date:20180110

Re: [Freesurfer] thickness measure in basal ganglia

2018-01-10 Thread Bruce Fischl


Hi Giovanni

the basal ganglia are little balls of gray matter, so I'm not sure how 
one would measure thickness there. We do supply volume for each nucleus


cheers
Bruce
On 
Thu, 11 Jan 2018, Giovanni de Marco wrote:




Hello,

In stats-table,
I did'n
t find the thickness of 
basal ganglia. 

Please,
 c
an we
get 
thickness 
in 
basal ganglia? 
(
Ma
ybe 
freesurfer measures
only the cortical thickness)

Many
 thanks for your response.

Giovanni

--

Tel: +33 (0) 6 74 61 01 65
demarco.giova...@gmail.com

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[Freesurfer] thickness measure in basal ganglia

2018-01-10 Thread Giovanni de Marco

Hello,







In stats-table,


I did'n

t find the thickness of




basal ganglia.























































Please, c

an we

get




thickness







in



basal ganglia?
(



Ma

ybe




freesurfer measures

only the cortical thickness)









































































































































































Many thanks for your response.





































Giovanni








-- 

Tel: +33 (0) 6 74 61 01 65
demarco.giova...@gmail.com
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Re: [Freesurfer] Nonlinear CVS registration into average brain rdinates

2018-01-10 Thread Lilla Zollei



Hi David and Noam,

I have fixed a bug in applyMorph. If you have access to the dev version of 
the code base that should be available to you in a day. If not, send and 
email to the list and we can provide you with it. Here are the steps:


(1) Run mri_cvs_register command. As the applyMorph code currently only 
works with tm3d files (not m3z) you will need to use the --nocleanup flag 
to obtain those files.


(2) Identify your coordinates in data coordinate space. This means that 
you need to find the numbers on Freeview that are next to 
"orig X []" in the braces.


(3) Run the below command:
applyMorph --template template/mri/orig.mgz \
   --transform subj/cvs/combined_tocolin27_elreg_afteraseg-norm.tm3d \
   point_list in_coords.txt out_coords.txt a

(4) The resulting coordinates will also be in data coordinate space in the 
template space.


Best, Lilla


On Fri, 15 Dec 2017, Peled, Noam wrote:



Hey David,

Have you managed to find a solution for that?


Best,

Noam

_
From: freesurfer-boun...@nmr.mgh.harvard.edu  
on behalf of Zhou, David Wei 
Sent: Thursday, April 7, 2016 3:10:38 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] Nonlinear CVS registration into average brain for 
coordinates  
Hi all,

I have a data set of 14 subjects with intracranial (both cortical and 
subcortical) electrode implants, already recon'ed in Freesurfer, with an 
average brain + surface computed of these subjects. I would like to map each 
subject's electrode coordinates (a set of RAS points) into the average brain 
using a
nonlinear transformation to account for individual deviations in surface 
topology.

I'm trying to figure out the steps that must be taken to achieve this. With my 
average brain as a template, it seems like I would use mri_cvs_register to 
produce each subject warped onto the template. After generating those warps, 
how does one apply the same warp to a set of coordinates, for example to find 
out
where my electrodes end up in the template brain? Which output file in .../cvs 
contains the data necessary to compute the coordinates in the template?

I'd appreciate any instruction, thanks!

David

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Re: [Freesurfer] hippocampal subfields in younger populations

2018-01-10 Thread Iglesias Gonzalez, Eugenio

Dear Christian,

They atlas is built using subfield segmentations on scans of older adult 
brains, but:
1. it’s also built with whole hippocampus segmentations of scans of subjects of 
a wider age range.
2. the deformation model should be able to account for large parts of the 
anatomical differences between subjects of different ages.

> I would think this would be an issue for young kids that have markedly 
> different brain volumes, but not for older kids and young adults that differ 
> less dramatically from older adults.

I agree with this statement.

I hope this helps!

/Eugenio

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


From:  on behalf of Christian Krog 
Tamnes 
Reply-To: Freesurfer support list 
Date: Wednesday, 10 January 2018 at 11:33
To: Freesurfer support list 
Subject: [Freesurfer] hippocampal subfields in younger populations


Dear FreeSurfer and hippocampal subfield segmentation developers,



I have noted that the FS6.0 hippocampal subfield segmentation procedure was 
developed using scans of older adult brains. Has the application of this method 
to kids, adolescents and/or young adults in any way been validated? Or do you 
have any thoughts regarding such use of the method?



I would think this would be an issue for young kids that have markedly 
different brain volumes, but not for older kids and young adults that differ 
less dramatically from older adults. But I would greatly appreciate any input 
regarding this.



Best regards,

Christian
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Re: [Freesurfer] Hippocampal segmentation flips on the left side

2018-01-10 Thread Iglesias Gonzalez, Eugenio

Dear Lauri,
Would you mind sending me the log of the subfield segmentation?
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 08/01/2018, 22:04, "freesurfer-boun...@nmr.mgh.harvard.edu on behalf of 
Tuominen, Lauri Johannes"  wrote:

Dear Freesurfers,
When I run freesurfer 6.0 recon-all -hippocampal-subfields-T1 command to 
segment an MNI152 template, the resulting segmentation of left hippocampus got 
flipped in left-right dimension. Otherwise the right hippocampus and other 
subcortical segmentations in the aseg-file look fine. I encountered a similar 
problem when I tried to segment a T1 acquired at 7T. I run the command both 
locally and then on launchpad. Would you know how to fix this? 

Thanks so much for your advice!  
Lauri Tuominen
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Re: [Freesurfer] reconstruction for very significant atrophy

2018-01-10 Thread Bruce Fischl

Hi Eli

it's hard to say without looking at an image. Can you upload a subject and 
point us at a spot you think is incorrect? And do you really think the 
thickness should be 0 - there is no gray matter left at all? That seems 
unlikely

cheers
Bruce


On Wed, 10 Jan 2018, Rockers, Elijah D. wrote:

> Hello,
> 
> We have some images that reflect severe atrophy in some subjects, in which 
> gray matter is virtually
> undetectable on the MRI in some regions. However, upon checking the 
> segmentations visually, the
> white/pial surfaces are reflecting a significant cortical thickness in these 
> areas.
> 
> Is there perhaps any recon-all setting that might extend the white matter 
> area out a little more
> aggressively than it does with the default settings?
> 
> Thanks,
> 
> - Eli
> 
> Houston Methodist. Leading Medicine.
> 
> Houston Methodist is ranked by U.S. News & World Report as the No. 1 hospital 
> in Texas for patient
> care. Houston Methodist is nationally ranked in 8 specialties and is 
> designated as a Magnet hospital
> for excellence in nursing. Visit us at houstonmethodist.org. Follow us at 
> twitter.com/MethodistHosp
> and facebook.com/HoustonMethodist.
> 
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> affiliates and may contain restricted and privileged material for the sole 
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> please contact the
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> 
>
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[Freesurfer] reconstruction for very significant atrophy

2018-01-10 Thread Rockers, Elijah D.

Hello,

We have some images that reflect severe atrophy in some subjects, in which gray 
matter is virtually undetectable on the MRI in some regions. However, upon 
checking the segmentations visually, the white/pial surfaces are reflecting a 
significant cortical thickness in these areas.

Is there perhaps any recon-all setting that might extend the white matter area 
out a little more aggressively than it does with the default settings?

Thanks,

- Eli

Houston Methodist. Leading Medicine. Houston Methodist is ranked by U.S. News & 
World Report as the No. 1 hospital in Texas for patient care. Houston Methodist 
is nationally ranked in 8 specialties and is designated as a Magnet hospital 
for excellence in nursing.  Visit us at  houstonmethodist.org. Follow us at  
twitter.com/MethodistHosp and facebook.com/HoustonMethodist.  
***CONFIDENTIALITY NOTICE*** This e-mail is the property of Houston Methodist 
and/or its relevant affiliates and may contain restricted and privileged 
material for the sole use of the intended recipient(s). Any review, use, 
distribution or disclosure by others is strictly prohibited. If you are not the 
intended recipient (or authorized to receive for the recipient), please contact 
the sender and delete all copies of the message. Thank you.
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Re: [Freesurfer] Error using chol - FS-FAST selxavg3-sess

2018-01-10 Thread stdp82

I have done the changes did you suggested:


mkanalysis-sess -analysis fc.rhipposeed.mni305 -mni305 -fwhm 6 -notask -taskreg 
R_Hippocampus.dat 1 -nuisreg vcsf.dat 5 -nuisreg wm.dat 5 -polyfit 5 -nskip 4 
-mcextreg -fsd rest -TR 3 -per-run -hpf 0.01 -lpf 0.1 -force


but the error persists:


GLS Beta Pass 

  run 1t= 0.0

Temporally filtering

GLS Residual Pass 

  run 1t= 0.0

Temporally filtering

Error using chol

Matrix must be positive definite.

Error in fast_selxavg3b (line 947)

Wseg = inv(chol(toeplitz(acfrun))');

>> --


IMPORTANT

Please take in account that before to update the MacOs system to version 11, 
the command run on the same data independently, if I choose -hpf 0.01 -lpf 0.1 
or viceversa.


> Il 5 gennaio 2018 alle 17.17 Douglas Greve  ha 
> scritto:
> 
> 
> You need to swap the values of the hpf and lpf. The way you have it,  you 
> are essentially filtering out everything above .01 Hz, which probably leaves 
> almost no signal
> 
> 
> On 1/3/18 3:00 PM, std...@virgilio.it mailto:std...@virgilio.it wrote:
> 
> > > 
> > mkanalysis-sess -analysis fc.lhamgseed.surf.lh -surface fsaverage 
> > lh -fwhm 6 -notask -taskreg L_Amygdala.dat 1 -nuisreg vcsf.dat 5 -nuisreg 
> > wm.dat 5 -polyfit 5 -nskip 4 -mcextreg -fsd rest -TR 3 -per-run -hpf 0.1 
> > -lpf 0.01
> > 
> > Thanks
> > 
> > > > > Il 31 dicembre 2017 alle 22.34 Douglas Greve 
> >  mailto:gr...@nmr.mgh.harvard.edu ha scritto:
> > > 
> > > 
> > > What is your mkanalysis-sess command line?
> > > 
> > > 
> > > On 12/28/17 8:53 AM, std...@virgilio.it 
> > > mailto:std...@virgilio.it wrote:
> > > 
> > > > > > > 
> > > > Running the "selxavg3-sess -s" command line in FS-FAST 
> > > > for seed-based functional connectivity analysis
> > > > 
> > > > the following errors occurred:
> > > > 
> > > > --
> > > > 
> > > > Temporally filtering
> > > > 
> > > > Error using chol
> > > > 
> > > > Matrix must be positive definite.
> > > > 
> > > > Error in fast_selxavg3b (line 947)
> > > > 
> > > > Wseg = inv(chol(toeplitz(acfrun))');
> > > > 
> > > > --
> > > > 
> > > > 
> > > > Thanks
> > > > 
> > > > Stefano
> > > > 
> > > > 
> > > > 
> > > > ___
> > > > Freesurfer mailing list
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> > > > mailto:Freesurfer@nmr.mgh.harvard.edu
> > > > 
> > > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> > > > 
> > > > > > > 
> > > > > 
> > 
> >  
> > 
> > > > > ___
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> > > mailto:Freesurfer@nmr.mgh.harvard.edu
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> > > 
> > > 
> > > The information in this e-mail is intended only for the 
> > > person to whom it is
> > > addressed. If you believe this e-mail was sent to you in 
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Re: [Freesurfer] combining masks

2018-01-10 Thread John Anderson

Yes!! this worked. Thank you so much!

I was afraid of that. You will need to either map wmparc to the brainstem space 
or the brainstem into the wmparc. Probably better to do the first. You can use 
mri_label2vol with --seg wmparc.mgz --temp brainstem.mgz --regheader wmparc.mgz 
--o wmparc.in-brainstem.mgz
swif�,7�&

>  Original Message 
> Subject: Re: combining masks
> Local Time: January 10, 2018 11:54 AM
> UTC Time: January 10, 2018 4:54 PM
> From: john.ande...@protonmail.com
> To: Freesurfer support list 
>
> Dear Dr Greeve,
> Thank you very much for the quick and detailed response.
> Before your response, I tried fslmaths instead of fslcalc and I got error 
> message complains about misorientation between the input masks.
>
> Now, I tried fslcalc and it failed as well to combine the masks due to a 
> mismatch sizes!
> Any suggestions are highly appreciated?
>
> you'll need to do it in 3 steps
>
> mri_binarize --i wmparc.mgz --match 1024 2024 3024 4024  --o wmparc.mask.mgz
>
> mri_binarize --i brainstemSsLabels.v10.mgz --match 173 --o bs.mask.mgz
>
> fscalc wmparc.mask.mgz and bs.mask.mgz -o final.mask.mgz
>
> The only problem will be if the brainstem seg is higher res than wmpar
>
> On 01/10/2018 11:10 AM, John Anderson wrote:
>
>> Dear Freesurfer experts,
>
>> I want to create mask for the midbrain and the precentral gyrus.
>
>> I used FSV6 to do the reconstruction. Then I used the flag
>
>> -brainstem-structures in recon-all to segment the brain stem.
>
>> How can I create _one mask_ that include structures from wmpac.mgz and
>
>> brainstemSsLabels.v10.mgz for instance I want to use mri_binarize to
>
>> create one mask contains the following labels
>
>> 1024 2024 3024 4024 from wmpar.mgz and 173 from
>
>> brainstemSsLabels.v10.mgz
>
>>
>
>> Any advice you provide is highly appreciated.
>
>> Thanks
>
>> John
>
>>  Original Message 
>> Subject: combining masks
>> Local Time: January 10, 2018 11:10 AM
>> UTC Time: January 10, 2018 4:10 PM
>> From: john.ande...@protonmail.com
>> To: Freesurfer support list 
>>
>> Dear Freesurfer experts,
>> I want to create mask for the midbrain and the precentral gyrus.
>> I used FSV6 to do the reconstruction. Then I used the flag 
>> -brainstem-structures in recon-all to segment the brain stem.
>> How can I create one mask that include structures from wmpac.mgz and 
>> brainstemSsLabels.v10.mgz for instance
>> I want to use mri_binarize to create one mask contains the following labels
>> 1024 2024 3024 4024 from wmpar.mgz and 173 from brainstemSsLabels.v10.mgz
>>
>> Any advice you provide is highly appreciated.
>> Thanks
>> John___
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Re: [Freesurfer] surfstat maps using freesurfer outputs on skull-stripped data

2018-01-10 Thread Duran, Tugce

I tried that and I got an error in the Mask function that excludes the 
inter-hemispheric cut in matlab.

It doesn’t like the lh/rh.pial surfaces of the fsaverage.



This is the code:



0001 function mask = SurfStatMaskCut( surf );

0002

0003 %Mask that excludes the inter-hemisphere cut.

0004 %

0005 % Usage: mask = SurfStatMaskCut( surf );

0006 %

0007 % surf.coord   = 3 x v matrix of surface coordinates, v=#vertices.

0008 %

0009 % mask = 1 x v vector, 1=inside, 0=outside, v=#vertices.

0010 %

0011 % It looks in -50thresh,

0012 % where thresh = 1.5 x arg max of a histogram of |x|.

0013

0014 f=(abs(surf.coord(2,:))<50 ...

0015 & abs(surf.coord(3,:)-10)<30 ...

0016 & abs(surf.coord(1,:))<3);

0017 b=(0:0.02:3);

0018 h=hist(abs(surf.coord(1,f)),b);

0019 t=b(find(h==max(h)))*1.5;

0020 mask=~(abs(surf.coord(1,:)) wrote:



You can map it onto fsaverage, which is made only from 40 subjects, so

there is a little more folding





On 01/09/2018 06:27 PM, Duran, Tugce wrote:

> Total N is 159. I have min # of 52 subjects for certain analyses. I used 
avgsubj. lh/rh.pial and lh/rh.thickness.10.mgh for reading surface and 
thickness data.

> Can the visualization issue be fixed?

>

> Thanks!

> Tugce

>

> dur...@iupui.edu

>

> On 1/9/18, 6:19 PM, "freesurfer-boun...@nmr.mgh.harvard.edu on behalf of 
Douglas N Greve"  wrote:

>

>  This is not entirely unexpected as the volume-based average of pial

>  surfaces will lose folds as you add subjects. How many subjects do 
you

>  have? Note that this is only a visualization issue if all your

>  underlying analysis is done on the surface.

>

>

>  On 01/08/2018 01:14 PM, Duran, Tugce wrote:

>  >

>  > Hi FS experts,

>  >

>  > I’m running SurfStat on my freesurfer skullstriped data (recon-all

>  > with –noskullstrip flag) and getting pecan shaped brain images as

>  > shown in the attached file.

>  >

>  > Do you know what freesurfer process (make_average_subject or glm or

>  > other)  is causing this issue?

>  >

>  > Thanks!

>  >

>  > *Tugce Duran, B.S.*

>  >

>  > /Research Technologist II/

>  >

>  > cid:image001.png@01D3861A.789F16C0

>  > 

>  >

>  > Indiana Alzheimer Disease Center (iADC)

>  >

>  > Office: 317-278-7015

>  >

>  > dur...@iupui.edu 

>  >

>  >

>  >

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>  --

>  Douglas N. Greve, Ph.D.

>  MGH-NMR Center

>  gr...@nmr.mgh.harvard.edu

>  Phone Number: 617-724-2358

>  Fax: 617-726-7422

>

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gr...@nmr.mgh.harvard.edu

Phone Number: 617-724-2358

Fax: 617-726-7422



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Re: [Freesurfer] combining masks

2018-01-10 Thread Douglas N Greve

I was afraid of that. You will need to either map wmparc to the 
brainstem space or the brainstem into the wmparc. Probably better to do 
the first. You can use mri_label2vol with --seg wmparc.mgz --temp 
brainstem.mgz --regheader wmparc.mgz --o wmparc.in-brainstem.mgz



On 01/10/2018 11:54 AM, John Anderson wrote:
> Dear Dr Greeve,
> Thank you very much for the quick and detailed response.
> Before your response, I tried fslmaths instead of fslcalc and I got 
> error message complains about misorientation between the input masks.
>
> Now, I tried fslcalc and it failed as well to combine the masks due to 
> a mismatch sizes!
> Any suggestions are highly appreciated?
>
>
> you'll need to do it in 3 steps
>
>
> mri_binarize --i wmparc.mgz --match 1024 2024 3024 4024  --o 
> wmparc.mask.mgz
>
>
> mri_binarize --i brainstemSsLabels.v10.mgz --match 173 --o bs.mask.mgz
>
>
> fscalc wmparc.mask.mgz and bs.mask.mgz -o final.mask.mgz
>
>
> The only problem will be if the brainstem seg is higher res than wmpar
>
>
>
> On 01/10/2018 11:10 AM, John Anderson wrote:
>
> > Dear Freesurfer experts,
>
> > I want to create mask for the midbrain and the precentral gyrus.
>
> > I used FSV6 to do the reconstruction. Then I used the flag
>
> > -brainstem-structures in recon-all to segment the brain stem.
>
> > How can I create _one mask_ that include structures from wmpac.mgz and
>
> > brainstemSsLabels.v10.mgz for instance I want to use mri_binarize to
>
> > create one mask contains the following labels
>
> > 1024 2024 3024 4024 from wmpar.mgz and 173 from
>
> > brainstemSsLabels.v10.mgz
>
> >
>
> > Any advice you provide is highly appreciated.
>
> > Thanks
>
> > John 
>
>>  Original Message 
>> Subject: combining masks
>> Local Time: January 10, 2018 11:10 AM
>> UTC Time: January 10, 2018 4:10 PM
>> From: john.ande...@protonmail.com
>> To: Freesurfer support list 
>>
>> Dear Freesurfer experts,
>> I want to create mask for the midbrain and the precentral gyrus.
>> I used FSV6 to do the reconstruction. Then I used the flag 
>> -brainstem-structures in recon-all to segment the brain stem.
>> How can I create _one mask_ that include structures from wmpac.mgz 
>> and brainstemSsLabels.v10.mgz for instance
>> I want to use mri_binarize to create one mask contains the following 
>> labels
>> 1024 2024 3024 4024 from wmpar.mgz and 173 from brainstemSsLabels.v10.mgz
>>
>> Any advice you provide is highly appreciated.
>> Thanks
>> John
>>
>
>
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

-- 
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MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
www.nmr.mgh.harvard.edu/facility/filedrop/index.html
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Re: [Freesurfer] LME

2018-01-10 Thread Tefera, Getaneh B

Dear Kersten,

Thank you so much.

When I run the procedure with left and right cortical thickness data I  get 
different phisqhat values
Phisqhat:0.2530 for the left and
Phisqhat:0.0903 for the right

The Dhat matrix is also different.

Is that Ok?

If so , shall  I consider two sample sizes  for the left and right?

With regards

Getaneh



-Original Message-
From: freesurfer-boun...@nmr.mgh.harvard.edu 
[mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Diers, Kersten 
/DZNE
Sent: Wednesday, January 10, 2018 7:10 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] LME

Hi Getaneh,

the estimates for D and phisq for a given analysis are contained within the 
data structure that is returned by the lme_fit_FS procedure.

I.e. for the tutorial data, the command was:

total_hipp_vol_stats = lme_fit_FS(X,[1 2],Y(:,1)+Y(:,2),ni);

Dhat and phisqhat are fields of the 'total_hipp_vol_stats' structure, and can 
be accessed by typing 'total_hipp_vol_stats.Dhat' and 
'total_hipp_vol_stats.phisqhat', respectively.

Best regards,

Kersten


-Original Message-
From: "Tefera, Getaneh B" 
Reply-to: Freesurfer support list 
To: Freesurfer support list 
Subject: Re: [Freesurfer] LME
Date: Tue, 9 Jan 2018 23:02:08 +0100

Hi Kersten.

Thank you very much .

I am not planning a new design for sample size calculation.

Can you please help me how to find those values?

Thank you

Getaneh 



From: freesurfer-boun...@nmr.mgh.harvard.edu  on behalf of Diers, Kersten /DZNE 
Sent: Tuesday, January 9, 2018 5:56 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] LME

Hi Getaneh,

please find my responses below.

-Original Message-
From: "Tefera, Getaneh B" 
Reply-to: Freesurfer support list 
To: freesurfer@nmr.mgh.harvard.edu 
Subject: [Freesurfer] LME
Date: Mon, 8 Jan 2018 22:54:49 +0100

Dear Freesurfer experts,


I have three groups g0, g1, and g2.

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+ …

The slope of g0 : 0 1 0 0 0 0
The slope of g1: 0 1 0 1 0  0
The slope of g2: 0 1 0 0 0 1

The slope difference between  g0 and g1: 0 0 0 1 0 0 The slope difference 
between  g0 and g2: 0 0 0 0 0 1 The slope difference between  g1 and g2: 0 0 0 
-1 0 1


1)  Is this contrast matrix correct to observe pairwise slope difference?

In the tutorial the contrast matrix   C = [zeros(3,3) [1 0 0 0 0; -1 0
1 0 0; 0 0 -1 0 1] zeros(3,6)]

This is a correct matrix, but only for the particular design given in the 
tutorial, i.e. 4 groups and several covariates. Also, it is not strictly 
speaking a pairwise test, but will indicate if there is *any* difference 
between the slopes of the groups (i.e. it will give only one
F- and p-value).
If you specifically want to test differences between particular pairs, use 
contrast matrices with just a single row.


2)  Is it necessary to combine contrast matrix of the pair difference the 
same as the tutorial?

If so, my contrast matrix can be  C=[0 0 0 1 0 0; 0 0 0 -1 0 1]

It makes sense to look at the overall effect prior to looking at pairwise 
differences. If you don't have any additional covariates, that matrix is OK for 
looking the overall effect. Otherwise, add as many columns of zeros as you have 
covariates, similar to the tutorial.

3)  How can we interpret the  result for this contrast matrix?

This is an F-test to detect if there is any difference between the slopes of 
the groups.


4)  How can I obtain B1, B2, … ?

Consider the following command from the tutorial:

total_hipp_vol_stats = lme_fit_FS(X,[1 2],Y(:,1)+Y(:,2),ni);

Then B1 and B2 will be the first two entries of total_hipp_vol_stats.Bhat


[sz1,sz2] = lme_plannedSampleSize(Zi,ZiCol,Dhat,phisqhat,effsz,...
 dr,pw,alpha,gr
_pr)


5)  For sample size calculation how can I get Dhat ( Estimated random 
effects covariance matrix) and phisqhat (Estimated intra-subject variability)?

If you are planning a new design, these estimates should be based on prior 
knowledge and can be derived e.g. from a pilot study or from the literature.

Best regards,

Kersten



With regards

Getaneh




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Re: [Freesurfer] combining masks

2018-01-10 Thread John Anderson

Dear Dr Greeve,
Thank you very much for the quick and detailed response.
Before your response, I tried fslmaths instead of fslcalc and I got error 
message complains about misorientation between the input masks.

Now, I tried fslcalc and it failed as well to combine the masks due to a 
mismatch sizes!
Any suggestions are highly appreciated?

you'll need to do it in 3 steps

mri_binarize --i wmparc.mgz --match 1024 2024 3024 4024  --o wmparc.mask.mgz

mri_binarize --i brainstemSsLabels.v10.mgz --match 173 --o bs.mask.mgz

fscalc wmparc.mask.mgz and bs.mask.mgz -o final.mask.mgz

The only problem will be if the brainstem seg is higher res than wmpar

On 01/10/2018 11:10 AM, John Anderson wrote:

> Dear Freesurfer experts,

> I want to create mask for the midbrain and the precentral gyrus.

> I used FSV6 to do the reconstruction. Then I used the flag

> -brainstem-structures in recon-all to segment the brain stem.

> How can I create _one mask_ that include structures from wmpac.mgz and

> brainstemSsLabels.v10.mgz for instance I want to use mri_binarize to

> create one mask contains the following labels

> 1024 2024 3024 4024 from wmpar.mgz and 173 from

> brainstemSsLabels.v10.mgz

>

> Any advice you provide is highly appreciated.

> Thanks

> John

>  Original Message 
> Subject: combining masks
> Local Time: January 10, 2018 11:10 AM
> UTC Time: January 10, 2018 4:10 PM
> From: john.ande...@protonmail.com
> To: Freesurfer support list 
>
> Dear Freesurfer experts,
> I want to create mask for the midbrain and the precentral gyrus.
> I used FSV6 to do the reconstruction. Then I used the flag 
> -brainstem-structures in recon-all to segment the brain stem.
> How can I create one mask that include structures from wmpac.mgz and 
> brainstemSsLabels.v10.mgz for instance
> I want to use mri_binarize to create one mask contains the following labels
> 1024 2024 3024 4024 from wmpar.mgz and 173 from brainstemSsLabels.v10.mgz
>
> Any advice you provide is highly appreciated.
> Thanks
> John___
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addressed. If you believe this e-mail was sent to you in error and the e-mail
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Re: [Freesurfer] combining masks

2018-01-10 Thread Douglas N Greve

you'll need to do it in 3 steps

mri_binarize --i wmparc.mgz --match 1024 2024 3024 4024  --o wmparc.mask.mgz

mri_binarize --i brainstemSsLabels.v10.mgz --match 173 --o bs.mask.mgz

fscalc wmparc.mask.mgz and bs.mask.mgz -o final.mask.mgz

The only problem will be if the brainstem seg is higher res than wmpar


On 01/10/2018 11:10 AM, John Anderson wrote:
> Dear Freesurfer experts,
> I want to create mask for the midbrain and the precentral gyrus.
> I used FSV6 to do the reconstruction. Then I used the flag 
> -brainstem-structures in recon-all to segment the brain stem.
> How can I create _one mask_ that include structures from wmpac.mgz and 
> brainstemSsLabels.v10.mgz for instance
> I want to use mri_binarize to create one mask contains the following 
> labels
> 1024 2024 3024 4024 from wmpar.mgz and 173 from brainstemSsLabels.v10.mgz
>
> Any advice you provide is highly appreciated.
> Thanks
> John
>
>
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

-- 
Douglas N. Greve, Ph.D.
MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
www.nmr.mgh.harvard.edu/facility/filedrop/index.html
Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/

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contains patient information, please contact the Partners Compliance HelpLine at
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[Freesurfer] combining masks

2018-01-10 Thread John Anderson

Dear Freesurfer experts,
I want to create mask for the midbrain and the precentral gyrus.
I used FSV6 to do the reconstruction. Then I used the flag 
-brainstem-structures in recon-all to segment the brain stem.
How can I create one mask that include structures from wmpac.mgz and 
brainstemSsLabels.v10.mgz for instance
I want to use mri_binarize to create one mask contains the following labels
1024 2024 3024 4024 from wmpar.mgz and 173 from brainstemSsLabels.v10.mgz

Any advice you provide is highly appreciated.
Thanks
John___
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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] Using MRS voxel mask in freesurfer surface space

2018-01-10 Thread Poortata Shirish Lalwani

Thank you so much for your response. I tried the 3rd solution and used
--trgsubject fsaverage and that works like a charm.

Best,
Pia

On Tue, Jan 9, 2018 at 6:04 PM, Douglas N Greve 
wrote:

> You probably set up the FSFAST analysis to sample onto the fsaverage
> surface (in your mkanalysis-sess command). There are a couple of things
> you can do: 1. redo the FSFAST analysis using "self" instead of
> fsaverage. 2. map the beta.nii to the subject's native anatomy using
> mri_surf2surf, or 3. Run mri_vol2surf with --trgsubject fsaverge to have
> your MRS output in fsaverage space
>
>
> On 01/09/2018 03:00 PM, Poortata Shirish Lalwani wrote:
> > Hello Freesurfer experts,
> > We are obtaining MRS data and functional MRI data on two separate days
> > for each subject. We use structural scan obtained during both these
> > sessions for the freesurfer segmentation.
> > MRS scan gives us a binary mask (nii format) in the same space as the
> > structural image obtained during that particular scan. We want to use
> > this binary mask during the surface based functional MRI analysis.
> > I tried the following process to do this:
> > 1) Registered the structural image to orig.mgz using:
> > bbregister --mov t1spgr.nii --s subject --t1 --init-fsl --reg
> > register.dat
> > 2) Applied the register.dat created by above process to the binary
> > mask to transform it into the orig.mgz space using:
> > mri_vol2vol --reg register.dat --mov gabarightxyz_mask.nii --fstarg
> > --o gabarightmask.mgh --interp nearest
> > (When I overlay this mask on orig.mgz using freeview they appear in
> > the correct position.)
> > 3) I then converted the volume to surface space using mri_vol2surf.
> > mri_vol2surf --src gabarightmask.mgh --out gabarightsurf.nii --srcreg
> > myregister.dat --hemi rh
> > However the size of this mask created by mri_vol2surf process is
> > (145236vertices) different from the size of beta.nii (163842 vertices)
> > that is created using selxavg. Is one of the above steps wrong? How to
> > resolve this discrepancy?
> >
> > Best,
> > Pia
> >
> > On Mon, Jan 8, 2018 at 2:58 PM, Poortata Shirish Lalwani
> > > wrote:
> >
> > Hi,
> > We are obtaining MRS data and functional MRI data on two separate
> > days for each subject. We use structural scan obtained during both
> > these sessions for the freesurfer segmentation. MRS scan gives us
> > a binary mask (nii format) in the same space as the structural
> > image obtained during that particular scan. We want to use this
> > binary mask during the surface based functional MRI analysis. I am
> > not sure how to transform this binary mask to the surface space.
> > Is there a way to do this?
> >
> > Best,
> > Pia
> >
> >
> >
> >
> > ___
> > Freesurfer mailing list
> > Freesurfer@nmr.mgh.harvard.edu
> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
> --
> Douglas N. Greve, Ph.D.
> MGH-NMR Center
> gr...@nmr.mgh.harvard.edu
> Phone Number: 617-724-2358
> Fax: 617-726-7422
>
> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
> www.nmr.mgh.harvard.edu/facility/filedrop/index.html
> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
>
> ___
> 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] LME

2018-01-10 Thread Diers, Kersten /DZNE

Hi Getaneh,

the estimates for D and phisq for a given analysis are contained within
the data structure that is returned by the lme_fit_FS procedure.

I.e. for the tutorial data, the command was:

total_hipp_vol_stats = lme_fit_FS(X,[1 2],Y(:,1)+Y(:,2),ni);

Dhat and phisqhat are fields of the 'total_hipp_vol_stats' structure,
and can be accessed by typing 'total_hipp_vol_stats.Dhat' and
'total_hipp_vol_stats.phisqhat', respectively.

Best regards,

Kersten


-Original Message-
From: "Tefera, Getaneh B" 
Reply-to: Freesurfer support list 
To: Freesurfer support list 
Subject: Re: [Freesurfer] LME
Date: Tue, 9 Jan 2018 23:02:08 +0100

Hi Kersten.

Thank you very much .

I am not planning a new design for sample size calculation.

Can you please help me how to find those values?

Thank you

Getaneh 



From: freesurfer-boun...@nmr.mgh.harvard.edu  on behalf of Diers, Kersten /DZNE 
Sent: Tuesday, January 9, 2018 5:56 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] LME

Hi Getaneh,

please find my responses below.

-Original Message-
From: "Tefera, Getaneh B" 
Reply-to: Freesurfer support list 
To: freesurfer@nmr.mgh.harvard.edu 
Subject: [Freesurfer] LME
Date: Mon, 8 Jan 2018 22:54:49 +0100

Dear Freesurfer experts,


I have three groups g0, g1, and g2.

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+ …

The slope of g0 : 0 1 0 0 0 0
The slope of g1: 0 1 0 1 0  0
The slope of g2: 0 1 0 0 0 1

The slope difference between  g0 and g1: 0 0 0 1 0 0
The slope difference between  g0 and g2: 0 0 0 0 0 1
The slope difference between  g1 and g2: 0 0 0 -1 0 1


1)  Is this contrast matrix correct to observe pairwise slope
difference?

In the tutorial the contrast matrix   C = [zeros(3,3) [1 0 0 0 0; -1 0
1 0 0; 0 0 -1 0 1] zeros(3,6)]

This is a correct matrix, but only for the particular design given in
the tutorial, i.e. 4 groups and several covariates. Also, it is not
strictly speaking a pairwise test, but will indicate if there is *any*
difference between the slopes of the groups (i.e. it will give only one
F- and p-value).
If you specifically want to test differences between particular pairs,
use contrast matrices with just a single row.


2)  Is it necessary to combine contrast matrix of the pair
difference the same as the tutorial?

If so, my contrast matrix can be  C=[0 0 0 1 0 0; 0 0 0 -1 0 1]

It makes sense to look at the overall effect prior to looking at
pairwise differences. If you don't have any additional covariates, that
matrix is OK for looking the overall effect. Otherwise, add as many
columns of zeros as you have covariates, similar to the tutorial.

3)  How can we interpret the  result for this contrast matrix?

This is an F-test to detect if there is any difference between the
slopes of the groups.


4)  How can I obtain B1, B2, … ?

Consider the following command from the tutorial:

total_hipp_vol_stats = lme_fit_FS(X,[1 2],Y(:,1)+Y(:,2),ni);

Then B1 and B2 will be the first two entries of
total_hipp_vol_stats.Bhat


[sz1,sz2] = lme_plannedSampleSize(Zi,ZiCol,Dhat,phisqhat,effsz,...
 dr,pw,alpha,gr
_pr)


5)  For sample size calculation how can I get Dhat ( Estimated
random effects covariance matrix) and phisqhat (Estimated intra-subject
variability)?

If you are planning a new design, these estimates should be based on
prior knowledge and can be derived e.g. from a pilot study or from the
literature.

Best regards,

Kersten



With regards

Getaneh




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Re: [Freesurfer] Is it poosible to redistribute a part of buckner_data for group work?

2018-01-10 Thread Kiyotaka Nemoto

Dear Allison,

Thank you! It will be a big help to us.

Best regards,

Kiyotaka


2018-01-10 21:17 GMT+09:00 Allison Stevens :

> Dear Kiyotaka,
> It is okay to distribute the buckner_data we post on our website for
> tutorial purposes.
> Allison
>
> On Jan 8, 2018, at 6:35 AM, Kiyotaka Nemoto  wrote:
>
> Dear FreeSurfer experts,
>
> We are planning to have a one-day neuroimaging workshop in Japan. One
> topic of the workshop is "FreeSurfer troubleshooting", in which we go
> through the online tutorial you provide (https://surfer.nmr.mgh.harvar
> d.edu/fswiki/FsTutorial/TroubleshootingData) in Japanese language.
>
> So we would like to use the buckner_data for the workshop. However, the
> problem is that some have difficulties downloading the data (It takes more
> than 2 days to download...)
>
> So I'm wondering if we can share the part of buckner_data with attendees
> for the workshop in a closed network (via a site with login requirements).
> I read through the FreeSurfer license, and README in the buckner_data, but
> it doesn't mention about redistributing the data. We would like to respect
> the license, so could you let me know if we can redistribute the part of
> buckner_data?
>
> Best regards,
>
> Kiyotaka
>
> --
> Kiyotaka Nemoto, M.D., Ph.D.
> Associate Professor
> Department of Neuropsychiatry
> Division of Clinical Medicine, Faculty of Medicine
> University of Tsukuba
> 1-1-1Tennodai Tsukuba, Ibaraki 305-8575, Japan
> E-mail: kiyot...@nemotos.net
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>
>
>
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>
>
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> is
> addressed. If you believe this e-mail was sent to you in error and the
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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.
>
>
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Re: [Freesurfer] Is it poosible to redistribute a part of buckner_data for group work?

2018-01-10 Thread Allison Stevens

Dear Kiyotaka,
It is okay to distribute the buckner_data we post on our website for tutorial 
purposes. 
Allison

On Jan 8, 2018, at 6:35 AM, Kiyotaka Nemoto  wrote:

> Dear FreeSurfer experts,
> 
> We are planning to have a one-day neuroimaging workshop in Japan. One topic 
> of the workshop is "FreeSurfer troubleshooting", in which we go through the 
> online tutorial you provide 
> (https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/TroubleshootingData) in 
> Japanese language.
> 
> So we would like to use the buckner_data for the workshop. However, the 
> problem is that some have difficulties downloading the data (It takes more 
> than 2 days to download...) 
> 
> So I'm wondering if we can share the part of buckner_data with attendees for 
> the workshop in a closed network (via a site with login requirements). I read 
> through the FreeSurfer license, and README in the buckner_data, but it 
> doesn't mention about redistributing the data. We would like to respect the 
> license, so could you let me know if we can redistribute the part of 
> buckner_data?
> 
> Best regards,
> 
> Kiyotaka
> 
> -- 
> Kiyotaka Nemoto, M.D., Ph.D.
> Associate Professor
> Department of Neuropsychiatry
> Division of Clinical Medicine, Faculty of Medicine
> University of Tsukuba
> 1-1-1Tennodai Tsukuba, Ibaraki 305-8575, Japan
> E-mail: kiyot...@nemotos.net
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
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[Freesurfer] hippocampal subfields in younger populations

2018-01-10 Thread Christian Krog Tamnes

Dear FreeSurfer and hippocampal subfield segmentation developers,



I have noted that the FS6.0 hippocampal subfield segmentation procedure was 
developed using scans of older adult brains. Has the application of this method 
to kids, adolescents and/or young adults in any way been validated? Or do you 
have any thoughts regarding such use of the method?



I would think this would be an issue for young kids that have markedly 
different brain volumes, but not for older kids and young adults that differ 
less dramatically from older adults. But I would greatly appreciate any input 
regarding this.



Best regards,

Christian
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