Re: [Freesurfer] contrast

[Dave Yas]

Thank you very much again Dough, I was hoping that i understood how to make a 
contrast!

Thank you!
To: freesurfer@nmr.mgh.harvard.edu
From: gr...@nmr.mgh.harvard.edu
Date: Thu, 9 Jun 2016 22:10:04 -0400
Subject: Re: [Freesurfer] contrast


  

  
  
I responded in the body of the email



On 6/9/16 7:57 PM, Dave Yas wrote:



  
  Helllo!



That was an empty email!

  



> To: freesurfer@nmr.mgh.harvard.edu

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

  > Date: Thu, 9 Jun 2016 16:33:48 -0400

  > Subject: Re: [Freesurfer] contrast

  > 

  > 

  > 

  > On 06/08/2016 11:40 PM, Dave Yas wrote:

  > > Thank you very much Dough!

  > >

  > > I need to check 4 contrasts. I made them based on
  the freesurfer page, 

  > > but cant decide if i interpreted them right!

  > > Are my contrasts Ok?

  > >

  > > If classes are:

  > > Patients, healthy control

  > >

  > > and variables are:

  > > Age, TIV, father age, mother age.

  > >

  > > Are these contrasts ok?

  > >

  > > R# = 2* (4+1) = 10

  > >

  > > *contrast1:* 0 0 0 0 0 0 -1 1 -1 1>> checking
  the differences between 

  > > groups in terms of father and mother age regression
  out the effect of 

  > > age and TIV

  > That will effectively compute the difference between the
  mean(father 

  > age + mother age), ie, it would be like analyzing with a
  regressor 

  > created by adding the father age and mother age (ie, mean
  parent age). 

  > Is that what you want?

  > >

  > > *contrast2:* 0 0 0 0 0 0 -1 1 0 0

  > > 0 0 0 0 0 0 0 0 1 -1 >> checking the
  differences 

  > > between groups in terms of father or mother age
  regression out the 

  > > effect of age and TIV

  > This will be significant if either the father age is diff
  OR the mother 

  > age is diff (or some combination thereof). It will be
  similar to 

  > contrast1 but not identical.

  > >

  > > *contrast3:* 0 0 0 0 0 0 -1 1 0 0 >> checking
  the differences between 

  > > groups in terms of father age regression out the
  effect of age and TIV 

  > > and mother age

  > Yes

  > >

  > > *contrast4: *0 0 0 0 0 0 0 0 -1 1 >> checking
  the differences between 

  > > groups in terms of mother age regression out the
  effect of age and TIV 

  > > and father age

  > Yes

  > >

  > > Yas

  > >

  > >

  > >

  > >
  


  > > To: freesurfer@nmr.mgh.harvard.edu

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

  > > Date: Wed, 8 Jun 2016 09:38:18 -0400

  > > Subject: Re: [Freesurfer] Coordinate system in
  mris_convert

  > >

  > >

  > > Try the group analysis tutorial

  > >
  http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis

  > >

  > > On 6/8/16 2:39 AM, Dave Yas wrote:

  > >

  > > Hello all,

  > >

  > > I'm new to surface analysis.

  > >

  > > I have 2 groups (patient and healthy control) that i
  want to check

  > > differences between.

  > > I want to perform cortical thickness/ surface
  analysis.

  > > My categories are

  > > Patients, healthy control, age, TIV, father age,
  mother age.

  > > Where age & TIV are covariates of no interest.
  and father and

  > > mother age are covariates of interest.

  > >

  > > I have already preprocessed the data (recon-all),
  but how can i

  > > proceed?

  > > Any online guide on steps for surface analysis? also
  making a

  > > design such as the above?

  > >

  > > Yas

  > >

  > >

  > >

  > > ___

  > > Freesurfer mailing list

  > > Freesurfer@nmr.mgh.harvard.edu
  

  > >
  https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

  > >

  > >

  > >

  > > ___
  Freesurfer mailing 

  > > list Freesurfer@nmr.mgh.harvard.edu 

  > >
  https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
  The 

  > > information in 

Re: [Freesurfer] contrast

[Douglas Greve]

I responded in the body of the email

On 6/9/16 7:57 PM, Dave Yas wrote:

/*Helllo!

That was an empty email!
*/

> To: freesurfer@nmr.mgh.harvard.edu
> From: gr...@nmr.mgh.harvard.edu
> Date: Thu, 9 Jun 2016 16:33:48 -0400
> Subject: Re: [Freesurfer] contrast
>
>
>
> On 06/08/2016 11:40 PM, Dave Yas wrote:
> > Thank you very much Dough!
> >
> > I need to check 4 contrasts. I made them based on the freesurfer 
page,

> > but cant decide if i interpreted them right!
> > Are my contrasts Ok?
> >
> > If classes are:
> > Patients, healthy control
> >
> > and variables are:
> > Age, TIV, father age, mother age.
> >
> > Are these contrasts ok?
> >
> > R# = 2* (4+1) = 10
> >
> > *contrast1:* 0 0 0 0 0 0 -1 1 -1 1>> checking the differences between
> > groups in terms of father and mother age regression out the effect of
> > age and TIV
> That will effectively compute the difference between the mean(father
> age + mother age), ie, it would be like analyzing with a regressor
> created by adding the father age and mother age (ie, mean parent age).
> Is that what you want?
> >
> > *contrast2:* 0 0 0 0 0 0 -1 1 0 0
> > 0 0 0 0 0 0 0 0 1 -1 >> checking the differences
> > between groups in terms of father or mother age regression out the
> > effect of age and TIV
> This will be significant if either the father age is diff OR the mother
> age is diff (or some combination thereof). It will be similar to
> contrast1 but not identical.
> >
> > *contrast3:* 0 0 0 0 0 0 -1 1 0 0 >> checking the differences between
> > groups in terms of father age regression out the effect of age and 
TIV

> > and mother age
> Yes
> >
> > *contrast4: *0 0 0 0 0 0 0 0 -1 1 >> checking the differences between
> > groups in terms of mother age regression out the effect of age and 
TIV

> > and father age
> Yes
> >
> > Yas
> >
> >
> >
> > 


> > To: freesurfer@nmr.mgh.harvard.edu
> > From: gr...@nmr.mgh.harvard.edu
> > Date: Wed, 8 Jun 2016 09:38:18 -0400
> > Subject: Re: [Freesurfer] Coordinate system in mris_convert
> >
> >
> > Try the group analysis tutorial
> > http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis
> >
> > On 6/8/16 2:39 AM, Dave Yas wrote:
> >
> > Hello all,
> >
> > I'm new to surface analysis.
> >
> > I have 2 groups (patient and healthy control) that i want to check
> > differences between.
> > I want to perform cortical thickness/ surface analysis.
> > My categories are
> > Patients, healthy control, age, TIV, father age, mother age.
> > Where age & TIV are covariates of no interest. and father and
> > mother age are covariates of interest.
> >
> > I have already preprocessed the data (recon-all), but how can i
> > proceed?
> > Any online guide on steps for surface analysis? also making a
> > design such as the above?
> >
> > Yas
> >
> >
> >
> > ___
> > Freesurfer mailing list
> > Freesurfer@nmr.mgh.harvard.edu 
> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> >
> >
> >
> > ___ 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
>
> --
> 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


___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


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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 error and the e-mail
contains patient information, please contact the Partners 

[Freesurfer] wm.mgz edits amygdala hippocampus cerebral cortex

[marco mcsweeney]

Dear all Freesurfer users,
I have a few questions regarding wm.mgz edits. 
I am very new to this area and have only recently started using Freesurfer so 
please excuse me if my questions appear naive or misinformed.
I have managed to make most of the necessary edits needed to fix skullstrip 
errors, intensity normalization errors and pial errors, but I am a bit stuck 
when it comes to fixing topological defects.
My question relates to what should or should not be included in the wm.mgz. 
Apart from the optic chiasm, which I have removed, is it normal to have, what 
appear to be, multiple specs included in the wm.mgz which when the aseg is 
loaded turn out to be parts of the amygdala and hippocampus. When I view the 
smoothwm.nofix these appear as jagged shard like shapes protruding out from the 
surface. In one publication I saw recently it was suggested that these should 
be removed but should this be done if they are parts of the amygdala and 
hippocampus. I am worried about this as these are the 2 main subcortical areas 
I will be focusing on.
Also, is it normal for the wm.mgz to include parts of the cerebral cortex 
(labelled as such in the aseg).
Also, most of the scans I am working with have numerous holes and handles and 
this is taking a very long time to fix. I have tried to run the automatic 
topology fixer again. This has helped a bit but the scans still require a lot 
of edits. Could this be down to the quality of the scans or could it be that I 
have edited too much - control points for example. I have followed the advice 
given and have tried not to make too many edits, but having said that it has 
taken me a very long time.
Any advice in relation to any of these questions would be very very very much 
appreciated.
Best wishes
fuzzy ___
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] contrast

[Dave Yas]

Helllo!

That was an empty email!
  

> To: freesurfer@nmr.mgh.harvard.edu
> From: gr...@nmr.mgh.harvard.edu
> Date: Thu, 9 Jun 2016 16:33:48 -0400
> Subject: Re: [Freesurfer] contrast
> 
> 
> 
> On 06/08/2016 11:40 PM, Dave Yas wrote:
> > Thank you very much Dough!
> >
> > I need to check 4 contrasts. I made them based on the freesurfer page, 
> > but cant decide if i interpreted them right!
> > Are my contrasts Ok?
> >
> > If classes are:
> > Patients, healthy control
> >
> > and variables are:
> > Age, TIV,  father age, mother age.
> >
> > Are these contrasts ok?
> >
> > R# = 2* (4+1) = 10
> >
> > *contrast1:* 0 0 0 0 0 0 -1 1 -1 1>> checking the differences between 
> > groups in terms of father and mother age regression out the effect of 
> > age and TIV
> That will effectively compute the  difference between the mean(father 
> age + mother age), ie, it would be like analyzing with a regressor 
> created by adding the father age and mother age (ie, mean parent age). 
> Is that what you want?
> >
> > *contrast2:* 0 0 0 0 0 0 -1 1 0 0
> >0 0 0 0 0 0 0 0 1 -1 >> checking the differences 
> > between groups in terms of father or mother age regression out the 
> > effect of age and TIV
> This will be significant if either the father age is diff OR the mother 
> age is diff (or some combination thereof). It will be similar to 
> contrast1 but not identical.
> >
> > *contrast3:* 0 0 0 0 0 0 -1 1 0 0 >> checking the differences between 
> > groups in terms of father age regression out the effect of age and TIV 
> > and  mother age
> Yes
> >
> > *contrast4: *0 0 0 0 0 0 0 0 -1 1 >> checking the differences between 
> > groups in terms of mother age regression out the effect of age and TIV 
> > and  father age
> Yes
> >
> > Yas
> >
> >
> >
> > 
> > To: freesurfer@nmr.mgh.harvard.edu
> > From: gr...@nmr.mgh.harvard.edu
> > Date: Wed, 8 Jun 2016 09:38:18 -0400
> > Subject: Re: [Freesurfer] Coordinate system in mris_convert
> >
> >
> > Try the group analysis tutorial
> > http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis
> >
> > On 6/8/16 2:39 AM, Dave Yas wrote:
> >
> > Hello all,
> >
> > I'm new to surface analysis.
> >
> > I have 2 groups (patient and healthy control) that i want to check
> > differences between.
> > I want to perform cortical thickness/ surface analysis.
> > My categories are
> >   Patients, healthy control, age, TIV,  father age, mother age.
> > Where age & TIV are covariates of no interest. and father and
> > mother age are covariates of interest.
> >
> > I have already preprocessed the data (recon-all), but how can i
> > proceed?
> > Any online guide on steps for surface analysis? also making a
> > design such as the above?
> >
> > Yas
> >
> >
> >
> > ___
> > Freesurfer mailing list
> > Freesurfer@nmr.mgh.harvard.edu 
> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> >
> >
> >
> > ___ 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
> 
> -- 
> 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
  ___
Freesurfer mailing list
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 error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
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Re: [Freesurfer] Coregister the CT image and MRI image

[HARI GURAGAIN]

Dear Douglas,

I have used the same file as you pointed, but it keeps on showing the same 
error message. I copied the file to my /Applications/freesurfer/bin directory 
but it still shows the same error message:
>> ‘dyld: Library not loaded: @executable_path/../lib/gcc/lib/libgomp.1.dylib’
>> Referenced from: /Applications/freesurfer/bin/mri_coreg.mac
>> Reason: image not found
>> Trace/BPT trap:5


Does it have something to do with the library issue with mac?
Any help is appreciated.
Thank you,


> On Jun 9, 2016, at 5:45 PM, Douglas N Greve  wrote:
> 
> try
> ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mri_coreg.mac
> 
> 
> 
> On 06/09/2016 06:21 PM, HARI GURAGAIN wrote:
>> Dear Douglas,
>> 
>> The executable is not working as it says ‘Library not loaded: 
>> @executable_path/../lib/gcc/lib/libgomp.1.dylib’
>> Referenced from: /Applications/freesurfer/bin/mri_coreg.mac
>> Reason: image not found
>> Trace/BPT trap:5
>> 
>> I am currently using the freeview: Version 1.0 and the operating system is: 
>> OS X EI Captain Version: 10.11.5
>> I wonder if the file you pointed works for the mac? Should I reinstall the 
>> freeview?
>> Any help would be greatly appreciated.
>> 
>> Thank you,
>> 
>> Hari
>> 
>> 
>>> On Jun 9, 2016, at 4:28 PM, Douglas N Greve  
>>> wrote:
>>> 
>>> No, it is not the same command line. If you run it without args, it will
>>> give you some info, but it is basically
>>> 
>>> mri_coreg --mov vol1.nii --targ vol2.nii --reg v1to2.lta
>>> 
>>> 
>>> On 06/09/2016 05:22 PM, HARI GURAGAIN wrote:
 Thank you Douglas.
 One more thing: Is there any syntax how to use it? I wonder if it is same 
 as the mri_robust_register?
 
 
> On Jun 9, 2016, at 3:43 PM, Douglas N Greve  
> wrote:
> 
> I don't think robust register will do cross-modal. You may be better off
> using mri_coreg, which you can get from here
> 
> ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mri_coreg
> 
> 
> On 06/09/2016 01:58 PM, HARI GURAGAIN wrote:
>> Dear Freesurfer community,
>> 
>> I am relatively new to this community.
>> 
>> I was trying to register the CT image and the MRI images (MRI as a the
>> target volume and CT as the movable volume). I used the
>> mri_robust_register to to do the registration as below:
>> 
>> /mri_robust_register --mov vol1.nii --dst vol2.nii --lta v1to2.lta
>> --mapmov v1to2.nii --weights v1to2-weights.mii --iscale —satit /
>> 
>> The problem is that:  after register, the new image (v1to2.nii) is not
>> exactly aligned with the original MRI image (vol2.nii). It gives a
>> very different output. I wonder if I am missing anything here or I
>> need to do some extra steps after the above command in order to get
>> the correct alignment of the two images. I was hoping to get the
>> resultant image should be well orient with the target volume image
>> (vol2.nii image in my case).
>> 
>> I really appreciate any help here.
>> 
>> Hari Guragain
>> 
>> 
>> 
>> ___
>> 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.
> 
 ___
 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
>>> 

Re: [Freesurfer] Coregister the CT image and MRI image

[Douglas N Greve]

try
ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mri_coreg.mac



On 06/09/2016 06:21 PM, HARI GURAGAIN wrote:
> Dear Douglas,
>
> The executable is not working as it says ‘Library not loaded: 
> @executable_path/../lib/gcc/lib/libgomp.1.dylib’
> Referenced from: /Applications/freesurfer/bin/mri_coreg.mac
> Reason: image not found
> Trace/BPT trap:5
>
> I am currently using the freeview: Version 1.0 and the operating system is: 
> OS X EI Captain Version: 10.11.5
> I wonder if the file you pointed works for the mac? Should I reinstall the 
> freeview?
> Any help would be greatly appreciated.
>
> Thank you,
>
> Hari
>
>
>> On Jun 9, 2016, at 4:28 PM, Douglas N Greve  
>> wrote:
>>
>> No, it is not the same command line. If you run it without args, it will
>> give you some info, but it is basically
>>
>> mri_coreg --mov vol1.nii --targ vol2.nii --reg v1to2.lta
>>
>>
>> On 06/09/2016 05:22 PM, HARI GURAGAIN wrote:
>>> Thank you Douglas.
>>> One more thing: Is there any syntax how to use it? I wonder if it is same 
>>> as the mri_robust_register?
>>>
>>>
 On Jun 9, 2016, at 3:43 PM, Douglas N Greve  
 wrote:

 I don't think robust register will do cross-modal. You may be better off
 using mri_coreg, which you can get from here

 ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mri_coreg


 On 06/09/2016 01:58 PM, HARI GURAGAIN wrote:
> Dear Freesurfer community,
>
> I am relatively new to this community.
>
> I was trying to register the CT image and the MRI images (MRI as a the
> target volume and CT as the movable volume). I used the
> mri_robust_register to to do the registration as below:
>
> /mri_robust_register --mov vol1.nii --dst vol2.nii --lta v1to2.lta
> --mapmov v1to2.nii --weights v1to2-weights.mii --iscale —satit /
>
> The problem is that:  after register, the new image (v1to2.nii) is not
> exactly aligned with the original MRI image (vol2.nii). It gives a
> very different output. I wonder if I am missing anything here or I
> need to do some extra steps after the above command in order to get
> the correct alignment of the two images. I was hoping to get the
> resultant image should be well orient with the target volume image
> (vol2.nii image in my case).
>
> I really appreciate any help here.
>
> Hari Guragain
>
>
>
> ___
> 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
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 e-mail
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 HelpLine at
 http://www.partners.org/complianceline . If the e-mail was sent to you in 
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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
>>
>> 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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>
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> 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: 

Re: [Freesurfer] Coregister the CT image and MRI image

[HARI GURAGAIN]

Dear Douglas,

The executable is not working as it says ‘Library not loaded: 
@executable_path/../lib/gcc/lib/libgomp.1.dylib’ 
Referenced from: /Applications/freesurfer/bin/mri_coreg.mac 
Reason: image not found
Trace/BPT trap:5

I am currently using the freeview: Version 1.0 and the operating system is: OS 
X EI Captain Version: 10.11.5
I wonder if the file you pointed works for the mac? Should I reinstall the 
freeview? 
Any help would be greatly appreciated.

Thank you,

Hari 


> On Jun 9, 2016, at 4:28 PM, Douglas N Greve  wrote:
> 
> No, it is not the same command line. If you run it without args, it will 
> give you some info, but it is basically
> 
> mri_coreg --mov vol1.nii --targ vol2.nii --reg v1to2.lta
> 
> 
> On 06/09/2016 05:22 PM, HARI GURAGAIN wrote:
>> Thank you Douglas.
>> One more thing: Is there any syntax how to use it? I wonder if it is same as 
>> the mri_robust_register?
>> 
>> 
>>> On Jun 9, 2016, at 3:43 PM, Douglas N Greve  
>>> wrote:
>>> 
>>> I don't think robust register will do cross-modal. You may be better off
>>> using mri_coreg, which you can get from here
>>> 
>>> ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mri_coreg
>>> 
>>> 
>>> On 06/09/2016 01:58 PM, HARI GURAGAIN wrote:
 Dear Freesurfer community,
 
 I am relatively new to this community.
 
 I was trying to register the CT image and the MRI images (MRI as a the
 target volume and CT as the movable volume). I used the
 mri_robust_register to to do the registration as below:
 
 /mri_robust_register --mov vol1.nii --dst vol2.nii --lta v1to2.lta
 --mapmov v1to2.nii --weights v1to2-weights.mii --iscale —satit /
 
 The problem is that:  after register, the new image (v1to2.nii) is not
 exactly aligned with the original MRI image (vol2.nii). It gives a
 very different output. I wonder if I am missing anything here or I
 need to do some extra steps after the above command in order to get
 the correct alignment of the two images. I was hoping to get the
 resultant image should be well orient with the target volume image
 (vol2.nii image in my case).
 
 I really appreciate any help here.
 
 Hari Guragain
 
 
 
 ___
 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.
>>> 
>> 
>> ___
>> 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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> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


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Re: [Freesurfer] converting ME-MPRAGE files

[Douglas N Greve]

That tells you there is one "series" in that folder. The series here 
means a volume, though there are many dicom files. 
dicomdir/mr_0006-e02/3d_t1_memprage-00533.dcm is just one in the series. 
To use this, you can run

recon-all -s yoursubject -all -i 
dicomdir/mr_0006-e02/3d_t1_memprage-00533.dcm

or

mri_convert dicomdir/mr_0006-e02/3d_t1_memprage-00533.dcm output.nii.gz





On 06/09/2016 05:11 PM, Limachia, Gaurang (NIH/NINDS) [F] wrote:
> Hello All,
>
> We have acquired our anatomical images on a Siemens scanner as 
> multiecho MPRAGE sequence (4 echos), and wish to unpack the runs so we 
> can perform morphometric analysis using FreeSurfer. What is the 
> optimal way to convert the DICOM files so we can use them with 
> FreeSurfer tools? Specifically, what command line do you recommend for 
> dcmunpack?
>
> When running the command: dcmunpack –src dicomdir  we get the 
> following output:
> Found 1 unique series: 6
> 6 3D_T1_MEMPRAGE 7.27 2530 7 unknown ROW 650 
> dicomdir/mr_0006-e02/3d_t1_memprage-00533.dcm
> Not sure how to interpret this.
>
> Thanks.
>
> Gaurang Limachia
>
>
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> 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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addressed. If you believe this e-mail was sent to you in error and the e-mail
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but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

Re: [Freesurfer] Coregister the CT image and MRI image

[Douglas N Greve]

No, it is not the same command line. If you run it without args, it will 
give you some info, but it is basically

mri_coreg --mov vol1.nii --targ vol2.nii --reg v1to2.lta


On 06/09/2016 05:22 PM, HARI GURAGAIN wrote:
> Thank you Douglas.
> One more thing: Is there any syntax how to use it? I wonder if it is same as 
> the mri_robust_register?
>
>
>> On Jun 9, 2016, at 3:43 PM, Douglas N Greve  
>> wrote:
>>
>> I don't think robust register will do cross-modal. You may be better off
>> using mri_coreg, which you can get from here
>>
>> ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mri_coreg
>>
>>
>> On 06/09/2016 01:58 PM, HARI GURAGAIN wrote:
>>> Dear Freesurfer community,
>>>
>>> I am relatively new to this community.
>>>
>>> I was trying to register the CT image and the MRI images (MRI as a the
>>> target volume and CT as the movable volume). I used the
>>> mri_robust_register to to do the registration as below:
>>>
>>> /mri_robust_register --mov vol1.nii --dst vol2.nii --lta v1to2.lta
>>> --mapmov v1to2.nii --weights v1to2-weights.mii --iscale —satit /
>>>
>>> The problem is that:  after register, the new image (v1to2.nii) is not
>>> exactly aligned with the original MRI image (vol2.nii). It gives a
>>> very different output. I wonder if I am missing anything here or I
>>> need to do some extra steps after the above command in order to get
>>> the correct alignment of the two images. I was hoping to get the
>>> resultant image should be well orient with the target volume image
>>> (vol2.nii image in my case).
>>>
>>> I really appreciate any help here.
>>>
>>> Hari Guragain
>>>
>>>
>>>
>>> ___
>>> 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.
>>
>
> ___
> 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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Re: [Freesurfer] Resampling the parametric map of brain activations onto a surface

[Zhao, Yue]

Thanks again. I will follow the new instructions!

Yue


From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Douglas N Greve 

Sent: Thursday, June 09, 2016 4:10:17 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] Resampling the parametric map of brain activations 
onto a surface

That one is out of date; we'll delete it. Thanks for pointing it out and
sorry for our wiki pointing you in the wrong direction. We're in the
process of weeding it out...

On 06/09/2016 04:54 PM, Zhao, Yue wrote:
> Hi Douglas,
>
> This is the instruction I am using.
> https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/FuncOverlay
>
> I cannot insert the picture in this email. I attach it. Hope it helps.
>
> Thanks very much!
>
> Yue
>
> 
> From: freesurfer-boun...@nmr.mgh.harvard.edu 
>  on behalf of Douglas N Greve 
> 
> Sent: Thursday, June 09, 2016 3:38:43 PM
> To: freesurfer@nmr.mgh.harvard.edu
> Subject: Re: [Freesurfer] Resampling the parametric map of brain activations 
> onto a surface
>
> Sorry for the delay. I can't see the image. Also, what instructions are
> you following? They look pretty old.
>
> check out our multimodal tutorial instead
> https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/MultiModal_freeview
>
>
> On 06/09/2016 10:19 AM, Zhao, Yue wrote:
>> Hi All,
>>
>>
>> I am not sure if the question is successfully posted. If the post is
>> there, does anyone has any idea? Thanks a lot!
>>
>>
>> Yue
>>
>> 
>> *From:* freesurfer-boun...@nmr.mgh.harvard.edu
>>  on behalf of Zhao, Yue
>> 
>> *Sent:* Tuesday, June 07, 2016 4:15:20 PM
>> *To:* freesurfer@nmr.mgh.harvard.edu
>> *Subject:* [Freesurfer] Resampling the parametric map of brain
>> activations onto a surface
>>
>> Hi All,
>>
>>
>> I am using a Ubuntu FreeSurfer v5.3.0 in the VirtualBox. I am trying
>> to overlay a parametric map onto a FreeSurfer surface. Here are the
>> tutorial codes I found:
>>
>> 1. To resample the paramatric map onto the individual's surface:
>>
>> mri_vol2surf --src spm001.img  --srcreg register.dat --hemi lh --projfrac 
>> 0.5 --out ./spm001-lh.w --out_type paint
>> 2. Visualize and overlay:
>> qsurfer -stat spm001 -hemi lh -subject bert-brf
>> 3. Configure the image by selecting "View -> Configure -> Overlay" and
>> play with the histogram
>>
>>
>> The image looks like this:
>>
>>
>> I assigned one single value to the voxels in each
>> cortical parcellation. So the white matter and subcortical regions
>> (e.g. caudate, putamen, hippocampus) are 0. The contrast represents
>> the variations of the parameter across the cortex. Everything looks
>> good to me except that I couldn't get rid of that green "noise"
>> appearing at the hippocampus and occipital area. Does anyone have any
>> idea why this is happening and how to get rid of it?
>>
>>
>> Another minor issue is that even though I play with the histogram in
>> "Overlay" to get the best contrast, the colorbar looks less dynamic.
>> Too much red but very little yellow. Any suggestion to improve that?
>>
>>
>> Thanks a lot!
>>
>>
>> Best,
>>
>> Yue
>>
>>
>>
>>
>> ___
>> 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.
>
>
>
> ___
> 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

Re: [Freesurfer] Coregister the CT image and MRI image

[HARI GURAGAIN]

Thank you Douglas.
One more thing: Is there any syntax how to use it? I wonder if it is same as 
the mri_robust_register?


> On Jun 9, 2016, at 3:43 PM, Douglas N Greve  wrote:
> 
> I don't think robust register will do cross-modal. You may be better off 
> using mri_coreg, which you can get from here
> 
> ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mri_coreg
> 
> 
> On 06/09/2016 01:58 PM, HARI GURAGAIN wrote:
>> Dear Freesurfer community,
>> 
>> I am relatively new to this community.
>> 
>> I was trying to register the CT image and the MRI images (MRI as a the 
>> target volume and CT as the movable volume). I used the 
>> mri_robust_register to to do the registration as below:
>> 
>> /mri_robust_register --mov vol1.nii --dst vol2.nii --lta v1to2.lta 
>> --mapmov v1to2.nii --weights v1to2-weights.mii --iscale —satit /
>> 
>> The problem is that:  after register, the new image (v1to2.nii) is not 
>> exactly aligned with the original MRI image (vol2.nii). It gives a 
>> very different output. I wonder if I am missing anything here or I 
>> need to do some extra steps after the above command in order to get 
>> the correct alignment of the two images. I was hoping to get the 
>> resultant image should be well orient with the target volume image 
>> (vol2.nii image in my case).
>> 
>> I really appreciate any help here.
>> 
>> Hari Guragain
>> 
>> 
>> 
>> ___
>> 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] mri_binarize --rmax option unknown

[Lakhani, Bimal]

Thanks very much, Doug! That version works perfectly.

Just out of curiosity now, is there potentially a way to create a binarized 
mask in the other way that I mentioned?

That is, to generate a mask that cuts maintains the middle 95% of the data 
(i.e. +- 2SDs of the signal mean) as a way to remove extreme values from the 
final mask?

Thanks again,
Bimal



On June 9, 2016 at 1:47:14 PM, Douglas N Greve 
(gr...@nmr.mgh.harvard.edu) wrote:

That was a bug which I have not fixed. Try this one

ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mri_binarize


On 06/09/2016 03:53 PM, Lakhani, Bimal wrote:
> Good afternoon,
>
> I am trying to run a fairly simple mri_binarize command on FS v 5.3,
> Linux 64bit, but when I use the option — rmax, I am getting an error
> that says the —rmax option is not recognized. It is made weirded
> because —rmin works perfectly.
>
> Here is the command line and the following error:
>
> boydsrv01:~/Desktop/Arrowsmith/Freesurfer/Output> mri_binarize --i
> '/home/boydadmin/Desktop/Arrowsmith/Freesurfer/Output/Scan1/R07_MWF2Brain.mgz'
> --rmax 1.95 --o
> '/home/boydadmin/Desktop/Arrowsmith/Freesurfer/Output/Scan1/R07__MWF2Brain.bin.mgz’
>
> ERROR: Option --rmax unknown
>
> Thanks very much!
> Bimal
>
>
>
> ___
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> 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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Re: [Freesurfer] Command to summarize 35 cortical thickness

[Douglas N Greve]

try aparcstats2table

On 06/09/2016 05:09 PM, shi yao wang wrote:
> Dear FS expert,
> I am using command "mris_anatomical_stats -a 
> subjid/label/lh.aparc.annot -b subjid lh" to calculate cortical 
> thickness in 35 regions.
> I have 50 subjects. I am wondering how can I summarize these results 
> and export to one document? (I just need cortical thickness results)
> thanks
> Lawrence
> Emory University
>
>
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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

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
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[Freesurfer] converting ME-MPRAGE files

[Limachia, Gaurang (NIH/NINDS) [F]]

Hello All,

We have acquired our anatomical images on a Siemens scanner as multiecho MPRAGE 
sequence (4 echos), and wish to unpack the runs so we can perform morphometric 
analysis using FreeSurfer. What is the optimal way to convert the DICOM files 
so we can use them with FreeSurfer tools? Specifically, what command line do 
you recommend for dcmunpack?

When running the command: dcmunpack –src dicomdir  we get the following output:
Found 1 unique series: 6
6 3D_T1_MEMPRAGE 7.27 2530 7 unknown ROW 650 
dicomdir/mr_0006-e02/3d_t1_memprage-00533.dcm
Not sure how to interpret this.

Thanks.

Gaurang Limachia
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Re: [Freesurfer] Resampling the parametric map of brain activations onto a surface

[Douglas N Greve]

That one is out of date; we'll delete it. Thanks for pointing it out and 
sorry for our wiki pointing you in the wrong direction. We're in the 
process of weeding it out...

On 06/09/2016 04:54 PM, Zhao, Yue wrote:
> Hi Douglas,
>
> This is the instruction I am using.
> https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/FuncOverlay
>
> I cannot insert the picture in this email. I attach it. Hope it helps.
>
> Thanks very much!
>
> Yue
>
> 
> From: freesurfer-boun...@nmr.mgh.harvard.edu 
>  on behalf of Douglas N Greve 
> 
> Sent: Thursday, June 09, 2016 3:38:43 PM
> To: freesurfer@nmr.mgh.harvard.edu
> Subject: Re: [Freesurfer] Resampling the parametric map of brain activations 
> onto a surface
>
> Sorry for the delay. I can't see the image. Also, what instructions are
> you following? They look pretty old.
>
> check out our multimodal tutorial instead
> https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/MultiModal_freeview
>
>
> On 06/09/2016 10:19 AM, Zhao, Yue wrote:
>> Hi All,
>>
>>
>> I am not sure if the question is successfully posted. If the post is
>> there, does anyone has any idea? Thanks a lot!
>>
>>
>> Yue
>>
>> 
>> *From:* freesurfer-boun...@nmr.mgh.harvard.edu
>>  on behalf of Zhao, Yue
>> 
>> *Sent:* Tuesday, June 07, 2016 4:15:20 PM
>> *To:* freesurfer@nmr.mgh.harvard.edu
>> *Subject:* [Freesurfer] Resampling the parametric map of brain
>> activations onto a surface
>>
>> Hi All,
>>
>>
>> I am using a Ubuntu FreeSurfer v5.3.0 in the VirtualBox. I am trying
>> to overlay a parametric map onto a FreeSurfer surface. Here are the
>> tutorial codes I found:
>>
>> 1. To resample the paramatric map onto the individual's surface:
>>
>> mri_vol2surf --src spm001.img  --srcreg register.dat --hemi lh --projfrac 
>> 0.5 --out ./spm001-lh.w --out_type paint
>> 2. Visualize and overlay:
>> qsurfer -stat spm001 -hemi lh -subject bert-brf
>> 3. Configure the image by selecting "View -> Configure -> Overlay" and
>> play with the histogram
>>
>>
>> The image looks like this:
>>
>>
>> I assigned one single value to the voxels in each
>> cortical parcellation. So the white matter and subcortical regions
>> (e.g. caudate, putamen, hippocampus) are 0. The contrast represents
>> the variations of the parameter across the cortex. Everything looks
>> good to me except that I couldn't get rid of that green "noise"
>> appearing at the hippocampus and occipital area. Does anyone have any
>> idea why this is happening and how to get rid of it?
>>
>>
>> Another minor issue is that even though I play with the histogram in
>> "Overlay" to get the best contrast, the colorbar looks less dynamic.
>> Too much red but very little yellow. Any suggestion to improve that?
>>
>>
>> Thanks a lot!
>>
>>
>> Best,
>>
>> Yue
>>
>>
>>
>>
>> ___
>> 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
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> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
> The information in this e-mail is intended only for the person to whom it is
> addressed. If you believe this e-mail was sent to you in error and the e-mail
> contains patient information, please contact the Partners Compliance HelpLine 
> at
> http://www.partners.org/complianceline . If the e-mail was sent to you in 
> error
> but does not contain patient information, please contact the sender and 
> properly
> dispose of the e-mail.
>
>
>
> ___
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> 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
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[Freesurfer] Command to summarize 35 cortical thickness

[shi yao wang]

Dear FS expert,
I am using command "mris_anatomical_stats -a subjid/label/lh.aparc.annot -b
subjid lh" to calculate cortical thickness in 35 regions.

I have 50 subjects. I am wondering how can I summarize these results and
export to one document? (I just need cortical thickness results)

thanks

Lawrence
Emory University
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Re: [Freesurfer] Resampling the parametric map of brain activations onto a surface

[Zhao, Yue]

Hi Douglas,

This is the instruction I am using.
https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/FuncOverlay

I cannot insert the picture in this email. I attach it. Hope it helps.

Thanks very much!

Yue


From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Douglas N Greve 

Sent: Thursday, June 09, 2016 3:38:43 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] Resampling the parametric map of brain activations 
onto a surface

Sorry for the delay. I can't see the image. Also, what instructions are
you following? They look pretty old.

check out our multimodal tutorial instead
https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/MultiModal_freeview


On 06/09/2016 10:19 AM, Zhao, Yue wrote:
>
> Hi All,
>
>
> I am not sure if the question is successfully posted. If the post is
> there, does anyone has any idea? Thanks a lot!
>
>
> Yue
>
> 
> *From:* freesurfer-boun...@nmr.mgh.harvard.edu
>  on behalf of Zhao, Yue
> 
> *Sent:* Tuesday, June 07, 2016 4:15:20 PM
> *To:* freesurfer@nmr.mgh.harvard.edu
> *Subject:* [Freesurfer] Resampling the parametric map of brain
> activations onto a surface
>
> Hi All,
>
>
> I am using a Ubuntu FreeSurfer v5.3.0 in the VirtualBox. I am trying
> to overlay a parametric map onto a FreeSurfer surface. Here are the
> tutorial codes I found:
>
> 1. To resample the paramatric map onto the individual's surface:
>
> mri_vol2surf --src spm001.img  --srcreg register.dat --hemi lh --projfrac 0.5 
> --out ./spm001-lh.w --out_type paint
> 2. Visualize and overlay:
> qsurfer -stat spm001 -hemi lh -subject bert-brf
> 3. Configure the image by selecting "View -> Configure -> Overlay" and
> play with the histogram
>
>
> The image looks like this:
>
>
> I assigned one single value to the voxels in each
> cortical parcellation. So the white matter and subcortical regions
> (e.g. caudate, putamen, hippocampus) are 0. The contrast represents
> the variations of the parameter across the cortex. Everything looks
> good to me except that I couldn't get rid of that green "noise"
> appearing at the hippocampus and occipital area. Does anyone have any
> idea why this is happening and how to get rid of it?
>
>
> Another minor issue is that even though I play with the histogram in
> "Overlay" to get the best contrast, the colorbar looks less dynamic.
> Too much red but very little yellow. Any suggestion to improve that?
>
>
> Thanks a lot!
>
>
> Best,
>
> Yue
>
>
>
>
> ___
> 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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Re: [Freesurfer] Hippocampal subfields segmentation - what is the voxel size of the input?

[Hibert, Matthew Louis]

Hi Eugenio,
Would it also be possible to use the -hires flag in the initial recon-all 
command to prevent the T1 from being downsampled and maintain the voxel size 
that the T1 was acquired at, and use that resulting recon for the hippocampal 
subfield segmentation?  I've tested this with MEMPRAGE scans acquired at 0.75mm 
isotropic and coronal T2 anisotropic scans acquired at 0.33mm in plane with 1mm 
thick slices, and the results look reasonable.  The "1mm" label files are 
correctly downsampled to 0.75mm instead of 1mm, and the higher resolution label 
files remain at 0.33mm resolution.

Thanks,
Matt

Stufflebeam Lab
Athinoula A. Martinos Center
Massachusetts General Hospital
149 13th Street, Room 1115S
Charlestown, MA 02129

From: freesurfer-boun...@nmr.mgh.harvard.edu 
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Iglesias, Eugenio 
[e.igles...@ucl.ac.uk]
Sent: Thursday, June 09, 2016 2:36 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] Hippocampal subfields segmentation - what is the 
voxel size of the input?

Hi Fernando,

Unfortunately, FreeSurfer does downsample the T1s to 1mm, and the subfield code 
assumes that the T1 comes from FreeSurfer… For the paper, I hacked the code to 
take advantage of multiple images with higher resolution, but it hasn’t been 
thoroughly tested and it’s not publicly available at this point.
That said, there are different things you can do at this point:
1. Use the T1+T2 as is (disadvantage: T1 will be resampled to 1 mm).
2. Use only the T2.
3. Use only the T1. To do this, you would use the T1 as additional scan on its 
own (i.e., the main and additional scans are the same, but the additional one 
won’t be resampled).
4. There might be a way (hack) of using both scans at full resolution. If you 
change the header of the T1 scan and specify that the voxel size is 1mm, no 
resampling will happen; FreeSurfer will believe that you’re dealing with a 
subject with a very large head. If you do this, you’ll also have to enlarge the 
voxel size of the T2 by a factor 1/0.7. Also, the resulting volumes will have 
to be divided by (1/0.7)^3 in order to correct for the “wrong” voxel size.

I hope this helps!

Cheers,

Eugenio

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


On 9 Jun 2016, at 19:23, Fernando Pasquini Santos 
> wrote:

Dear,

I have a doubt regarding the input T1 image used for the Hippocampal Subfield 
segmentation in Freesurfer 6.0 - 
https://surfer.nmr.mgh.harvard.edu/fswiki/HippocampalSubfields

In this documentation it says that I can use a standard 1mm T1 image or the 
same standard 1mm T1 image with an additional scan. However, I want to use a 
0.7mm T1 image as input, with an additional T2 scan. When I run the program 
with it, the output images (nu.mgz and orig.mgz) are downsampled to 1mm voxel 
size. So, I don't know if this happens just because of the recon-all program or 
if the segmentation is being done in the downsampled T1 image or in the 
original 0.7mm.

By reading the article "A computational atlas of the hippocampal formation 
using ex vivo, ultra-high resolution MRI: Application to adaptive segmentation 
of in vivo MRI" I saw that, in the methods section, the algorithm is used to 
segment 0.6mm T1 images. But is this possible to do in the Freesurfer package? 
Obviously, doing the segmentation directly on 0.7mm data would be better than a 
downsampled version to 1mm...

Thanks,

Fernando Pasquini Santos
PhD student in Dynamic Systems
fernandosan...@pitt.edu
fernando.pasquini.san...@usp.br
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Re: [Freesurfer] mri_binarize --rmax option unknown

[Douglas N Greve]

That was a bug which I have not fixed. Try this one

ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mri_binarize


On 06/09/2016 03:53 PM, Lakhani, Bimal wrote:
> Good afternoon,
>
> I am trying to run a fairly simple mri_binarize command on FS v 5.3, 
> Linux 64bit, but when I use the option — rmax, I am getting an error 
> that says the —rmax option is not recognized. It is made weirded 
> because —rmin works perfectly.
>
> Here is the command line and the following error:
>
> boydsrv01:~/Desktop/Arrowsmith/Freesurfer/Output> mri_binarize --i 
> '/home/boydadmin/Desktop/Arrowsmith/Freesurfer/Output/Scan1/R07_MWF2Brain.mgz'
>  
> --rmax 1.95 --o 
> '/home/boydadmin/Desktop/Arrowsmith/Freesurfer/Output/Scan1/R07__MWF2Brain.bin.mgz’
>
> ERROR: Option --rmax unknown
>
> Thanks very much!
> Bimal
>
>
>
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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

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] Coregister the CT image and MRI image

[Douglas N Greve]

I don't think robust register will do cross-modal. You may be better off 
using mri_coreg, which you can get from here

ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mri_coreg


On 06/09/2016 01:58 PM, HARI GURAGAIN wrote:
> Dear Freesurfer community,
>
> I am relatively new to this community.
>
> I was trying to register the CT image and the MRI images (MRI as a the 
> target volume and CT as the movable volume). I used the 
> mri_robust_register to to do the registration as below:
>
> /mri_robust_register --mov vol1.nii --dst vol2.nii --lta v1to2.lta 
> --mapmov v1to2.nii --weights v1to2-weights.mii --iscale —satit /
>
> The problem is that:  after register, the new image (v1to2.nii) is not 
> exactly aligned with the original MRI image (vol2.nii). It gives a 
> very different output. I wonder if I am missing anything here or I 
> need to do some extra steps after the above command in order to get 
> the correct alignment of the two images. I was hoping to get the 
> resultant image should be well orient with the target volume image 
> (vol2.nii image in my case).
>
> I really appreciate any help here.
>
> Hari Guragain
>
>
>
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-- 
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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
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Re: [Freesurfer] Resampling the parametric map of brain activations onto a surface

[Douglas N Greve]

Sorry for the delay. I can't see the image. Also, what instructions are 
you following? They look pretty old.

check out our multimodal tutorial instead
https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/MultiModal_freeview


On 06/09/2016 10:19 AM, Zhao, Yue wrote:
>
> Hi All,
>
>
> I am not sure if the question is successfully posted. If the post is 
> there, does anyone has any idea? Thanks a lot!
>
>
> Yue
>
> 
> *From:* freesurfer-boun...@nmr.mgh.harvard.edu 
>  on behalf of Zhao, Yue 
> 
> *Sent:* Tuesday, June 07, 2016 4:15:20 PM
> *To:* freesurfer@nmr.mgh.harvard.edu
> *Subject:* [Freesurfer] Resampling the parametric map of brain 
> activations onto a surface
>
> Hi All,
>
>
> I am using a Ubuntu FreeSurfer v5.3.0 in the VirtualBox. I am trying 
> to overlay a parametric map onto a FreeSurfer surface. Here are the 
> tutorial codes I found:
>
> 1. To resample the paramatric map onto the individual's surface:
>
> mri_vol2surf --src spm001.img  --srcreg register.dat --hemi lh --projfrac 0.5 
> --out ./spm001-lh.w --out_type paint
> 2. Visualize and overlay:
> qsurfer -stat spm001 -hemi lh -subject bert-brf
> 3. Configure the image by selecting "View -> Configure -> Overlay" and 
> play with the histogram
>
>
> The image looks like this:
>
>
> I assigned one single value to the voxels in each 
> cortical parcellation. So the white matter and subcortical regions 
> (e.g. caudate, putamen, hippocampus) are 0. The contrast represents 
> the variations of the parameter across the cortex. Everything looks 
> good to me except that I couldn't get rid of that green "noise" 
> appearing at the hippocampus and occipital area. Does anyone have any 
> idea why this is happening and how to get rid of it?
>
>
> Another minor issue is that even though I play with the histogram in 
> "Overlay" to get the best contrast, the colorbar looks less dynamic. 
> Too much red but very little yellow. Any suggestion to improve that?
>
>
> Thanks a lot!
>
>
> Best,
>
> Yue
>
>
>
>
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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

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
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Re: [Freesurfer] Regarding: Surface projection of WMHs volume

[Douglas N Greve]

You could create a label of the WMH (mri_cor2label), then use 
mri_label2label to map it on to the surface with the --paint option (run 
it with --help to see an example)

On 06/09/2016 09:07 AM, Dr Sampada Sinha wrote:
> Dear freesurfer expert,
>
> I don't know if this question make any sense but is there a way to 
> project white matter hypointensities volume onto the surface?
>
> Thanks and kind regards,
>
> Sampada
>
>
> -- 
> Sampada
> Pre-doctoral student
> Department of Geriatric Mental Health (DGMH)
> King George Medical University
> Lucknow-226003
> India
>
>
>
>
>
>
> */
> /*
>
>
>
>
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-- 
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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] contrast

[Douglas N Greve]

On 06/08/2016 11:40 PM, Dave Yas wrote:
> Thank you very much Dough!
>
> I need to check 4 contrasts. I made them based on the freesurfer page, 
> but cant decide if i interpreted them right!
> Are my contrasts Ok?
>
> If classes are:
> Patients, healthy control
>
> and variables are:
> Age, TIV,  father age, mother age.
>
> Are these contrasts ok?
>
> R# = 2* (4+1) = 10
>
> *contrast1:* 0 0 0 0 0 0 -1 1 -1 1>> checking the differences between 
> groups in terms of father and mother age regression out the effect of 
> age and TIV
That will effectively compute the  difference between the mean(father 
age + mother age), ie, it would be like analyzing with a regressor 
created by adding the father age and mother age (ie, mean parent age). 
Is that what you want?
>
> *contrast2:* 0 0 0 0 0 0 -1 1 0 0
>0 0 0 0 0 0 0 0 1 -1 >> checking the differences 
> between groups in terms of father or mother age regression out the 
> effect of age and TIV
This will be significant if either the father age is diff OR the mother 
age is diff (or some combination thereof). It will be similar to 
contrast1 but not identical.
>
> *contrast3:* 0 0 0 0 0 0 -1 1 0 0 >> checking the differences between 
> groups in terms of father age regression out the effect of age and TIV 
> and  mother age
Yes
>
> *contrast4: *0 0 0 0 0 0 0 0 -1 1 >> checking the differences between 
> groups in terms of mother age regression out the effect of age and TIV 
> and  father age
Yes
>
> Yas
>
>
>
> 
> To: freesurfer@nmr.mgh.harvard.edu
> From: gr...@nmr.mgh.harvard.edu
> Date: Wed, 8 Jun 2016 09:38:18 -0400
> Subject: Re: [Freesurfer] Coordinate system in mris_convert
>
>
> Try the group analysis tutorial
> http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis
>
> On 6/8/16 2:39 AM, Dave Yas wrote:
>
> Hello all,
>
> I'm new to surface analysis.
>
> I have 2 groups (patient and healthy control) that i want to check
> differences between.
> I want to perform cortical thickness/ surface analysis.
> My categories are
>   Patients, healthy control, age, TIV,  father age, mother age.
> Where age & TIV are covariates of no interest. and father and
> mother age are covariates of interest.
>
> I have already preprocessed the data (recon-all), but how can i
> proceed?
> Any online guide on steps for surface analysis? also making a
> design such as the above?
>
> Yas
>
>
>
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>
>
>
> ___ Freesurfer mailing 
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> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The 
> information in this e-mail is intended only for the person to whom it 
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> 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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>
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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

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] mri_binarize --rmax option unknown

[Lakhani, Bimal]

Alternatively, is there another way to calculate the binzarized threshold min 
and max based on multiples of the standard deviation of the global mean?

Thanks!



On June 9, 2016 at 12:54:25 PM, Lakhani, Bimal 
(bimal.lakh...@ubc.ca) wrote:

Good afternoon,

I am trying to run a fairly simple mri_binarize command on FS v 5.3, Linux 
64bit, but when I use the option — rmax, I am getting an error that says the 
—rmax option is not recognized. It is made weirded because —rmin works 
perfectly.

Here is the command line and the following error:

boydsrv01:~/Desktop/Arrowsmith/Freesurfer/Output> mri_binarize --i 
'/home/boydadmin/Desktop/Arrowsmith/Freesurfer/Output/Scan1/R07_MWF2Brain.mgz' 
--rmax 1.95 --o 
'/home/boydadmin/Desktop/Arrowsmith/Freesurfer/Output/Scan1/R07__MWF2Brain.bin.mgz’

ERROR: Option --rmax unknown

Thanks very much!
Bimal

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[Freesurfer] mri_binarize --rmax option unknown

[Lakhani, Bimal]

Good afternoon,

I am trying to run a fairly simple mri_binarize command on FS v 5.3, Linux 
64bit, but when I use the option — rmax, I am getting an error that says the 
—rmax option is not recognized. It is made weirded because —rmin works 
perfectly.

Here is the command line and the following error:

boydsrv01:~/Desktop/Arrowsmith/Freesurfer/Output> mri_binarize --i 
'/home/boydadmin/Desktop/Arrowsmith/Freesurfer/Output/Scan1/R07_MWF2Brain.mgz' 
--rmax 1.95 --o 
'/home/boydadmin/Desktop/Arrowsmith/Freesurfer/Output/Scan1/R07__MWF2Brain.bin.mgz’

ERROR: Option --rmax unknown

Thanks very much!
Bimal

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Re: [Freesurfer] Hippocampal subfields segmentation - what is the voxel size of the input?

[Matt Glasser]

Hi Eugenio,

Did you already do this?  If so, a published reference would be more useful
to me than instructions for how to do it, as I¹m more interested in making
an argument for an acquisition protocol modification.

Matt.

From:   on behalf of "Iglesias,
Eugenio" 
Reply-To:  Freesurfer support list 
Date:  Thursday, June 9, 2016 at 1:37 PM
To:  Freesurfer support list 
Subject:  Re: [Freesurfer] Hippocampal subfields segmentation - what is the
voxel size of the input?

Hi Matt, 
you can use strategy 3 of my previous email ;-)
Cheers,
Eugenio

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


> On 9 Jun 2016, at 19:31, Matt Glasser  wrote:
> 
> I would be interested to know how well 0.7mm isotropic resolution data
> performs at hippocampal segmentation.  It would be better if folks could do
> this then needing to acquire specialized anisotropic scans for hippocampal
> segmentation.
> 
> Peace,
> 
> Matt.
> 
> From:  on behalf of Fernando Pasquini
> Santos 
> Reply-To: Freesurfer support list 
> Date: Thursday, June 9, 2016 at 1:23 PM
> To: "freesurfer@nmr.mgh.harvard.edu" 
> Subject: [Freesurfer] Hippocampal subfields segmentation - what is the voxel
> size of the input?
> 
> Dear,
> 
> I have a doubt regarding the input T1 image used for the Hippocampal Subfield
> segmentation in Freesurfer 6.0 -
> https://surfer.nmr.mgh.harvard.edu/fswiki/HippocampalSubfields
> 
> In this documentation it says that I can use a standard 1mm T1 image or the
> same standard 1mm T1 image with an additional scan. However, I want to use a
> 0.7mm T1 image as input, with an additional T2 scan. When I run the program
> with it, the output images (nu.mgz and orig.mgz) are downsampled to 1mm voxel
> size. So, I don't know if this happens just because of the recon-all program
> or if the segmentation is being done in the downsampled T1 image or in the
> original 0.7mm.
> 
> By reading the article "A computational atlas of the hippocampal formation
> using ex vivo, ultra-high resolution MRI: Application to adaptive segmentation
> of in vivo MRI" I saw that, in the methods section, the algorithm is used to
> segment 0.6mm T1 images. But is this possible to do in the Freesurfer package?
> Obviously, doing the segmentation directly on 0.7mm data would be better than
> a downsampled version to 1mm...
> 
> Thanks,
> 
> Fernando Pasquini Santos
> PhD student in Dynamic Systems
> fernandosan...@pitt.edu
> fernando.pasquini.san...@usp.br
> ___ Freesurfer mailing list
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> in this e-mail is intended only for the person to whom it is addressed. If you
> believe this e-mail was sent to you in error and the e-mail contains patient
> information, please contact the Partners Compliance HelpLine at
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> 
> 
> 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] Hippocampal subfields segmentation - what is the voxel size of the input?

[Iglesias, Eugenio]

Hi Matt,
you can use strategy 3 of my previous email ;-)
Cheers,
Eugenio

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


On 9 Jun 2016, at 19:31, Matt Glasser > 
wrote:

I would be interested to know how well 0.7mm isotropic resolution data performs 
at hippocampal segmentation.  It would be better if folks could do this then 
needing to acquire specialized anisotropic scans for hippocampal segmentation.

Peace,

Matt.

From: 
>
 on behalf of Fernando Pasquini Santos 
>
Reply-To: Freesurfer support list 
>
Date: Thursday, June 9, 2016 at 1:23 PM
To: "freesurfer@nmr.mgh.harvard.edu" 
>
Subject: [Freesurfer] Hippocampal subfields segmentation - what is the voxel 
size of the input?

Dear,

I have a doubt regarding the input T1 image used for the Hippocampal Subfield 
segmentation in Freesurfer 6.0 - 
https://surfer.nmr.mgh.harvard.edu/fswiki/HippocampalSubfields

In this documentation it says that I can use a standard 1mm T1 image or the 
same standard 1mm T1 image with an additional scan. However, I want to use a 
0.7mm T1 image as input, with an additional T2 scan. When I run the program 
with it, the output images (nu.mgz and orig.mgz) are downsampled to 1mm voxel 
size. So, I don't know if this happens just because of the recon-all program or 
if the segmentation is being done in the downsampled T1 image or in the 
original 0.7mm.

By reading the article "A computational atlas of the hippocampal formation 
using ex vivo, ultra-high resolution MRI: Application to adaptive segmentation 
of in vivo MRI" I saw that, in the methods section, the algorithm is used to 
segment 0.6mm T1 images. But is this possible to do in the Freesurfer package? 
Obviously, doing the segmentation directly on 0.7mm data would be better than a 
downsampled version to 1mm...

Thanks,

Fernando Pasquini Santos
PhD student in Dynamic Systems
fernandosan...@pitt.edu
fernando.pasquini.san...@usp.br
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Re: [Freesurfer] Hippocampal subfields segmentation - what is the voxel size of the input?

[Iglesias, Eugenio]

Hi Fernando,

Unfortunately, FreeSurfer does downsample the T1s to 1mm, and the subfield code 
assumes that the T1 comes from FreeSurfer… For the paper, I hacked the code to 
take advantage of multiple images with higher resolution, but it hasn’t been 
thoroughly tested and it’s not publicly available at this point.
That said, there are different things you can do at this point:
1. Use the T1+T2 as is (disadvantage: T1 will be resampled to 1 mm).
2. Use only the T2.
3. Use only the T1. To do this, you would use the T1 as additional scan on its 
own (i.e., the main and additional scans are the same, but the additional one 
won’t be resampled).
4. There might be a way (hack) of using both scans at full resolution. If you 
change the header of the T1 scan and specify that the voxel size is 1mm, no 
resampling will happen; FreeSurfer will believe that you’re dealing with a 
subject with a very large head. If you do this, you’ll also have to enlarge the 
voxel size of the T2 by a factor 1/0.7. Also, the resulting volumes will have 
to be divided by (1/0.7)^3 in order to correct for the “wrong” voxel size.

I hope this helps!

Cheers,

Eugenio

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


On 9 Jun 2016, at 19:23, Fernando Pasquini Santos 
> wrote:

Dear,

I have a doubt regarding the input T1 image used for the Hippocampal Subfield 
segmentation in Freesurfer 6.0 - 
https://surfer.nmr.mgh.harvard.edu/fswiki/HippocampalSubfields

In this documentation it says that I can use a standard 1mm T1 image or the 
same standard 1mm T1 image with an additional scan. However, I want to use a 
0.7mm T1 image as input, with an additional T2 scan. When I run the program 
with it, the output images (nu.mgz and orig.mgz) are downsampled to 1mm voxel 
size. So, I don't know if this happens just because of the recon-all program or 
if the segmentation is being done in the downsampled T1 image or in the 
original 0.7mm.

By reading the article "A computational atlas of the hippocampal formation 
using ex vivo, ultra-high resolution MRI: Application to adaptive segmentation 
of in vivo MRI" I saw that, in the methods section, the algorithm is used to 
segment 0.6mm T1 images. But is this possible to do in the Freesurfer package? 
Obviously, doing the segmentation directly on 0.7mm data would be better than a 
downsampled version to 1mm...

Thanks,

Fernando Pasquini Santos
PhD student in Dynamic Systems
fernandosan...@pitt.edu
fernando.pasquini.san...@usp.br
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but does not contain patient information, please contact the sender and properly
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Re: [Freesurfer] Hippocampal subfields segmentation - what is the voxel size of the input?

[Matt Glasser]

I would be interested to know how well 0.7mm isotropic resolution data
performs at hippocampal segmentation.  It would be better if folks could do
this then needing to acquire specialized anisotropic scans for hippocampal
segmentation.

Peace,

Matt.

From:   on behalf of Fernando
Pasquini Santos 
Reply-To:  Freesurfer support list 
Date:  Thursday, June 9, 2016 at 1:23 PM
To:  "freesurfer@nmr.mgh.harvard.edu" 
Subject:  [Freesurfer] Hippocampal subfields segmentation - what is the
voxel size of the input?

Dear,

I have a doubt regarding the input T1 image used for the Hippocampal
Subfield segmentation in Freesurfer 6.0 -
https://surfer.nmr.mgh.harvard.edu/fswiki/HippocampalSubfields

In this documentation it says that I can use a standard 1mm T1 image or the
same standard 1mm T1 image with an additional scan. However, I want to use a
0.7mm T1 image as input, with an additional T2 scan. When I run the program
with it, the output images (nu.mgz and orig.mgz) are downsampled to 1mm
voxel size. So, I don't know if this happens just because of the recon-all
program or if the segmentation is being done in the downsampled T1 image or
in the original 0.7mm.

By reading the article "A computational atlas of the hippocampal formation
using ex vivo, ultra-high resolution MRI: Application to adaptive
segmentation of in vivo MRI" I saw that, in the methods section, the
algorithm is used to segment 0.6mm T1 images. But is this possible to do in
the Freesurfer package? Obviously, doing the segmentation directly on 0.7mm
data would be better than a downsampled version to 1mm...

Thanks,

Fernando Pasquini Santos
PhD student in Dynamic Systems
fernandosan...@pitt.edu
fernando.pasquini.san...@usp.br
___ Freesurfer mailing list
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[Freesurfer] Hippocampal subfields segmentation - what is the voxel size of the input?

[Fernando Pasquini Santos]

Dear,

I have a doubt regarding the input T1 image used for the Hippocampal
Subfield segmentation in Freesurfer 6.0 -
https://surfer.nmr.mgh.harvard.edu/fswiki/HippocampalSubfields

In this documentation it says that I can use a standard 1mm T1 image or the
same standard 1mm T1 image with an additional scan. However, I want to use
a 0.7mm T1 image as input, with an additional T2 scan. When I run the
program with it, the output images (nu.mgz and orig.mgz) are downsampled to
1mm voxel size. So, I don't know if this happens just because of the
recon-all program or if the segmentation is being done in the downsampled
T1 image or in the original 0.7mm.

By reading the article "A computational atlas of the hippocampal formation
using ex vivo, ultra-high resolution MRI: Application to adaptive
segmentation of in vivo MRI" I saw that, in the methods section, the
algorithm is used to segment 0.6mm T1 images. But is this possible to do in
the Freesurfer package? Obviously, doing the segmentation directly on 0.7mm
data would be better than a downsampled version to 1mm...

Thanks,

Fernando Pasquini Santos
PhD student in Dynamic Systems
fernandosan...@pitt.edu
fernando.pasquini.san...@usp.br
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Re: [Freesurfer] Symmetric label on fsaverage

[Alexandre Routier]

Hello,

Sorry for my late reply but I just tried these commands today. In fact, I
don't have mris_left_right_register on Freesurfer 5.3 so I used this one :
https://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/dev_binaries/ and it
seems to work.

Concerning mris_apply_reg, I am not sure how to use it.
1) My custom label is on fsaverage. I use the command:
mri_label2label --srcsubject fsaverage --srclabel
fsaverage/lh.manual_label.label --trgsubject IdSubject --trglabel
IdSubject/lh.manual_label.label --hemi lh --regmethod surface
to come back to the native space

2) mris_left_right_register enables me to have symetric hemispheres on the
subject

3) Then I want to correspond my label (defined on left hemisphere) to the
right hemisphere. I specify IdSubject/lh.manual_label.label for the --src-label
flag but the output flag, is "   --streg lh.sphere rh.sphere.left_right"
correct ? I can choose between "--trg trgvalfile" and "--streg srcreg1
trgreg1 " but I don't know what is the difference and how to use it.

(To be sure, do I need to use one on these following flags:
   --jac : use jacobian correction
   --no-rev : do not do reverse mapping
   --randn : replace input with WGN
   --ones  : replace input with ones
?)

Alexandre

2016-05-04 21:07 GMT+02:00 Douglas N Greve :

>
> ive put a copy here
>
> ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mris_apply_reg
>
>
> On 05/03/2016 04:21 AM, Alexandre Routier wrote:
> > Hello Douglas,
> >
> > Unfortunately, I didn't find the command mris_apply_reg in FreeSurfer
> > 5.3. Is there anything to do to solve this problem ?
> >
> > Alex
> >
> > 2016-04-28 18:15 GMT+02:00 Douglas N Greve  > >:
> >
> > You can use mris_left_right_register, then use mris_apply_reg with
> the
> > --src-label option. I can't remember whether these are in 5.3 (or
> > whether 5.3 has the --src-label), so let me know if you need updates
> >
> >
> > On 04/28/2016 09:06 AM, Alexandre Routier wrote:
> > > Hello everyone,
> > >
> > > We used tksurfer to draw a specific region on the left hemisphere
> of
> > > fsaverage subject and we would like to automatically register the
> > > label from the left hemisphere to the right hemisphere.
> > >
> > > Since FreeSurfer provides tools to compute a symmetric fsaverage
> > > (https://surfer.nmr.mgh.harvard.edu/fswiki/Xhemi), I was
> > wondering if
> > > there was any command to have the manually drawn label on the left
> > > hemisphere to the right hemisphere.
> > >
> > > Thanks in advance for your help.
> > > Alexandre
> > >
> > >
> > > ___
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> > 
> > > 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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> >
> >
> > 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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>
> --
> 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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[Freesurfer] Coregister the CT image and MRI image

[HARI GURAGAIN]

Dear Freesurfer community,

I am relatively new to this community.

I was trying to register the CT image and the MRI images (MRI as a the target 
volume and CT as the movable volume). I used the mri_robust_register to to do 
the registration as below:

mri_robust_register --mov vol1.nii --dst vol2.nii --lta v1to2.lta --mapmov 
v1to2.nii --weights v1to2-weights.mii --iscale —satit

The problem is that:  after register, the new image (v1to2.nii) is not exactly 
aligned with the original MRI image (vol2.nii). It gives a very different 
output. I wonder if I am missing anything here or I need to do some extra steps 
after the above command in order to get the correct alignment of the two 
images. I was hoping to get the resultant image should be well orient with the 
target volume image (vol2.nii image in my case).

I really appreciate any help here. 

Hari Guragain

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[Freesurfer] Segmentation Fault with mri_convert

[Christopher Finuf]

I'm trying to convert the dicom to the original 001.mgz file using the
following command on a Mac OSX Yosemite version 10.10.5. My
SUBJECTS_DIR is /Users/csfinuf/Desktop/freesurfer/morerepeat/subjects/
. My current working directory is /Users/csfinuf/Desktop/freesurfer/morerepeat/
. The following is the output and error that I get. I'm running the latest
version v 5.3.0 of freesurfer. Any suggestions on what the problem is? What
is strange that it works with half my data set but the other has this
error. I've run this command in the exact way many times before and have
never had this issue.





bash-3.2$ recon-all -i
/Users/csfinuf/Desktop/freesurfer/morerepeat/Bigler_Repeatability_0005Ad_M1/IM-0027-0001.dcm
-subjid Bigler_Repeatability_0005Ad_M1


Subject Stamp: freesurfer-Darwin-lion-stable-pub-v5.3.0

Current Stamp: freesurfer-Darwin-lion-stable-pub-v5.3.0

INFO: SUBJECTS_DIR is /Users/csfinuf/Desktop/freesurfer/morerepeat/subjects

Actual FREESURFER_HOME /Applications/freesurfer

Darwin NS112201PSY2.byu.edu 14.5.0 Darwin Kernel Version 14.5.0: Tue Sep  1
21:23:09 PDT 2015; root:xnu-2782.50.1~1/RELEASE_X86_64 x86_64

/Users/csfinuf/Desktop/freesurfer/morerepeat/subjects/Bigler_Repeatability_0005Ad_M1

\n mri_convert
/Users/csfinuf/Desktop/freesurfer/morerepeat/Bigler_Repeatability_0005Ad_M1/IM-0027-0001.dcm
/Users/csfinuf/Desktop/freesurfer/morerepeat/subjects/Bigler_Repeatability_0005Ad_M1/mri/orig/001.mgz
\n

mri_convert
/Users/csfinuf/Desktop/freesurfer/morerepeat/Bigler_Repeatability_0005Ad_M1/IM-0027-0001.dcm
/Users/csfinuf/Desktop/freesurfer/morerepeat/subjects/Bigler_Repeatability_0005Ad_M1/mri/orig/001.mgz

$Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $

reading from
/Users/csfinuf/Desktop/freesurfer/morerepeat/Bigler_Repeatability_0005Ad_M1/IM-0027-0001.dcm...

Getting Series No

INFO: Found 178 files in
/Users/csfinuf/Desktop/freesurfer/morerepeat/Bigler_Repeatability_0005Ad_M1

INFO: Scanning for Series Number 2

Scanning Directory

INFO: found 176 files in series

INFO: loading series header info.


RunNo = 1

INFO: sorting.

INFO: (224 256 176), nframes = 1, ismosaic=0

PE Dir ROW ROW

AutoAlign matrix detected

AutoAlign Matrix -

 1.000   0.000   0.000   0.000;

 0.000   1.000   0.000   0.000;

 0.000   0.000   1.000   0.000;

 0.000   0.000   0.000   1.000;


FileName
/Users/csfinuf/Desktop/freesurfer/morerepeat/Bigler_Repeatability_0005Ad_M1/IM-0027-0001.dcm

Identification

NumarisVersyngo MR B17

ScannerModel  TrioTim

PatientName   Bigler_Repeatability_AD_M

Date and time

StudyDate 20160512

StudyTime 075942.531000

SeriesTime081401.859000

AcqTime   080647.62

Acquisition parameters

PulseSeq  *tfl3d1_ns

Protocol  t1_mpr_sag_iso_ave2_ipat2_(mprage)

PhEncDir  ROW

EchoNo1

FlipAngle 9

EchoTime  2.26

InversionTime 900

RepetitionTime1900

PhEncFOV  218.75

ReadoutFOV250

Image information

RunNo 1

SeriesNo  2

ImageNo   1

NImageRows256

NImageCols224

NFrames   1

SliceArraylSize   1

IsMosaic  0

ImgPos 75.8389 136.8499 125.

VolRes  0.9766   0.9766   1.

VolDim224  256  176

Vc  0.0767  -0.9971   0.

Vr -0.   0.  -1.

Vs -0.9971  -0.0767   0.

VolCenter  -3.5106  21.0460   0.

TransferSyntaxUID 1.2.840.10008.1.2.1

UseSliceScaleFactor 0 (slice 0: 1)

Segmentation fault

Darwin NS112201PSY2.byu.edu 14.5.0 Darwin Kernel Version 14.5.0: Tue Sep  1
21:23:09 PDT 2015; root:xnu-2782.50.1~1/RELEASE_X86_64 x86_64


recon-all -s Bigler_Repeatability_0005Ad_M1 exited with ERRORS at Wed Jun
8 13:39:08 MDT 2016


For more details, see the log file
/Users/csfinuf/Desktop/freesurfer/morerepeat/subjects/Bigler_Repeatability_0005Ad_M1/scripts/recon-all.log

To report a problem, see
http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
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Re: [Freesurfer] Resampling the parametric map of brain activations onto a surface

[Zhao, Yue]

Hi All,


I am not sure if the question is successfully posted. If the post is there, 
does anyone has any idea? Thanks a lot!


Yue


From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Zhao, Yue 

Sent: Tuesday, June 07, 2016 4:15:20 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] Resampling the parametric map of brain activations onto a 
surface


Hi All,


I am using a Ubuntu FreeSurfer v5.3.0 in the VirtualBox. I am trying to overlay 
a parametric map onto a FreeSurfer surface. Here are the tutorial codes I found:

1. To resample the paramatric map onto the individual's surface:

mri_vol2surf --src spm001.img  --srcreg register.dat --hemi lh --projfrac 0.5 
--out ./spm001-lh.w --out_type paint

2. Visualize and overlay:

qsurfer -stat spm001 -hemi lh -subject bert-brf

3. Configure the image by selecting "View -> Configure -> Overlay" and play 
with the histogram


The image looks like this:

[https://mail.google.com/mail/u/0/?ui=2=fffa1c9b37=fimg=1552b8aa077ac979=0.1=emb=ANGjdJ-pqlhFTJE2srxoou8y6c01tMI8Eewf-ICJtNACyUAHlD_817oQYfKULQ9ELG6ujIbOeI4-BaiWb8MEYUJrNVc1_0eYQdj5aeC2OAw5GYoPb0BPNmTWuB9yEck=s0-l75-ft=1465314364876=1552b8aa077ac979=1]

I assigned one single value to the voxels in each cortical parcellation. So the 
white matter and subcortical regions (e.g. caudate, putamen, hippocampus) are 
0. The contrast represents the variations of the parameter across the cortex. 
Everything looks good to me except that I couldn't get rid of that green 
"noise" appearing at the hippocampus and occipital area. Does anyone have any 
idea why this is happening and how to get rid of it?


Another minor issue is that even though I play with the histogram in "Overlay" 
to get the best contrast, the colorbar looks less dynamic. Too much red but 
very little yellow. Any suggestion to improve that?


Thanks a lot!


Best,

Yue

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Re: [Freesurfer] Longitudinal Studies Question

[Martin Reuter]

Hi Carolyn,

from you longitudinal qdec table you can create one that qdec can use by 
simply manually concatenating the first two collumns with a ".long." in 
the middle


tpid.long.baseid

and call that column "fsid" in the first row.
This will instruct qdec to load the data from the longitudinal 
directories of this subject. However, Qdec will not understand that 
these data points come from the same subject. It will assume these are 6 
different subjects. It is really only to load the data and investigate. 
All I am saying is that you cannot really do any longitudinal statistics 
with a single subject and only a few time points. If you want to use 
other statistical tools (note we also have Linear Mixed Effects Models 
in Matlab), you can use asegstats2table and aparcstats2table with the 
--qdec-long flag (passing the longitudinal qdec table). This will 
collect the stats values from your time points into a single csv table.


Best, Martin

On 06/08/2016 01:36 PM, Carolyn Drobak wrote:
So if these aren't useful for only 1 subject, what would be the best 
way to look at data over multiple scans for just the one subject?


On Mon, Jun 6, 2016 at 2:12 PM, Martin Reuter 
> wrote:


Hi Carolyn,

not sure what you are asking. You want to do statistics on N=1
subject ?

Anyway, in order to use QDEC, you'd have to reduce the
longitudinal data (thickness, measured at different time points)
to a single number: the slope of a linear fit. This is called the
2-stage-approach.

Or you skip Qdec and do a Linear Mixed Effects model directly.

Either approach only makes sense if you have a bunch of subjects
(per group).

Best, Martin

Ps info on longituidnal statistics:
https://surfer.nmr.mgh.harvard.edu/fswiki/LongitudinalStatistics

On 06/06/2016 09:45 AM, Carolyn Drobak wrote:

Hello,

I have six scans for a single subject. I have performed "group
analysis," but wish to use longitudinal data analysis. In
particular, I was able to get a base for the subjects, so can
view in freeview and all of that. My issue arises when I try to
use QDEC. Because QDEC can't use my long.qdec.table.dat file, nor
does it like my cross.qdec.table.dat file. The problem seems to
be that I only have one base, i.e. one subject. Is there some way
to run analysis on this so I can still get all the statistics I
want (mostly interested in cortical thickness) using just my one
subject?

I'm still fairly new to FS, but have done the large majority of
the tutorials, so am pretty sure I'm not just messing up my files
here.

Thanks,
CMD

On Mon, Jun 6, 2016 at 9:40 AM, Carolyn Drobak
>
wrote:

Hello,

I have six scans for a single subject. I have performed
"group analysis," but wish to use longitudinal data analysis.
In particular, I was able to get a base for the subjects, so
can view in freeview and all of that. My issue arises when I
try to use QDEC. Because QDEC can't use my
long.qdec.table.dat file, nor does it like my
cross.qdec.table.dat file. The problem seems to be that I
only have one base, i.e. one subject. Is there some way to
run analysis on this so I can still get all the statistics I
want (mostly interested in cortical thickness) using just my
one subject?

I'm still fairly new to FS, but have done the large majority
of the tutorials, so am pretty sure I'm not just messing up
my files here.

Thanks,
CD




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-- 
Martin Reuter, PhD

Assistant Professor of Radiology, Harvard Medical School
Assistant Professor of Neurology, Harvard Medical School
A.A.Martinos Center for Biomedical Imaging
Massachusetts General Hospital
Research Affiliate, CSAIL, MIT
Phone:+1-617-724-5652 
Web  :http://reuter.mit.edu  



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Re: [Freesurfer] tutorial data

[Arkadiy Maksimovskiy]

Hi Everyone,

I have found a solution and wanted to update this thread in case anyone
runs into the same problem.

I was able to download the tutorial data directly from this link:

http://ftp.nmr.mgh.harvard.edu/pub/data/

- Arkadiy

On Wed, Jun 8, 2016 at 7:44 PM, Arkadiy Maksimovskiy 
wrote:

> Hello,
>
> I am trying to download the light tutorial dataset from this page:
>
> http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Data
>
> The file link is titled: tutorial_data.tar.gz
> 
>
> I have tried clicking on the link as well as using terminal and neither
> method is working.
>
> Might these data be available elsewhere?
>
> Thank you for your help,
> Arkadiy
>
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[Freesurfer] Regarding: Surface projection of WMHs volume

[Dr Sampada Sinha]

Dear freesurfer expert,

I don't know if this question make any sense but is there a way to project
white matter hypointensities volume onto the surface?

Thanks and kind regards,

Sampada


-- 
Sampada
Pre-doctoral student
Department of Geriatric Mental Health (DGMH)
King George Medical University
Lucknow-226003
India
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Re: [Freesurfer] Brainmask edit error

[Ani Varjabedian]

Hi Sabrina,

I talked to Bruce and he said we can improve the surfaces further if we  
try labeling the lesion as "Left_Lesion" in the aseg and then running 
recon-all from that point onward.  It should freeze the white surface 
exactly where you draw voxels (so be careful with it) but still let the 
pial deform outwards. Right now, labeling the wm.mgz helps improve 
things but the ?h.white surf still ignores the edits in some places. If 
you directly edit the aseg then the surfaces will follow those 
boundaries exactly.


I'll try it on a few slices of the data and let you know the results, 
but you can also do it if you like.


-Ani



On 06/07/2016 04:46 PM, Sabrina Yu wrote:


Hi Ani,


I really appreciate the time and effort you are putting in to help me 
find a solution to this problem. The surface does look much more 
promising.



Following your instructions in the email, I have been playing around 
with editing the wm.mgz and have been able to generate better wm 
surfaces. With these edits, will I also be able to improve the 
aparc.mgz and aparc+aseg.mgz?



Thanks so much,
Sabrina


*From:* freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Ani Varjabedian 


*Sent:* Tuesday, June 7, 2016 5:45:43 AM
*To:* freesurfer@nmr.mgh.harvard.edu
*Subject:* Re: [Freesurfer] Brainmask edit error
Hi Sabrina,
Just wanted to update you on my progress.

I tried editing the wm.mgz and filling in the hole to see if that 
might help things. If we can get the wm surface accurate then there is 
a good chance the pial surf (which grows from the white) will follow 
suit.
After I edited the wm surf I ran this command to quickly generate the 
next step and check prelim surfaces


 recon-all -fill -tessellate -s SUBJECT01_wmedit

I made a copy of your subject to keep track of my edits, that's why 
the name is a bit different. But basically I generated the filled 
volume (from the wm.mgz) and then made the surfaces ?h.orig.nofix. 
These are prelim surfaces to what will eventually become the wm 
surfaces. If they look good then there is hope that this edit might do 
the trick!


I've attached a screenshot and you can see that it did help push the 
surfs out a bit more. I obviously did not edit the wm.mgz as carefully 
or accurately as I could have but if this works then you can try it 
yourself with more knowledge of the stroke region.


So! The next step is to see what the ?h.white surfs look like and to 
do that I ran this command:


 recon-all -smooth1 -inflate1 -qshpere -fix -white  -s SUBJECT01_wmedit

I am getting these commands here:
https://surfer.nmr.mgh.harvard.edu/fswiki/ReconAllDevTable
This is a really helpful table that lists the FS pipeline and all the 
different steps so you can pick and choose which ones to run if you 
want to see a result quickly.


I didn't check which version of FS you were using. I'm running the dev 
version of 6.0 so some things might be a bit different but overall the 
major steps should be the same enough to make a comparison.
To see a list of your recon-all steps you can always use the -dontrun 
flag with your subject and it will just print out all the commands to 
the logfile without actually running them. It's a really good way to 
get a list of the steps and then you can look into what they do!


Anyways, when this is done I will update you on the white surfs. If 
they look good then I will try the next step which will be generating 
the pial!


Hope all is well and thank you again for being so patient during this 
busy time.

-Ani


On 06/02/2016 02:15 PM, Ani Varjabedian wrote:

Hi Sabrina,

I'm not entirely sure about that, but if my manual edits don't work 
I'll let Bruce know and we can discuss other workarounds.


-Ani

On 06/02/2016 12:55 PM, Sabrina Yu wrote:

Hi Ani,

Thanks so much for your explanation, it makes sense that the brain 
is too deformed for one continuous surface. If we are not able to 
find a workaround that creates a continuous surface, can I create a 
separate surface just for the stroke region? And generate average 
voxel intensity for that region?


Thanks,
Sabrina

On Jun 2, 2016, at 6:21 PM, Ani Varjabedian 
 wrote:



Hi Sabrina,

Usually we don't add voxels in the brainmask. We usually add to the 
wm.mgz which pushes the white surf out and ultimately the pial surf 
out (because it grows from the white).
If the area around the stroke on both sides looks good but there is 
a hole in the middle where there is no information or labels, then 
the surfaces will not connect all the way around it. They treat it 
like two separate pieces. Does this make sense? I'll try to play 
around with some different things (like adding to the wm.mgz) and 
see if I can get the surfaces to be continuous around this region.


Like Bruce said, it might end up being that the brain is too 
different from what