[Freesurfer] Pial surface running into white surface

[Kevin Aquino]

External Email - Use Caution

Hi free surfer mailing list!

I am having a problem with some subjects where the pial surface is running
into the white surface (and terminating at some points terminating within
white matter). Apologies if the solution is in the mailing list (all I
could find is that this could be fixed with FS v6). The build stamp is:

freesurfer-Linux-centos6_x86_64-dev-20170915-

what kind of edits should I be doing?

I have added the necessary files to https://github.com/KevinAquino/errorPial
if you could be so kind to have a look!


Cheers,
*Dr Kevin Aquino*
Research fellow,
School of Psychology, Monash University, Australia.

Hon. Research Fellow
Sir Peter Mansfield Magnetic Resonance Center, The University of
Nottingham.

--

The brain is a wonderful organ. It starts working the moment you get up and
does not stop until you get into the office.
-
Robert Frost
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Re: [Freesurfer] Tilting / orienting brain slices

[Kevin Aquino]

Something quick: mricro 
http://www.cabi.gatech.edu/mricro/mricro/



Cheers,
Kevo

> On 23 Nov 2017, at 9:05 pm, Sam Norman-Haignere  wrote:
> 
> I would like to tilt/rotate a brain image so that I can see multiple 
> activations in a single slice. I don't believe this is possible in Freeview, 
> am I'm curious if there is a brain viewer with this capability (would 
> presumably require some type of activate interpolation)? It seems like a 
> feature that would be quite useful.
> 
> My best,
> Sam Norman-Haignere
> ___
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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
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> at
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[Freesurfer] Fixed effects fMRI {Disarmed}

[Kevin Aquino]

Hi all,

I would like to perform a fixed effects analysis on a small sample of
subjects with FS-fast -- where the time series from all subjects are
concatenated together and analysed in a large design matrix.

Is there an easy way to do this? I don't know if I'm looking in the wrong
place but I can't seem to find it.


Cheers,


*Dr Kevin Aquino*
Research fellow,
Sir Peter Mansfield Magnetic Resonance Center, The University of
Nottingham.

Honorary Research Fellow
School of Physics, Faculty of Science, University of Sydney

*E* kevin.aqu...@nottingham.ac.uk, aqu...@physics.usyd.edu.au | *W*
https://kevinaquino.github.io <http://www.physics.usyd.edu.au/~aquino/>

--

The brain is a wonderful organ. It starts working the moment you get up and
does not stop until you get into the office.
-
Robert Frost

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Re: [Freesurfer] FS-FAST outputs is X.mat used? {Disarmed}

[Kevin Aquino]

Thanks for that Doug!

Cheers,


*Dr Kevin Aquino*
Research fellow,
Sir Peter Mansfield Magnetic Resonance Center, The University of
Nottingham.

Honorary Research Fellow
School of Physics, Faculty of Science, University of Sydney

*E* kevin.aqu...@nottingham.ac.uk, aqu...@physics.usyd.edu.au | *W*
https://kevinaquino.github.io <http://www.physics.usyd.edu.au/~aquino/>

--

The brain is a wonderful organ. It starts working the moment you get up and
does not stop until you get into the office.
-
Robert Frost

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On Fri, Aug 18, 2017 at 7:28 AM, Douglas N Greve <gr...@nmr.mgh.harvard.edu>
wrote:

> selxavg uses scenario #1, which corresponds to the 2nd image below, ie,
> all the task regressors are in a single column and not pulled out on a
> run-by-run basis. The nuisance regressors are specific to each run.
>
>
> >
>
> On 08/16/2017 08:24 PM, Kevin Aquino wrote:
> > Thanks for that Doug,
> >
> > [I was hoping i could do the parametric modulation in the contrast
> > weights -- SPM style of doing this after the betas were fit].
> >
> > Regarding the X.mat question, sorry I wasn't clear. I can see it has
> > the nuisance regressors and constant terms, but is that x.mat used to
> > estimate the betas?
> Yes
> >
> > In the beta estimation which scenario is happening?
> >
> > 1. concatenate all the model regressors onto one column, add the
> > nuisance regressors and constant terms into one big matrix (X.mat) to
> > estimate the beta values
> > 2. create a matrix for each run separately and estimate the betas.
> > Save regression coefficients, compute contrasts and significances of
> > contrasts. The end (default) result is the average (i guess average of
> > all the estimated quantities).
> >
> > From the help message it looks like it is #2, and if thats the case
> > then X.mat looks like its a summary. I ask this because I would like
> > to use a X that looks something like below:
> > Inline image 1,
> >
> > which is essentially the scenario in #2, but the output of X.mat looks
> > like this:
> >
> > Inline image 2
> > (the image hasn't been normalized so that is why there are blank
> > spaces for 3 of the 6 nuisance regressors)
> >
> > There are slight differences between the two (so it doesn't matter in
> > the long run) but I just want to know which one is being used. On a
> > quick look of selxag3-sess, the matlab files look like compiled mex
> > files, so I can't access them.
>
> >
> > Thanks!
> >
> >
> > *Dr Kevin Aquino*
> > Research fellow,
> > Sir Peter Mansfield Magnetic Resonance Center, The University of
> > Nottingham.
> >
> > Honorary Research Fellow
> > School of Physics, Faculty of Science, University of Sydney
> >
> >
> > --
> >
> > The brain is a wonderful organ. It starts working the moment you get
> > up and does not stop until you get into the office.
> > -
> > Robert Frost
> >
> > CRICOS 00026A
> > This email plus any attachments to it are confidential. Any
> > unauthorised use is strictly prohibited. If you receive this email in
> > error, please delete it and any attachments.
> >
> > Please think of our environment and only print this e-mail if necessary.
> >
> >
> > On Thu, Aug 17, 2017 at 8:24 AM, Douglas N Greve
> > <gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu>> wrote:
> >
> > It has the design matrix plus a lot of other stuff in it. For
> > parametric
> > modulation, have you seen this page
> >
> > https://surfer.nmr.mgh.harvard.edu/fswiki/FsFastParametricModulation
> > <https://surfer.nmr.mgh.harvard.edu/fswiki/
> FsFastParametricModulation>
> >
> > On 08/15/2017 09:52 PM, Kevin Aquino wrote:
> > > Dear all,
> > >
> > > I have a question regarding the output from selxavg3-sess. I
> noticed
> > > that within an analysis there  is a X.mat that looks like a design
> > > matrix -- however is this used at any stage of the analysis?
> > The help
> > > message in selxavg3-sess reads:
> > >
> > > "This program will construct the design matrix for each run, fit
> > > the

Re: [Freesurfer] FS-FAST outputs is X.mat used? {Disarmed}

[Kevin Aquino]

Thanks for that Doug,

[I was hoping i could do the parametric modulation in the contrast weights
-- SPM style of doing this after the betas were fit].

Regarding the X.mat question, sorry I wasn't clear. I can see it has the
nuisance regressors and constant terms, but is that x.mat used to estimate
the betas?

In the beta estimation which scenario is happening?

1. concatenate all the model regressors onto one column, add the nuisance
regressors and constant terms into one big matrix (X.mat) to estimate the
beta values
2. create a matrix for each run separately and estimate the betas. Save
regression coefficients, compute contrasts and significances of contrasts.
The end (default) result is the average (i guess average of all the
estimated quantities).

>From the help message it looks like it is #2, and if thats the case then
X.mat looks like its a summary. I ask this because I would like to use a X
that looks something like below:
[image: Inline image 1],

which is essentially the scenario in #2, but the output of X.mat looks like
this:

[image: Inline image 2]
(the image hasn't been normalized so that is why there are blank spaces for
3 of the 6 nuisance regressors)

There are slight differences between the two (so it doesn't matter in the
long run) but I just want to know which one is being used. On a quick look
of selxag3-sess, the matlab files look like compiled mex files, so I can't
access them.


Thanks!


*Dr Kevin Aquino*
Research fellow,
Sir Peter Mansfield Magnetic Resonance Center, The University of
Nottingham.

Honorary Research Fellow
School of Physics, Faculty of Science, University of Sydney


--

The brain is a wonderful organ. It starts working the moment you get up and
does not stop until you get into the office.
-
Robert Frost

CRICOS 00026A
This email plus any attachments to it are confidential. Any unauthorised
use is strictly prohibited. If you receive this email in error, please
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On Thu, Aug 17, 2017 at 8:24 AM, Douglas N Greve <gr...@nmr.mgh.harvard.edu>
wrote:

> It has the design matrix plus a lot of other stuff in it. For parametric
> modulation, have you seen this page
>
> https://surfer.nmr.mgh.harvard.edu/fswiki/FsFastParametricModulation
>
> On 08/15/2017 09:52 PM, Kevin Aquino wrote:
> > Dear all,
> >
> > I have a question regarding the output from selxavg3-sess. I noticed
> > that within an analysis there  is a X.mat that looks like a design
> > matrix -- however is this used at any stage of the analysis?  The help
> > message in selxavg3-sess reads:
> >
> > "This program will construct the design matrix for each run, fit
> > the GLM, save regression coefficients, compute contrasts and
> > significances of contrasts. The runs are combined together so the
> > output is the average across runs (some would call this a
> > "second-level" analysis)."
> >
> > so this looks like that x.mat is constructed and used for each run
> > (and not saved by default). This then looks like X.mat is not used in
> > the analysis -- it is just there for illustrative purposes? or have I
> > misinterpreted the help message.
> >
> >
> > If this is correct (i.e. X.mat in the output is not used) when making
> > contrasts using mkcontrast-sess, is there a way to parametrically
> > modulate each run? e.g. to model behavioural changes per run etc.
> >
> > Cheers,
> >
> >
> > *Dr Kevin Aquino*
> > Research fellow,
> > Sir Peter Mansfield Magnetic Resonance Center, The University of
> > Nottingham.
> >
> > Honorary Research Fellow
> > School of Physics, Faculty of Science, University of Sydney
> >
> > *E* kevin.aqu...@nottingham.ac.uk
> > <mailto:kevin.aqu...@nottingham.ac.uk>, aqu...@physics.usyd.edu.au
> > <mailto:aqu...@physics.usyd.edu.au> | *W* *MailScanner has detected a
> > possible fraud attempt from "www.physics.usyd.edu.au" claiming to be*
> > https://kevinaquino.github.io <http://www.physics.usyd.edu.au/%7Eaquino/
> >
> >
> > --
> >
> > The brain is a wonderful organ. It starts working the moment you get
> > up and does not stop until you get into the office.
> > -
> > Robert Frost
> >
> > CRICOS 00026A
> > This email plus any attachments to it are confidential. Any
> > unauthorised use is strictly prohibited. If you receive this email in
> > error, please delete it and any attachments.
> >
> > Please think of our environment and only print this e-mail if necessary.
> >
> >
> >
>

[Freesurfer] FS-FAST outputs is X.mat used? {Disarmed}

[Kevin Aquino]

Dear all,

I have a question regarding the output from selxavg3-sess. I noticed that
within an analysis there  is a X.mat that looks like a design matrix --
however is this used at any stage of the analysis?  The help message in
selxavg3-sess reads:

"This program will construct the design matrix for each run, fit the GLM,
save regression coefficients, compute contrasts and significances of
contrasts. The runs are combined together so the output is the average
across runs (some would call this a "second-level" analysis)."

so this looks like that x.mat is constructed and used for each run (and not
saved by default). This then looks like X.mat is not used in the analysis
-- it is just there for illustrative purposes? or have I misinterpreted the
help message.


If this is correct (i.e. X.mat in the output is not used) when making
contrasts using mkcontrast-sess, is there a way to parametrically modulate
each run? e.g. to model behavioural changes per run etc.


Cheers,


*Dr Kevin Aquino*
Research fellow,
Sir Peter Mansfield Magnetic Resonance Center, The University of
Nottingham.

Honorary Research Fellow
School of Physics, Faculty of Science, University of Sydney

*E* kevin.aqu...@nottingham.ac.uk, aqu...@physics.usyd.edu.au | *W*
https://kevinaquino.github.io <http://www.physics.usyd.edu.au/~aquino/>

--

The brain is a wonderful organ. It starts working the moment you get up and
does not stop until you get into the office.
-
Robert Frost

CRICOS 00026A
This email plus any attachments to it are confidential. Any unauthorised
use is strictly prohibited. If you receive this email in error, please
delete it and any attachments.

Please think of our environment and only print this e-mail if necessary.
___
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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
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Re: [Freesurfer] 7T recon {Disarmed}

[Kevin Aquino]

Does adding control points help?

https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/ControlPoints_freeview



Cheers,


*Dr Kevin Aquino*
Research fellow,
Sir Peter Mansfield Magnetic Resonance Center, The University of
Nottingham.

Honorary Research Fellow
School of Physics, Faculty of Science, University of Sydney

*E* kevin.aqu...@nottingham.ac.uk, aqu...@physics.usyd.edu.au | *W*
https://kevinaquino.github.io <http://www.physics.usyd.edu.au/~aquino/>

--

The brain is a wonderful organ. It starts working the moment you get up and
does not stop until you get into the office.
-
Robert Frost

CRICOS 00026A
This email plus any attachments to it are confidential. Any unauthorised
use is strictly prohibited. If you receive this email in error, please
delete it and any attachments.

Please think of our environment and only print this e-mail if necessary.


On Wed, Jun 7, 2017 at 3:39 PM, Hibert, Matthew Louis <
mhib...@mgh.harvard.edu> wrote:

> Hi Bruce,
> I edited the wm.mgz with the recon-editing tool this time, removing the
> problem areas near this defect (primarily lots of dura originally
> included), and confirmed that my edits remained after re-processing.
> However, the left STG is still being removed, images attached (red is the
> lh.orig.nofix with lh.defect_labels overlayed, yellow is lh.white).  The
> entire left STG is still being marked as a defect despite my edits.  Any
> suggestions?
>
> Thanks,
> Matt
> 
> From: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.
> harvard.edu] on behalf of Hibert, Matthew Louis [mhib...@mgh.harvard.edu]
> Sent: Tuesday, June 06, 2017 5:22 PM
> To: Freesurfer support list
> Subject: Re: [Freesurfer] 7T recon
>
> Ah ok, thanks Bruce.
>
> Matt
> 
> 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, June 06, 2017 4:35 PM
> To: Freesurfer support list
> Subject: Re: [Freesurfer] 7T recon
>
> Hi Matt
> we keep track of edits by setting erased voxels to 1, not 0. If you do
> the editing within freeview using the "recon edit" tool, this will happen
> automatically
>
> cheers
> Bruce
> On Tue, 6 Jun 2017, Hibert, Matthew Louis wrote:
>
> > Hi Bruce,
> > Thanks again for your help so far.  I've tried removing the problem
> voxels from the wm.mgz (setting their value to 0), saving the wm.mgz, and
> then running "recon-all -autorecon2-wm -autorecon3 -hires -s $SUBJECT
> -xopts-use -openmp 2".  However, the edits to the wm.mgz are not
> incorporated and the surfaces are not changed; when I open the wm.mgz
> again, the voxels I removed are now present again.  What am I doing wrong?
> >
> > Thanks,
> > Matt
> > 
> > From: freesurfer-boun...@nmr.mgh.harvard.edu [
> freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Bruce Fischl [
> fis...@nmr.mgh.harvard.edu]
> > Sent: Friday, May 26, 2017 1:57 PM
> > To: Freesurfer support list
> > Subject: Re: [Freesurfer] 7T recon
> >
> > yes, and autorecon3
> > On Fri, 26 May 2017, Hibert, Matthew Louis wrote:
> >
> >> Thanks Bruce.  After I remove the problem voxels in wm.mgz, do I then
> re-run the recon from autorecon2-wm?
> >>
> >> Thanks,
> >> Matt
> >> 
> >> From: freesurfer-boun...@nmr.mgh.harvard.edu [
> freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Bruce Fischl [
> fis...@nmr.mgh.harvard.edu]
> >> Sent: Friday, May 26, 2017 1:40 PM
> >> To: Freesurfer support list
> >> Subject: Re: [Freesurfer] 7T recon
> >>
> >> Hi Matt
> >>
> >> yes, that means there was a topological defect that was incorrectly
> >> fixed. If you load the wm.mgz over the lh.orig.nofix, then in the
> >> orig.nofix load the file defect_labels as an overlay and change the
> overlay
> >> settings to that the min is 1 and click the "use overlay color" button
> it
> >> will show you the regions of the surface that are defective. You will
> then
> >> need to edit the wm.mgz to remove the handle/hole that is the defect.
> >>
> >> cheers
> >> Bruce
> >>
> >>
> >> On Fri, 26 May 2017, Hibert, Matthew Louis wrote:
> >>
> >>> Hi All,
> >>> I reconstructed 20 subjects with a 750um isotropic MPRAGE collected at
> 7T
> >>> and while most look good, 4 of the subjects have a similar s

Re: [Freesurfer] mac mghread and freeview error {Disarmed}

[Kevin Aquino]

Cheers,


*Dr Kevin Aquino*
Research fellow,
Sir Peter Mansfield Magnetic Resonance Center, The University of
Nottingham.

Honorary Research Fellow
School of Physics, Faculty of Science, University of Sydney

*E* kevin.aqu...@nottingham.ac.uk, aqu...@physics.usyd.edu.au | *W*
https://kevinaquino.github.io <http://www.physics.usyd.edu.au/~aquino/>

--

The brain is a wonderful organ. It starts working the moment you get up and
does not stop until you get into the office.
-
Robert Frost

CRICOS 00026A
This email plus any attachments to it are confidential. Any unauthorised
use is strictly prohibited. If you receive this email in error, please
delete it and any attachments.

Please think of our environment and only print this e-mail if necessary.


On Sun, May 21, 2017 at 10:36 PM, Fekonja <l.feko...@fekonja.ch> wrote:

> Hi FreeSurfer Developers,
>
> I’ve just installed FreeSurfer on my MacBook Pro and experience several
> Problems.
>
> 1. If I generate a .profile file with the command to source FS as soon as
> I open the Terminal, nothing happens.
> If I source FS manually it works (e.g. the extract below).
>

Have you tried putting the commands into .bash_profile instead? as far as i
know that is the standard practice for doing this in macos.


>
> 2. If I open Freeview, it crashes as soon as I try to load anything.
>
> 3. The command to target the subject sample „sample-001.mgz“ works, but
> the command to convert it doesn’t – e.g. extracted Terminal-Log below.
>
> I’ve searched the list and found some similar errors, but unfortunately I
> couldn’t find working solutions.
> My Security & Privacy settings allow to open apps downloaded from anywhere.
>
> 1)FreeSurfer version: freesurfer-Darwin-OSX-stable-pub-v6.0.0-2beb96c /
> freesurfer-i386-apple-darwin11.4.2-stable6-20170119
> 2)Platform: MacOS Sierra 10.12.5
> 3)uname -a:Darwin Luciuss-MacBook-Pro.local 16.6.0 Darwin Kernel Version
> 16.6.0: Fri Apr 14 16:21:16 PDT 2017; root:xnu-3789.60.24~6/RELEASE_X86_64
> x86_64
> 4)recon-all.log: see below
>
> Last login: Sun May 21 14:04:09 on ttys001
> Luciuss-MacBook-Pro:~ luciusfekonja$ export FREESURFER_HOME=/Applications/
> freesurfer
> Luciuss-MacBook-Pro:~ luciusfekonja$ source $FREESURFER_HOME/
> SetUpFreeSurfer.sh
>  freesurfer-Darwin-OSX-stable-pub-v6.0.0-2beb96c 
> Setting up environment for FreeSurfer/FS-FAST (and FSL)
> FREESURFER_HOME   /Applications/freesurfer
> FSFAST_HOME   /Applications/freesurfer/fsfast
> FSF_OUTPUT_FORMAT nii.gz
> SUBJECTS_DIR  /Applications/freesurfer/subjects
> MNI_DIR   /Applications/freesurfer/mni
> FSL_DIR   /Applications/fsl
> Luciuss-MacBook-Pro:~ luciusfekonja$ cp $FREESURFER_HOME/subjects/
> sample-001.mgz
> usage: cp [-R [-H | -L | -P]] [-fi | -n] [-apvX] source_file target_file
>cp [-R [-H | -L | -P]] [-fi | -n] [-apvX] source_file ...
> target_directory
> Luciuss-MacBook-Pro:~ luciusfekonja$ mri_convert sample-001.mgz
> sample-001.nii.gz
> mri_convert.bin sample-001.mgz sample-001.nii.gz
> $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $
> reading from sample-001.mgz...
> mghRead(/Users/luciusfekonja/sample-001.mgz, -1): could not open file
> Luciuss-MacBook-Pro:~ luciusfekonja$
> Luciuss-MacBook-Pro:~ luciusfekonja$ recon-all
>
> USAGE: recon-all
>
>  Required Arguments:
>-subjid 
>-
>
>  Fully-Automated Directive:
>   -all   : performs all stages of cortical reconstruction
>   -autorecon-all : same as -all
>
>  Manual-Intervention Workflow Directives:
>   -autorecon1: process stages 1-5 (see below)
>   -autorecon2: process stages 6-23
>after autorecon2, check white surfaces:
>  a. if wm edit was required, then run -autorecon2-wm
>  b. if control points added, then run -autorecon2-cp
>  c. proceed to run -autorecon3
>   -autorecon2-cp : process stages 12-23 (uses -f w/ mri_normalize, -keep
> w/ mri_seg)
>   -autorecon2-wm : process stages 15-23
>   -autorecon2-inflate1 : 6-18
>   -autorecon2-perhemi : tess, sm1, inf1, q, fix, sm2, inf2, finalsurf,
> ribbon
>   -autorecon3: process stages 24-34
>  if edits made to correct pial, then run
> -autorecon-pial
>   -hemi ?h   : just do lh or rh (default is to do both)
>
>   Autorecon Processing Stages (see -autorecon# flags above):
> 1.  Motion Correction and Conform
> 2.  NU (Non-Uniform intensity normalization)
> 3.  Talairach transform computation
> 4.  Intensity Normalization 1
> 5.  Skull Strip
>
> 6.  EM Register (linear volumetric registration)
> 7.  CA Intensity Norma

Re: [Freesurfer] mri_mcsim for individual subjects and references {Disarmed}

[Kevin Aquino]

Hi Doug,

Thanks for that! with regards to your last point

Unfortunately, it does not help much. Much was made of the bug that Eklund,
et al, found in the alphasim program (the AFNI mc simulator), but even
after fixing it, the volume-based analyses still had very high false
positive rates. This is because the problem is that the smoothness in the
data is not Gaussian, so any method that assumes Gaussianity will be
inaccurate.


>From what I read, the MC simulations on the surface uses this Gaussian
assumption. Do you have any ideas (or something in the works) on how to
handle these issues on a single subject level? - since the permutation test
won't be applicable.


Cheers,


*Dr Kevin Aquino*
Research fellow,
Sir Peter Mansfield Magnetic Resonance Center, The University of
Nottingham.

Honorary Research Fellow
School of Physics, Faculty of Science, University of Sydney

*E* kevin.aqu...@nottingham.ac.uk, aqu...@physics.usyd.edu.au | *W*
https://kevinaquino.github.io <http://www.physics.usyd.edu.au/~aquino/>

--

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does not stop until you get into the office.
-
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On Wed, May 17, 2017 at 1:18 AM, Douglas Greve <gr...@nmr.mgh.harvard.edu>
wrote:

>
>
> On 5/15/17 10:34 PM, Kevin Aquino wrote:
>
> Hi all,
>
> First of all, Freesurfer V6 is working like a dream, my 0.7 mm
> segmentations are running really well and in comparisons to hi-resrecon in
> 5.3 and early beta, I'm having to do fewer manual corrections!
>
>
> Now for my questions,
>
> 1. I'm running mri_mcsim in order to correct for multiple comparisons via
> the FS-FAST stream. I'm wondering how many iterations are advised, and how
> can one check for convergence in an automatic fashion.
>
> I've run the simulations with 1000 and 10,000 iterations on a 1mm
> segmentation with the FWHM simulations at 8mm. (i.e. using mri_mcsim --o .
> --base mc-z --save-iter  --surf subject lh/rh --nreps 1 --fwhm 8) and I
> can't see many differences between the two when correcting for multiple
> comparisons (i.e. using cluster-sess -analysis  myanalysis -thresh 3 -cwp
> .05 -s SESSION -sign pos).
>
> For the tables hat we distribute I ran it to 10,000, but there will
> probably not be much difference with 1000. If you look in the cluster
> summary file, it will actually give the 95% confidence intervals on the
> cluster p-values. If the worst is ok, then you don't really need to run it
> more.
>
>
> 2. I'm trying to find some references that detail the simulations and form
> the corrections, does anyone have advice which list I can read/start off
> with, as well as some key papers that use it (esp on a single subject
> level).
>
> You can check out "Smoothing and cluster thresholding for cortical
> surface-based group analysis of fMRI data" by Don Hagler
>
> I really like this approach and It does look to circumvent (I think...) a
> lot of the problems of cluster-wise corrections described with Eklund et
> al. (Cluster failure paper).
>
> Unfortunately, it does not help much. Much was made of the bug that
> Eklund, et al, found in the alphasim program (the AFNI mc simulator), but
> even after fixing it, the volume-based analyses still had very high false
> positive rates. This is because the problem is that the smoothness in the
> data is not Gaussian, so any method that assumes Gaussianity will be
> inaccurate.
> doug
>
>
> Cheers,
>
>
> *Dr Kevin Aquino*
> Research fellow,
> Sir Peter Mansfield Magnetic Resonance Center, The University of
> Nottingham.
>
> Honorary Research Fellow
> School of Physics, Faculty of Science, University of Sydney
>
> *E* kevin.aqu...@nottingham.ac.uk, aqu...@physics.usyd.edu.au | *W* 
> *MailScanner
> has detected a possible fraud attempt from "www.physics.usyd.edu.au"
> claiming to be* https://kevinaquino.github.io
> <http://www.physics.usyd.edu.au/%7Eaquino/>
>
> --
>
> The brain is a wonderful organ. It starts working the moment you get up
> and does not stop until you get into the office.
> -
> Robert Frost
>
> CRICOS 00026A
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Re: [Freesurfer] mri_mcsim for individual subjects and references {Disarmed}

[Kevin Aquino]

Actually,

would would be preferable would be running a permutations test something
that you describe in:

http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg49846.html

is there an easy to run mri_glmfit-sim's permutation simulations on a
single subject?
I've run through the FS-FAST pipeline

mkanalysis-sess -fsd bold -surface self rh -fwhm 4.5 -event-related
-paradigm attn.par -nconditions 4 -spmhrf 0 -TR 1.9 -analysis
myanalysis -per-session
-refeventdur 450 -force -nuisreg moco.txt -1 -polyfit 0
mkcontrast-sess -analysis myanalysis -contrast attn -c 1 -a 2 -a 3 -c 4
selxavg3-sess -s SESSION -analysis self_attn_sm_reg.rh -no-preproc -fwhm

But mri_glmfit-sim is expecting the output from mri_glmfit

mri_glmfit-sim --glmdir . --perm 1000 3 pos --log ./selxavg3.log
>> ERROR: cannot find ./mri_glmfit.log

should I just run mri_glmfit with the appropriate flags, or is there a
mri_glmfit-sim version for data that has passed through selxavg3 ?


Cheers,


*Dr Kevin Aquino*
Research fellow,
Sir Peter Mansfield Magnetic Resonance Center, The University of
Nottingham.

Honorary Research Fellow
School of Physics, Faculty of Science, University of Sydney

*E* kevin.aqu...@nottingham.ac.uk, aqu...@physics.usyd.edu.au | *W*
https://kevinaquino.github.io <http://www.physics.usyd.edu.au/~aquino/>

--

The brain is a wonderful organ. It starts working the moment you get up and
does not stop until you get into the office.
-
Robert Frost

CRICOS 00026A
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On Tue, May 16, 2017 at 12:34 PM, Kevin Aquino <aqu...@physics.usyd.edu.au>
wrote:

> Hi all,
>
> First of all, Freesurfer V6 is working like a dream, my 0.7 mm
> segmentations are running really well and in comparisons to hi-resrecon in
> 5.3 and early beta, I'm having to do fewer manual corrections!
>
>
> Now for my questions,
>
> 1. I'm running mri_mcsim in order to correct for multiple comparisons via
> the FS-FAST stream. I'm wondering how many iterations are advised, and how
> can one check for convergence in an automatic fashion.
>
> I've run the simulations with 1000 and 10,000 iterations on a 1mm
> segmentation with the FWHM simulations at 8mm. (i.e. using mri_mcsim --o .
> --base mc-z --save-iter  --surf subject lh/rh --nreps 1 --fwhm 8) and I
> can't see many differences between the two when correcting for multiple
> comparisons (i.e. using cluster-sess -analysis  myanalysis -thresh 3 -cwp
> .05 -s SESSION -sign pos).
>
> 2. I'm trying to find some references that detail the simulations and form
> the corrections, does anyone have advice which list I can read/start off
> with, as well as some key papers that use it (esp on a single subject
> level). I really like this approach and It does look to circumvent (I
> think...) a lot of the problems of cluster-wise corrections described with
> Eklund et al. (Cluster failure paper).
>
> Cheers,
>
>
> *Dr Kevin Aquino*
> Research fellow,
> Sir Peter Mansfield Magnetic Resonance Center, The University of
> Nottingham.
>
> Honorary Research Fellow
> School of Physics, Faculty of Science, University of Sydney
>
> *E* kevin.aqu...@nottingham.ac.uk, aqu...@physics.usyd.edu.au | *W* 
> *MailScanner
> has detected a possible fraud attempt from "www.physics.usyd.edu.au"
> claiming to be* https://kevinaquino.github.io
> <http://www.physics.usyd.edu.au/~aquino/>
>
> --
>
> The brain is a wonderful organ. It starts working the moment you get up
> and does not stop until you get into the office.
> -
> Robert Frost
>
> CRICOS 00026A
> This email plus any attachments to it are confidential. Any unauthorised
> use is strictly prohibited. If you receive this email in error, please
> delete it and any attachments.
>
> Please think of our environment and only print this e-mail if necessary.
>
>
> ___
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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.
>
>
_

[Freesurfer] mri_mcsim for individual subjects and references {Disarmed}

[Kevin Aquino]

Hi all,

First of all, Freesurfer V6 is working like a dream, my 0.7 mm
segmentations are running really well and in comparisons to hi-resrecon in
5.3 and early beta, I'm having to do fewer manual corrections!


Now for my questions,

1. I'm running mri_mcsim in order to correct for multiple comparisons via
the FS-FAST stream. I'm wondering how many iterations are advised, and how
can one check for convergence in an automatic fashion.

I've run the simulations with 1000 and 10,000 iterations on a 1mm
segmentation with the FWHM simulations at 8mm. (i.e. using mri_mcsim --o .
--base mc-z --save-iter  --surf subject lh/rh --nreps 1 --fwhm 8) and I
can't see many differences between the two when correcting for multiple
comparisons (i.e. using cluster-sess -analysis  myanalysis -thresh 3 -cwp
.05 -s SESSION -sign pos).

2. I'm trying to find some references that detail the simulations and form
the corrections, does anyone have advice which list I can read/start off
with, as well as some key papers that use it (esp on a single subject
level). I really like this approach and It does look to circumvent (I
think...) a lot of the problems of cluster-wise corrections described with
Eklund et al. (Cluster failure paper).

Cheers,


*Dr Kevin Aquino*
Research fellow,
Sir Peter Mansfield Magnetic Resonance Center, The University of
Nottingham.

Honorary Research Fellow
School of Physics, Faculty of Science, University of Sydney

*E* kevin.aqu...@nottingham.ac.uk, aqu...@physics.usyd.edu.au | *W*
https://kevinaquino.github.io <http://www.physics.usyd.edu.au/~aquino/>

--

The brain is a wonderful organ. It starts working the moment you get up and
does not stop until you get into the office.
-
Robert Frost

CRICOS 00026A
This email plus any attachments to it are confidential. Any unauthorised
use is strictly prohibited. If you receive this email in error, please
delete it and any attachments.

Please think of our environment and only print this e-mail if necessary.
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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] Re. display SPM results on inflated surface? {Disarmed}

[Kevin Aquino]

Hi Douglas,

I am wondering, where did you find the mini 152 T1 map? :)

Regarding this...
Would it be better to instead run recon-all on a higher-res MNI atlas? and
then run mri_vol2surf for that segmentation?






Cheers,


*Dr Kevin Aquino*
Research fellow,
Sir Peter Mansfield Magnetic Resonance Center, The University of
Nottingham.

Honorary Research Fellow
School of Physics, Faculty of Science, University of Sydney

*E* kevin.aqu...@nottingham.ac.uk, aqu...@physics.usyd.edu.au | *W*
https://kevinaquino.github.io <http://www.physics.usyd.edu.au/~aquino/>

--

The brain is a wonderful organ. It starts working the moment you get up and
does not stop until you get into the office.
-
Robert Frost

CRICOS 00026A
This email plus any attachments to it are confidential. Any unauthorised
use is strictly prohibited. If you receive this email in error, please
delete it and any attachments.

Please think of our environment and only print this e-mail if necessary.


On Thu, Mar 23, 2017 at 7:53 AM, Douglas Greve <gr...@nmr.mgh.harvard.edu>
wrote:

> Just map your mni152-spm volume to the surface with mri_vol2surf and
> --regheader, eg,
>
> mri_vol2surf --mov yourspm152.nii.gz --hemi lh --projfrac 0.5 --s mni152
> --o lh.yourspm152.nii.gz
>
> then visualize
>
> tksurferfv mni152 lh inflated -ov lh.yourmni152.nii.gz
>
>
> On 3/22/17 3:46 PM, Schoot, Lotte wrote:
> > Thanks so much, I appreciate the help.
> > However, I am not sure what I am supposed to do with the output of the
> recon-all process.
> > Can I simply use the .dat file that is outputted there in MRI_vol2surf?
> >
> > Lotte
> >
> >
> > Date: Wed, 22 Mar 2017 13:01:42 -0400
> > From: Douglas Greve <gr...@nmr.mgh.harvard.edu>
> > Subject: Re: [Freesurfer] display SPM results on inflated surface?
> > To: freesurfer@nmr.mgh.harvard.edu
> > Message-ID: <41134c50-bb0b-792c-c52b-b6850bcec...@nmr.mgh.harvard.edu>
> > Content-Type: text/plain; charset="windows-1252"
> >
> > If you have the T1 for the mni152 (which is somewhere in the bowels of
> the spm distribution), then you just run recon-all on it. I've done this
> for myself, so you can just download the result (which I have not checked
> thoroughly) from here https://gate.nmr.mgh.harvard.
> edu/safelinks/greve/mni152.tar.gz
> >
> >
> >
> > On 3/21/17 1:27 PM, Schoot, Lotte wrote:
> >> Hi Doug and others,
> >>
> >> A while ago, I got this reply to my question below (thanks!). I tried
> to look in to it, but I am a bit confused (probably because I am very new
> to Freesurfer).
> >> My results are on the MNI 152, but I don't understand what you mean
> with 'run the mni152 through freesurfer'. Is this the process to get the
> register.dat file that is required in mri_vol2surf?
> >> What would you recommend to get the register.dat file? Is it possible
> to use bbregister for that? I have tried this, but I don't know whether it
> is correct:
> >>
> >> bbregister --s fsaverage --mov con_0001.nii --init-spm --reg
> >> register.dat --bold
> >>
> >>
> >> Thanks!
> >> Lotte
> >>
> >>
> >>> If your results are on the MNI152, you can run the mni152 through
> >>> freesurfer, then use mri_vol2surf to map the data to the surface then
> >>> view it with freeview (or tksurfer). You should not confuse this with
> >>> doing the fMRI analysis on the surface. You will not have the
> >>> benefits of surface-based analysis
> >>
> >> On 02/15/2017 03:37 PM, Schoot, Lotte wrote:
> >>> /Hi all, />//>/I was wondering if you knew of a way to display SPM
> >>> results onto the />/inflated surface in Freesurfer. />//>/I have
> >>> tried using SurfRend but there seem to be problems which might />/be
> >>> due to the fact the results are obtained with SPM12 and SurfRend
> >>> />/was designed to work with SPM5. />//>/Thanks, />/Lotte
> >>> />//>//>/___
> >>> />/Freesurfer mailing list />/Freesurfer at nmr.mgh.harvard.edu
> >> <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>
> >> />/https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer /
> >> --
> >> Douglas N. Greve, Ph.D.
> >> MGH-NMR Center
> >> greve at nmr.mgh.harvard.edu
> >> <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>
> >> Phone Number: 617-724-2358
> >> Fax: 617-726-7422
> >>
> >>
> >> 

Re: [Freesurfer] Smooth overlay in command line {Disarmed}

[Kevin Aquino]

You can use mri_surf2surf with the -nsmooth flag but just remember to set
the target and source subject as the same subject,

[check out the info in --help :) ]

Cheers,


*Dr Kevin Aquino*
Research fellow,
Sir Peter Mansfield Magnetic Resonance Center, The University of
Nottingham.

Honorary Research Fellow
School of Physics, Faculty of Science, University of Sydney

*E* kevin.aqu...@nottingham.ac.uk, aqu...@physics.usyd.edu.au | *W*
https://kevinaquino.github.io <http://www.physics.usyd.edu.au/~aquino/>

--

The brain is a wonderful organ. It starts working the moment you get up and
does not stop until you get into the office.
-
Robert Frost

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On Fri, Mar 24, 2017 at 8:11 AM, Dorian P. <alb@gmail.com> wrote:

> Is it possible to set the smooth overlay option (i.e. no of iterations)
> from command line instead of freeview? I am taking some screenshots that
> would look nicer with a smoothed overlay.
>
> Dorian
>
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Re: [Freesurfer] FS 6.0 Freeview

[Kevin Aquino]

I've had the same problem, 
the only solution I have is to only open Freeview from terminal

Cheers,
Kevo

> On 23 Feb 2017, at 10:58 pm, peng  wrote:
> 
> Dear Ruopeng,
> 
>I have the same problem even before the current version 6 release, and it 
> was "solved" by invoke freeview from the command line (term). I guess, to 
> start from the icon, it might use different setup files.
> 
> best
> Peng
> 
>> On Fri, Feb 17, 2017 at 4:41 PM, Ruopeng Wang  
>> wrote:
>> Or would it be possible to send us the full crash report?
>> 
>>> On Feb 17, 2017, at 10:17 AM, Z K  wrote:
>>> 
>>> Hi Dan. Is there an error output to the screen or terminal window? We 
>>> will probably need that to help diagnose the issue.
>>> 
>>> 
>>> 
 On 02/17/2017 05:31 AM, Daniel Carey wrote:
 Dear All,
 
 I've recently installed FS 6.0 on Mac (OS 10.7.5), and have been unable
 to load volumes in Freeview. When selecting 'File > Load volume', the
 dialog box appears, but when I select any T1.mgz and click Ok, Freeview
 immediately crashes.
 
 Has anyone encountered this same issue?
 
 Best wishes,
 
 Dan
 
 ---
 Dr. Daniel Carey
 Post-Doctoral Research Fellow - Statistician
 The Irish LongituDinal Study on Ageing (TILDA)
 Trinity College Dublin
 Dublin 2, Ireland.
 Email: care...@tcd.ie 
 
 
 
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>> 
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[Freesurfer] Re-running recon-all in V6 {Disarmed}

[Kevin Aquino]

Hi all,

When V6 is released I'd want to re-run all my (10) subjects through
recon-all again (they were processed with v6 alpha). I'd like to keep all
my wm edits, mask and control points, is it as easy as just running
recon-all on the same folder again? They are 0.7mm so I'd like to keep all
the corrections.


Cheers!


*Dr Kevin Aquino*
Research fellow,
Sir Peter Mansfield Magnetic Resonance Center, The University of
Nottingham.

Honorary Research Fellow
School of Physics, Faculty of Science, University of Sydney

*E* kevin.aqu...@nottingham.ac.uk, aqu...@physics.usyd.edu.au | *W*
https://kevinaquino.github.io <http://www.physics.usyd.edu.au/~aquino/>

--

The brain is a wonderful organ. It starts working the moment you get up and
does not stop until you get into the office.
-
Robert Frost

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Re: [Freesurfer] question white matter

[Kevin Aquino]

I believe they are mean and Gaussian curvature respectively. 


Cheers, 

Kevin Aquino

> On 13 Dec 2016, at 17:23, tom parker <tomparker...@gmail.com> wrote:
> 
> Dear Freesurfers,
> 
> Could anyone tell me what the white.H and white.K measures in Qdec are?
> 
> Thank you so much!
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Re: [Freesurfer] Processing 7T data

[Kevin Aquino]

Hi Damien,

I have tested using the HighResRecon vs Freesurfer beta on 0.7 mm^3 data
and have preferred the segmentations on the beta version.

Cheers,


*Dr Kevin Aquino*
Research fellow,
Sir Peter Mansfield Magnetic Resonance Center, The University of
Nottingham.

Honorary Research Fellow
School of Physics, Faculty of Science, University of Sydney

*E* kevin.aqu...@nottingham.ac.uk, aqu...@physics.usyd.edu.au | *W*
www.physics.usyd.edu.au/~aquino/

--

The brain is a wonderful organ. It starts working the moment you get up and
does not stop until you get into the office.
-
Robert Frost

CRICOS 00026A
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On Thu, Oct 6, 2016 at 1:01 PM, Damien MARIE <damien.ma...@unige.ch> wrote:

> Dear experts,
>
> I plan to process some MRI 7T data, 0.6 mm^3 isotropic voxel size. The aim
> is to look a R1 maps.
>
> I was wondering what was your opinion concerning the downsampling to 1
> mm^3 (performed by the current FreeSurfer version if I am correct). What do
> you think would be the best: FreeSurfer 5.3 , FreeSurfer 5.3-HCP or
> FreeSurfer beta 6.0?
>
> Thank You and Best,
>
> Damien
>
> ___
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>
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> 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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[Freesurfer] Using freesurfer on a partial brain

[Kevin Aquino]

Dear Freesurfer list,

I was wondering if anyone here has used freesurfer on anatomical scans
acquired on a partial brain?

I realise that recon-all and many of the tools are suited for a full brain,
but I was wondering if anyone out there has had experience making the tools
work for this scenario? Not necessarily the parcellations and the full
set-up, but other tools such as segmentation, creating a white and pial
surface and topology fixes.


Cheers,


*Dr Kevin Aquino*
Research fellow,
Sir Peter Mansfield Magnetic Resonance Center, The University of
Nottingham.

Honorary Research Fellow
School of Physics, Faculty of Science, University of Sydney

*E* kevin.aqu...@nottingham.ac.uk, aqu...@physics.usyd.edu.au | *W*
www.physics.usyd.edu.au/~aquino/

--

The brain is a wonderful organ. It starts working the moment you get up and
does not stop until you get into the office.
-
Robert Frost

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[Freesurfer] Freesurfer V6 (beta) and MacOS 10.11 (El Capitan)

[Kevin Aquino]

Dear all,

I was wondering if many users have had freesurfer 6 (beta) working (well)
with Mac OS 10.11?

(or Freesurfer V5.3)

Thanks!


*Dr Kevin Aquino*
Research fellow,
Sir Peter Mansfield Magnetic Resonance Center, The University of
Nottingham.

Honorary Research Fellow
School of Physics, Faculty of Science, University of Sydney

*E* kevin.aqu...@nottingham.ac.uk, aqu...@physics.usyd.edu.au | *W*
www.physics.usyd.edu.au/~aquino/

--

The brain is a wonderful organ. It starts working the moment you get up and
does not stop until you get into the office.
-
Robert Frost

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Re: [Freesurfer] high resolution data using recon-all

[Kevin Aquino]

Hi Falk,

Just to jump on this as well – does FS 6.0 make HiResRecon redundant?

– I've been using HiResRecon [working like a charm :) ] and wondering if FS
6.0 will cut the need for that workaround.

Cheers,


*Dr Kevin Aquino*
Research fellow,
Sir Peter Mansfield Magnetic Resonance Center, The University of
Nottingham.

Honorary Research Fellow
School of Physics, Faculty of Science, University of Sydney

*E* kevin.aqu...@nottingham.ac.uk, aqu...@physics.usyd.edu.au | *W*
www.physics.usyd.edu.au/~aquino/

--

The brain is a wonderful organ. It starts working the moment you get up and
does not stop until you get into the office.
-
Robert Frost

CRICOS 00026A
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On Mon, Oct 12, 2015 at 9:24 AM, Falk Lüsebrink <falk.luesebr...@ovgu.de>
wrote:

> Hi Yun,
>
> if it is for some reason impractical to use a beta version of FreeSurfer
> you can also try to follow the HiResRecon (
> http://freesurfer.net/fswiki/HiResRecon) I put together some time ago.
> This solves the issues related to high resolution data and will circumvent
> conformation to 1 mm^3.
>
> However, if the subcortical segmentation is of interest or if you want to
> have a look at a future-proof processing pipeline you should aim for the
> beta version of FreeSurfer. Several improvements have been made to v6.0 so
> it's definitely worth checking out, especially for high resolution data.
>
> Best,
> Falk
>
> -Ursprüngliche Nachricht-
> Von: freesurfer-boun...@nmr.mgh.harvard.edu [mailto:
> freesurfer-boun...@nmr.mgh.harvard.edu] Im Auftrag von Bruce Fischl
> Gesendet: Samstag, 10. Oktober 2015 19:23
> An: Freesurfer support list
> Cc: Kyoko Fujimoto
> Betreff: Re: [Freesurfer] high resolution data using recon-all
>
> Hi Yun
>
> you should probably get a beta version of 6.0 - it has much improved
> highres support. 7T can be hard though. Kyoko Fujimoto (ccd) put together a
> pipeline for 7T that worked pretty well. You might check in with her Bruce
>
>
> On Sat, 10 Oct 2015, Yun Wang wrote:
>
> > Hi All,
> >
> > I have 7T high resolution data 0.625mm.  Is it  appropriate to process
> the data using recon-all ? If not, any idea?
> >
> > Thanks!
> >
> >
> > Yun Wang
> > ___
> > 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 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] mris_surf2vol

[Kevin Aquino]

Hi Doug,

sorry to be a bother, this doesn't work on my machine,
running:
file mri_surf2vol.mac64

gets me:

mri_surf2vol.mac64: ELF 64-bit LSB executable, x86-64, version 1 (SYSV),
dynamically linked (uses shared libs), for GNU/Linux 2.4.0, not stripped



Cheers,


*Dr Kevin Aquino*
Research fellow,
Sir Peter Mansfield Magnetic Resonance Center, The University of
Nottingham.

Honorary Research Fellow
School of Physics, Faculty of Science, University of Sydney

*E* kevin.aqu...@nottingham.ac.uk, aqu...@physics.usyd.edu.au | *W*
www.physics.usyd.edu.au/~aquino/

--

The brain is a wonderful organ. It starts working the moment you get up and
does not stop until you get into the office.
-
Robert Frost

CRICOS 00026A
This email plus any attachments to it are confidential. Any unauthorised
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On Tue, Oct 6, 2015 at 12:35 AM, Douglas Greve <gr...@nmr.mgh.harvard.edu>
wrote:

> here you go
>
> ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mri_surf2vol.mac64
>
>
> On 10/5/15 11:24 AM, Kevin Aquino wrote:
>
> Hi Doug,
>
> Thanks for the file, do you happen to have one that is compiled for a
> 64bit mac installation of freesurfer?
>
> Cheers!
>
> Cheers,
>
>
> *Dr Kevin Aquino*
> Research fellow,
> Sir Peter Mansfield Magnetic Resonance Center, The University of
> Nottingham.
>
> Honorary Research Fellow
> School of Physics, Faculty of Science, University of Sydney
>
> *E* kevin.aqu...@nottingham.ac.uk, aqu...@physics.usyd.edu.au | *W*
> www.physics.usyd.edu.au/~aquino/
> <http://www.physics.usyd.edu.au/%7Eaquino/>
>
> --
>
> The brain is a wonderful organ. It starts working the moment you get up
> and does not stop until you get into the office.
> -
> Robert Frost
>
> CRICOS 00026A
> This email plus any attachments to it are confidential. Any unauthorised
> use is strictly prohibited. If you receive this email in error, please
> delete it and any attachments.
>
> Please think of our environment and only print this e-mail if necessary.
>
>
> On Fri, Oct 2, 2015 at 6:26 PM, Douglas Greve <gr...@nmr.mgh.harvard.edu>
> wrote:
>
>>
>> Try using Method 1 from this version of mri_surf2vol
>>
>> ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mri_surf2vol
>>
>>
>> On 10/2/15 11:38 AM, Kevin Aquino wrote:
>>
>> Ah sorry for not being clear,
>>
>> Basically I would like the output from mris_surf2vol with the mask option
>> to be less speckled.
>>
>> For example, in the image attached:
>> http://www.physics.usyd.edu.au/~aquino/example_mri_surf2vol.png
>>
>> there are some voxels missing. Is there an option to fill these voxels?
>>
>>
>> Cheers,
>>
>>
>> *Dr Kevin Aquino*
>> Research fellow,
>> Sir Peter Mansfield Magnetic Resonance Center, The University of
>> Nottingham.
>>
>> Honorary Research Fellow
>> School of Physics, Faculty of Science, University of Sydney
>>
>> *E* kevin.aqu...@nottingham.ac.uk, aqu...@physics.usyd.edu.au | *W*
>> www.physics.usyd.edu.au/~aquino/
>> <http://www.physics.usyd.edu.au/%7Eaquino/>
>>
>> --
>>
>> The brain is a wonderful organ. It starts working the moment you get up
>> and does not stop until you get into the office.
>> -
>> Robert Frost
>>
>> CRICOS 00026A
>> This email plus any attachments to it are confidential. Any unauthorised
>> use is strictly prohibited. If you receive this email in error, please
>> delete it and any attachments.
>>
>> Please think of our environment and only print this e-mail if necessary.
>>
>>
>> On Fri, Oct 2, 2015 at 1:42 PM, Bruce Fischl <fis...@nmr.mgh.harvard.edu>
>> wrote:
>>
>>> Hi Kevin
>>>
>>> I'm not clear on what you need. Would mri_surf2vol --fillribbon do what
>>> you want? I don't really know what else "voxelize" means
>>>
>>> cheers
>>> Bruce
>>>
>>>
>>> On Fri, 2 Oct 2015, Kevin Aquino wrote:
>>>
>>> Hi all,
>>>> I am trying to "voxelize" the cortical surfaces generated in freesurfer
>>>> and
>>>> I am a little stuck.
>>>>
>>>> I have been using mris_surf2vol with the --mask option however this
>>>> generates a very speckled representatio

Re: [Freesurfer] mris_surf2vol

[Kevin Aquino]

Hi Doug,

Thanks for the file, do you happen to have one that is compiled for a 64bit
mac installation of freesurfer?

Cheers!

Cheers,


*Dr Kevin Aquino*
Research fellow,
Sir Peter Mansfield Magnetic Resonance Center, The University of
Nottingham.

Honorary Research Fellow
School of Physics, Faculty of Science, University of Sydney

*E* kevin.aqu...@nottingham.ac.uk, aqu...@physics.usyd.edu.au | *W*
www.physics.usyd.edu.au/~aquino/

--

The brain is a wonderful organ. It starts working the moment you get up and
does not stop until you get into the office.
-
Robert Frost

CRICOS 00026A
This email plus any attachments to it are confidential. Any unauthorised
use is strictly prohibited. If you receive this email in error, please
delete it and any attachments.

Please think of our environment and only print this e-mail if necessary.


On Fri, Oct 2, 2015 at 6:26 PM, Douglas Greve <gr...@nmr.mgh.harvard.edu>
wrote:

>
> Try using Method 1 from this version of mri_surf2vol
>
> ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mri_surf2vol
>
>
> On 10/2/15 11:38 AM, Kevin Aquino wrote:
>
> Ah sorry for not being clear,
>
> Basically I would like the output from mris_surf2vol with the mask option
> to be less speckled.
>
> For example, in the image attached:
> http://www.physics.usyd.edu.au/~aquino/example_mri_surf2vol.png
>
> there are some voxels missing. Is there an option to fill these voxels?
>
>
> Cheers,
>
>
> *Dr Kevin Aquino*
> Research fellow,
> Sir Peter Mansfield Magnetic Resonance Center, The University of
> Nottingham.
>
> Honorary Research Fellow
> School of Physics, Faculty of Science, University of Sydney
>
> *E* kevin.aqu...@nottingham.ac.uk, aqu...@physics.usyd.edu.au | *W*
> www.physics.usyd.edu.au/~aquino/
> <http://www.physics.usyd.edu.au/%7Eaquino/>
>
> --
>
> The brain is a wonderful organ. It starts working the moment you get up
> and does not stop until you get into the office.
> -
> Robert Frost
>
> CRICOS 00026A
> This email plus any attachments to it are confidential. Any unauthorised
> use is strictly prohibited. If you receive this email in error, please
> delete it and any attachments.
>
> Please think of our environment and only print this e-mail if necessary.
>
>
> On Fri, Oct 2, 2015 at 1:42 PM, Bruce Fischl <fis...@nmr.mgh.harvard.edu>
> wrote:
>
>> Hi Kevin
>>
>> I'm not clear on what you need. Would mri_surf2vol --fillribbon do what
>> you want? I don't really know what else "voxelize" means
>>
>> cheers
>> Bruce
>>
>>
>> On Fri, 2 Oct 2015, Kevin Aquino wrote:
>>
>> Hi all,
>>> I am trying to "voxelize" the cortical surfaces generated in freesurfer
>>> and
>>> I am a little stuck.
>>>
>>> I have been using mris_surf2vol with the --mask option however this
>>> generates a very speckled representation of the cortical surface on the
>>> voxels. What I would prefer would be the level sets of the cortical
>>> surface
>>> interpolated onto voxels, even if they are at a different resolution that
>>> could be enough. Is this possible with any of the available commands?
>>>
>>> I also went down the route of mris_volmask however, this generates the
>>> cortical ribbon, which is something that I don't need.
>>>
>>> Cheers,
>>>
>>>
>>> Dr Kevin Aquino
>>> Research fellow,
>>> Sir Peter Mansfield Magnetic Imaging Center,
>>> School of Physics & astronomy, The University of Nottingham.
>>>
>>> Honorary Research Fellow
>>> School of Physics, Faculty of Science, University of Sydney.
>>>
>>> E kevin.aqu...@nottingham.ac.uk, aqu...@physics.usyd.edu.au | W
>>> www.physics.usyd.edu.au/~aquino/
>>> <http://www.physics.usyd.edu.au/%7Eaquino/>
>>>
>>> --
>>>
>>> The brain is a wonderful organ. It starts working the moment you get up
>>> and
>>> does not stop until you get into the office.
>>> -
>>> Robert Frost
>>>
>>> CRICOS 00026A
>>> This email plus any attachments to it are confidential. Any unauthorised
>>> use
>>> is strictly prohibited. If you receive this email in error, please
>>> delete it
>>> and any attachments.
>>>
>>> Please think of our environment and only print this e-mail if necessary.
>>>
>>>
>>>
>> _

[Freesurfer] mris_surf2vol

[Kevin Aquino]

Hi all,

I am trying to "voxelize" the cortical surfaces generated in freesurfer and
I am a little stuck.

I have been using mris_surf2vol with the --mask option however this
generates a very speckled representation of the cortical surface on the
voxels. What I would prefer would be the level sets of the cortical surface
interpolated onto voxels, even if they are at a different resolution that
could be enough. Is this possible with any of the available commands?

I also went down the route of mris_volmask however, this generates the
cortical ribbon, which is something that I don't need.

Cheers,


*Dr Kevin Aquino*
Research fellow,
Sir Peter Mansfield Magnetic Imaging Center,
School of Physics & astronomy, The University of Nottingham.

Honorary Research Fellow
School of Physics, Faculty of Science, University of Sydney.

*E* kevin.aqu...@nottingham.ac.uk, aqu...@physics.usyd.edu.au | *W*
www.physics.usyd.edu.au/~aquino/

--

The brain is a wonderful organ. It starts working the moment you get up and
does not stop until you get into the office.
-
Robert Frost

CRICOS 00026A
This email plus any attachments to it are confidential. Any unauthorised
use is strictly prohibited. If you receive this email in error, please
delete it and any attachments.

Please think of our environment and only print this e-mail if necessary.
___
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addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
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but does not contain patient information, please contact the sender and properly
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Re: [Freesurfer] mris_surf2vol

[Kevin Aquino]

Ah sorry for not being clear,

Basically I would like the output from mris_surf2vol with the mask option
to be less speckled.

For example, in the image attached:
http://www.physics.usyd.edu.au/~aquino/example_mri_surf2vol.png

there are some voxels missing. Is there an option to fill these voxels?


Cheers,


*Dr Kevin Aquino*
Research fellow,
Sir Peter Mansfield Magnetic Resonance Center, The University of
Nottingham.

Honorary Research Fellow
School of Physics, Faculty of Science, University of Sydney

*E* kevin.aqu...@nottingham.ac.uk, aqu...@physics.usyd.edu.au | *W*
www.physics.usyd.edu.au/~aquino/

--

The brain is a wonderful organ. It starts working the moment you get up and
does not stop until you get into the office.
-
Robert Frost

CRICOS 00026A
This email plus any attachments to it are confidential. Any unauthorised
use is strictly prohibited. If you receive this email in error, please
delete it and any attachments.

Please think of our environment and only print this e-mail if necessary.


On Fri, Oct 2, 2015 at 1:42 PM, Bruce Fischl <fis...@nmr.mgh.harvard.edu>
wrote:

> Hi Kevin
>
> I'm not clear on what you need. Would mri_surf2vol --fillribbon do what
> you want? I don't really know what else "voxelize" means
>
> cheers
> Bruce
>
>
> On Fri, 2 Oct 2015, Kevin Aquino wrote:
>
> Hi all,
>> I am trying to "voxelize" the cortical surfaces generated in freesurfer
>> and
>> I am a little stuck.
>>
>> I have been using mris_surf2vol with the --mask option however this
>> generates a very speckled representation of the cortical surface on the
>> voxels. What I would prefer would be the level sets of the cortical
>> surface
>> interpolated onto voxels, even if they are at a different resolution that
>> could be enough. Is this possible with any of the available commands?
>>
>> I also went down the route of mris_volmask however, this generates the
>> cortical ribbon, which is something that I don't need.
>>
>> Cheers,
>>
>>
>> Dr Kevin Aquino
>> Research fellow,
>> Sir Peter Mansfield Magnetic Imaging Center,
>> School of Physics & astronomy, The University of Nottingham.
>>
>> Honorary Research Fellow
>> School of Physics, Faculty of Science, University of Sydney.
>>
>> E kevin.aqu...@nottingham.ac.uk, aqu...@physics.usyd.edu.au | W
>> www.physics.usyd.edu.au/~aquino/
>>
>> --
>>
>> The brain is a wonderful organ. It starts working the moment you get up
>> and
>> does not stop until you get into the office.
>> -
>> Robert Frost
>>
>> CRICOS 00026A
>> This email plus any attachments to it are confidential. Any unauthorised
>> use
>> is strictly prohibited. If you receive this email in error, please delete
>> it
>> and any attachments.
>>
>> Please think of our environment and only print this e-mail if necessary.
>>
>>
>>
> ___
> 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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The information in this e-mail is intended only for the person to whom it is
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