[Freesurfer] NeuroHackademy 2019

[Ariel Rokem]

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We are happy to announce a call for applications to participate in
Neurohackademy 2019!

This two-week hands-on workshop held at the University of Washington
eScience Institute in Seattle, July 29th - August 9th, 2019, focuses on
tools and techniques used to analyze human neuroscience data, on methods
used to extract information from large datasets of publicly available data
(such as the Human Connectome Project, OpenfMRI, etc.), and on tools for
making human neuroscience research open and reproducible.

Neurohackademy sessions in the first week will include lectures and
tutorials on data science, machine learning, data visualization, and data
resources. The second week will be devoted to participant-directed
activities: guided work on team projects, hackathon sessions, and breakout
sessions on topics of interest.

*For more details and a preliminary list of instructors, see:
**https://neurohackademy.org/
*

We are now accepting applications to participate at
https://neurohackademy.org/apply/

Ideally, applicants should have some prior experience with programming and
with neuroscience data analysis, but we welcome applications from
participants with a variety of relevant backgrounds.

Accepted applicants will be asked to pay a fee of $200 upon final
registration. This fee will include participation in the course,
accommodation in the UW dorms, and two meals a day (breakfast and lunch),
for the duration of the course. A limited number of fee waivers and travel
grants will be available. We encourage students with financial need and
students from groups that are underrepresented in neuroimaging and data
science to apply for these grants (see application form for details).

*Important dates:*
*February 18th: Application deadline*
*March 15th: Notification of acceptance*
*April 1st: Final registration deadline*
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[Freesurfer] How to make grey matter edits

[Rosalia Dacosta Aguayo]

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Dear FreeSufer team,

I have been working with MS patients using T1 lesion filled images. I
corrected pial surface and I did control points for white matter. However,
I have not found how to edit gray matter segmentation.
I would much appreciate if you tell me where I could find a TUTORIAL fir
this issue.

Best regards,
Rosalia
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[Freesurfer] LME MATLAB Tools

[Tefera, Getaneh B]

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Dear Freesurfer Experts,



I have a question about how to interpret  cortical thickness difference between 
groups using LME MATLAB tools.


I have three groups(g0, g1, and g2) and five time points(t= 0,0.5, 1,2,3).



I am trying to use  LME model  with random effects y-int and time from the base 
line.

Based on the LME tutorial  and the questions and answers from Freesurfer 
support list:

Y=B1+B2*t+B3*g1+B4*g1*t+B5*g2+B6*g2*t+ 

To see the difference between group g0 and group g1,  I constructed the 
following contrast matrix using the tutorial provided in LME MATLAB tools

C = [zeros(1,3) [1 0 0] zeros(1,4)];
CM.C=[zeros(1,3) [1 0 0] zeros(1,4)];

Based on the tutorial I run the following functions.

rhstats = lme_mass_fit_Rgw(X,[1 2],rhY,ni,rhTh0,rhRgs,rhsphere);
F_rhstats = lme_mass_F(rhstats,CM);
fs_write_fstats(F_rhstats,rhmri,'/backup/cross/rh_AB_cross_sig.mgh','sig');

nv=length(rhstats);
Beta2 = zeros(1,nv);
for i=1:nv
  if ~isempty(rhstats(i).Bhat)
  Beta2(i) = rhstats(i).Bhat(2);
   end;
end;

rhmri1 = rhmri;
rhmri1.volsz(4) = 1;
fs_write_Y(Beta2,rhmri1,'rhBeta2.mgh');

[detvtx,sided_pval,pth] = 
lme_mass_FDR2(F_rhstats.pval,F_rhstats.sgn,rhcortex,0.05,0);

fs_write_Y(sided_pval,rhmri1,'spval.mgh');


When I view sig.mgh using tksurfer I see regions with red and blue color.


1) Does the result shows the oveall change for all the five time points?
2) How do I know the difference between the two groups for each 5 time points?
3) Does red means thickness of group A is larger than thickness of group B?
4) what does rhBeta2.mgh and spval.mgh tell us? How can I extract the 
information from the file?



With regards

Getaneh
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Re: [Freesurfer] Large cluster size significant clusters

[Greve, Douglas N.,Ph.D.]

Try raising the threshold

On 1/10/19 1:42 PM, Azeez, Azeezat wrote:
>
> External Email - Use Caution
>
>
> Hello ,
> I have results for my mri_glmfit-sim. I find a significant results in 
> my cache.th20abs.sig.cluster.summary.
> Yet, the cluster size of the significant cluster is almost the size of 
> the total cortical surface area. I am not sure what to make of this 
> any help would be helpful.
>
> # Total Cortical Surface Area 65416.6 (mm^2)
> # ClusterNo  Max   VtxMax   Size(mm^2)  MNIX   MNIY MNIZ    CWP    
> CWPLow    CWPHi   NVtxs   Annot
>    1  -44.154    9733  55204.38 -4.9  -47.1 29.6  0.00020  
> 0.0  0.00040  108257  isthmuscingulate
>
>
> -- 
> Azeezat Azeez
>
>
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[Freesurfer] Large cluster size significant clusters

[Azeez, Azeezat]

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Hello ,
I have results for my mri_glmfit-sim. I find a significant results in my
cache.th20abs.sig.cluster.summary.
Yet, the cluster size of the significant cluster is almost the size of the
total cortical surface area. I am not sure what to make of this any help
would be helpful.

# Total Cortical Surface Area 65416.6 (mm^2)
# ClusterNo  Max   VtxMax   Size(mm^2)  MNIX   MNIY   MNIZCWP
CWPLowCWPHi   NVtxs   Annot
   1  -44.1549733  55204.38 -4.9  -47.1   29.6  0.00020
0.0  0.00040  108257  isthmuscingulate


-- 
Azeezat Azeez
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Re: [Freesurfer] fsaverage, brainstem and cerebellum

[john Anderson]

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Ah! great!! thank you so much for the great help!!
Have a good day,
John


Sent with ProtonMail Secure Email.

‐‐‐ Original Message ‐‐‐
On Thursday, January 10, 2019 1:03 PM, Bruce Fischl 
 wrote:

> Hi John
>
> we distribute an aseg.mgs with fsaverage I believe. You can just
> tesselate that.
>
> cheers
> Bruce
> On Thu, 10 Jan 2019, john Anderson wrote:
>
> > External Email - Use Caution
> > Hi Dr Bruce, I highly appreciate your guidance.
> > I would like to load the cerebellum and brain stem structures as an average 
> > structure similar to
> > "fsaverage" , I usually use the command
> > tksurferfv fsaverage lh pial -overlay 
> > mri_tessellate or mri_mc would create a surface for every subject, how can 
> > I create the average of the
> > surfaces of those structures similar to "fsaverage"?
> > Thanks again for any highlights
> > John
> > Hi John
> >
> > you could use mri_tessellate or mri_mc to create a surface for those 
> > structures, then smooth them with
> > mris_smooth and load them into freeview.
> > Shouldn't be too hard.
> >
> > cheers
> > Bruce
> >
> > On Thu, 10 Jan 2019, john Anderson
> > wrote:
> > ‐‐‐ Original Message ‐‐‐
> > On Thursday, January 10, 2019 7:40 AM, john Anderson 
> > john.ande...@protonmail.com wrote:
> >
> >   Dear FS experts,
> >
> >
> > For visualization purposes, is there any way to show the cerebellum and 
> > brain stem regions
> > (similar to the attached figure), this figure was published used CONN 
> > toolbox but I am not sure
> > how they were able to map functional data in brain surface and show the 
> > cerebellum and brain
> > stem with fsaverage.
> > I appreciate any suggestion
> > Jon



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Re: [Freesurfer] fsaverage, brainstem and cerebellum

[Bruce Fischl]

Hi John

we distribute an aseg.mgs with fsaverage I believe. You can just 
tesselate that.


cheers
Bruce
On Thu, 10 Jan 2019, john Anderson wrote:



External Email - Use Caution

Hi Dr Bruce, I highly appreciate your guidance.
I would like to load the cerebellum and brain stem structures as an average 
structure similar to
"fsaverage" , I usually use the command 

tksurferfv fsaverage lh pial -overlay 

mri_tessellate or mri_mc would create a surface for every subject, how can I 
create the average of the
surfaces of those structures similar to "fsaverage"?

Thanks again for any highlights
John


Hi John

 

you could use mri_tessellate or mri_mc to create a surface for those 
structures, then smooth them with
mris_smooth and load them into freeview.

Shouldn't be too hard.

 

cheers

Bruce

 

 

On Thu, 10 Jan 2019, john Anderson

wrote:

‐‐‐ Original Message ‐‐‐
On Thursday, January 10, 2019 7:40 AM, john Anderson 
 wrote:

  Dear FS experts,
For visualization purposes, is there any way to show the cerebellum and brain 
stem regions
(similar to the attached figure), this figure was published used CONN toolbox 
but I am not sure
how they were able to map functional data in brain surface and show the 
cerebellum and brain
stem with fsaverage.
I appreciate any suggestion
Jon






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Re: [Freesurfer] fsaverage, brainstem and cerebellum

[john Anderson]

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Hi Dr Bruce, I highly appreciate your guidance.
I would like to load the cerebellum and brain stem structures as an average 
structure similar to "fsaverage" , I usually use the command

tksurferfv fsaverage lh pial -overlay 

mri_tessellate or mri_mc would create a surface for every subject, how can I 
create the average of the surfaces of those structures similar to "fsaverage"?

Thanks again for any highlights
John

Hi John

you could use mri_tessellate or mri_mc to create a surface for those 
structures, then smooth them with mris_smooth and load them into freeview.

Shouldn't be too hard.

cheers

Bruce

On Thu, 10 Jan 2019, john Anderson

wrote:

‐‐‐ Original Message ‐‐‐
On Thursday, January 10, 2019 7:40 AM, john Anderson 
 wrote:

> Dear FS experts,
> For visualization purposes, is there any way to show the cerebellum and brain 
> stem regions (similar to the attached figure), this figure was published used 
> CONN toolbox but I am not sure how they were able to map functional data in 
> brain surface and show the cerebellum and brain stem with fsaverage.
> I appreciate any suggestion
> Jon___
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Re: [Freesurfer] MRI sequence parameter difference and effect on cortical thickness values

[Greve, Douglas N.,Ph.D.]

I imagine it will have some systematic effect. If your design is such 
that the two scan types are divided across your contrast of interest 
(eg, diagnosis), then including it as a nuisance regressor is probably 
fine.

On 1/3/19 4:31 PM, Arsenije Subotic wrote:
>  External Email - Use Caution
>
> Dear experts,
>
> For our study, we are planning on combining two different datasets to examine 
> cortical thickness. There is a slight difference in the inversion time (400 
> vs 650) and flip angle ( 8 vs 11) between the two datasets. I know that free 
> surfer measurements are fairly consistent across different scanner types and 
> strengths, but do you know if slight differences in mri sequence parameters 
> have an affect on cortical thickness? I was planning on adding it as a 
> covariate in our analysis just in case.
>
> Thank you!
> Arsenije
>
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Re: [Freesurfer] Questions About Effect Sizes in Vertexwise GLM Anlaysis

[Greve, Douglas N.,Ph.D.]

On 1/9/19 10:35 AM, Max Owens wrote:
>
> External Email - Use Caution
>
> Hi,
>
> I just wanted to follow up and see if there was anyone who could 
> answer my questions:
>
> 1.What is the unit of effect size for the gamma.mgh file created by 
> vertexwise GLM Analysis using mri_glmfit?
Same units as the input (ie, --y)
>
> 2.Based on two previous posts 
> (https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg52144.html 
> and 
> https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg57316.html) 
> I tried to calculate Cohen’s d in all significant clusters resulting 
> from clusterwise multiple comparison correction of a vertexwise GLM 
> using mri_glmfit. I did this by dividing the gamma.mgh file by 
> rstd.mgh to create a cohensd.mgh file (fscalc gamma.mgh div 
> ../rstd.mgh -o cohensd.mgh). Then from the output of that operation I 
> extracted the mean value in each significant cluster from my 
> vertexwise analysis using mri_segstats (mri_segstats --i cohensd.mgh 
> --seg cluster.sig.ocn.mgh --exclude 0 --o sum.dat). My understanding 
> was that this would yield the average Cohen’s d of each cluster. 
> However, if it is indeed Cohen’s d the effect sizes yielded (between 
> .01 and .02) are so small that they should be undetectable given my 
> sample size (N=1104). This leads me to believe that the outputs are 
> not in fact the average Cohen’s d of the cluster. Can anyone provide 
> any clarification of what the output file of this process means? 
> Specifically, what is the unit of effect size?
Cohen's D  is defined for a two group analysis as 
(mean1-mean2)/PooledStdDev. Do you have a two-group design? If not, then 
Cohen's D might not be the right effect size to use.
>
> Please let me know if I can clarify anything.
>
> Thanks,
>
> Max
>
> On Fri, Dec 7, 2018 at 1:02 PM Max Owens  > wrote:
>
> Hi Freesurfer Experts,
>
> I have two related questions about the measures of effect size
> that can be derived from a vertexwise GLM analyses conducted in
> Freesurfer:
>
> 1.What is the unit of effect size for the gamma.mgh file created
> by vertexwise GLM Analysis using mri_glmfit?
>
> 2.Based on two previous posts
> (https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg52144.html
> and
> https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg57316.html)
> I tried to calculate Cohen’s d in all significant clusters
> resulting from clusterwise multiple comparison correction of a
> vertexwise GLM using mri_glmfit. I did this by dividing the
> gamma.mgh file by rstd.mgh to create a cohensd.mgh file (fscalc
> gamma.mgh div ../rstd.mgh -o cohensd.mgh). Then from the output of
> that operation I extracted the mean value in each significant
> cluster from my vertexwise analysis using mri_segstats
> (mri_segstats --i cohensd.mgh --seg cluster.sig.ocn.mgh --exclude
> 0 --o sum.dat). My understanding was that this would yield the
> average Cohen’s d of each cluster. However, if it is indeed
> Cohen’s d the effect sizes yielded (between .01 and .02) are so
> small that they should be undetectable given my sample size
> (N=1104). This leads me to believe that the outputs are not in
> fact the average Cohen’s d of the cluster. Can anyone provide any
> clarification of what the output file of this process means?
> Specifically, what is the unit of effect size?
>
> Thanks in advance for your help!
>
> Max
>
>
>
> -- 
>
> Max M Owens
>
> Postdoctoral Fellow
>
> NERVE Laboratory
>
> University of Vermont
>
>
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Re: [Freesurfer] Subcortical divide parcellation

[Bruce Fischl]

Hi Huifang

sorry, we don't have tools for dividing up the subcortical segmentations. 
For cortical parcels we find the first eigenvector and divide it along that


cheers
Bruce


On Thu, 10 Jan 
2019, WANG Huifang wrote:




External Email - Use Caution


Hi Bruce,


Thank you so much for your response. 

I would like to divide them into two/three uniformed parts, not considering the 
subfields. 


Now I made some python codes to do it. I am trying to test it with the more 
datasets now. If you have
tools to do it that it will be great for me to compare. Thank you. 


Thank you so much,

Looking forward to hearing you,

Best,

Huifang

__
De : freesurfer-boun...@nmr.mgh.harvard.edu 
 de la part de
Bruce Fischl 
Envoyé : mercredi 9 janvier 2019 16:25:53
À : Freesurfer support list
Objet : Re: [Freesurfer] Subcortical divide parcellation  
Hi Huifang

what is your goal? We do have tools that will generate sub-segmentations of
some structures (thalamus, amygdala and hippocampus). These are along
anatomical lines rather than purely geometric ones.

cheers
Bruce


On Wed, 9 Jan 2019, WANG Huifang wrote:

>
> External Email - Use Caution
>
> Dear freesurfer experts,
>
>
> I would like to do subcortical divide parcellation, such as the hippocampus. 
>
>
> By my understanding in freesurfer, the cortical parcellation can be saved as 
vertices but
> subcortical parcellation is only saved as volumes. 
>
>
> There are a few ways I can do the cortical divide parcellation, seems do not 
fit
> for subcortical parcellation, such as: mris_divide_parcellation. 
>
>
> Can this function also do for the subcortical regions? 
>
> Is any other suggestion for this-subcortical divide parcellation?
>
>
> Thank you so much,
>
> Huifang
>
>
>

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Re: [Freesurfer] fsaverage, brainstem and cerebellum

[Bruce Fischl]

Hi John

you could use mri_tessellate or mri_mc to create a surface for those 
structures, then smooth them with mris_smooth and load them into freeview. 
Shouldn't be too hard.


cheers
Bruce


On Thu, 10 Jan 2019, john Anderson 
wrote:




External Email - Use Caution

Dear FS experts,
For visualization purposes, is there any way to show the cerebellum and brain 
stem regions (similar to
the attached figure), this figure was published used CONN toolbox but I am not 
sure how they were able
to map functional data in brain surface and show the cerebellum and brain stem 
with fsaverage.
I appreciate any suggestion
Jon





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Re: [Freesurfer] Pial surface error (failing dura removal)

[Rusche, Johann]

Dear Douglas,

This is just a friendly reminder concerning the data I send you. I'd much 
appreciate if there is any advice on how to advance our pial surfacing other 
than manual editing.

Thanks!

Johann



From: Rusche, Johann
Sent: Monday, January 07, 2019 1:03 PM
To: Freesurfer support list
Subject: RE: [Freesurfer] Pial surface error (failing dura removal)

Hi Douglas,

Thanks for your swift reply. I just shared a link to a Partners Dropbox folder 
with you as our group (lazargp) does not have a folder in /cluster/outgoing.

No T2 or FLAIR unfortunately. Other than MPRAGE T1 we only have fMRI and DTI 
scans.

Thanks,
Johann


From: freesurfer-boun...@nmr.mgh.harvard.edu 
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Greve, Douglas N.,Ph.D. 
[dgr...@mgh.harvard.edu]
Sent: Monday, January 07, 2019 11:05 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] Pial surface error (failing dura removal)

Do you have a T2 or a FLAIR? Can you upload the subject so we can take a look?

On 1/6/19 6:20 PM, Rusche, Johann wrote:

Dear Freesurfers,

I have been processing my T1 dataset through the longitudinal pipeline with the 
-3T flag (scanned at Martinos). Unfortunately in 50% of all subjects large 
areas of dura are being included in the pial surface.

Both gcut and adjustment of watershed parameters (down to 5) did not bring 
significant improvements. I understand intensity characteristics are very 
similar for GM and dura. However, I wonder whether you can recommend a more 
elegant solution than painfully recon-editing all brainmasks by hand.

Attached is a screenshot depicting the issue with and without gcut. I am using 
stable v6.0. Thanks for your time!

Best,
Johann

__
Johann Rusche

Graduate Research Student, Lazar Lab
Department of Psychiatry – Neurosciences
Massachusetts General Hospital




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Re: [Freesurfer] Help with Reviewer Comment

[Bruce Fischl]

Hi Shane

that's a pretty tough one to answer. Certainly some developmental 
conditions (e.g. dramatic FCDs) can mess up the thickness. It really 
depends on the details.


sorry I don't have a better answer
Bruce

On Thu, 10 Jan 2019, Shane Schofield wrote:



External Email - Use Caution

Hi Freesurfer

A reviewer asked whether there are concerns about whether Freesurfer may obtain 
accurate cortical
thickness data in people with developmental conditions - the main focus in my 
study. I did a search
and could not find any validation studies in these cohorts.  Any idea? Thanks a 
lot.

Regards,
Shane

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Re: [Freesurfer] segmentation problem

[Bruce Fischl]

Hi Manuela

you can certainly do manual editing in freeview

cheers
Bruce
On Thu, 10 Jan 2019, Manuela 
Costa wrote:




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Dear all,
We have a subject for whom we would like to do hippocampal subfield and 
amygdalar nuclei
segmentation.  Unfortunately, this subject has a large lesion in the right 
hemisphere.  Looking at the
aseg, the segmentation of the bilateral amygdala are fine, but the right 
hippocampus becomes
incorrectly segmented towards the posterior end (shown in the attached images). 
 Is there any way that
this can be corrected, manually or otherwise?  Will there be further problems 
down the line when we
proceed with the subfield segmentation?  

We are running freesurfer-linux-centos6_x86_64-dev-20181121-910b841.  

Thanks in advance!

Regards,
Manuela
--
Manuela Costa, PhD
Cognitive Neuroscientist
Lab. for Clinical Neuroscience,CTB, Madrid

[icon-envelope-tick-round-orange-animated-no-repeat-v1.gif]
Libre de virus. www.avast.com

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Re: [Freesurfer] Subcortical divide parcellation

[WANG Huifang]

External Email - Use Caution

Hi Bruce,


Thank you so much for your response.

I would like to divide them into two/three uniformed parts, not considering the 
subfields.


Now I made some python codes to do it. I am trying to test it with the more 
datasets now. If you have tools to do it that it will be great for me to 
compare. Thank you.


Thank you so much,

Looking forward to hearing you,

Best,

Huifang


De : freesurfer-boun...@nmr.mgh.harvard.edu 
 de la part de Bruce Fischl 

Envoyé : mercredi 9 janvier 2019 16:25:53
À : Freesurfer support list
Objet : Re: [Freesurfer] Subcortical divide parcellation

Hi Huifang

what is your goal? We do have tools that will generate sub-segmentations of
some structures (thalamus, amygdala and hippocampus). These are along
anatomical lines rather than purely geometric ones.

cheers
Bruce


On Wed, 9 Jan 2019, WANG Huifang wrote:

>
> External Email - Use Caution
>
> Dear freesurfer experts,
>
>
> I would like to do subcortical divide parcellation, such as the hippocampus.
>
>
> By my understanding in freesurfer, the cortical parcellation can be saved as 
> vertices but
> subcortical parcellation is only saved as volumes.
>
>
> There are a few ways I can do the cortical divide parcellation, seems do not 
> fit
> for subcortical parcellation, such as: mris_divide_parcellation.
>
>
> Can this function also do for the subcortical regions?
>
> Is any other suggestion for this-subcortical divide parcellation?
>
>
> Thank you so much,
>
> Huifang
>
>
>
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[Freesurfer] fsaverage, brainstem and cerebellum

[john Anderson]

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Dear FS experts,
For visualization purposes, is there any way to show the cerebellum and brain 
stem regions (similar to the attached figure), this figure was published used 
CONN toolbox but I am not sure how they were able to map functional data in 
brain surface and show the cerebellum and brain stem with fsaverage.
I appreciate any suggestion
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[Freesurfer] Help with Reviewer Comment

[Shane Schofield]

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Hi Freesurfer
A reviewer asked whether there are concerns about whether Freesurfer may obtain 
accurate cortical thickness data in people with developmental conditions - the 
main focus in my study. I did a search and could not find any validation 
studies in these cohorts.  Any idea? Thanks a lot.
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[Freesurfer] Problem with checking registration quality using tkregister-sess: if: Expression Syntax.

[Keri Woods]

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Hi


I’m having a problem that I’m hoping someone could help me with.


I’m trying to check the quality of the alignment of structural and
functional data, using the command:


tkregister-sess -s 20_1 -fsd bold -per-run


where 20_1 is the subject ID. Nothing opens, and I get the following error:




--

tkregister-sess logfile is /home/keri/audio2/log/tkregister-sess.log

--

Session: 20_1 

if: Expression Syntax.





I’ve opened the log file, which doesn’t shed much light on the problem. Its
contents are:





tkregister-sess log file

$Id: tkregister-sess,v 1.42 2015/12/10 22:51:31 zkaufman Exp $


setenv SUBJECTS_DIR /home/keri/recon_all/subjects

cd /home/keri/audio

/usr/local/freesurfer/fsfast/bin/tkregister-sess -s 20_1 -fsd bold -per-run


buddha

/usr/local/freesurfer/bin/tkregister2

Session: 20_1 




The SUBJECTS_DIR show here is correct.


I’ve been looking through the archives, and someone suggested checking
whether tkmedit works when having problems with tkregister. I’ve done this,
and it works fine.




On a side note, when checking the quality of registration using the command
in the format of:


tkregister-sess -s sess01 -s sess02 -s sess03 -fsd bold -per-run -bbr-sum


I get very poor results for many of the subjects (some of them are even >
1, which I didn’t think was possible). Could this be part of the problem?
The subject 20_1 I used as a example did have a fairly good result (eg
0.5090 for one run).


Thanks in advance.


Best wishes,

Keri
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[Freesurfer] segmentation problem

[Manuela Costa]

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Dear all,

We have a subject for whom we would like to do hippocampal subfield and
amygdalar nuclei segmentation.  Unfortunately, this subject has a large
lesion in the right hemisphere.  Looking at the aseg, the segmentation of
the bilateral amygdala are fine, but the right hippocampus becomes
incorrectly segmented towards the posterior end (shown in the attached
images).  Is there any way that this can be corrected, manually or
otherwise?  Will there be further problems down the line when we proceed
with the subfield segmentation?

We are running freesurfer-linux-centos6_x86_64-dev-20181121-910b841.

Thanks in advance!

Regards,
Manuela
-- 
Manuela Costa, PhD
Cognitive Neuroscientist
Lab. for Clinical Neuroscience,CTB, Madrid


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