Re: [Freesurfer] improving white/grey segmentation in recon -all for better volume estmation

[Bruce Fischl]

hmm, that looks pretty bad. If you upload the subject we will take a 
look. It might be a residual bias field - what are the values of the 
white matter in the brain.mgz in those regions?
On Sat, 23 Apr 2016, 
Ramtilak Gattu wrote:



Hello Bruce,

Thanks a lot for your earlier expert option suggestion in improving the
segmentation during the recon process. I am attaching a snap shot where
yellow is with expert options and red is with default options. My concern is
where I have indicated with blue arrows . Could you please suggest why is it
still failing to pick up those areas. Is it because of 

a) misregistration with the atlas
         (i)  if so where can I find the results after the non linear
registration and 
         (ii) would it be possible to improve with any more expert options
during  the registration and the segmentation subsequently.

b) or is it should be just changing the lower limit values for the WM and
higher limit values for the GM. I am not sure which way to tune the values
should I go low on WM values and go high on GM values. These are the actual
values 

mri_segment -wlo 87.7  -ghi 103.3
mris_make_surfaces -min_gray_at_white_border 79.4  -max_border_white 109.3
 -min_border_white 90  -max_csf 68.7  -max_gray 98.7 -max_gray_at_csf_border
84.7  -min_gray_at_csf_border 58.1

For example Should these be changed to 

mri_segment -wlo 80  -ghi 110

Thanks for your help in advance.

Regards
Tilak


Thanks

Regards
Tilak


From: Ramtilak Gattu
Sent: Wednesday, March 30, 2016 4:26 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] improving white/grey segmentation in recon -all
for better volume estmation

Thank you for recommending the expert options. I have run this on two
subjects (rows) and you can see the post analysis results on the right
(column) in the attached  image  . As you have mentioned it didnt work well
in the cerebellum any other ways to improve in the inferior regions?

Thanks

Regards
Tilak

From: Ramtilak Gattu
Sent: Monday, March 28, 2016 5:12 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] improving white/grey segmentation in recon -all
for better volume estmation

Thank you,

Attached is the scripts folder for one subject .

Thanks

Regards
Tilak

From: Ramtilak Gattu
Sent: Monday, March 28, 2016 4:11 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] improving white/grey segmentation in recon -all
for better volume estmation

Sorry, Actually just found out that the receiving coil is the 12 channel
head coil and the transmitting coil is the body coil. I am attaching a
snapshot showing the sag orientation of the three cases that I previously
mentioned and uploaded for your review.

>From these figures do you really think there is not enough contrast, just
wondering

1) why it worked in the bottom image and it failed in the upper two
(T1_sag_comparison.jpg)
2) it failed in the left image and did good in the right image
(T1_sag_comparison_2.jpg).

We have similar data in 25 of the subjects. Is there a way to salvage the
existing data and improve our results we will certainly follow your input in
changing the existing protocol and collect some data and run the analysis to
see if it improves the results.

One more thought is if is there any other way around to increase the
contrast by taking help from T2 image and run recon-all. Do you think it
will help?

Thanks for you help .

Regards
Tilak


From: Bruce Fischl 
Sent: Monday, March 28, 2016 11:22 AM
To: Ramtilak Gattu
Subject: Re: [Freesurfer] improving white/grey segmentation in recon -all
for better volume estmation

what was the transmit coil? I think I would either reduce the voxel sizes a
bit or not use grappa. Probably go to 1.2 mm or so, which would be a 70%
increase in SNR. That won't help the transmit bias field though if you have
one. The 8 channel can also sometimes be a problem. The 32 channel coils
work much better

On Mon, 28 Mar 2016, Ramtilak Gattu wrote:

> Hey Bruce,
>
> The scans are done on 3T Siemens TRIO and 8 coil head channel with a
GRAPPA of 2.
>
> Here is the screen shot of protocol used.
>
>https://waynestateprod-my.sharepoint.com/personal/ao3080_wayne_edu/_layouts
/15/guestaccess.aspx?guestaccesstoken=VJ0QiLxUz9fI6GCUofGHq7IAQY6k4uG50U0ic
0zBkHE%3d=034b186e0a218401590414fc271f3cf5f
>
> Thanks
>
> Regards
> Tilak
>
>
>
> 
> From: Ramtilak Gattu
> Sent: Sunday, March 27, 2016 3:23 PM
> To: Bruce Fischl
> Subject: Re: [Freesurfer] improving white/grey segmentation in recon -all
for better volume estmation
>
> Hey Bruce,
>
> I have uploaded the files in
>
>https://waynestateprod-my.sharepoint.com/personal/ao3080_wayne_edu/_layouts
/15/guestaccess.aspx?guestaccesstoken=0MdoYLvWY2ZYOdi983YqZtMFGMns%2b5WB6dN

[Freesurfer] improving white/grey segmentation in recon -all for better volume estmation

[Ramtilak Gattu]

Hello Bruce,

Thanks a lot for your earlier expert option suggestion in improving the
segmentation during the recon process. I am attaching a snap shot where
yellow is with expert options and red is with default options. My concern
is where I have indicated with blue arrows . Could you please suggest why
is it still failing to pick up those areas. Is it because of

a) misregistration with the atlas
 (i)  if so where can I find the results after the non linear
registration and
 (ii) would it be possible to improve with any more expert options
during  the registration and the segmentation subsequently.

b) or is it should be just changing the lower limit values for the WM and
higher limit values for the GM. I am not sure which way to tune the values
should I go low on WM values and go high on GM values. These are the actual
values

mri_segment -wlo 87.7  -ghi 103.3
mris_make_surfaces -min_gray_at_white_border 79.4  -max_border_white 109.3
 -min_border_white 90  -max_csf 68.7  -max_gray 98.7
-max_gray_at_csf_border 84.7  -min_gray_at_csf_border 58.1

For example Should these be changed to

mri_segment -wlo 80  -ghi 110

Thanks for your help in advance.

Regards
Tilak


Thanks

Regards
Tilak


From: Ramtilak Gattu
Sent: Wednesday, March 30, 2016 4:26 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] improving white/grey segmentation in recon -all
for better volume estmation

Thank you for recommending the expert options. I have run this on two
subjects (rows) and you can see the post analysis results on the right
(column) in the attached  image  . As you have mentioned it didnt work well
in the cerebellum any other ways to improve in the inferior regions?

Thanks

Regards
Tilak

From: Ramtilak Gattu
Sent: Monday, March 28, 2016 5:12 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] improving white/grey segmentation in recon -all
for better volume estmation

Thank you,

Attached is the scripts folder for one subject .

Thanks

Regards
Tilak

From: Ramtilak Gattu
Sent: Monday, March 28, 2016 4:11 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] improving white/grey segmentation in recon -all
for better volume estmation

Sorry, Actually just found out that the receiving coil is the 12 channel
head coil and the transmitting coil is the body coil. I am attaching a
snapshot showing the sag orientation of the three cases that I previously
mentioned and uploaded for your review.

>From these figures do you really think there is not enough contrast, just
wondering

1) why it worked in the bottom image and it failed in the upper two
(T1_sag_comparison.jpg)
2) it failed in the left image and did good in the right image
(T1_sag_comparison_2.jpg).

We have similar data in 25 of the subjects. Is there a way to salvage the
existing data and improve our results we will certainly follow your input
in changing the existing protocol and collect some data and run the
analysis to see if it improves the results.

One more thought is if is there any other way around to increase the
contrast by taking help from T2 image and run recon-all. Do you think it
will help?

Thanks for you help .

Regards
Tilak


From: Bruce Fischl 
Sent: Monday, March 28, 2016 11:22 AM
To: Ramtilak Gattu
Subject: Re: [Freesurfer] improving white/grey segmentation in recon -all
for better volume estmation

what was the transmit coil? I think I would either reduce the voxel sizes a
bit or not use grappa. Probably go to 1.2 mm or so, which would be a 70%
increase in SNR. That won't help the transmit bias field though if you have
one. The 8 channel can also sometimes be a problem. The 32 channel coils
work much better

On Mon, 28 Mar 2016, Ramtilak Gattu wrote:

> Hey Bruce,
>
> The scans are done on 3T Siemens TRIO and 8 coil head channel with a
GRAPPA of 2.
>
> Here is the screen shot of protocol used.
>
>
https://waynestateprod-my.sharepoint.com/personal/ao3080_wayne_edu/_layouts/15/guestaccess.aspx?guestaccesstoken=VJ0QiLxUz9fI6GCUofGHq7IAQY6k4uG50U0ic0zBkHE%3d=034b186e0a218401590414fc271f3cf5f
>
> Thanks
>
> Regards
> Tilak
>
>
>
> 
> From: Ramtilak Gattu
> Sent: Sunday, March 27, 2016 3:23 PM
> To: Bruce Fischl
> Subject: Re: [Freesurfer] improving white/grey segmentation in recon -all
for better volume estmation
>
> Hey Bruce,
>
> I have uploaded the files in
>
>
https://waynestateprod-my.sharepoint.com/personal/ao3080_wayne_edu/_layouts/15/guestaccess.aspx?guestaccesstoken=0MdoYLvWY2ZYOdi983YqZtMFGMns%2b5WB6dNeC3osudU%3d=000b5dcba90f2419e9bdf4ce77dfd7a5e
>
> I have also included the 001.mgz in there.
>
> Thanks
>
> Regards
> Tilak
>
> 
> From: Bruce Fischl 
> Sent: Saturday, March 26, 2016 8:35 PM
> To: 

[Freesurfer] Postdoctoral Fellow in Machine Learning in Neuroimaging

[Thomas Yeo]

Dear All,

I am looking to hire a postdoc to develop machine learning algorithms for fMRI.

Topics are flexible. Example topics include individual-subject brain
parcellations, dynamic functional connectivity, meta-analysis, neural
mass modeling, monkey-human homologies, mental disorder subtypes, etc.

Other details below.

Regards,
Thomas

Requirements: Ph.D. in computer science, electrical engineering,
statistics, computational neuroscience or related fields. The
successful applicant will work with an interdisciplinary team of
computer scientists and neuroscientists, and must be willing to learn
some neuroscience.

Research Webpage: https://sites.google.com/site/yeoyeo02/home

Compensation: Competitive and commensurate with experience

Attraction: Perform ground-breaking research at the National
University of Singapore (NUS), while enjoying the beautiful sceneries
and cultures of South-East Asia. NUS is a research-intensive
university consistently ranked among the top 30 universities in the
world 
(http://en.wikipedia.org/wiki/National_University_of_Singapore#University_rankings).

Contact: Email BT Thomas Yeo (ytho...@csail.mit.edu) with your CV.

Deadline: Whenever the position is filled.
___
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.

[Freesurfer] lh-WhiteSurfArea

[Hassan bakhshi]

Hello,

In Freesurfer stats there is a feature named lh-WhiteSurfArea.

where is exactly this WhiteSurfArea and how can I show it in freeview on
surface or image?

Kind Regards,
Hassan
___
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.

[Freesurfer] Coordinates of voxels in matlab

[Mohamed Abdelhack]

Dear all,

So I am doing some matlab based analysis where I have to align several fmri
volumes.

To load the data from Freesurfer I used f = MRIread('filename.nii') where I
have f.vol is the voxel intensity series.

How is it possible to extract the [x,y,z] coordinates of the voxels from
that structure to match the registered volume space?

Thank you,
Best,
Mohamed =)
___
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] hippo subfield segmentation new beta version (version 6)

[Eugenio Iglesias]

Hi Barbara, 
Sorry for the late response. 
- the type of sequence does not matter much as long as the contrast between 
gray and white matter is good. 
- the resolution is important, because you need to be able to see the internal 
thin layer of white matter in the hippocampus to be able to infer its internal 
structure; otherwise, the segmentation of the internal boundarie will indeed be 
dominated by the prior knowledge, rather than the intensities. 
- the algorithm operates at 0.33mm (isotropic) resolution; the segmentation is 
provided both at that resolution and at 1mm isotropic (FS space); please see 
the details in the wiki: 
https://surfer.nmr.mgh.harvard.edu/fswiki/HippocampalSubfields 
If you send me the T2FLAIR and T2STIR images for a sample subject, I can take a 
look and give you more accurate answers ;-) 
Cheers, 
Eugenio 

Juan Eugenio Iglesias 
Postdoctoral researcher BCBL 
www.jeiglesias.com 
www.bcbl.eu 

Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer 


From: "Barbara Kreilkamp"  
To: "Freesurfer support list"  
Sent: Friday, April 22, 2016 5:28:44 PM 
Subject: [Freesurfer] hippo subfield segmentation new beta version (version 6) 

Dear all, 

Would you please help me on this one? 
Thank you, 
best wishes, 
Barbara 


 Forwarded Message  
Subject:hippo subfield segmentation new beta version (version 6) 
Date:   Wed, 20 Apr 2016 11:45:02 +0100 
From:   Barbara Kreilkamp  
To: Freesurfer support list  

Dear all,

I've been reading the manuscript on version 6 freesurfer hippocampal 
subfield segmentation "A computational atlas of the hippocampal 
formation using ex vivo, ultra-high resolution MRI: application to 
adaptive segmentation of in vivo MRI"

Can you please tell me if the type of sequence (e.g. coronal T2FLAIR vs 
T2STIR) and voxel sizes of .4x.4x2mm^3 vs .4x.4x4mm^3 really make a 
difference for this multi-modal algorithm?
I previously ran recon-all on 1mm isotropic T1-w scans all with similar 
contrast.

It seems that the mesh fitting in version 6 is driven by the relation of 
the subfields to each other rather than by contrast or signal 
intensities; and also I notice the algorithm brings everything to 
isotropic space anyway.

Is this correct?
Do you see a major methodological issue when using T2FLAIR (.4x.4x4mm^3) 
and T2STIR (.4x.4x2mm^3) subfield volumes together?

Thank you very much,
Best wishes,
Barbara

P.s. as a side-note, I've not noticed any major differences in subfield 
segmentations visually, when comparing segmentations via these two 
different T2 scans. 



___ 
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. 
___
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.