 01, 2016 2:31 PM
 To: Freesurfer support list
 Subject: Re: [Freesurfer] white matter segmentation incorrect after 
 intensity change

 hmmm, that's awfully bright. Is it also bright on the orig.mgz? It's not
 really possible to diagnose from a single slice from a single subject. If
 you tar, gzip and upload the subject one of us will take a look

 cheers
 Bruce
 On Thu, 1
 Dec 2016, Rizvi, Batool wrote:

>
> Hi FreeSurfer experts,
>
>
>
> After running -autorecon2 and -autorecon3, we're seeing issues for some of
> the subjects, which now start showing changes in intensity/brightness in
> some voxels, and this increased intensity is now missed by the white 
> matter
> and grey matter segmentation, and is labeled as non-brain matter.
>
>
>
>  Attached is an example of a subject's brain that was segmented 
> incorrectly,
> which we think is due to the intensity around that frontal region. We 
> hadn't
> added 

Re: [Freesurfer] MS Lesions effects on cortical thickness in FS 6.0

[Bruce Fischl]

because filling in the T1 may cause artifacts
On Mon, 12 Dec 2016, Ismail 
Koubiyr wrote:



Would you please give me the reasons why the former would be better ?
Ismail

PhD candidate
Neurocentre Magendie, INSERM
Bordeaux, France


2016-12-12 15:47 GMT+01:00 Bruce Fischl :
  the former I think, but it's an empirical question
  Bruce
  On Mon, 12 Dec 2016, Ismail Koubiyr wrote:

  > Hi Bruce,
  > Thanks for your answer.
  > What do you think would be better, run recon-all on the original data 
(with
  > lesions) then edit the aseg for the juxtacortical lesions or use a 
lesion
  > filling on the T1 and then run recon-all on it.
  > Thanks again.
  >
  > Cheers,
  >
  > Ismail
  >
  > PhD candidate
  > Neurocentre Magendie, INSERM
  > Bordeaux, France
  >
  > 2016-12-09 22:58 GMT+01:00 Bruce Fischl :
  >       I Ismail
  >
  >       yes, if you have juxtacortical lesions you should label them as
  >       such in
  >       the aseg, then I think it should work
  >
  >       cheers
  >       Bruce
  >       On Fri, 9 Dec 2016, Ismail Koubiyr
  >       wrote:
  >
  >       > Dear Freesurfer experts,
  >       > We are facing a problem in our study and would need your
  >       advice on it.
  >       > We want to get an accurate measurement for the cortical
  >       thickness from our
  >       > MS patients data. For that we are using 3D T1 and FLAIR
  >       (recon-all will be
  >       > used with the FLAIR option so that we can a more accurate pial
  >       surface).
  >       > However, we were wondering if running recon-all on the raw
  >       data would lead
  >       > to some errors specially because of the juxtacortical lesions
  >       or not. Or, is
  >       > it better to first apply a lesion filling using our lesion
  >       mask ?
  >       > I should specify that we will use the longitudinal pipeline if
  >       it is of any
  >       > use.
  >       >
  >       > Thank you all.
  >       >
  >       > Ismail
  >       >
  >       > PhD candidate
  >       > Neurocentre Magendie, INSERM
  >       > Bordeaux, France
  >       >
  >       >
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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 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] white matter segmentation incorrect after intensity change

[Rizvi, Batool]

Hi Bruce,
We re-ran these subjects using recon-all -all -autorecon2-cp -aurorecon3 
-subjid freesurferfolder.
We got no output files from that, but I'm wondering if freesurfer didn't run 
only because we incorrectly ran this command with the '-all', or do you think 
there was some other reason? We ran this on the cluster, and it generated no 
error logs.

Thanks again for your help!

Batool___
From: freesurfer-boun...@nmr.mgh.harvard.edu 
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Bruce Fischl 
[fis...@nmr.mgh.harvard.edu]
Sent: Thursday, December 01, 2016 5:21 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] white matter segmentation incorrect after intensity 
change

sure, good luck
Bruce
On Thu, 1 Dec 2016, Rizvi, Batool wrote:

> Sounds great, thanks again for your help and will try out your 
> recommendations.
> Have a great day!
>
> B
>
> 
> From: freesurfer-boun...@nmr.mgh.harvard.edu 
> [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Bruce Fischl 
> [fis...@nmr.mgh.harvard.edu]
> Sent: Thursday, December 01, 2016 4:27 PM
> To: Freesurfer support list
> Subject: Re: [Freesurfer] white matter segmentation incorrect after intensity 
> change
>
> yes, you can remove the control.dat file and run autorecon2-cp and
> autorecon3. Should only take a couple of hours depending on your
> processor
> On Thu, 1 Dec 2016, Rizvi, Batool wrote:
>
>>
>> Hi Bruce,
>> Thanks so much for the feedback, that is very helpful. We'll try deleting 
>> the control points then. Is there a quick way to rerun recon-all without 
>> having it take up to 5-8 hours?
>>
>> Also, a separate question, when running autorecon, after edits to the white 
>> matter and pial surfaces, should we run the command -autorecon2 -autorecon3, 
>> or would that include too many steps? I read that it's recommended to run 
>> from -autorecon2-cp instead?
>>
>>
>> Thanks so much for your help,
>> B
>>
>> 
>> From: freesurfer-boun...@nmr.mgh.harvard.edu 
>> [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Bruce Fischl 
>> [fis...@nmr.mgh.harvard.edu]
>> Sent: Thursday, December 01, 2016 4:04 PM
>> To: Freesurfer support list
>> Subject: Re: [Freesurfer] white matter segmentation incorrect after 
>> intensity change
>>
>> the problme is that you have several control points in voxels that aren't
>> entirely wm. For example, 129, 134, 173 is a control point and it has no wm
>> in it. This causes the intensity in that region to go up way too high, as
>> we will normalize the control points to the desired wm intensity (110). I
>> ran it without any control points and it worked pretty well. You should
>> probably get rid of your control.dat. If you think that those thin frontal
>> strands should go out a bit further, since some voxels that are entirely
>> white matter (e.g. 134, 135, 162) but have an intensity that is less than
>> 110 (this one is 103 after normalizating) and it will bring the intensity
>> up a bit in that entire region (by the ratio of 110/103).
>>
>> On Thu, 1 Dec 2016, Rizvi, Batool wrote:
>>
>>> Hi Bruce,
>>> Thanks for your reply. It is actually brighter on the brainmask.mgz than 
>>> the orig.mgz when I checked. I'm uploading the freesurfer subject here.
>>>
>>> Thanks!
>>> BR
>>>
>>> 
>>> From: freesurfer-boun...@nmr.mgh.harvard.edu 
>>> [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Bruce Fischl 
>>> [fis...@nmr.mgh.harvard.edu]
>>> Sent: Thursday, December 01, 2016 2:31 PM
>>> To: Freesurfer support list
>>> Subject: Re: [Freesurfer] white matter segmentation incorrect after 
>>> intensity change
>>>
>>> hmmm, that's awfully bright. Is it also bright on the orig.mgz? It's not
>>> really possible to diagnose from a single slice from a single subject. If
>>> you tar, gzip and upload the subject one of us will take a look
>>>
>>> cheers
>>> Bruce
>>> On Thu, 1
>>> Dec 2016, Rizvi, Batool wrote:
>>>

 Hi FreeSurfer experts,



 After running -autorecon2 and -autorecon3, we're seeing issues for some of
 the subjects, which now start showing changes in intensity/brightness in
 some voxels, and this increased intensity is now missed by the white matter
 and grey matter segmentation, and is labeled as non-brain matter.



  Attached is an example of a subject's brain that was segmented 
 incorrectly,
 which we think is due to the intensity around that frontal region. We 
 hadn't
 added control points in that region, so we are unsure what the cause of the
 intensity change is. In our first pass before running -autorecon2
 -autorecon3, we did not notice this error or the intensity values to be so
 bright for that region.



 Thanks for your help!

 BR



>> ___
>> Freesurfer mailing list
>> 

Re: [Freesurfer] MS Lesions effects on cortical thickness in FS 6.0

[Ismail Koubiyr]

Would you please give me the reasons why the former would be better ?

Ismail

PhD candidate
Neurocentre Magendie, INSERM
Bordeaux, France


2016-12-12 15:47 GMT+01:00 Bruce Fischl :

> the former I think, but it's an empirical question
> Bruce
> On Mon, 12 Dec 2016, Ismail Koubiyr wrote:
>
> > Hi Bruce,
> > Thanks for your answer.
> > What do you think would be better, run recon-all on the original data
> (with
> > lesions) then edit the aseg for the juxtacortical lesions or use a lesion
> > filling on the T1 and then run recon-all on it.
> > Thanks again.
> >
> > Cheers,
> >
> > Ismail
> >
> > PhD candidate
> > Neurocentre Magendie, INSERM
> > Bordeaux, France
> >
> > 2016-12-09 22:58 GMT+01:00 Bruce Fischl :
> >   I Ismail
> >
> >   yes, if you have juxtacortical lesions you should label them as
> >   such in
> >   the aseg, then I think it should work
> >
> >   cheers
> >   Bruce
> >   On Fri, 9 Dec 2016, Ismail Koubiyr
> >   wrote:
> >
> >   > Dear Freesurfer experts,
> >   > We are facing a problem in our study and would need your
> >   advice on it.
> >   > We want to get an accurate measurement for the cortical
> >   thickness from our
> >   > MS patients data. For that we are using 3D T1 and FLAIR
> >   (recon-all will be
> >   > used with the FLAIR option so that we can a more accurate pial
> >   surface).
> >   > However, we were wondering if running recon-all on the raw
> >   data would lead
> >   > to some errors specially because of the juxtacortical lesions
> >   or not. Or, is
> >   > it better to first apply a lesion filling using our lesion
> >   mask ?
> >   > I should specify that we will use the longitudinal pipeline if
> >   it is of any
> >   > use.
> >   >
> >   > Thank you all.
> >   >
> >   > Ismail
> >   >
> >   > PhD candidate
> >   > Neurocentre Magendie, INSERM
> >   > Bordeaux, France
> >   >
> >   >
> > ___
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> > 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
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> > in error
> > but does not contain patient information, please contact the sender
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> > dispose of the e-mail.
> >
> >
> >
> >
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Re: [Freesurfer] MS Lesions effects on cortical thickness in FS 6.0

[Bruce Fischl]

the former I think, but it's an empirical question
Bruce
On Mon, 12 Dec 2016, Ismail Koubiyr wrote:

> Hi Bruce,
> Thanks for your answer.
> What do you think would be better, run recon-all on the original data (with
> lesions) then edit the aseg for the juxtacortical lesions or use a lesion
> filling on the T1 and then run recon-all on it.
> Thanks again.
> 
> Cheers,
> 
> Ismail
> 
> PhD candidate
> Neurocentre Magendie, INSERM
> Bordeaux, France
> 
> 2016-12-09 22:58 GMT+01:00 Bruce Fischl :
>   I Ismail
>
>   yes, if you have juxtacortical lesions you should label them as
>   such in
>   the aseg, then I think it should work
>
>   cheers
>   Bruce
>   On Fri, 9 Dec 2016, Ismail Koubiyr
>   wrote:
>
>   > Dear Freesurfer experts,
>   > We are facing a problem in our study and would need your
>   advice on it.
>   > We want to get an accurate measurement for the cortical
>   thickness from our
>   > MS patients data. For that we are using 3D T1 and FLAIR
>   (recon-all will be
>   > used with the FLAIR option so that we can a more accurate pial
>   surface).
>   > However, we were wondering if running recon-all on the raw
>   data would lead
>   > to some errors specially because of the juxtacortical lesions
>   or not. Or, is
>   > it better to first apply a lesion filling using our lesion
>   mask ?
>   > I should specify that we will use the longitudinal pipeline if
>   it is of any
>   > use.
>   >
>   > Thank you all.
>   >
>   > Ismail
>   >
>   > PhD candidate
>   > Neurocentre Magendie, INSERM
>   > Bordeaux, France
>   >
>   >
> ___
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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
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> in error
> but does not contain patient information, please contact the sender
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> dispose of the e-mail.
> 
> 
> 
>
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Re: [Freesurfer] MS Lesions effects on cortical thickness in FS 6.0

[Ismail Koubiyr]

Hi Bruce,

Thanks for your answer.
What do you think would be better, run recon-all on the original data (with
lesions) then edit the aseg for the juxtacortical lesions or use a lesion
filling on the T1 and then run recon-all on it.
Thanks again.

Cheers,

Ismail

PhD candidate
Neurocentre Magendie, INSERM
Bordeaux, France

2016-12-09 22:58 GMT+01:00 Bruce Fischl :

> I Ismail
>
> yes, if you have juxtacortical lesions you should label them as such in
> the aseg, then I think it should work
>
> cheers
> Bruce
> On Fri, 9 Dec 2016, Ismail Koubiyr
> wrote:
>
> > Dear Freesurfer experts,
> > We are facing a problem in our study and would need your advice on it.
> > We want to get an accurate measurement for the cortical thickness from
> our
> > MS patients data. For that we are using 3D T1 and FLAIR (recon-all will
> be
> > used with the FLAIR option so that we can a more accurate pial surface).
> > However, we were wondering if running recon-all on the raw data would
> lead
> > to some errors specially because of the juxtacortical lesions or not.
> Or, is
> > it better to first apply a lesion filling using our lesion mask ?
> > I should specify that we will use the longitudinal pipeline if it is of
> any
> > use.
> >
> > Thank you all.
> >
> > Ismail
> >
> > PhD candidate
> > Neurocentre Magendie, INSERM
> > Bordeaux, France
> >
> >
> ___
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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
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Re: [Freesurfer] longHippoSubfields

[Iglesias Gonzalez, Eugenio]

Dear Christian,
Both options are OK, as long as you report on your paper how you obtained your 
results. Rerunning everything with 6.0 has the advantage that the results are 
easier to reproduce but, if you’ve already QCed large amounts of data processed 
with 5.3, not rerunning in understandable and, in my opinion, a perfectly valid 
option.
Cheers,
/Eugenio

Juan Eugenio Iglesias
ERC Senior Research Fellow
Translational Imaging Group
University College London
http://www.jeiglesias.com
http://cmictig.cs.ucl.ac.uk/


On 12 Dec 2016, at 09:39, Christian Krog Tamnes 
> wrote:

Hi again Eugenio,



Sorry for the picky follow-up question regarding the longitudinal hippocampal 
subfields processing, but do you suggest that when the official version 6 comes 
out, we rerun everything (including the standard FS long processing) or would 
it be ok to just rerun the hippocampal part (on scan processed with 5.3)?



For us, the first option might necessitate a new round of QC, which would be 
very time consuming for a large longitudinal dataset.



regards,
Christian




From: 
freesurfer-boun...@nmr.mgh.harvard.edu
 
>
 on behalf of Christian Krog Tamnes 
>
Sent: 30 November 2016 15:57
To: Freesurfer support list
Subject: Re: [Freesurfer] longHippoSubfields

We will get the beta for now then.
Thanks Eugenio!



regards,
Christian








From: 
freesurfer-boun...@nmr.mgh.harvard.edu
 
>
 on behalf of Iglesias Gonzalez, Eugenio 
>
Sent: 30 November 2016 15:46
To: Freesurfer support list
Subject: Re: [Freesurfer] longHippoSubfields

Hi Christian,
I believe you were unlucky enough to download the dev version during the days 
that this module was broken.
I would strongly suggest that you either download the beta version of 6.0 or 
wait until the official release of this version, which should be happening soon.
Cheers,
/Eugenio

Juan Eugenio Iglesias
ERC Senior Research Fellow
Translational Imaging Group
University College London
http://www.jeiglesias.com
http://cmictig.cs.ucl.ac.uk/


On 30 Nov 2016, at 14:26, Christian Krog Tamnes 
> wrote:

Dear Juan and FreeSurfer team,



We are trying to test out the longitudinal hippocampus subfield segmentation 
pipeline, but can’t seem to run/find the script (longHippoSubfieldsT1.sh). We 
have done the standard processing in v5.3 and have the following dev version: 
freesurfer-Linux-centos6_x86_64-dev-20160914-bdac8bc. Sorry for the basic 
question, but do we simply need a later dev build?



Best regards,
Christian
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Re: [Freesurfer] longHippoSubfields

[Christian Krog Tamnes]

Hi again Eugenio,



Sorry for the picky follow-up question regarding the longitudinal hippocampal 
subfields processing, but do you suggest that when the official version 6 comes 
out, we rerun everything (including the standard FS long processing) or would 
it be ok to just rerun the hippocampal part (on scan processed with 5.3)?



For us, the first option might necessitate a new round of QC, which would be 
very time consuming for a large longitudinal dataset.



regards,
Christian




From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Christian Krog Tamnes 

Sent: 30 November 2016 15:57
To: Freesurfer support list
Subject: Re: [Freesurfer] longHippoSubfields


We will get the beta for now then.

Thanks Eugenio!



regards,

Christian








From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Iglesias Gonzalez, 
Eugenio 
Sent: 30 November 2016 15:46
To: Freesurfer support list
Subject: Re: [Freesurfer] longHippoSubfields

Hi Christian,
I believe you were unlucky enough to download the dev version during the days 
that this module was broken.
I would strongly suggest that you either download the beta version of 6.0 or 
wait until the official release of this version, which should be happening soon.
Cheers,
/Eugenio

Juan Eugenio Iglesias
ERC Senior Research Fellow
Translational Imaging Group
University College London
http://www.jeiglesias.com
http://cmictig.cs.ucl.ac.uk/


On 30 Nov 2016, at 14:26, Christian Krog Tamnes 
> wrote:

Dear Juan and FreeSurfer team,



We are trying to test out the longitudinal hippocampus subfield segmentation 
pipeline, but can't seem to run/find the script (longHippoSubfieldsT1.sh). We 
have done the standard processing in v5.3 and have the following dev version: 
freesurfer-Linux-centos6_x86_64-dev-20160914-bdac8bc. Sorry for the basic 
question, but do we simply need a later dev build?



Best regards,
Christian
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Re: [Freesurfer] Revisiting GM ROI list

[P Taylor]

And, a minor clarification on one of the ROIs in question--

I should have phrase the comment about ROI #80 as follows:
 80 non-WM-hypointensities  ---> *should be in list of FS_nongm?

... since the name clearly implies that it is non-WM.

Basically, I am first wanting to check that the above list of ROIs does
form the "whole brain" returned by recon-all;  there are a lot more ROIs
listed in the LUT, of all sorts of tissue types, but it seems like those
don't often appear in the output.

And following on that, it seems like presently a map of various non-GM
tissues is made by summing up ROIs of a given type, and then:
GM_map = whole_brain - WM_map - CSF_map - vent_map.
However, am I interpreting things correctly that the four ROIs flagged
above (#30, 62, 80 and 85) seem to be an "other" class that should be
subtracted away from the whole_brain, as well, such that:
GM_map = whole_brain - WM_map - CSF_map - vent_map - other_four_regions ?

Thanks,
pt



On Mon, Dec 12, 2016 at 1:04 AM, P Taylor  wrote:

> Hi, Doug-
>
>
> I've looked more into my earlier question of identifying FS-returned
> regions, in particular:
> 1) which regions of the whole FreeSurferColorLUT.txt seem to get returned
> by default recon-all calls (for either the 2000- or 2009-parc+segs); and
> 2) which of those regions are GM and non-GM (WM/CSF/other), based both on
> the mri_binarize list you had posted earlier in this thread and on the
> names given in the LUT.
>
> I'd like to pick your brain on this.
>
> A) The main questions I have relate to the regions labeled from [0, 256],
> which seem have the same labelling in both the 2000 and 2009 parc+segs.
> From a few different FreeSurfer recon-alls on healthy adults, below is a
> list of the ROIs that seem to be consistently returned by recon-all (a much
> sparser subset than all 256).
> For each, I have included the number and label, as well as put arrows by
> the numbers that, according to the MatchValues list in mri_binarize, should
> be in either the WM or Vent masks, (and hence non-arrowed regions should be
> GM, by how that function returns "--gm").
> My main questions arise about #30, 62, 80 and 85, as they don't appear to
> be GM-- therefore, am I correct that I should also *exclude* those four
> regions from a list of GM regions?
> (Here, "FS_nongm*" means that it was in the list of non-GM regions in
> mri_binarize, as either unknown, WM, CSF or ventricle.)
> 
> -
>   0 Unknown   -> FS_nongm
>
>   2 Left-Cerebral-White-Matter-> FS_nongm_wm
>
>   4 Left-Lateral-Ventricle-> FS_nongm_vent
>   5 Left-Inf-Lat-Vent -> FS_nongm_vent
>
>   7 Left-Cerebellum-White-Matter  -> FS_nongm_wm
>   8 Left-Cerebellum-Cortex
>
>  10 Left-Thalamus-Proper
>  11 Left-Caudate
>  12 Left-Putamen
>  13 Left-Pallidum
>  14 3rd-Ventricle -> FS_nongm_vent
>  15 4th-Ventricle -> FS_nongm_vent
>  16 Brain-Stem
>  17 Left-Hippocampus
>  18 Left-Amygdala
>
>  24 CSF   -> FS_nongm_csf
>
>  26 Left-Accumbens-area
>
>  28 Left-VentralDC
>
>  30 Left-vessel ---> *should be in list of FS_nongm?
>  31 Left-choroid-plexus   -> FS_nongm_vent
>
>  41 Right-Cerebral-White-Matter   -> FS_nongm_wm
>
>  43 Right-Lateral-Ventricle   -> FS_nongm_vent
>  44 Right-Inf-Lat-Vent-> FS_nongm_vent
>
>  46 Right-Cerebellum-White-Matter -> FS_nongm_wm
>  47 Right-Cerebellum-Cortex
>
>  49 Right-Thalamus-Proper
>  50 Right-Caudate
>
>  52 Right-Pallidum
>  53 Right-Hippocampus
>  54 Right-Amygdala
>
>  58 Right-Accumbens-area
>
>  60 Right-VentralDC
>
>  62 Right-vessel---> *should be in list of FS_nongm?
>  63 Right-choroid-plexus  -> FS_nongm_vent
>
>  72 5th-Ventricle -> FS_nongm_vent
>
>  77 WM-hypointensities-> FS_nongm_wm
>
>  80 non-WM-hypointensities  ---> *should be in list of FS_nongm_wm?
>
>  85 Optic-Chiasm---> *should be in list of FS_nongm?
>
> 251 CC_Posterior  -> FS_nongm_wm
> 252 CC_Mid_Posterior  -> FS_nongm_wm
> 253 CC_Central-> FS_nongm_wm
> 254 CC_Mid_Anterior   -> FS_nongm_wm
> 255 CC_Anterior   -> FS_nongm_wm
> 
> 
>
> It seem that the new version of mri_binarize that you had sent me might
> still include those four flagged regions in the 'mri_binarize --gm' output.
>
>
> B) For the ROIs specific to the 2000aparc+aseg, I think it also seems
> pretty clear:
> + 1000 and 2000 are returned as "ctx_*_unknown";
> + All ROIs in the intervals [1001, 1003] and [1005, 1035] can be returned,
> and these are all LH GM;
> + All ROIs in the intervals [2001, 2003] and [2005, 2035] can be returned,
> and these are all RH