Re: [Freesurfer] recon-all on newborn

[Das S.]

Thanks for the reply. If you let me know, among the below list of steps of 
current recon-all, currently which is not suitable to perform on neonates MRI 
image, will really appreciate.

Autorecon Processing Stages:
Motion Correction and Conform
NU (Non-Uniform intensity normalization)
Talairach transform computation
Intensity Normalization 1
Skull Strip
EM Register (linear volumetric registration)
CA Intensity Normalization
CA Non-linear Volumetric Registration
Remove Neck
LTA with Skull
CA Label (Volumetric Labeling, ie Aseg) and Statistics
Intensity Normalization 2 (start here for control points)
White matter segmentation
Edit WM With ASeg
Fill (start here for wm edits)
Tessellation (begins per-hemisphere operations)
Smooth1
Inflate1
QSphere
Automatic Topology Fixer
Final Surfs (start here for brain edits for pial surf)
Smooth2
Inflate2
Spherical Mapping
Spherical Registration
Spherical Registration, Contralateral hemisphere
Map average curvature to subject
Cortical Parcellation - Desikan_Killiany and Christophe (Labeling)
Cortical Parcellation Statistics
Cortical Ribbon Mask
Cortical Parcellation mapping to Aseg 

BW
S Das

From: freesurfer-boun...@nmr.mgh.harvard.edu 
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Lilla Zollei 
[lzol...@nmr.mgh.harvard.edu]
Sent: 04 July 2017 22:04
To: Freesurfer support list
Subject: Re: [Freesurfer] recon-all on newborn

Hi S Das,

We are trying to release the infant pipeline by the end of the summer.

Lilla

On Tue, 4 Jul 2017, Das S. wrote:

> Dear Freesurfer expert,
> I want to perform recon-all pipeline on neonates data.Can I do so?
> I was going through some mail archives and there it is said that on T1 image 
> of neonates data we can't perform recon-all.
> But again there is another paper where it says Freesurfer can perform 
> segmentation of neonates image.
> Any input will be appreciated.
> Thanks
> S Das
>
>
> ___
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> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
>
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Re: [Freesurfer] Problem with drawing gifti contour on nifty volume in Freeview 2.0 but not in 1.0

[Ruopeng Wang]

Hi Torben,

Would it be possible to send us the volume and the surface file? 

Best,
Ruopeng

> On Jul 4, 2017, at 3:32 AM, Torben Lund  wrote:
> 
> Hello FreeSurfer Developers
> 
> I'm attempting to evaluate a segmentation result from CAT12, (sorry) with the 
> Freeview program. For version 1.0 superimposing a gifti surface on top of a 
> nifti volume works beautifully, but with the new version 2.0 the orientation 
> is messed up, for the exact same files (see screenshots in attached jpeg’s). 
> Has anybody else experienced this problem, and could it potentially be caused 
> by recent changes in the minc tools which nifti converter I know have been 
> changed between the two Freeview versions, or are they not used in Freeview.
> 
> Best
> Torben
> 
> 
> 
> 
> 
> Torben Ellegaard Lund
> Associate Professor, PhD
> Center of Functionally Integrative Neuroscience (CFIN)
> Aarhus University
> Aarhus University Hospital
> Building 10G, 5th floor, room 31
> Noerrebrogade 44
> 8000 Aarhus C
> Denmark
> Phone: +45 7846 4380
> Fax: +45 7846 4400
> http://www.cfin.au.dk 
> torbenel...@cfin.au.dk  (for official stuff)
> torbenel...@me.com (for faster response) 
> 
> 
> 
> 
> 
> 
> 
> 
> 
> ___
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[Freesurfer] petsurfer stats for multiple segmentations

[Lu Zhao]

Dear freesurfer support,

I am using the PetSurfer to process our PET data. But by default, it would only 
generate stats for the segmentation with the aparc atlas. 
However, I want to obtain the stats for different freesurfer atlases, like in 
the freesurfer outputs (aseg,stats, ?h,BA_exvivo.stats, 
?h.aparc.DKTatlas.stats, etc.)
How should I set the ‘gtmseg' to make it produce segmentations for the GTM with 
different freesurfer atlases? 
I checked the help doc of gtmseg. The annotation to use for GM/WM segmentation 
can be set using --ctx-annot --wm-annot. However, I still don’t know how 
exactly these should be set. I will be very grateful if you could give me some 
suggestions and detailed guidance to help me obtain the PetSurfer stats for 
different freesurfer segmentations.

Best regards,

Lu
 
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Re: [Freesurfer] recon-all on newborn

[Lilla Zollei]

Hi S Das,

We are trying to release the infant pipeline by the end of the summer.

Lilla

On Tue, 4 Jul 2017, Das S. wrote:

> Dear Freesurfer expert,
> I want to perform recon-all pipeline on neonates data.Can I do so?
> I was going through some mail archives and there it is said that on T1 image 
> of neonates data we can't perform recon-all.
> But again there is another paper where it says Freesurfer can perform 
> segmentation of neonates image.
> Any input will be appreciated.
> Thanks
> S Das
>
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
>
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Re: [Freesurfer] lopsided hemisphere

[Michael Davies]

Hello Bruce,


Thank you for your advice! I really appreciate it! Happy 4th July.


Kind regards, Michael


From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Bruce Fischl 

Sent: 04 July 2017 20:09:10
To: Freesurfer support list
Subject: Re: [Freesurfer] lopsided hemisphere

Hi Michael

I don't think there is really a problem here - it is just that either the
brain is oriented strangely or it indeed asymmetric. In any case the
segmentations and surfaces look accurate

cheers
Bruce
On Tue, 4 Jul 2017, Michael Davies
wrote:

>
> Hello, I have encountered a lopsided hemisphere when analysing the data.
> What procedure do i need to employ to fix the problem? Any advice would be
> greatly appreciated!
>
>
> Kind regards, Michael
>
>
>
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Re: [Freesurfer] lopsided hemisphere

[Bruce Fischl]

Hi Michael

I don't think there is really a problem here - it is just that either the 
brain is oriented strangely or it indeed asymmetric. In any case the 
segmentations and surfaces look accurate


cheers
Bruce
On Tue, 4 Jul 2017, Michael Davies 
wrote:




Hello, I have encountered a lopsided hemisphere when analysing the data.
What procedure do i need to employ to fix the problem? Any advice would be
greatly appreciated!


Kind regards, Michael  


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[Freesurfer] lopsided hemisphere

[Michael Davies]

Hello, I have encountered a lopsided hemisphere when analysing the data. What 
procedure do i need to employ to fix the problem? Any advice would be greatly 
appreciated!


Kind regards, Michael
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Re: [Freesurfer] Pial surface editing

[Bruce Fischl]

Hi Michelle

yes, you can try putting already stripped data through, or I think if you 
convert the afni skull stripped volume to $subject/mri/brainmask.mgz
recon-all should recognize that it is different from the auto stripping and 
use it instead


cheers
Bruce


On Tue, 4 Jul 2017, Michelle VanTieghem wrote:


Hello, 
I am just following up on this question.

Thanks!
Michelle

On Tue, Jun 27, 2017 at 4:46 PM, Michelle VanTieghem
 wrote:
  Hi Bruce, 
The -gcut does not appear to make any difference on our skull
stripping. I also saw that you can change flags for watershed option.
Do you recommend this? If so, how would you implement this on
freesurfer output that was already run? 

We achieve fairly good skull stripping with this dataset using afni's
skullstrip function. Would it be possible to enter the already-skull
stripped data into freesurfer? if so, how would you set this up? Right
now, I am entering the original dicom files as input to freesurfer --
is it possible to use other file formats as input? 

Thanks!
Michelle 

On Mon, Jun 12, 2017 at 4:49 PM, Bruce Fischl
 wrote:
  -gcut should do the trick

  cheers
  Bruce
  On Mon, 12 Jun 2017, Michelle VanTieghem wrote:

Hi, 
Thanks for your response. Maybe I am missing
something, but I haven't been
able to find any documentation about how to
use graph cuts skull stripping
in the freesurfer pipeline. can you please
advise?

Thanks,
Michelle

On Mon, Jun 12, 2017 at 2:48 PM, Bruce Fischl

wrote:
      Hi Michelle

      you can try using the graph cuts skull
stripping. It is more
      aggressive and more likely to remove
more skull/dura (and also
      to remove some brain)

      cheers
      Bruce
      On Mon, 12 Jun 2017, Michelle VanTieghem
wrote:

            Hello, 
            We have assessed freesurfer output
for 160+ brains,
            and about 50% have poor
            segmentation of pial matter that
includes too much
            skull.  Manual edits and
            re-running does work to improve
the problem, but is
            very time/labor
            intensive for so many scans.

            I saw on the freesurfer wiki that
you can include T2
            or Flair images to
            improve the segmentation for this
problem. However,
            we do not have these
            extra scans. What do you recommend
to do otherwise? 

            Thank you!


            --
            Michelle VanTieghem
            PhD student in Psychology
            Developmental Affective
Neuroscience Lab
            Columbia University 
            mrv2...@columbia.edu


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it is
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e-mail
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HelpLine at
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--
Michelle VanTieghem
PhD student in Psychology
Developmental Affective Neuroscience Lab
Columbia University 
mrv2...@columbia.edu


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--
Michelle VanTieghem
PhD student in Psychology
Developmental Affective Neuroscience Lab

Re: [Freesurfer] Fwd: wm topological defects

[Bruce Fischl]

Hi Manuel

it's impossible to tell from a single slice.
cheers
Bruce


On Tue, 4 Jul 2017, Manuel 
Delgado wrote:

> To illustrate the previous case here there is an image in which there is a
> discrepancy between the wm surface and the smoothwm.nofix. Is it necessary
> to fix it or not?
> Thanks
> --
> Manuel Delgado Alvarado, MD
> 
> Predoctoral Researcher
> Neuroimaging Unit, IDIVAL
> [LogoIDIVAL.PNG?ver=2015-10-14-180234-000]
> Avda. Cardenal Herrera Oria s/n
> 39011 Santander, Spain
> 
> 
> 
> 
> --
> Manuel Delgado Alvarado, MD
> 
> Predoctoral Researcher
> Neuroimaging Unit, IDIVAL
> [LogoIDIVAL.PNG?ver=2015-10-14-180234-000]
> Avda. Cardenal Herrera Oria s/n
> 39011 Santander, Spain
> 
> 
>
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Re: [Freesurfer] wm topological defects

[Bruce Fischl]

Hi Manuel

you should examine the ?h.white and ?h.pial for accuracy, and only use the 
.nofix surfaces if you are trying to figure out why the white/pial are not 
as accurate as you would like
Bruce


On Tue, 4 Jul 2017, Manuel Delgado wrote:

> Dear all:
> Regarding wm edits, it is shown in the tutorial how to proceed with "holes"
> that appear in the smoothwm.nofix. However, those holes do not necessarily
> affect the wm matter surface. So is it recommendable to check if holes in
> the smoothwm.nofix surface affect the real wm surface before correcting
> them? And, what is the purpose of the smoothwm.nofix, is it used for other
> issues?
> Thank you
> 
> --
> Manuel Delgado Alvarado, MD
> 
> Predoctoral Researcher
> Neuroimaging Unit, IDIVAL
> [LogoIDIVAL.PNG?ver=2015-10-14-180234-000]
> Avda. Cardenal Herrera Oria s/n
> 39011 Santander, Spain
> 
> 
>
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Re: [Freesurfer] Medial Surface Problem

[Bruce Fischl]

sure. Can you upload the data again to our ftp site? Don't use the filedrop 
- use ftp and make sure you include the cross and the long of all the 
timepoints for this subject, and also the coordinates of the location you 
are seeing the problem



cheers
Bruce


On Tue, 4 Jul 2017, 
Bronwyn Overs wrote:



Thanks Bruce.

Kind regards,

Bronwyn Overs
Research Assistant

Neuroscience Research Australia

Neuroscience Research Australia
Margarete Ainsworth Building
Barker Street Randwick Sydney NSW 2031 Australia
M 0411 308 769 T +61 2 9399 1883 F +61 2 9399 1265

neura.edu.au

Follow @neuraustralia on twitter Follow NeuRA on facebook Subscribe to the
NeuRA Magazine


  On 3 Jul 2017, at 11:55 pm, Bruce Fischl
   wrote:

Hi Bronwyn

not yet, but we'll get to it soon

cheers
Bruce
On Mon, 3 Jul 2017, Bronwyn Overs wrote:

  Hi Bruce,
  Just wanted to check in on the status of reviewing our
  medial surface
  problem. Any luck so far?
  Kind regards,
  Bronwyn Overs
  Research Assistant
  Neuroscience Research Australia
  Neuroscience Research Australia
  Margarete Ainsworth Building
  Barker Street Randwick Sydney NSW 2031 Australia
  M 0411 308 769 T +61 2 9399 1883 F +61 2 9399 1265
  neura.edu.au
  Follow @neuraustralia on twitter Follow NeuRA on facebook
  Subscribe to the
  NeuRA Magazine

   On 14 Jun 2017, at 9:52 am, Bronwyn Overs
  
   wrote:
  Hi Bruce,
  That's fine, thanks very much.
  Bronwyn Overs
  Research Assistant
  
  Neuroscience Research Australia
  Margarete Ainsworth Building
  Barker Street Randwick Sydney NSW 2031 Australia
  M 0411 308 769 T +61 2 9399 1883
  neura.edu.au 
  Twitter | Facebook | Subscribe
___
  _
  From: "Bruce Fischl" 
  To: "Freesurfer support list"
  
  Sent: Wednesday, 14 June, 2017 00:02:04
  Subject: Re: [Freesurfer] Medial Surface Problem
  thanks Bronwyn
  I got them. It will take a bit for us to get to as this is
  in the long
  stream and we have a new postdoc who will be taking it
  over.
  cheers
  Bruce
  On Tue, 13 Jun
  2017, Bronwyn Overs wrote:
  > Hi Bruce,
  > Sure, files have been dropped again.
  >
  > Kind regards,
  >
  > Bronwyn Overs
  > Research Assistant
  >
  > Neuroscience Research Australia
  >
  > Neuroscience Research Australia
  > Margarete Ainsworth Building
  > Barker Street Randwick Sydney NSW 2031 Australia
  > M 0411 308 769 T +61 2 9399 1883 F +61 2 9399 1265
  >
  > neura.edu.au
  >
  > Follow @neuraustralia on twitter Follow NeuRA on
  facebook Subscribe
  to the
  > NeuRA Magazine
  >
  >
  >       On 13 Jun 2017, at 11:44 am, Bruce Fischl
  >        wrote:
  >
  > Hi Bronwyn 
  > Can you filedrop it again? I don't think I have it
  > Thanks
  > Bruce
  >
  > On May 15, 2017, at 8:27 PM, Bronwyn Overs
  
  > wrote:
  >
  >       Hi Bruce,
  > Thank you for offering to take a look at this medial
  surface
  > problem.
  >
  > I have uploaded all of the relevant files to through the
  > Martinos Centre FileDrop v2.0 to your email address
  > (fis...@nmr.mgh.harvard.edu). Please let me know if you
  require
  > any additional information.
  >
  > Kind regards,
  >
  > Bronwyn Overs
  > Research Assistant
  >
  > Neuroscience Research Australia
  >
  > Neuroscience Research Australia
  > Margarete Ainsworth Building
  > Barker Street Randwick Sydney NSW 2031 Australia
  > M 0411 308 769 T +61 2 9399 1883 F +61 2 9399 1265
  >
  > neura.edu.au
  >
  > Follow @neuraustralia on twitter Follow NeuRA on
  facebook
  > Subscribe to the NeuRA Magazine
  >
  >
  >       On 5 May 2017, at 8:25 am, Bruce Fischl
  >        wrote:
  >
  > if someone can upload a dataset as well as the exact
  > coordinates of the problem I'll take a look
  >
  > cheers
  > Bruce
  >
  > On Fri, 5 May 2017, Yann Quidé wrote:
  >
  >       Hi all,
  >       We also have the same issue, any
  >       idea/suggestion?
  >       Thanks.
  >       Yann
  >
  >        On 27 Apr 2017, at 9:43 am, Bronwyn Overs
  >       
  >        wrote:
  >       Hi Mailing List,
  >       Still trying to solve the below medial surface
  >       problem. Does anyone
  >       have any ideas?
  >       Kind regards,
  >       Bronwyn Overs
  >  

[Freesurfer] MNI Coordinates

[AKUDJEDU, THEOPHILUS]

Hi All,

I am trying to visualise nodes of a brain network reconstructed using 
FreeSurfer Desikan-Killiany Atlas parcellation scheme (aparc+aseg.mgz) on Brain 
Net Viewer and Network Based Statistics software.
In order to do so, I need to upload a .txt file listing Freesurfer labels 
coordinates in MNI space. Is there any way I can get a list of MNI coordinates 
for my set of labels?

Many thanks,


Theo



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Re: [Freesurfer] Pial surface editing

[Michelle VanTieghem]

Hello,

I am just following up on this question.

Thanks!
Michelle

On Tue, Jun 27, 2017 at 4:46 PM, Michelle VanTieghem <
michelle.vantieg...@gmail.com> wrote:

> Hi Bruce,
>
> The -gcut does not appear to make any difference on our skull stripping. I
> also saw that you can change flags for watershed option. Do you recommend
> this? If so, how would you implement this on freesurfer output that was
> already run?
>
> We achieve fairly good skull stripping with this dataset using afni's
> skullstrip function. Would it be possible to enter the already-skull
> stripped data into freesurfer? if so, how would you set this up? Right now,
> I am entering the original dicom files as input to freesurfer -- is it
> possible to use other file formats as input?
>
> Thanks!
> Michelle
>
> On Mon, Jun 12, 2017 at 4:49 PM, Bruce Fischl 
> wrote:
>
>> -gcut should do the trick
>>
>>
>> cheers
>> Bruce
>> On Mon, 12 Jun 2017, Michelle VanTieghem wrote:
>>
>> Hi,
>>> Thanks for your response. Maybe I am missing something, but I haven't
>>> been
>>> able to find any documentation about how to use graph cuts skull
>>> stripping
>>> in the freesurfer pipeline. can you please advise?
>>>
>>> Thanks,
>>> Michelle
>>>
>>> On Mon, Jun 12, 2017 at 2:48 PM, Bruce Fischl <
>>> fis...@nmr.mgh.harvard.edu>
>>> wrote:
>>>   Hi Michelle
>>>
>>>   you can try using the graph cuts skull stripping. It is more
>>>   aggressive and more likely to remove more skull/dura (and also
>>>   to remove some brain)
>>>
>>>   cheers
>>>   Bruce
>>>   On Mon, 12 Jun 2017, Michelle VanTieghem wrote:
>>>
>>> Hello,
>>> We have assessed freesurfer output for 160+ brains,
>>> and about 50% have poor
>>> segmentation of pial matter that includes too much
>>> skull.  Manual edits and
>>> re-running does work to improve the problem, but is
>>> very time/labor
>>> intensive for so many scans.
>>>
>>> I saw on the freesurfer wiki that you can include T2
>>> or Flair images to
>>> improve the segmentation for this problem. However,
>>> we do not have these
>>> extra scans. What do you recommend to do otherwise?
>>>
>>> Thank you!
>>>
>>>
>>> --
>>> Michelle VanTieghem
>>> PhD student in Psychology
>>> Developmental Affective Neuroscience Lab
>>> Columbia University
>>> mrv2...@columbia.edu
>>>
>>>
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>>> and properly
>>> dispose of the e-mail.
>>>
>>>
>>>
>>>
>>> --
>>> Michelle VanTieghem
>>> PhD student in Psychology
>>> Developmental Affective Neuroscience Lab
>>> Columbia University
>>> mrv2...@columbia.edu
>>>
>>>
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>
>
> --
> Michelle VanTieghem
> PhD student in Psychology
> Developmental Affective Neuroscience Lab
> Columbia University
> mrv2...@columbia.edu
>



-- 
Michelle VanTieghem
PhD student in Psychology
Developmental Affective Neuroscience Lab
Columbia University
mrv2...@columbia.edu
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[Freesurfer] remove skull from gtmseg.mgz

[miracle ozzoude]

Hello Freesurfer,

After running the first step of PETsurfer (
https://surfer.nmr.mgh.harvard.edu/fswiki/PetSurfer). I viewed the image it
created using freeview. When I change, the color map to Lookup Table, the
image also included the skull. How can I remove the skull from
gtmseg.mgz/prevent it from showing? Any help will be appreciated. Thanks.
Please, see attached image

Best,
Paul
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[Freesurfer] Problem with drawing gifti contour on nifty volume in Freeview 2.0 but not in 1.0 - with links to files

[Torben Lund]

Hello FreeSurfer Developers

I'm attempting to evaluate a segmentation result from CAT12, (sorry) with the 
Freeview program. For version 1.0 superimposing a gifti surface on top of a 
nifti volume works beautifully (see results here: 
https://www.dropbox.com/s/lwhonnzy7n2t87x/Freeview1.0.pdf?dl=0 
 ), but with 
the new version 2.0 the orientation is messed up (see result here: 
https://www.dropbox.com/s/ma6p4batv2cc6w4/Freeview2.0.pdf?dl=0 
 ), for the 
exact same files. Has anybody else experienced this problem, and could it 
potentially be caused by recent changes in the minc tools which nifti converter 
I know have been changed between the two Freeview versions.


The issue seems to be platform independent and exist for both MacOS 10.12.15 
and linux (Ubuntu 16.04.1 LTS)

Best
Torben





Torben Ellegaard Lund
Associate Professor, PhD
Center of Functionally Integrative Neuroscience (CFIN)
Aarhus University
Aarhus University Hospital
Building 10G, 5th floor, room 31
Noerrebrogade 44
8000 Aarhus C
Denmark
Phone: +45 7846 4380
Fax: +45 7846 4400
http://www.cfin.au.dk 
torbenel...@cfin.au.dk  (for official stuff)
torbenel...@me.com (for faster response) 









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[Freesurfer] recon-all on newborn

[Das S.]

Dear Freesurfer expert,
I want to perform recon-all pipeline on neonates data.Can I do so?
I was going through some mail archives and there it is said that on T1 image of 
neonates data we can't perform recon-all.
But again there is another paper where it says Freesurfer can perform 
segmentation of neonates image.
Any input will be appreciated.
Thanks
S Das


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[Freesurfer] Fwd: wm topological defects

[Manuel Delgado]

To illustrate the previous case here there is an image in which there is a
discrepancy between the wm surface and the smoothwm.nofix. Is it necessary
to fix it or not?
Thanks
-- 
*Manuel Delgado Alvarado, MD*

*Predoctoral Researcher*
*Neuroimaging Unit, IDIVAL*

*Avda. Cardenal Herrera Oria s/n*
*39011 Santander, Spain*




-- 
*Manuel Delgado Alvarado, MD*

*Predoctoral Researcher*
*Neuroimaging Unit, IDIVAL*

*Avda. Cardenal Herrera Oria s/n*
*39011 Santander, Spain*
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[Freesurfer] wm topological defects

[Manuel Delgado]

Dear all:
Regarding wm edits, it is shown in the tutorial how to proceed with "holes"
that appear in the smoothwm.nofix. However, those holes do not necessarily
affect the wm matter surface. So is it recommendable to check if holes in
the smoothwm.nofix surface affect the real wm surface before correcting
them? And, what is the purpose of the smoothwm.nofix, is it used for other
issues?
Thank you

-- 
*Manuel Delgado Alvarado, MD*

*Predoctoral Researcher*
*Neuroimaging Unit, IDIVAL*

*Avda. Cardenal Herrera Oria s/n*
*39011 Santander, Spain*
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