Re: [Freesurfer] viewing mri_glmfit FDR corrected results

[marco mcsweeney]

Dear Doug,

thank you so much for the feedback and all of your help!

Best wishes

Marco



On Thu, Jul 6, 2017 at 1:45 AM, Douglas Greve 
wrote:

> You can use mri_surfcluster. Set the sig.mgh as the --in file. Set --fdr
> to the FDR you want. Set --subject fsaverage and set the ---hemi. Set
> --annot aparc. Set --sum to the output summary file. This should give you
> something similar to the output of mri_glmfit-sim.
>
> On 6/29/17 4:29 PM, marco mcsweeney wrote:
>
> Dear FreeSurfer experts,
>
> I ran my group analysis using mri_glmfit and found a number of significant
> clusters showing cortical thickness differences between 2 groups. I used
> tksurfer to visualize the results and used FDR to correct for multiple
> comparisons.
>
> My question is about how do I correctly get the FDR corrected results
> showing cluster number, size, MNI coordinates etc. as I would if I used
> QDEC?
>
> I have searched through the archives and have found what looks like the
> answer, but I'm not convinced that the method I used is correct.
>
> I used
>
> 1) mri_glmfit-sim --glmdir lh.group_diff.glmdir --cache 1.3 abs
> --cwpvalthresh .99
>
> and
>
> 2) less lh.group_diff.glmdir/contrast.txt/cache.th13.abs.sig.
> cluster.summary
>
> However when I visualize the FDR corrected results with tksurfer or
> freeview I can see a couple of clusters not listed in the summary. Am I
> missing something?
>
> Thank you so much in advance.
>
> Any help or advice would be greatly appreciated.
>
> Best wishes
>
> Marco
>
>
> ___
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[Freesurfer] Stanford University Job Opportunities: Postdoctoral Fellowships in Computational Modeling of Brain Networks

[Sheena Chand]

Stanford University's Department of Psychiatry & Behavioral Sciences is seeking 
to hire full time post-doctoral fellows in Computational Modeling of Brain 
Networks for their Cognitive & Systems Neuroscience Laboratory.
This lab is headed by Dr. Vinod Menon who has broad multidisciplinary expertise 
that spans several scientific disciplines and has published extensively on 
various aspects of human cognition and brain function.

Explore our lab website for more information: 
http://med.stanford.edu/scsnl.html.

Please, distribute job posting (below) appropriately in your department. We 
thank you for your support.

POSTDOCTORAL FELLOWSHIP IN COMPUTATIONAL MODELING OF BRAIN NETWORKS
The Stanford Cognitive and Systems Neuroscience Laboratory invites applications 
for a postdoctoral fellowship in human brain network analysis and modeling. We 
seek candidates with strong research backgrounds in one or more of the 
following areas: resting-state and task-evoked fMRI connectivity, structural 
HARDI-based connectivity, neurophysiological modeling of brain networks, 
Bayesian modeling, machine learning, and deep neural networks. Candidates must 
have strong computational skills and a PhD in computational neuroscience, 
computer science, physics, biomedical engineering or related fields. This is an 
exciting opportunity to work on multiple NIH- and Stanford-funded projects 
using multimodal (fMRI, optogenetic, DTI, EEG) brain imaging techniques in 
multiple clinical populations and normative groups. The successful candidate 
will develop a vigorous research program that contributes to, and complements, 
ongoing research studies. The candidate will have access to state-of-the-art 
brain imaging and HPC/GPU facilities.Please email a CV, statement of research 
interests and relevant background, and names of three referees to Drs. Vinod 
Menon and Aarthi Padmanabhan at 
scsnl.stanford+post...@gmail.com


Best,
Sheena

_
Sheena Chand
Research Administrative Assistant
Department of Psychiatry & Behavioral Sciences
Stanford University|School of Medicine
Email: schan...@stanford.edu
Desk: (650) 498-9821

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[Freesurfer] Please post to list: Subject: Stanford University Job Opportunities: Postdoctoral Fellowships in Computational Modeling of Brain Networks

[Sheena Chand]

Stanford University's Department of Psychiatry & Behavioral Sciences is seeking 
to hire full time post-doctoral fellows in Computational Modeling of Brain 
Networks for their Cognitive & Systems Neuroscience Laboratory.
This lab is headed by Dr. Vinod Menon who has broad multidisciplinary expertise 
that spans several scientific disciplines and has published extensively on 
various aspects of human cognition and brain function.

Explore our lab website for more information: 
http://med.stanford.edu/scsnl.html.

Please, distribute job posting (below) appropriately in your department. We 
thank you for your support.

POSTDOCTORAL FELLOWSHIP IN COMPUTATIONAL MODELING OF BRAIN NETWORKS
The Stanford Cognitive and Systems Neuroscience Laboratory invites applications 
for a postdoctoral fellowship in human brain network analysis and modeling. We 
seek candidates with strong research backgrounds in one or more of the 
following areas: resting-state and task-evoked fMRI connectivity, structural 
HARDI-based connectivity, neurophysiological modeling of brain networks, 
Bayesian modeling, machine learning, and deep neural networks. Candidates must 
have strong computational skills and a PhD in computational neuroscience, 
computer science, physics, biomedical engineering or related fields. This is an 
exciting opportunity to work on multiple NIH- and Stanford-funded projects 
using multimodal (fMRI, optogenetic, DTI, EEG) brain imaging techniques in 
multiple clinical populations and normative groups. The successful candidate 
will develop a vigorous research program that contributes to, and complements, 
ongoing research studies. The candidate will have access to state-of-the-art 
brain imaging and HPC/GPU facilities.Please email a CV, statement of research 
interests and relevant background, and names of three referees to Drs. Vinod 
Menon and Aarthi Padmanabhan at 
scsnl.stanford+post...@gmail.com


Best,
Sheena

_
Sheena Chand
Research Administrative Assistant
Department of Psychiatry & Behavioral Sciences
Stanford University|School of Medicine
Email: schan...@stanford.edu
Desk: (650) 498-9821

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[Freesurfer] mkbrainmask-sess: couldn't find register.dof6.lta

[Li Guo]

Dear freesurfer developers,

I’d like to ask about an error I encountered in Freesurfer v6.0 with 
mkbrainmask-sess. I am using macOS Sierra.
Here is the error:

error:"ERROR: cannot find 
/Users/lguo15/Documents/MATLAB/fMRI_P3/Fisch_P3_01/bold/register.dof6.lta, you 
might need to run register-sess”

The error goes away if I run register-sess before mkbrainmask-sess. However, my 
lab mates use v5.3 and ran the exact same preprocess pipeline without this 
error. The order for them is mkbrainmask-sess first and register-sess later.

I’d like to ask whether it is true that maybe in v6.0 mkbrainmask-sess now 
depends on register-sess to generate the register.dof6.lta file? Or how should 
I interpret this? Does running registration and masks have some fixed order at 
all or it doesn’t matter?

Best,
Li
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Re: [Freesurfer] freeview command error

[Bruce Fischl]

then you shouldn't be sourcing a script that uses setenv. Try sourcing 
$FREESURFER_HOME/FreeSurferEnv.sh


cheers
Bruce
On Tue, 11 Jul 2017, Yagmur Ozdemir 19 
wrote:



It is using bash.

Idil

From: freesurfer-boun...@nmr.mgh.harvard.edu 
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Bruce Fischl 
[fis...@nmr.mgh.harvard.edu]
Sent: Tuesday, July 11, 2017 6:30 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] freeview command error

Hi Idil

do you know what shell you are using in the terminal that you are trying
to call freeview from?
On Tue, 11 Jul 2017, Yagmur Ozdemir 19 wrote:


Hello,
I only followed the steps in the install/download page and installed tcsh 
because it was not running recon-all. Are you saying that I should set up 
freeview by sourcing those three files and use the *.csh extension? When 
opening the terminal again after recon-all to run this I did not do any 
additional set up. I also remember using .sh when following the steps on the 
install page. The system does not recognize freeview even when I just use the 
command alone.
Sorry my knowledge pertaining to software use is pretty elementary and there is 
no one to ask.

Thank you for the help,
Idil


From: freesurfer-boun...@nmr.mgh.harvard.edu 
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Bruce Fischl 
[fis...@nmr.mgh.harvard.edu]
Sent: Tuesday, July 11, 2017 6:03 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] freeview command error

Hi Idil

how do you setup freesurfer? If you are using bash (and it looks like you
are) you should source the *.sh file, not the *.csh. Also, note that you
should use T1.mgz not T1/mgz in your freeview command line
cheers
Bruce
On Tue, 11 Jul
2017, Yagmur Ozdemir 19 wrote:


Hello,

I am installing Freesurfer with my limited coding knowledge and this problem 
with freeview came up when I was trying to view the volumes of recon-ed subject.

lab@lab-ThinkStation-E31:~/Desktop/freesurfer/subjects$ freeview -v 
practice/mri/T1/mgz
No command 'freeview' found, did you mean:
 Command 'treeview' from package 'treeview' (multiverse)
freeview: command not found

I checked and freeview is in the bin, and I even tried to install it according 
to its file by sourcing tcl_setup and others, but then this error comes up:

lab@lab-ThinkStation-E31:~/Desktop/freesurfer/bin$ source tcl_setup
bash: tcl_setup: line 47: syntax error near unexpected token `setenv'
bash: tcl_setup: line 47: `    if ( -e $TCLLIBPATH/tcl8.3 ) setenv TCL_LIBRARY 
$TCLLIBPATH/tcl8.3'

Can someone please give me any direction for how to solve this issue. I would 
appreciate the help very much.
(Freesurfer version 6 & Ubuntu 16.04)

Thank you all,
Idil





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Re: [Freesurfer] GLM question

[Yann Ying Chye]

Thanks for your reply,

I have a follow up on my first question - if however I was not looking for
a main effect of gender, but for the main effect of something else (e.g.
diagnosis), will it then be ok to include the unbalanced group (i.e.
A-male), to control for gender?

Thanks!

Regards
Yann

On 7 July 2017 at 18:34,  wrote:

> Send Freesurfer mailing list submissions to
> freesurfer@nmr.mgh.harvard.edu
>
> To subscribe or unsubscribe via the World Wide Web, visit
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> or, via email, send a message with subject or body 'help' to
> freesurfer-requ...@nmr.mgh.harvard.edu
>
> You can reach the person managing the list at
> freesurfer-ow...@nmr.mgh.harvard.edu
>
>
>
> On 7/7/17 1:58 PM, Yann Ying Chye wrote:
> > Dear FreeSurfer mailing list,
> >
> > I've got two questions regarding the freesurfer GLM analysis.
> >
> > 1. I am trying to run mri_glmfit on the cortical thickness of a
> > dataset that has a few interacting factors of unequal levels.
> > For example, my dataset may have groups A, B, C, and D. Within the
> > groups, subjects are further divided by gender - male and female.
> > However, group A only has males, such that the classes in my FSGD file
> > = A-male, B-male, B-female, C-male, C-female, D-male, and D-female.
> > Will this design be a problem? Will it be statistically sound?
> > Additionally if I was looking for an effect of gender, how would I
> > weigh my contrast? I was thinking 0.25 0.25 -0.33 0.25 -0.33 0.25
> > -0.33. Would that be valid?
> I think I would lean against including A-male. Otherwise, what is the
> null hypothesis? Without A-male, it would be that males and females
> differ when regeressing out the effect of group, but you can't say that
> if you include A-male. Eg, if there were no difference between A-male
> and A-female but A tended to be larger than the other groups, then
> including A-male and not A-female would create a confound making males
> look bigger than females.
> > 2. Does mri_glmfit have a limit to the number of subjects it can run
> > with? If I have say upwards of a few thousand subjects, will this be
> > possible to run/how long would that take?
> I don't think it has a limit.
> >
> > Thanks for your help!
> >
> > Regards
> > Yann
> >
> >
> > ___
> > Freesurfer mailing list
> > Freesurfer@nmr.mgh.harvard.edu
> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
> End of Freesurfer Digest, Vol 161, Issue 17
> ***
>
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Re: [Freesurfer] Simple math with freesurfer surface

[Van Der Deijl, Rosanne]

Dear Bruce,

To be honest, I'm not sure, but I think I want the average of the scalar fields 
over the surface. I want to have some way of putting the thickness overlays on 
the surfaces of all my subjects together and visualizing this (I have pre-post 
data so I'd like to have a visualization of pre-average/added and one for 
post-average/added). 

Hope this makes sense, thank you!

- Rose

From: freesurfer-boun...@nmr.mgh.harvard.edu 
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of 
freesurfer-requ...@nmr.mgh.harvard.edu [freesurfer-requ...@nmr.mgh.harvard.edu]
Sent: Tuesday, July 11, 2017 12:00 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Freesurfer Digest, Vol 161, Issue 21

Send Freesurfer mailing list submissions to
freesurfer@nmr.mgh.harvard.edu

To subscribe or unsubscribe via the World Wide Web, visit
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
or, via email, send a message with subject or body 'help' to
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You can reach the person managing the list at
freesurfer-ow...@nmr.mgh.harvard.edu

When replying, please edit your Subject line so it is more specific
than "Re: Contents of Freesurfer digest..."


Today's Topics:

   1. Re: Extract smoothed cortical thickness whole-brain
  vertex-wise (Nicolette Schwarz)
   2. Re: help with code interpretation (Leanne Hunt)
   3. Re: Fwd: surface inaccuracies around the optic chiasm
  (Bruce Fischl)
   4. Re: Extract smoothed cortical thickness whole-brain
  vertex-wise (Bruce Fischl)
   5. error with mri_glmfit --frame-mask (Sadie Marvel)
   6. Re: Extract smoothed cortical thickness whole-brain
  vertex-wise (Nicolette Schwarz)
   7. questions mri_glmfit-sim (Van Der Deijl, Rosanne)
   8. Simple math with freesurfer surfaces (Van Der Deijl, Rosanne)
   9. Re: Simple math with freesurfer surfaces (Bruce Fischl)
  10. Re: Extract smoothed cortical thickness whole-brain
  vertex-wise (Bruce Fischl)
  11. 'Best practice' for dealing with lesioned brains
  (King, Daniel (Research Student))
  12. BBRegister + partial FoV fail (Paul Glad Mihai)
  13. Re: BBRegister + partial FoV fail (Bruce Fischl)
  14. Re: BBRegister + partial FoV fail (Paul Glad Mihai)
  15. Re: BBRegister + partial FoV fail (Bruce Fischl)
  16. freeview command error (Yagmur Ozdemir 19)
  17. Re: freeview command error (Bruce Fischl)
  18. Re: freeview command error (Yagmur Ozdemir 19)
  19. Re: freeview command error (Bruce Fischl)
  20. Re: freeview command error (Yagmur Ozdemir 19)


--

Message: 1
Date: Mon, 10 Jul 2017 12:12:57 -0400
From: Nicolette Schwarz 
Subject: Re: [Freesurfer] Extract smoothed cortical thickness
whole-brain vertex-wise
To: Freesurfer support list 
Message-ID:

Re: [Freesurfer] freeview command error

[Yagmur Ozdemir 19]

It is using bash.

Idil

From: freesurfer-boun...@nmr.mgh.harvard.edu 
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Bruce Fischl 
[fis...@nmr.mgh.harvard.edu]
Sent: Tuesday, July 11, 2017 6:30 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] freeview command error

Hi Idil

do you know what shell you are using in the terminal that you are trying
to call freeview from?
On Tue, 11 Jul 2017, Yagmur Ozdemir 19 wrote:

> Hello,
> I only followed the steps in the install/download page and installed tcsh 
> because it was not running recon-all. Are you saying that I should set up 
> freeview by sourcing those three files and use the *.csh extension? When 
> opening the terminal again after recon-all to run this I did not do any 
> additional set up. I also remember using .sh when following the steps on the 
> install page. The system does not recognize freeview even when I just use the 
> command alone.
> Sorry my knowledge pertaining to software use is pretty elementary and there 
> is no one to ask.
>
> Thank you for the help,
> Idil
>
> 
> From: freesurfer-boun...@nmr.mgh.harvard.edu 
> [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Bruce Fischl 
> [fis...@nmr.mgh.harvard.edu]
> Sent: Tuesday, July 11, 2017 6:03 PM
> To: Freesurfer support list
> Subject: Re: [Freesurfer] freeview command error
>
> Hi Idil
>
> how do you setup freesurfer? If you are using bash (and it looks like you
> are) you should source the *.sh file, not the *.csh. Also, note that you
> should use T1.mgz not T1/mgz in your freeview command line
> cheers
> Bruce
> On Tue, 11 Jul
> 2017, Yagmur Ozdemir 19 wrote:
>
>> Hello,
>>
>> I am installing Freesurfer with my limited coding knowledge and this problem 
>> with freeview came up when I was trying to view the volumes of recon-ed 
>> subject.
>>
>> lab@lab-ThinkStation-E31:~/Desktop/freesurfer/subjects$ freeview -v 
>> practice/mri/T1/mgz
>> No command 'freeview' found, did you mean:
>>  Command 'treeview' from package 'treeview' (multiverse)
>> freeview: command not found
>>
>> I checked and freeview is in the bin, and I even tried to install it 
>> according to its file by sourcing tcl_setup and others, but then this error 
>> comes up:
>>
>> lab@lab-ThinkStation-E31:~/Desktop/freesurfer/bin$ source tcl_setup
>> bash: tcl_setup: line 47: syntax error near unexpected token `setenv'
>> bash: tcl_setup: line 47: `    if ( -e $TCLLIBPATH/tcl8.3 ) setenv 
>> TCL_LIBRARY $TCLLIBPATH/tcl8.3'
>>
>> Can someone please give me any direction for how to solve this issue. I 
>> would appreciate the help very much.
>> (Freesurfer version 6 & Ubuntu 16.04)
>>
>> Thank you all,
>> Idil
>>
>>
>>
>
> ___
> Freesurfer mailing list
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> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
>

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contains patient information, please contact the Partners Compliance HelpLine at
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but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

Re: [Freesurfer] freeview command error

[Bruce Fischl]

Hi Idil

do you know what shell you are using in the terminal that you are trying 
to call freeview from?

On Tue, 11 Jul 2017, Yagmur Ozdemir 19 wrote:


Hello,
I only followed the steps in the install/download page and installed tcsh 
because it was not running recon-all. Are you saying that I should set up 
freeview by sourcing those three files and use the *.csh extension? When 
opening the terminal again after recon-all to run this I did not do any 
additional set up. I also remember using .sh when following the steps on the 
install page. The system does not recognize freeview even when I just use the 
command alone.
Sorry my knowledge pertaining to software use is pretty elementary and there is 
no one to ask.

Thank you for the help,
Idil


From: freesurfer-boun...@nmr.mgh.harvard.edu 
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Bruce Fischl 
[fis...@nmr.mgh.harvard.edu]
Sent: Tuesday, July 11, 2017 6:03 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] freeview command error

Hi Idil

how do you setup freesurfer? If you are using bash (and it looks like you
are) you should source the *.sh file, not the *.csh. Also, note that you
should use T1.mgz not T1/mgz in your freeview command line
cheers
Bruce
On Tue, 11 Jul
2017, Yagmur Ozdemir 19 wrote:


Hello,

I am installing Freesurfer with my limited coding knowledge and this problem 
with freeview came up when I was trying to view the volumes of recon-ed subject.

lab@lab-ThinkStation-E31:~/Desktop/freesurfer/subjects$ freeview -v 
practice/mri/T1/mgz
No command 'freeview' found, did you mean:
 Command 'treeview' from package 'treeview' (multiverse)
freeview: command not found

I checked and freeview is in the bin, and I even tried to install it according 
to its file by sourcing tcl_setup and others, but then this error comes up:

lab@lab-ThinkStation-E31:~/Desktop/freesurfer/bin$ source tcl_setup
bash: tcl_setup: line 47: syntax error near unexpected token `setenv'
bash: tcl_setup: line 47: `    if ( -e $TCLLIBPATH/tcl8.3 ) setenv TCL_LIBRARY 
$TCLLIBPATH/tcl8.3'

Can someone please give me any direction for how to solve this issue. I would 
appreciate the help very much.
(Freesurfer version 6 & Ubuntu 16.04)

Thank you all,
Idil





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The information in this e-mail is intended only for the person to whom it is
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Re: [Freesurfer] freeview command error

[Yagmur Ozdemir 19]

Hello, 
I only followed the steps in the install/download page and installed tcsh 
because it was not running recon-all. Are you saying that I should set up 
freeview by sourcing those three files and use the *.csh extension? When 
opening the terminal again after recon-all to run this I did not do any 
additional set up. I also remember using .sh when following the steps on the 
install page. The system does not recognize freeview even when I just use the 
command alone. 
Sorry my knowledge pertaining to software use is pretty elementary and there is 
no one to ask.

Thank you for the help,
Idil


From: freesurfer-boun...@nmr.mgh.harvard.edu 
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Bruce Fischl 
[fis...@nmr.mgh.harvard.edu]
Sent: Tuesday, July 11, 2017 6:03 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] freeview command error

Hi Idil

how do you setup freesurfer? If you are using bash (and it looks like you
are) you should source the *.sh file, not the *.csh. Also, note that you
should use T1.mgz not T1/mgz in your freeview command line
cheers
Bruce
On Tue, 11 Jul
2017, Yagmur Ozdemir 19 wrote:

> Hello,
>
> I am installing Freesurfer with my limited coding knowledge and this problem 
> with freeview came up when I was trying to view the volumes of recon-ed 
> subject.
>
> lab@lab-ThinkStation-E31:~/Desktop/freesurfer/subjects$ freeview -v 
> practice/mri/T1/mgz
> No command 'freeview' found, did you mean:
>  Command 'treeview' from package 'treeview' (multiverse)
> freeview: command not found
>
> I checked and freeview is in the bin, and I even tried to install it 
> according to its file by sourcing tcl_setup and others, but then this error 
> comes up:
>
> lab@lab-ThinkStation-E31:~/Desktop/freesurfer/bin$ source tcl_setup
> bash: tcl_setup: line 47: syntax error near unexpected token `setenv'
> bash: tcl_setup: line 47: `    if ( -e $TCLLIBPATH/tcl8.3 ) setenv 
> TCL_LIBRARY $TCLLIBPATH/tcl8.3'
>
> Can someone please give me any direction for how to solve this issue. I would 
> appreciate the help very much.
> (Freesurfer version 6 & Ubuntu 16.04)
>
> Thank you all,
> Idil
>
>
>

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Re: [Freesurfer] freeview command error

[Bruce Fischl]

Hi Idil

how do you setup freesurfer? If you are using bash (and it looks like you 
are) you should source the *.sh file, not the *.csh. Also, note that you 
should use T1.mgz not T1/mgz in your freeview command line

cheers
Bruce
On Tue, 11 Jul 
2017, Yagmur Ozdemir 19 wrote:



Hello,

I am installing Freesurfer with my limited coding knowledge and this problem 
with freeview came up when I was trying to view the volumes of recon-ed subject.

lab@lab-ThinkStation-E31:~/Desktop/freesurfer/subjects$ freeview -v 
practice/mri/T1/mgz
No command 'freeview' found, did you mean:
 Command 'treeview' from package 'treeview' (multiverse)
freeview: command not found

I checked and freeview is in the bin, and I even tried to install it according 
to its file by sourcing tcl_setup and others, but then this error comes up:

lab@lab-ThinkStation-E31:~/Desktop/freesurfer/bin$ source tcl_setup
bash: tcl_setup: line 47: syntax error near unexpected token `setenv'
bash: tcl_setup: line 47: `    if ( -e $TCLLIBPATH/tcl8.3 ) setenv TCL_LIBRARY 
$TCLLIBPATH/tcl8.3'

Can someone please give me any direction for how to solve this issue. I would 
appreciate the help very much.
(Freesurfer version 6 & Ubuntu 16.04)

Thank you all,
Idil


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[Freesurfer] freeview command error

[Yagmur Ozdemir 19]

Hello,

I am installing Freesurfer with my limited coding knowledge and this problem 
with freeview came up when I was trying to view the volumes of recon-ed subject.

lab@lab-ThinkStation-E31:~/Desktop/freesurfer/subjects$ freeview -v 
practice/mri/T1/mgz
No command 'freeview' found, did you mean:
 Command 'treeview' from package 'treeview' (multiverse)
freeview: command not found

I checked and freeview is in the bin, and I even tried to install it according 
to its file by sourcing tcl_setup and others, but then this error comes up:

lab@lab-ThinkStation-E31:~/Desktop/freesurfer/bin$ source tcl_setup
bash: tcl_setup: line 47: syntax error near unexpected token `setenv'
bash: tcl_setup: line 47: `if ( -e $TCLLIBPATH/tcl8.3 ) setenv TCL_LIBRARY 
$TCLLIBPATH/tcl8.3'

Can someone please give me any direction for how to solve this issue. I would 
appreciate the help very much.
(Freesurfer version 6 & Ubuntu 16.04)

Thank you all,
Idil

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Re: [Freesurfer] BBRegister + partial FoV fail

[Bruce Fischl]

sure. I'll leave the rest to Doug except to say that a full head EPI is a 
pretty cheap and useful thing to get, and that it is not surprising the 
using the header (assuming they are same session) works better than 
anything else

cheers
Bruce

On Tue, 11 Jul 2017, Paul Glad Mihai wrote:

> Hi Bruce,
>
> Thanks for the quick reply. I've just finished rerunning it with spm,
> fsl and header init and the latter seemed to work if I write out a
> _bbreg.nii file. The former two failed, however. Apparently using the
> header seems to work for this one subject and one run. I'm testing the
> rest of the runs.
>
> This is an example from the FSL init. Please note that I'm running it
> through nipype, hence the jumbled subdirectory strucutre.
>
> bbregister --t2 --epi-mask --init-fsl --fslmat
> /data/pt_nmc002/TDMGB_FMRI_coreg/tmp/preproc/_subject_id_sub-01/_init_fsl/bbreg/mapflow/_bbreg0/meanusub-01_task-spespk_run-01_bold_bbreg_sub-01.mat
> --reg
> /data/pt_nmc002/TDMGB_FMRI_coreg/tmp/preproc/_subject_id_sub-01/_init_fsl/bbreg/mapflow/_bbreg0/meanusub-01_task-spespk_run-01_bold_bbreg_sub-01.dat
> --o
> /data/pt_nmc002/TDMGB_FMRI_coreg/tmp/preproc/_subject_id_sub-01/_init_fsl/bbreg/mapflow/_bbreg0/meanusub-01_task-spespk_run-01_bold_bbreg.nii
> --mov
> /data/pt_nmc002/TDMGB_FMRI_coreg/tmp/preproc/_subject_id_sub-01/_init_fsl/bbreg/mapflow/_bbreg0/meanusub-01_task-spespk_run-01_bold.nii
> --s sub-01
>
> The output is attached. Details are under the heading 'Terminal output'.
> I'm also attaching a screenshot of the T2 with a white overlay for the
> header init. It seems to be alright. The output from the header init is
> also attached. The difference in the command line is --init-header
> instead of --init-fsl.
>
> Downstream, however, the registration to MNI through ANTs seems to fail,
> even though I've converted the transformation matrices to ITK through
> C3D. H... I just had a revelation. I may have used the wrong T1 to
> calculate the registration matrix through ANTs. Instead of using the T1
> from the ReconAll output, I used the one from the fsl.bet. I'll make
> sure to use the ReconAll T1 and get back to you.
>
> I would appreciate a comment, however, on how to get better registration
> of partial FoV T2 images to T1 images through BBRegister. It seems that
> the easiest option is a full head EPI at the time of the experiment.
>
> Regards,
> Glad
>
>
>
> On 07/11/2017 03:33 PM, Bruce Fischl wrote:
>> Hi Glad
>>
>> can you send us the full command line you are using and screen output?
>>
>> thanks
>>
>> Bruce
>> On
>> Tue, 11 Jul 2017, Paul Glad Mihai wrote:
>>
>>> Dear List,
>>>
>>> I've been quite frustrated with the BBRegister results when trying to
>>> register a partial field of view EPI mean functional image to a T1 scan.
>>> I've tried different init arguments (fsl, spm, header) and none really
>>> work. I've found that the initial registration is causing the problem,
>>> since the T1 and mean EPi are in reasonable alignment, but not perfect.
>>> As soon as it passes the initial alignment it's totally off and
>>> obviously fails in the BBR step. I have no full head EPI, unfortunately.
>>> I have a full head scout which seems to be a T1 image with really poor
>>> contrast. If I try to register this to the T1 through BBRegister it
>>> works. But if I use it as an intermediate file it still fails. What can
>>> I do? How does the intermediate file come into play? Will it get
>>> registered to the T1 initially and then the resulting matrix is used
>>> further? I also tried to feed the resulting registration matrix as
>>> init-reg but that didn't work either.
>>>
>>> Is there a way to skip the initial registration?
>>>
>>> Can I mask the T1 image with the FoV of the functional scan if they are
>>> initially in reasonable alignment? Would that work? Would that mean that
>>> I have to re-run ReconAll with the masked T1?
>>>
>>> Would love to hear back from someone.
>>>
>>> Regards,
>>> Glad
>>>
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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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Re: [Freesurfer] BBRegister + partial FoV fail

[Bruce Fischl]

Hi Glad

can you send us the full command line you are using and screen output?

thanks

Bruce
On 
Tue, 11 Jul 2017, Paul Glad Mihai wrote:

> Dear List,
>
> I've been quite frustrated with the BBRegister results when trying to
> register a partial field of view EPI mean functional image to a T1 scan.
> I've tried different init arguments (fsl, spm, header) and none really
> work. I've found that the initial registration is causing the problem,
> since the T1 and mean EPi are in reasonable alignment, but not perfect.
> As soon as it passes the initial alignment it's totally off and
> obviously fails in the BBR step. I have no full head EPI, unfortunately.
> I have a full head scout which seems to be a T1 image with really poor
> contrast. If I try to register this to the T1 through BBRegister it
> works. But if I use it as an intermediate file it still fails. What can
> I do? How does the intermediate file come into play? Will it get
> registered to the T1 initially and then the resulting matrix is used
> further? I also tried to feed the resulting registration matrix as
> init-reg but that didn't work either.
>
> Is there a way to skip the initial registration?
>
> Can I mask the T1 image with the FoV of the functional scan if they are
> initially in reasonable alignment? Would that work? Would that mean that
> I have to re-run ReconAll with the masked T1?
>
> Would love to hear back from someone.
>
> Regards,
> Glad
>
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[Freesurfer] BBRegister + partial FoV fail

[Paul Glad Mihai]

Dear List,

I've been quite frustrated with the BBRegister results when trying to
register a partial field of view EPI mean functional image to a T1 scan.
I've tried different init arguments (fsl, spm, header) and none really
work. I've found that the initial registration is causing the problem,
since the T1 and mean EPi are in reasonable alignment, but not perfect.
As soon as it passes the initial alignment it's totally off and
obviously fails in the BBR step. I have no full head EPI, unfortunately.
I have a full head scout which seems to be a T1 image with really poor
contrast. If I try to register this to the T1 through BBRegister it
works. But if I use it as an intermediate file it still fails. What can
I do? How does the intermediate file come into play? Will it get
registered to the T1 initially and then the resulting matrix is used
further? I also tried to feed the resulting registration matrix as
init-reg but that didn't work either.

Is there a way to skip the initial registration?

Can I mask the T1 image with the FoV of the functional scan if they are
initially in reasonable alignment? Would that work? Would that mean that
I have to re-run ReconAll with the masked T1?

Would love to hear back from someone.

Regards,
Glad
-- 
Paul Glad Mihai, PhD

Independent Research Group "Neural Mechanisms of Human Communication"
Max Planck Institute for Human Cognitive and Brain Sciences
Stephanstraße 1A, 04103 Leipzig, Germany

Phone:   +49 (0) 341-9940-2478
E-mail:  mi...@cbs.mpg.de

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[Freesurfer] 'Best practice' for dealing with lesioned brains

[King, Daniel (Research Student)]

Dear Freesurfer Team,

I am attempting to complete a surface reconstruction on a dataset with 
traumatic lesions both to the grey and white matter.

I am hoping to get some opinions on what would be considered as the 'Best 
practice' pipeline for dealing with such a dataset. We have access to T1 and 
T2-FLAIR images for a moderately large dataset and thus require a pipeline as 
fully-automated as is possible whilst still relatively accurate. I have 
seaerched the mailing list archives but many just relate to white matter 
lesions in MS for example.

My current thoughts were to use the T1 and Fair images with the -FLAIRpial flag 
 in recon-all to improve pial segmentation, but also using an automated lesion 
segmentation tool to conduct lesion filling. However, I know this is more 
effective for white than Gray matter lesions due to the greater intensity 
variability in the Gray matter compared to the white matter.

Any reccomendations would be greatly appreciated.

Cheers
Dan

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