Re: [Freesurfer] Surface based analysis using FA maps

[Alshikho, Mohamad J.]

This is theoritically correct!
If we do DTI to study the liver. How these measures can explain the tissue? It 
is not only white matter and gray matter! 

All DTI measures can explain how much space we have between the cells. More 
space means low FA and high RD. The opposit correct as well.
Given that they share the same formula. If we accept RD as a marker for gray 
matter integrity. We should accept FA a marker for gray matter integrity.

Yes I am looking for an optimal measure to evaluate tissue damage.

Mohamad

From: freesurfer-boun...@nmr.mgh.harvard.edu 
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Matt Glasser 
[m...@ma-tea.com]
Sent: Wednesday, March 23, 2016 9:29 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] Surface based analysis using FA maps

FA or fractional anisotropy explains the fraction of the diffusion that is
along the long axis of the diffusion tensor.  In so far as the diffusion
tensor is an accurate model of the underlying structural architecture,
what you say might be true (e.g. in the small number of white matter
regions with only one main fiber orientation).  Most of white matter has
multiple fiber orientations and thus the diffusion tensor is not a great
model.  In grey matter, the principle orientation of processes is radial
to the surface (e.g. radial fibers, major dendrites), but there are are
also tangential processes (e.g. Bands of Baillarger).  To get a decrease
in FA, one could do a number of things:

1) Decrease the strength of radial diffusion
2) Increase the strength of tangential diffusion
3) Decrease the strength of both radial and tangential diffusion

Are you looking for a measure that shows tissue damage?

Matt.

On 3/23/16, 7:55 PM, "Alshikho, Mohamad J."
 wrote:

>It can explain one thing "tissue integrity"
>
>It will tell us neurobiologically exactly what can tell us in tissues
>other than the brain such as liver, lung, heart, joints,  etc
>
>Mohamad
>
>
>-Original Message-
>From: freesurfer-boun...@nmr.mgh.harvard.edu
>[mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Matt Glasser
>Sent: Wednesday, March 23, 2016 8:49 PM
>To: Freesurfer support list 
>Subject: Re: [Freesurfer] Surface based analysis using FA maps
>
>Right but what do you think FA, MD, AD, RD, etc are telling you
>neurobiologically in the grey matter?
>
>Matt.
>
>On 3/23/16, 7:18 PM, "Alshikho, Mohamad J."
>malshi...@mgh.harvard.edu> wrote:
>
>>Hi Matt,
>>I highly appreciate your input on this!!
>>
>>Actually my goal is to study the difference in FA values between groups
>>within the cortex. I know that diffusivities ( MD, AD and RD) can be
>>used to evaluate gray matter and many people claim that it is much
>>better to use diffusivities to evaluate gray matter But my interest is
>>specifically in FA within the gray matter.
>>
>>For that reason I want to do surface based analysis to study the
>>differences in FA between my study groups. I checked for the optimal
>>ways to do it:
>>1. I found https://surfer.nmr.mgh.harvard.edu/fswiki/dt_recon
>>2. And I found
>>https://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/2013-February/028
>>109
>>.html
>>
>>I ran the analysis using both methods.
>>
>>For the second method I replaced PET maps by FA maps and this was the
>>reason for my question! If we can do the analysis that way using PET
>>maps, why we can't do it using FA maps?
>>
>>I will be more than happy if you can suggest me an alternative approach
>>to study FA on a surface.
>>
>>
>>Best,
>>Mohamad
>>
>>-Original Message-
>>From: freesurfer-boun...@nmr.mgh.harvard.edu
>>[mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Matt
>>Glasser
>>Sent: Wednesday, March 23, 2016 8:04 PM
>>To: Freesurfer support list 
>>Subject: Re: [Freesurfer] Surface based analysis using FA maps
>>
>>I too am puzzled as to why you would want to do this.  In terms of
>>getting improvement in the alignment across subjects TBSS is one way to
>>approach this.  Another would be to use the fiber orientations in the
>>registration like these folks have done:
>>http://dti-tk.sourceforge.net/pmwiki/pmwiki.php?n=Main.HomePage
>>
>>If you are interested in studying the properties of cortical grey
>>matter there might be better modalities than FA.  If you can provide
>>more details on what you are trying to do, perhaps that would clarify
>>how to go about it?
>>
>>Peace,
>>
>>Matt.
>>
>>On 3/22/16, 2:49 PM, "Douglas N Greve"
>>>gr...@nmr.mgh.harvard.edu> wrote:
>>
>>>I don't know of a reference where someone has done this (though I
>>>would be surprised if it is not out there), so just be aware of this
>>>if you try to publish. The commands look correct, however, you may or
>>>may not want to sample in the middle of the cortical ribbon (--projfrac
>>>0.5).
>>>Since this is a DTI analysis, wouldn't you want to sample in the WM?
>>>Doing that is a little tricky, but you can use something like
>>>--projabs
>>>-1 to sample 1mm *away* fr

Re: [Freesurfer] Surface based analysis using FA maps

[Matt Glasser]

FA or fractional anisotropy explains the fraction of the diffusion that is
along the long axis of the diffusion tensor.  In so far as the diffusion
tensor is an accurate model of the underlying structural architecture,
what you say might be true (e.g. in the small number of white matter
regions with only one main fiber orientation).  Most of white matter has
multiple fiber orientations and thus the diffusion tensor is not a great
model.  In grey matter, the principle orientation of processes is radial
to the surface (e.g. radial fibers, major dendrites), but there are are
also tangential processes (e.g. Bands of Baillarger).  To get a decrease
in FA, one could do a number of things:

1) Decrease the strength of radial diffusion
2) Increase the strength of tangential diffusion
3) Decrease the strength of both radial and tangential diffusion

Are you looking for a measure that shows tissue damage?

Matt.

On 3/23/16, 7:55 PM, "Alshikho, Mohamad J."
 wrote:

>It can explain one thing "tissue integrity"
>
>It will tell us neurobiologically exactly what can tell us in tissues
>other than the brain such as liver, lung, heart, joints,  etc
>
>Mohamad
>
>
>-Original Message-
>From: freesurfer-boun...@nmr.mgh.harvard.edu
>[mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Matt Glasser
>Sent: Wednesday, March 23, 2016 8:49 PM
>To: Freesurfer support list 
>Subject: Re: [Freesurfer] Surface based analysis using FA maps
>
>Right but what do you think FA, MD, AD, RD, etc are telling you
>neurobiologically in the grey matter?
>
>Matt.
>
>On 3/23/16, 7:18 PM, "Alshikho, Mohamad J."
>malshi...@mgh.harvard.edu> wrote:
>
>>Hi Matt,
>>I highly appreciate your input on this!!
>>
>>Actually my goal is to study the difference in FA values between groups
>>within the cortex. I know that diffusivities ( MD, AD and RD) can be
>>used to evaluate gray matter and many people claim that it is much
>>better to use diffusivities to evaluate gray matter But my interest is
>>specifically in FA within the gray matter.
>>
>>For that reason I want to do surface based analysis to study the
>>differences in FA between my study groups. I checked for the optimal
>>ways to do it:
>>1. I found https://surfer.nmr.mgh.harvard.edu/fswiki/dt_recon
>>2. And I found
>>https://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/2013-February/028
>>109
>>.html
>>
>>I ran the analysis using both methods.
>>
>>For the second method I replaced PET maps by FA maps and this was the
>>reason for my question! If we can do the analysis that way using PET
>>maps, why we can't do it using FA maps?
>>
>>I will be more than happy if you can suggest me an alternative approach
>>to study FA on a surface.
>>
>>
>>Best,
>>Mohamad
>>
>>-Original Message-
>>From: freesurfer-boun...@nmr.mgh.harvard.edu
>>[mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Matt
>>Glasser
>>Sent: Wednesday, March 23, 2016 8:04 PM
>>To: Freesurfer support list 
>>Subject: Re: [Freesurfer] Surface based analysis using FA maps
>>
>>I too am puzzled as to why you would want to do this.  In terms of
>>getting improvement in the alignment across subjects TBSS is one way to
>>approach this.  Another would be to use the fiber orientations in the
>>registration like these folks have done:
>>http://dti-tk.sourceforge.net/pmwiki/pmwiki.php?n=Main.HomePage
>>
>>If you are interested in studying the properties of cortical grey
>>matter there might be better modalities than FA.  If you can provide
>>more details on what you are trying to do, perhaps that would clarify
>>how to go about it?
>>
>>Peace,
>>
>>Matt.
>>
>>On 3/22/16, 2:49 PM, "Douglas N Greve"
>>>gr...@nmr.mgh.harvard.edu> wrote:
>>
>>>I don't know of a reference where someone has done this (though I
>>>would be surprised if it is not out there), so just be aware of this
>>>if you try to publish. The commands look correct, however, you may or
>>>may not want to sample in the middle of the cortical ribbon (--projfrac
>>>0.5).
>>>Since this is a DTI analysis, wouldn't you want to sample in the WM?
>>>Doing that is a little tricky, but you can use something like
>>>--projabs
>>>-1 to sample 1mm *away* from the ribbon into the WM.
>>>
>>>On 03/22/2016 11:08 AM, Alshikho, Mohamad J. wrote:

 Dear FS experts,

 I would like to run surface based analysis using FA maps. I am not
 exactly sure that what I am doing is totally right specially step 2 .
 I used the following commands:

 1.I registered the FA maps to T1 using the command:  bbregister --s
 bert --mov dtifit_FA.nii --bold --init-fsl --reg  reg.dat

 2.I concatenated the subject¹s FA maps using the command :
  mris_preproc ­target fsaverage ­hemi lh ­iv .bert1/dtifit_FA.nii
reg.dat ­iv bert2/dtifit_FA.nii reg.dat Š. --projfrac 0.5 --out
lh.FA.mgz

 3.Then smoothing mri_surf2surf --hemi lh --s fsaverage --fwhm 5
 --cortex --sval  lh.FA.mgz --tval lh.FA_5mm.mgz

 4.Then GLM analysis using 

Re: [Freesurfer] Surface based analysis using FA maps

[Alshikho, Mohamad J.]

It can explain one thing "tissue integrity"

It will tell us neurobiologically exactly what can tell us in tissues other 
than the brain such as liver, lung, heart, joints,  etc

Mohamad


-Original Message-
From: freesurfer-boun...@nmr.mgh.harvard.edu 
[mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Matt Glasser
Sent: Wednesday, March 23, 2016 8:49 PM
To: Freesurfer support list 
Subject: Re: [Freesurfer] Surface based analysis using FA maps

Right but what do you think FA, MD, AD, RD, etc are telling you 
neurobiologically in the grey matter?

Matt.

On 3/23/16, 7:18 PM, "Alshikho, Mohamad J."
 
wrote:

>Hi Matt,
>I highly appreciate your input on this!!
>
>Actually my goal is to study the difference in FA values between groups 
>within the cortex. I know that diffusivities ( MD, AD and RD) can be 
>used to evaluate gray matter and many people claim that it is much 
>better to use diffusivities to evaluate gray matter But my interest is 
>specifically in FA within the gray matter.
>
>For that reason I want to do surface based analysis to study the 
>differences in FA between my study groups. I checked for the optimal 
>ways to do it:
>1. I found https://surfer.nmr.mgh.harvard.edu/fswiki/dt_recon
>2. And I found
>https://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/2013-February/028
>109
>.html
>
>I ran the analysis using both methods.
>
>For the second method I replaced PET maps by FA maps and this was the 
>reason for my question! If we can do the analysis that way using PET 
>maps, why we can't do it using FA maps?
>
>I will be more than happy if you can suggest me an alternative approach 
>to study FA on a surface.
>
>
>Best,
>Mohamad
>
>-Original Message-
>From: freesurfer-boun...@nmr.mgh.harvard.edu
>[mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Matt 
>Glasser
>Sent: Wednesday, March 23, 2016 8:04 PM
>To: Freesurfer support list 
>Subject: Re: [Freesurfer] Surface based analysis using FA maps
>
>I too am puzzled as to why you would want to do this.  In terms of 
>getting improvement in the alignment across subjects TBSS is one way to 
>approach this.  Another would be to use the fiber orientations in the 
>registration like these folks have done:
>http://dti-tk.sourceforge.net/pmwiki/pmwiki.php?n=Main.HomePage
>
>If you are interested in studying the properties of cortical grey 
>matter there might be better modalities than FA.  If you can provide 
>more details on what you are trying to do, perhaps that would clarify 
>how to go about it?
>
>Peace,
>
>Matt.
>
>On 3/22/16, 2:49 PM, "Douglas N Greve"
>gr...@nmr.mgh.harvard.edu> wrote:
>
>>I don't know of a reference where someone has done this (though I 
>>would be surprised if it is not out there), so just be aware of this 
>>if you try to publish. The commands look correct, however, you may or 
>>may not want to sample in the middle of the cortical ribbon (--projfrac 0.5).
>>Since this is a DTI analysis, wouldn't you want to sample in the WM?
>>Doing that is a little tricky, but you can use something like 
>>--projabs
>>-1 to sample 1mm *away* from the ribbon into the WM.
>>
>>On 03/22/2016 11:08 AM, Alshikho, Mohamad J. wrote:
>>>
>>> Dear FS experts,
>>>
>>> I would like to run surface based analysis using FA maps. I am not 
>>> exactly sure that what I am doing is totally right specially step 2 .
>>> I used the following commands:
>>>
>>> 1.I registered the FA maps to T1 using the command:  bbregister --s 
>>> bert --mov dtifit_FA.nii --bold --init-fsl --reg  reg.dat
>>>
>>> 2.I concatenated the subject¹s FA maps using the command :
>>>  mris_preproc ­target fsaverage ­hemi lh ­iv .bert1/dtifit_FA.nii 
>>>reg.dat ­iv bert2/dtifit_FA.nii reg.dat Š. --projfrac 0.5 --out 
>>>lh.FA.mgz
>>>
>>> 3.Then smoothing mri_surf2surf --hemi lh --s fsaverage --fwhm 5 
>>> --cortex --sval  lh.FA.mgz --tval lh.FA_5mm.mgz
>>>
>>> 4.Then GLM analysis using mri_glmfit
>>>
>>> 5.Correction for multiple comparison mri_glmfit-sim
>>>
>>> Kindly, are these steps correct? I used the previous steps to do 
>>> surface based analysis using PET images and it worked very well.
>>> While for the FA maps it seems that there is something wrong and I 
>>> can¹t figure out what it is!
>>>
>>> I highly appreciate any input on this!
>>>
>>> Best,
>>>
>>> Mohamad
>>>
>>>
>>>
>>> ___
>>> 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
>>http

Re: [Freesurfer] Surface based analysis using FA maps

[Matt Glasser]

Right but what do you think FA, MD, AD, RD, etc are telling you
neurobiologically in the grey matter?

Matt.

On 3/23/16, 7:18 PM, "Alshikho, Mohamad J."
 wrote:

>Hi Matt,
>I highly appreciate your input on this!!
>
>Actually my goal is to study the difference in FA values between groups
>within the cortex. I know that diffusivities ( MD, AD and RD) can be used
>to evaluate gray matter and many people claim that it is much better to
>use diffusivities to evaluate gray matter But my interest is specifically
>in FA within the gray matter.
>
>For that reason I want to do surface based analysis to study the
>differences in FA between my study groups. I checked for the optimal ways
>to do it: 
>1. I found https://surfer.nmr.mgh.harvard.edu/fswiki/dt_recon
>2. And I found 
>https://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/2013-February/028109
>.html
>
>I ran the analysis using both methods.
>
>For the second method I replaced PET maps by FA maps and this was the
>reason for my question! If we can do the analysis that way using PET
>maps, why we can't do it using FA maps?
>
>I will be more than happy if you can suggest me an alternative approach
>to study FA on a surface.
>
>
>Best,
>Mohamad
>
>-Original Message-
>From: freesurfer-boun...@nmr.mgh.harvard.edu
>[mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Matt Glasser
>Sent: Wednesday, March 23, 2016 8:04 PM
>To: Freesurfer support list 
>Subject: Re: [Freesurfer] Surface based analysis using FA maps
>
>I too am puzzled as to why you would want to do this.  In terms of
>getting improvement in the alignment across subjects TBSS is one way to
>approach this.  Another would be to use the fiber orientations in the
>registration like these folks have done:
>http://dti-tk.sourceforge.net/pmwiki/pmwiki.php?n=Main.HomePage
>
>If you are interested in studying the properties of cortical grey matter
>there might be better modalities than FA.  If you can provide more
>details on what you are trying to do, perhaps that would clarify how to
>go about it?
>
>Peace,
>
>Matt.
>
>On 3/22/16, 2:49 PM, "Douglas N Greve"
>gr...@nmr.mgh.harvard.edu> wrote:
>
>>I don't know of a reference where someone has done this (though I would
>>be surprised if it is not out there), so just be aware of this if you
>>try to publish. The commands look correct, however, you may or may not
>>want to sample in the middle of the cortical ribbon (--projfrac 0.5).
>>Since this is a DTI analysis, wouldn't you want to sample in the WM?
>>Doing that is a little tricky, but you can use something like --projabs
>>-1 to sample 1mm *away* from the ribbon into the WM.
>>
>>On 03/22/2016 11:08 AM, Alshikho, Mohamad J. wrote:
>>>
>>> Dear FS experts,
>>>
>>> I would like to run surface based analysis using FA maps. I am not
>>> exactly sure that what I am doing is totally right specially step 2 .
>>> I used the following commands:
>>>
>>> 1.I registered the FA maps to T1 using the command:  bbregister --s
>>> bert --mov dtifit_FA.nii --bold --init-fsl --reg  reg.dat
>>>
>>> 2.I concatenated the subject¹s FA maps using the command :
>>>  mris_preproc ­target fsaverage ­hemi lh ­iv .bert1/dtifit_FA.nii
>>>reg.dat ­iv bert2/dtifit_FA.nii reg.dat Š. --projfrac 0.5 --out
>>>lh.FA.mgz
>>>
>>> 3.Then smoothing mri_surf2surf --hemi lh --s fsaverage --fwhm 5
>>> --cortex --sval  lh.FA.mgz --tval lh.FA_5mm.mgz
>>>
>>> 4.Then GLM analysis using mri_glmfit
>>>
>>> 5.Correction for multiple comparison mri_glmfit-sim
>>>
>>> Kindly, are these steps correct? I used the previous steps to do
>>> surface based analysis using PET images and it worked very well.
>>> While for the FA maps it seems that there is something wrong and I
>>> can¹t figure out what it is!
>>>
>>> I highly appreciate any input on this!
>>>
>>> Best,
>>>
>>> Mohamad
>>>
>>>
>>>
>>> ___
>>> 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.
>>
>
>
>

Re: [Freesurfer] Surface based analysis using FA maps

[Alshikho, Mohamad J.]

Hi Matt,
I highly appreciate your input on this!!

Actually my goal is to study the difference in FA values between groups within 
the cortex. I know that diffusivities ( MD, AD and RD) can be used to evaluate 
gray matter and many people claim that it is much better to use diffusivities 
to evaluate gray matter But my interest is specifically in FA within the gray 
matter.

For that reason I want to do surface based analysis to study the differences in 
FA between my study groups. I checked for the optimal ways to do it: 
1. I found https://surfer.nmr.mgh.harvard.edu/fswiki/dt_recon
2. And I found 
https://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/2013-February/028109.html

I ran the analysis using both methods. 

For the second method I replaced PET maps by FA maps and this was the reason 
for my question! If we can do the analysis that way using PET maps, why we 
can't do it using FA maps?

I will be more than happy if you can suggest me an alternative approach to 
study FA on a surface.


Best,
Mohamad

-Original Message-
From: freesurfer-boun...@nmr.mgh.harvard.edu 
[mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Matt Glasser
Sent: Wednesday, March 23, 2016 8:04 PM
To: Freesurfer support list 
Subject: Re: [Freesurfer] Surface based analysis using FA maps

I too am puzzled as to why you would want to do this.  In terms of getting 
improvement in the alignment across subjects TBSS is one way to approach this.  
Another would be to use the fiber orientations in the registration like these 
folks have done:
http://dti-tk.sourceforge.net/pmwiki/pmwiki.php?n=Main.HomePage

If you are interested in studying the properties of cortical grey matter there 
might be better modalities than FA.  If you can provide more details on what 
you are trying to do, perhaps that would clarify how to go about it?

Peace,

Matt.

On 3/22/16, 2:49 PM, "Douglas N Greve"
 
wrote:

>I don't know of a reference where someone has done this (though I would 
>be surprised if it is not out there), so just be aware of this if you 
>try to publish. The commands look correct, however, you may or may not 
>want to sample in the middle of the cortical ribbon (--projfrac 0.5).
>Since this is a DTI analysis, wouldn't you want to sample in the WM?
>Doing that is a little tricky, but you can use something like --projabs
>-1 to sample 1mm *away* from the ribbon into the WM.
>
>On 03/22/2016 11:08 AM, Alshikho, Mohamad J. wrote:
>>
>> Dear FS experts,
>>
>> I would like to run surface based analysis using FA maps. I am not 
>> exactly sure that what I am doing is totally right specially step 2 .
>> I used the following commands:
>>
>> 1.I registered the FA maps to T1 using the command:  bbregister --s 
>> bert --mov dtifit_FA.nii --bold --init-fsl --reg  reg.dat
>>
>> 2.I concatenated the subject¹s FA maps using the command :
>>  mris_preproc ­target fsaverage ­hemi lh ­iv .bert1/dtifit_FA.nii  
>>reg.dat ­iv bert2/dtifit_FA.nii reg.dat Š. --projfrac 0.5 --out 
>>lh.FA.mgz
>>
>> 3.Then smoothing mri_surf2surf --hemi lh --s fsaverage --fwhm 5 
>> --cortex --sval  lh.FA.mgz --tval lh.FA_5mm.mgz
>>
>> 4.Then GLM analysis using mri_glmfit
>>
>> 5.Correction for multiple comparison mri_glmfit-sim
>>
>> Kindly, are these steps correct? I used the previous steps to do 
>> surface based analysis using PET images and it worked very well. 
>> While for the FA maps it seems that there is something wrong and I 
>> can¹t figure out what it is!
>>
>> I highly appreciate any input on this!
>>
>> Best,
>>
>> Mohamad
>>
>>
>>
>> ___
>> 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
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Re: [Freesurfer] Surface based analysis using FA maps

[Matt Glasser]

I too am puzzled as to why you would want to do this.  In terms of getting
improvement in the alignment across subjects TBSS is one way to approach
this.  Another would be to use the fiber orientations in the registration
like these folks have done:
http://dti-tk.sourceforge.net/pmwiki/pmwiki.php?n=Main.HomePage

If you are interested in studying the properties of cortical grey matter
there might be better modalities than FA.  If you can provide more details
on what you are trying to do, perhaps that would clarify how to go about
it?

Peace,

Matt.

On 3/22/16, 2:49 PM, "Douglas N Greve"
 wrote:

>I don't know of a reference where someone has done this (though I would
>be surprised if it is not out there), so just be aware of this if you
>try to publish. The commands look correct, however, you may or may not
>want to sample in the middle of the cortical ribbon (--projfrac 0.5).
>Since this is a DTI analysis, wouldn't you want to sample in the WM?
>Doing that is a little tricky, but you can use something like --projabs
>-1 to sample 1mm *away* from the ribbon into the WM.
>
>On 03/22/2016 11:08 AM, Alshikho, Mohamad J. wrote:
>>
>> Dear FS experts,
>>
>> I would like to run surface based analysis using FA maps. I am not
>> exactly sure that what I am doing is totally right specially step 2 .
>> I used the following commands:
>>
>> 1.I registered the FA maps to T1 using the command:  bbregister --s
>> bert --mov dtifit_FA.nii --bold --init-fsl --reg  reg.dat
>>
>> 2.I concatenated the subject¹s FA maps using the command :
>>  mris_preproc ­target fsaverage ­hemi lh ­iv .bert1/dtifit_FA.nii
>> reg.dat ­iv bert2/dtifit_FA.nii reg.dat Š. --projfrac 0.5 --out
>>lh.FA.mgz
>>
>> 3.Then smoothing mri_surf2surf --hemi lh --s fsaverage --fwhm 5
>> --cortex --sval  lh.FA.mgz --tval lh.FA_5mm.mgz
>>
>> 4.Then GLM analysis using mri_glmfit
>>
>> 5.Correction for multiple comparison mri_glmfit-sim
>>
>> Kindly, are these steps correct? I used the previous steps to do
>> surface based analysis using PET images and it worked very well. While
>> for the FA maps it seems that there is something wrong and I can¹t
>> figure out what it is!
>>
>> I highly appreciate any input on this!
>>
>> Best,
>>
>> Mohamad
>>
>>
>>
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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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>
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>contains patient information, please contact the Partners Compliance
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Re: [Freesurfer] mri_label2vol check-up

[Ji Won Bang]

Dear. Experts.

Please ignore the previous email.

It works.

Thank you.

Best,
Ji Won

2016-03-23 17:24 GMT-04:00 Ji Won Bang :

> Dear. Freesurfer experts.
>
> Hi. How are you?
>
> I'd appreciate it a lot if you can help me with this problem.
>
> I'm trying to check the ROI (.nii) after creating it by using
> mri_label2vol command.
>
> I used the command:
>
> mri_label2vol --label $SUBJECTS_DIR/$SUBJECT/label/lh.v1vt.label --label
> $SUBJECTS_DIR/$SUBJECT/label/lh.v1dt.label --temp
> $DATA_DIR/$SUBJECT/bold_retino/025/fmcpr.nii.gz --reg
> $DATA_DIR/$SUBJECT/bold_retino/025/register.dof6.dat --o
> $DATA_DIR/$SUBJECT/roimask/test.nii
>
> tkmedit -f $SUBJECTS_DIR/$SUBJECT/mri/norm.mgz -overlay
> $DATA_DIR/$SUBJECT/roimask/test.nii -overlay-reg
> $DATA_DIR/$SUBJECT/bold_retino/025/register.dof6.dat -fthresh 0.01
>
> However, this tkmedit command looks for test.dat file instead of test.nii
> and does not show ROI.
>
> Could you please tell me what's going wrong?
>
> Thank you!
>
> Best,
> Ji Won
>
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[Freesurfer] mri_label2vol check-up

[Ji Won Bang]

Dear. Freesurfer experts.

Hi. How are you?

I'd appreciate it a lot if you can help me with this problem.

I'm trying to check the ROI (.nii) after creating it by using mri_label2vol
command.

I used the command:

mri_label2vol --label $SUBJECTS_DIR/$SUBJECT/label/lh.v1vt.label --label
$SUBJECTS_DIR/$SUBJECT/label/lh.v1dt.label --temp
$DATA_DIR/$SUBJECT/bold_retino/025/fmcpr.nii.gz --reg
$DATA_DIR/$SUBJECT/bold_retino/025/register.dof6.dat --o
$DATA_DIR/$SUBJECT/roimask/test.nii

tkmedit -f $SUBJECTS_DIR/$SUBJECT/mri/norm.mgz -overlay
$DATA_DIR/$SUBJECT/roimask/test.nii -overlay-reg
$DATA_DIR/$SUBJECT/bold_retino/025/register.dof6.dat -fthresh 0.01

However, this tkmedit command looks for test.dat file instead of test.nii
and does not show ROI.

Could you please tell me what's going wrong?

Thank you!

Best,
Ji Won
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[Freesurfer] whole hemisphere is yellow

[Miracle Ozzoude]

hello doug, 
i performed a group analysis and after correction for multiple comparisons when 
i tried to load the corrected clusters the whole hemisphere was completely 
yellow. what should i do? 
Best, 
Miracle
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[Freesurfer] XNAT Freesurfer custom datatype

[Rockers, Elijah D.]

Trying to integrate freesurfer data with our XNAT database.

Are there any freesurfer schemas for XNAT available, or is it pretty much I 
have to try to make my own?

Thanks,

--
Elijah Rockers
Research Data Analyst
Houston Methodist Neurological Institute
O: 713 363 7729

Houston Methodist. Leading Medicine. Houston Methodist is ranked by U.S.News & 
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has also been named to FORTUNE®  Magazine's "100 Best Companies to Work For®" 
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***CONFIDENTIALITY NOTICE*** This e-mail is the property of Houston Methodist 
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material for the sole use of the intended recipient(s). Any review, use, 
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intended recipient (or authorized to receive for the recipient), please contact 
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[Freesurfer] Mismatch in dimensions using mri_label2vol

[Afzal, Afsana]

Hi,

I'm using mri_label2vol with the parameters below but the output .nii volume 
has the shape 163842x1x1 while the input volume is 27307x1x6. This dimension 
mismatch is causing issues in our gPPI pipeline.

How can I generate a .nii output file with the 27307x1x6 dimension?

mri_label2vol
--temp fmcpr.sm4.fsaverage.lh.b0dc.nii (output file generated from preproc 
step)
--label label_name.label
--o label_name.nii
--identity

Thanks,

Afsana

__
Afsana Afzal
Clinical Research Coordinator
Massachusetts General Hospital
Division of Neurotherapeutics
Department of Psychiatry: Neurosciences
149 13th St, Room 2612
Charlestown, MA 02129
Phone: 617-643-5129
Fax: 617-726-4078
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Re: [Freesurfer] cannot allocate memory

[Ehsan Tadayon]

Hi Doug,

Thanks. I was wondering if you think this would do the job: 1) use
fmcpr.nii.gz   2) split it to 3d volumes  3) do mri_vol2vol for all the
volumes separely  4) concatenate the resampled volumes together to get a 4d
volume. If you don't think this is a good approach, I appreciate it if you
could walk me through the steps.

Thanks in advance for your help
Best regards,
Ehsan



On Tue, Mar 22, 2016 at 3:53 PM, Douglas N Greve 
wrote:

> The problem is not the command, it is the size of the data it generates.
> You can try reducing the size of the anatomical to a bounding box around
> the brain. This is a bit tricky as you also have to compute a new
> registration. I can help step you through the process if you want to go
> in that direction.
>
> On 03/22/2016 11:50 AM, Ehsan Tadayon wrote:
> > Hi Doug,
> >
> > Thanks for your response. What I'm trying to do is to get each voxel's
> > times course in structural space and I was under the impression that
> > mri_vol2vol --mov func.nii would be the right way to go. Would you
> > please let me know what the best way would be to do this?
> >
> > best,
> > Ehsan,.
> >
> >
> > On Wed, Mar 16, 2016 at 11:27 PM, Douglas Greve
> > mailto:gr...@nmr.mgh.harvard.edu>> wrote:
> >
> > that's going to create a pretty big volume as it will map your
> > functional time course to a 256^3 float volume. If you have 100
> > time points, then that will be about 7G.
> >
> > On 3/16/16 3:27 PM, Ehsan Tadayon wrote:
> >> Hi Bruce,
> >>
> >> Thanks for your response. I'm using :
> >>
> >> freesurfer version:
> >> freesurfer-Darwin-leopard-i686-stable-pub-v5.1.0 on OS X Yosemite
> >> 10.10.5 with 16 GB 1333 MHz DDR3 memory. The command that I'm using:
> >>
> >> mri_vol2vol --mov func.nii.gz --fstarg --reg register.dat --o
> >> func.anat.nii.gz
> >>
> >> Thanks in advance for your help.
> >>
> >> best regards,
> >> Ehsan.
> >>
> >>
> >>
> >>
> >> On Tue, Mar 15, 2016 at 11:49 PM, Bruce Fischl
> >> mailto:fis...@nmr.mgh.harvard.edu>>
> >> wrote:
> >>
> >> Hi Ehsan
> >>
> >> We need the full command line and screen output and also what
> >> your hardware and software environments are to help you.
> >> Certainly sounds like you ran out of memory though
> >>
> >> Cheers
> >> Bruce
> >>
> >> > On Mar 15, 2016, at 11:41 PM, Ehsan Tadayon
> >>  >> > wrote:
> >> >
> >> > Ehsan
> >>
> >> ___
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> >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> >>
> >>
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> >> 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
> >
> >
> > ___
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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
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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
> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
>
> 

Re: [Freesurfer] REPOST: registering longitudinal data to template

[Martin Reuter]

Hi Clara,

1) You'd create a different table for your time point with fsid being 
the longitudinal directories s1.long.sbase , no fsid-base column. then 
you can map and stack these using cross sectional commands (mris_preproc 
--qdec  ...)
2) You should use Qdec or glm_fit for cross sectional analysis
3) Yes, only for 2 stage model, so don't use it (for long you use LME 
anyway and for cross see 2))
4) that commands create a table with one entry for each subject 
(referring to the base), this is also for 2 stage model (the second 
stage works on a subject by subject basis)
5) the -qcache in recon all maps and smoothes surface data to the 
template, so that it is available later. You can do that even on the 
long runs, or you can just manually map ans smooth things with preproc.
6) A different preproc call using a fsgd file rather than a qdec table. 
see the glm_fit tutorial for these things.

Best, Martin

On 03/23/2016 12:28 PM, Clara Kühn wrote:
> Dear FreeSurfer experts,
>
> I would like to analyze my longitudinal data also cross-sectionally at single 
> time points. I am a little confused as to how to register my data to the 
> template and smooth it accordingly.
>
> So far, I have registered my longitudinal data to my template to use in LMEs 
> with this command:
> mris_preproc --qdec-long ./qdec/long.qdec.table.dat --target 30kids_template 
> --hemi lh --meas thickness --out lh.thickness.mg
>
> and then smoothed it with this command:
> mri_surf2surf --hemi lh --s study_average --sval lh.thickness.mgh --tval 
> lh.thickness_sm10.mgh --fwhm-trg 10 --cortex  --noreshape
>
> (1) Do I have to do it once with a cross-sectional command and once with a 
> longitudinal command?
> (2) Should I do the cross-sectional analyses in QDEC or with LME?
>
> Now the question is what these other commands are for?
>
> (3) long_mris_slopes --qdec ct/qdec/long.qdec.table.dat --meas thickness 
> --hemi lh --do-avg --do-rate --do-pc1 --do-spc --do-stack --do-label --time 
> years --qcache kids_template --sd $SUBJECTS_DIR
> --> I understood this is only for Two-Stage-Models, is that correct?
>
> (4) long_qdec_table --qdec qdec/long.qdec.table.dat --cross --out 
> qdec/cross.qdec.table.dat
>
> (5) recon-all -s name -qcache -target  name_of_template
>
> (6) mris_preproc --fsgd gender_age.fsgd --cache-in thickness.fwhm10.fsaverage 
> --target fsaverage --hemi lh --out lh.gender_age.thickness.10.mgh
>
>
> Please help clear up my confusion :)
> Thanks in advance,
> Clara
>
>
>

-- 
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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[Freesurfer] REPOST: registering longitudinal data to template

[Clara Kühn]

Dear FreeSurfer experts,

I would like to analyze my longitudinal data also cross-sectionally at single 
time points. I am a little confused as to how to register my data to the 
template and smooth it accordingly.

So far, I have registered my longitudinal data to my template to use in LMEs 
with this command:
mris_preproc --qdec-long ./qdec/long.qdec.table.dat --target 30kids_template 
--hemi lh --meas thickness --out lh.thickness.mg 

and then smoothed it with this command:
mri_surf2surf --hemi lh --s study_average --sval lh.thickness.mgh --tval 
lh.thickness_sm10.mgh --fwhm-trg 10 --cortex  --noreshape

(1) Do I have to do it once with a cross-sectional command and once with a 
longitudinal command? 
(2) Should I do the cross-sectional analyses in QDEC or with LME?

Now the question is what these other commands are for?

(3) long_mris_slopes --qdec ct/qdec/long.qdec.table.dat --meas thickness --hemi 
lh --do-avg --do-rate --do-pc1 --do-spc --do-stack --do-label --time years 
--qcache kids_template --sd $SUBJECTS_DIR 
--> I understood this is only for Two-Stage-Models, is that correct?

(4) long_qdec_table --qdec qdec/long.qdec.table.dat --cross --out 
qdec/cross.qdec.table.dat

(5) recon-all -s name -qcache -target  name_of_template

(6) mris_preproc --fsgd gender_age.fsgd --cache-in thickness.fwhm10.fsaverage 
--target fsaverage --hemi lh --out lh.gender_age.thickness.10.mgh


Please help clear up my confusion :)
Thanks in advance,
Clara



-- 
Clara Kühn, Phd Student
 
Max-Planck-Institute for Human Cognitive and Brain Science
Department of Neuropsychology
Stephanstrasse 1A
04103 Leipzig, Germany

Phone: +49 341 - 9940 2271
Fax: +49 341 - 9940 2260
Web: www.cbs.mpg.de
E-Mail: cku...@cbs.mpg.de

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Re: [Freesurfer] PET voxelwise

[Douglas Greve]

No, you'll need to pass the new registration to mri_vol2surf. You should 
also check that freeview is producing the correct registration file. 
We've had several problems with it that are definitely fixed in 6.0, but 
not sure about 5.3. Try loading it in tkregister (--lta your.lta --reg 
your.reg --ltaout your.lta). In fact, I would probably just not use 
freeview to adjust the registration in 5.3, use tkregister.


On 3/23/16 7:55 AM, Elijah Mak wrote:

Hi Doug,

Thanks!

I manually tweaked the registration of the PET to T1 on a number of 
subjects to bring the mincost down to < 0.5. After saving the pet2free 
volume in Freeview, I noticed that a new .lta is produced in the same 
directory (i.e. pet2free_fsl.mgz.lta).


Will the option --regheader tell the subsequent commands (i.e. 
mri_vol2surf) to use the updated registration .lta instead of the 
original .dat that was produced via bbregister?


Best Wishes,
Elijah




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Re: [Freesurfer] PET voxelwise

[Douglas Greve]

On 3/23/16 9:07 AM, Elijah Mak wrote:
mri_concat --f pib_lh_fsaverage (textfile of subjects and their 
images) --o concat_lh_pet.mgh


Should I add -mean here for the GLM?

No, that is handled by glmfit


mri_glmfit  --y  concat_lh_pet.mgh  --fsgd  pib_fsgd  --C 
group1.group2.mtx  --surf fsaverage lh  --cortex  --glmdir lh.pet.glmdir


My simple 2 group-no-covariates FSGD is as follows. Can I also check 
that it is alright to have the Groups interspersed throughout the order?

Yes, that is fine.


GroupDescriptorFile 1
Title OSGM
Class Group1
Class Group2
inputFS6_16084_MPRAGE_Neuro.niiGroup1
inputFS6_22769_MPRAGE_Neuro.niiGroup1
inputFS6_22863_MPRAGE_Neuro.niiGroup1
inputFS6_22899_MPRAGE_Neuro.niiGroup1
inputFS6_22995_MPRAGE_Neuro.niiGroup2
inputFS6_23008_MPRAGE_Neuro.niiGroup1
inputFS6_23173_MPRAGE_Neuro.niiGroup2
inputFS6_23243_MPRAGE_Neuro.niiGroup2
inputFS6_23244_MPRAGE_Neuro.niiGroup1
inputFS6_23619_MPRAGE_Neuro.niiGroup1
inputFS6_23623_MPRAGE_Neuro.niiGroup1
inputFS6_23755_MPRAGE_Neuro.niiGroup2

Thanks again, Doug. Appreciate it so much!

Best Wishes,
Elijah




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Re: [Freesurfer] Troubleshooting for error - neither NIfTI-1 qform or sform are valid

[Douglas Greve]

On 3/23/16 1:04 AM, Reema Jayakar wrote:

Hi Dr. Greve,

Thank you very much for getting back to me so promptly. If memory 
serves me right, I am pretty sure that the orientations were incorrect 
in tkmedit but will double check soon. Based on what you are saying 
and based on what I read in the wiki about mri_convert it seems that I 
will be able to change all of my nifti files using mri_convert and 
then I can use the newly generated niftis to run reconall? Is this 
correct?

Yes


As I am very new to FS, I don't know what it means to give it an 
orientation string? Is there some documentation where I can look this 
up further?
If you run mri_convert without options it will print out a bunch of 
text. Info about the orientation string is in there


In any case, thank you very much and I will keep you posted!

Best,
Reema

--
*Reema Jayakar, M.A.*
Doctoral Candidate - Clinical Neuropsychology
Health Resources and Services Administration (HRSA) Fellow
Department of Psychology
Georgia State University
Email: rjayak...@student.gsu.edu 


Message: 24
Date: Tue, 22 Mar 2016 10:56:40 -0400
From: Douglas Greve mailto:gr...@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] Troubleshooting for error - neither NIfTI-1
qform or sform are valid
To: freesurfer@nmr.mgh.harvard.edu

Message-ID: <56f15d28.7040...@nmr.mgh.harvard.edu
>
Content-Type: text/plain; charset="windows-1252"

To check whether the orientation is correct, you can view it in
freeview
or tkmedit. When you click on the axial view it should show up
axially,
etc. Though you cannot tell whether it is left-right reversed this
way.
You cannot feed it a matrix, but you can specify the direction cosines
on the mri_convert command line (-iid, -ijd, -ikd). You'll have to
play
with it a bit. You can also try giving it an orientation string
instead.
if you run mri_convert without any options, then it will give you lots
of documentation.

On 3/20/16 8:44 PM, Reema Jayakar wrote:
> Hello FS list subscribers,
>
> Is there a way to manually feed FS with NIfTI-1 qform or sform
> information? Or correctly add this information to the original .nii
> files? My sense of the problem is that there is a problem with the
> header information in my .nii files and FS cannot tell what is
> anterior, posterior, left, right.
>
> That said, I am very new to FS and my interpretation of the error
> could be wrong. So I am laying out the details below
(recon-all.log is
> also attached to this email):
>
>   * When I try to run recon-all there are no output images/files
> generated and the message I get is that the Talairach transform
> failed
>   * When I try to run autorecon1 an autorecon2 with the "-notal
check"
> flag, FS does not give me any error message and proceeds with
> generating output. However, I can visually see (via
brainmask.mgz)
> that oreintations are messed up (e.g., tried to register coronal
> orientation on top of sagittal orientation)
>   * This problem only occurs with .nii files from a particular study
> that came out of a specific scanner. All my other data are
running
> through FS smoothly, which is why I think there is some problem
> with the .nii files
>   * Also, when I view my raw .nii images in FSL view none of the
usual
> orientation markers are visible to me, which again suggest that
> they may be missing?
>   * Unfortunately, I do not currently have the original .dcm files
> available as this is a multi-site archival study
>
>
> Any help you can provide to resolve this issue would be really
> appreciated!
>
> Thank you,
> Reema
>
>
>
> --
> *Reema Jayakar, M.A.*
> Doctoral Candidate - Clinical Neuropsychology
> Health Resources and Services Administration (HRSA) Fellow
> Department of Psychology
> Georgia State University
> Email: rjayak...@student.gsu.edu

>
***







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Re: [Freesurfer] PET voxelwise

[Elijah Mak]

mri_concat --f pib_lh_fsaverage (textfile of subjects and their images) --o
concat_lh_pet.mgh

Should I add -mean here for the GLM?

mri_glmfit  --y  concat_lh_pet.mgh  --fsgd  pib_fsgd  --C group1.group2.mtx
 --surf fsaverage lh  --cortex  --glmdir lh.pet.glmdir

My simple 2 group-no-covariates FSGD is as follows. Can I also check that
it is alright to have the Groups interspersed throughout the order?

GroupDescriptorFile 1
Title OSGM
Class Group1
Class Group2
input FS6_16084_MPRAGE_Neuro.nii Group1
input FS6_22769_MPRAGE_Neuro.nii Group1
input FS6_22863_MPRAGE_Neuro.nii Group1
input FS6_22899_MPRAGE_Neuro.nii Group1
input FS6_22995_MPRAGE_Neuro.nii Group2
input FS6_23008_MPRAGE_Neuro.nii Group1
input FS6_23173_MPRAGE_Neuro.nii Group2
input FS6_23243_MPRAGE_Neuro.nii Group2
input FS6_23244_MPRAGE_Neuro.nii Group1
input FS6_23619_MPRAGE_Neuro.nii Group1
input FS6_23623_MPRAGE_Neuro.nii Group1
input FS6_23755_MPRAGE_Neuro.nii Group2

Thanks again, Doug. Appreciate it so much!

Best Wishes,
Elijah
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Re: [Freesurfer] Matlabpool has been removed

[Martin Reuter]

Hi Kasper,

the fix is that someone needs to sit down and port all matlabpool to 
parpool, which is straightforward. It needs to be done in a way that is 
backward compatible, as not everyone has the new version of Matlab. 
Maybe someone on the list want's to take this on, should only be a 
couple hours or a day with matlab experience.


Cheers, Martin


On 03/23/2016 06:57 AM, Kasper Jessen wrote:

Hi Clara,
Your right, an older version of Matlab, could be a solution. However, 
i am thinking that there must be a fix?

Cheers,
Kasper

2016-03-23 11:16 GMT+01:00 Clara Kühn >:


Hi Kaspar,

I had the same problem. The last version that supports matlabpool
is Matlab 8.2. Maybe try it with that version.

Cheers, Clara

- Ursprüngliche Mail -
Von: "Kasper Jessen" mailto:kaspe...@cnsr.dk>>
An: "Freesurfer support list" mailto:freesurfer@nmr.mgh.harvard.edu>>
Gesendet: Mittwoch, 23. März 2016 09:41:51
Betreff: [Freesurfer] Matlabpool has been removed

Dear FreeSurfer experts,

Thanks again for a great FreeSurfer forum.

I have been trying to run the linear mixed effects model on a
longitudinal dataset. However, i get the an error in matlab:
"matlabpool has been removed. Use PARPOOL instead". I can see in
the forum that others have experienced the same. Unfortunately i
cannot find the answer, which fixes the problem. As far as i
understand, it may be because i am using a new version of Matlab.
However, is there a way to fix the problem?
Best regards,
Kasper Jessen
MD, PhD student



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--
Kasper Jessen,
MD, PhD student
Center for neuropsychiatric Schizophrenia Research (CNSR)
Mental Health Centre Glostrup
Nordre Ringvej 29-67
2600 Glostrup
Tlf.: 24430136
E-mail: kaspe...@cnsr.dk  eller 
kasper.jes...@regionh.dk 



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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] PET voxelwise

[Elijah Mak]

Hi Doug,

Thanks!

I manually tweaked the registration of the PET to T1 on a number of
subjects to bring the mincost down to < 0.5.  After saving the pet2free
volume in Freeview, I noticed that a new .lta is produced in the same
directory (i.e. pet2free_fsl.mgz.lta).

Will the option --regheader tell the subsequent commands (i.e.
mri_vol2surf) to use the updated registration .lta instead of the original
.dat that was produced via bbregister?

Best Wishes,
Elijah
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Re: [Freesurfer] Matlabpool has been removed

[Kasper Jessen]

Hi Clara,
Your right, an older version of Matlab, could be a solution. However, i am
thinking that there must be a fix?
Cheers,
Kasper

2016-03-23 11:16 GMT+01:00 Clara Kühn :

> Hi Kaspar,
>
> I had the same problem. The last version that supports matlabpool is
> Matlab 8.2. Maybe try it with that version.
>
> Cheers, Clara
>
> - Ursprüngliche Mail -
> Von: "Kasper Jessen" 
> An: "Freesurfer support list" 
> Gesendet: Mittwoch, 23. März 2016 09:41:51
> Betreff: [Freesurfer] Matlabpool has been removed
>
> Dear FreeSurfer experts,
>
> Thanks again for a great FreeSurfer forum.
>
> I have been trying to run the linear mixed effects model on a longitudinal
> dataset. However, i get the an error in matlab: "matlabpool has been
> removed. Use PARPOOL instead". I can see in the forum that others have
> experienced the same. Unfortunately i cannot find the answer, which fixes
> the problem. As far as i understand, it may be because i am using a new
> version of Matlab. However, is there a way to fix the problem?
> Best regards,
> Kasper Jessen
> MD, PhD student
>
>
>
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-- 
Kasper Jessen,
MD, PhD student
Center for neuropsychiatric Schizophrenia Research (CNSR)
Mental Health Centre Glostrup
Nordre Ringvej 29-67
2600 Glostrup
Tlf.: 24430136
E-mail: kaspe...@cnsr.dk eller kasper.jes...@regionh.dk
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Re: [Freesurfer] Matlabpool has been removed

[Clara Kühn]

Hi Kaspar,

I had the same problem. The last version that supports matlabpool is Matlab 
8.2. Maybe try it with that version.

Cheers, Clara

- Ursprüngliche Mail -
Von: "Kasper Jessen" 
An: "Freesurfer support list" 
Gesendet: Mittwoch, 23. März 2016 09:41:51
Betreff: [Freesurfer] Matlabpool has been removed

Dear FreeSurfer experts, 

Thanks again for a great FreeSurfer forum. 

I have been trying to run the linear mixed effects model on a longitudinal 
dataset. However, i get the an error in matlab: "matlabpool has been removed. 
Use PARPOOL instead". I can see in the forum that others have experienced the 
same. Unfortunately i cannot find the answer, which fixes the problem. As far 
as i understand, it may be because i am using a new version of Matlab. However, 
is there a way to fix the problem? 
Best regards, 
Kasper Jessen 
MD, PhD student 



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[Freesurfer] Matlabpool has been removed

[Kasper Jessen]

Dear FreeSurfer experts,

Thanks again for a great FreeSurfer forum.

I have been trying to run the linear mixed effects model on a longitudinal
dataset. However, i get the an error in matlab: "matlabpool has been
removed. Use PARPOOL instead". I can see in the forum that others have
experienced the same. Unfortunately i cannot find the answer, which fixes
the problem. As far as i understand, it may be because i am using a new
version of Matlab. However, is there a way to fix the problem?

Best regards,
Kasper Jessen
MD, PhD student
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