Re: [Freesurfer] Matlab 2016b and localGI

[Chris Watson]

Hi, I took a look at this and saw that the error comes from the "getmatlab"
script ($FREESURFER_HOME/fsfast/bin/getmatlab). It is a CSH script, which I
thought might be the issue.

Specifically, the script checks for the existence of matlab by
(unsurprisingly)

set MATLAB = `which matlab`;

On Dr. J's system, this was problematic due to "matlab" being aliased, so
calling "getmatlab" directly exited with the error. Hard-coding the path
for matlab in the "getmatlab" script is a (non-portable) solution.

However, I am not sure why it would throw an error, in any case. I tried it
on my system and it returned the correct location of matlab. I am running
CentOS 7.3 and using Freesurfer v5.3
(x86_64-unknown-linux-gnu-stable5-20130513). The version of "getmatlab" is
Revision 1.2

Chris

On Fri, Aug 11, 2017 at 12:27 PM, Alan Francis 
wrote:

> Hi Jennifer -
>
> Ostensibly your pathways and environment variables look correct. I ran
> into this problem once before, so I changed from BASH to the enhanced C
> shell and it worked. You may want to try that. All you need to do is to
> exit out of bash and set the environment in tcsh and it could work.
>
> best,
>
> Alan
>
> On Thu, Aug 10, 2017 at 4:56 PM, Juranek, Jenifer <
> jenifer.jura...@uth.tmc.edu> wrote:
>
>> Hi,
>>
>> Hope someone can identify my user error...I've listed below key bits of
>> info (system info, cmdline and error message, echo $PATH, cat .bashrc, cat
>> startup.m).
>>
>> Really appreciate someone taking a look and walking me through a solution
>> to my error?
>>
>> Many Thanks!
>>
>> Jenifer
>>
>>
>> 1) Running Freesurfer_v6 on RHEL Centos7.3
>>
>> and matlab 2016b (with imaging processing toolbox)
>>
>> 2) recon-all -s  -localGI
>>
>> returns the following:
>>
>> #@# Local Gyrification Index lh Thu Aug 10 15:39:03 CDT 2017
>>
>>  mris_compute_lgi --i lh.pial
>>
>> ERROR: Matlab is required to run mris_compute_lgi!
>> Linux localhost.localdomain 3.10.0-514.el7.x86_64 #1 SMP Wed Oct 19
>> 11:24:13 EDT 2016 x86_64 x86_64 x86_64 GNU/Linux
>>
>>
>> 3) matlab is in my path
>>
>> [jjuranek@localhost subjects]$ echo $PATH
>> /home/jjuranek/freesurfer/bin:/home/jjuranek/freesurfer/fsfa
>> st/bin:/home/jjuranek/freesurfer/tktools:/home/jjuranek/fsl/
>> bin:/home/jjuranek/freesurfer/mni/bin:/home/jjuranek/fsl/
>> bin:/home/jjuranek/freesurfer/bin:/home/jjuranek/freesurfer/
>> fsfast/bin:/home/jjuranek/freesurfer/tktools:/home/
>> jjuranek/freesurfer/mni/bin:/usr/local/bin:/usr/local/sbin:
>> /usr/bin:/usr/sbin:/bin:/sbin:/home/jjuranek/.local/bin:/
>> home/jjuranek/bin:/home/jjuranek/matlab/R2016b/bin/matlab
>>
>>
>> 4) my .bashrc file is as follows
>>
>> # .bashrc
>>
>> # Source global definitions
>> if [ -f /etc/bashrc ]; then
>> . /etc/bashrc
>> fi
>>
>> # User specific aliases and functions
>>
>> export FREESURFER_HOME=/home/jjuranek/freesurfer
>> source $FREESURFER_HOME/SetUpFreeSurfer.sh
>>
>> matlab=/home/jjuranek/matlab/R2016b/bin/matlab
>> alias matlab=$matlab
>>
>> export PATH=$PATH:/home/jjuranek/matlab/R2016b/bin/matlab
>>
>> #/home/jjuranek/matlab/R2016b/bin/matlab
>> #MATLAB is selecting SOFTWARE OPENGL rendering.
>>
>>
>> 5) my startup.m file is as follows
>>
>> % FreeSurfer -%
>> fshome = getenv('FREESURFER_HOME');
>> fsmatlab = sprintf('%s/matlab',fshome);
>> if (exist(fsmatlab) == 7)
>> addpath(genpath(fsmatlab));
>> end
>> clear fshome fsmatlab;
>> %-%
>>
>> % FreeSurfer FAST %
>> fsfasthome = getenv('FSFAST_HOME');
>> fsfasttoolbox = sprintf('%s/toolbox',fsfasthome);
>> if (exist(fsfasttoolbox) == 7)
>> path(path,fsfasttoolbox);
>> end
>> clear fsfasthome fsfasttoolbox;
>> %-%
>>
>> % FreeSurfer LGI %
>> FSH = getenv('FREESURFER_HOME');
>>
>> fshmatlab = sprintf('%s/matlab',FSH);
>> path(path,fshmatlab);
>> clear fshmatlab FSH;
>>
>>
>>
>> ___
>> 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
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>> dispose of the e-mail.
>>
>>
>
>
> --
> |~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|
>
> *Alan N. Francis PhD*
> Instructor - Imaging Neuroscience
> Brain Imaging Center
> McLean Hospital
> Harvard Medical School
> 115 Mill Street, Belmont, MA 02478
> al...@bwh.harvard.edu 
> afran...@mclean.harvard.edu
>
>
> 

Re: [Freesurfer] Matlab 2016b and localGI

[Alan Francis]

Hi Jennifer -

Ostensibly your pathways and environment variables look correct. I ran into
this problem once before, so I changed from BASH to the enhanced C shell
and it worked. You may want to try that. All you need to do is to exit out
of bash and set the environment in tcsh and it could work.

best,

Alan

On Thu, Aug 10, 2017 at 4:56 PM, Juranek, Jenifer <
jenifer.jura...@uth.tmc.edu> wrote:

> Hi,
>
> Hope someone can identify my user error...I've listed below key bits of
> info (system info, cmdline and error message, echo $PATH, cat .bashrc, cat
> startup.m).
>
> Really appreciate someone taking a look and walking me through a solution
> to my error?
>
> Many Thanks!
>
> Jenifer
>
>
> 1) Running Freesurfer_v6 on RHEL Centos7.3
>
> and matlab 2016b (with imaging processing toolbox)
>
> 2) recon-all -s  -localGI
>
> returns the following:
>
> #@# Local Gyrification Index lh Thu Aug 10 15:39:03 CDT 2017
>
>  mris_compute_lgi --i lh.pial
>
> ERROR: Matlab is required to run mris_compute_lgi!
> Linux localhost.localdomain 3.10.0-514.el7.x86_64 #1 SMP Wed Oct 19
> 11:24:13 EDT 2016 x86_64 x86_64 x86_64 GNU/Linux
>
>
> 3) matlab is in my path
>
> [jjuranek@localhost subjects]$ echo $PATH
> /home/jjuranek/freesurfer/bin:/home/jjuranek/freesurfer/
> fsfast/bin:/home/jjuranek/freesurfer/tktools:/home/jjuranek/fsl/bin:/home/
> jjuranek/freesurfer/mni/bin:/home/jjuranek/fsl/bin:/home/
> jjuranek/freesurfer/bin:/home/jjuranek/freesurfer/fsfast/
> bin:/home/jjuranek/freesurfer/tktools:/home/jjuranek/
> freesurfer/mni/bin:/usr/local/bin:/usr/local/sbin:/usr/bin:/
> usr/sbin:/bin:/sbin:/home/jjuranek/.local/bin:/home/
> jjuranek/bin:/home/jjuranek/matlab/R2016b/bin/matlab
>
>
> 4) my .bashrc file is as follows
>
> # .bashrc
>
> # Source global definitions
> if [ -f /etc/bashrc ]; then
> . /etc/bashrc
> fi
>
> # User specific aliases and functions
>
> export FREESURFER_HOME=/home/jjuranek/freesurfer
> source $FREESURFER_HOME/SetUpFreeSurfer.sh
>
> matlab=/home/jjuranek/matlab/R2016b/bin/matlab
> alias matlab=$matlab
>
> export PATH=$PATH:/home/jjuranek/matlab/R2016b/bin/matlab
>
> #/home/jjuranek/matlab/R2016b/bin/matlab
> #MATLAB is selecting SOFTWARE OPENGL rendering.
>
>
> 5) my startup.m file is as follows
>
> % FreeSurfer -%
> fshome = getenv('FREESURFER_HOME');
> fsmatlab = sprintf('%s/matlab',fshome);
> if (exist(fsmatlab) == 7)
> addpath(genpath(fsmatlab));
> end
> clear fshome fsmatlab;
> %-%
>
> % FreeSurfer FAST %
> fsfasthome = getenv('FSFAST_HOME');
> fsfasttoolbox = sprintf('%s/toolbox',fsfasthome);
> if (exist(fsfasttoolbox) == 7)
> path(path,fsfasttoolbox);
> end
> clear fsfasthome fsfasttoolbox;
> %-%
>
> % FreeSurfer LGI %
> FSH = getenv('FREESURFER_HOME');
>
> fshmatlab = sprintf('%s/matlab',FSH);
> path(path,fshmatlab);
> clear fshmatlab FSH;
>
>
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
> The information in this e-mail is intended only for the person to whom it
> is
> addressed. If you believe this e-mail was sent to you in error and the
> e-mail
> contains patient information, please contact the Partners Compliance
> HelpLine at
> http://www.partners.org/complianceline . If the e-mail was sent to you in
> error
> but does not contain patient information, please contact the sender and
> properly
> dispose of the e-mail.
>
>


-- 
|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|

*Alan N. Francis PhD*
Instructor - Imaging Neuroscience
Brain Imaging Center
McLean Hospital
Harvard Medical School
115 Mill Street, Belmont, MA 02478
al...@bwh.harvard.edu 
afran...@mclean.harvard.edu


|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|
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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] Mean diffusivity on cortex?

[Yendiki, Anastasia]

Agreed, especially so with MD. Keep in mind that you¹re upsampling MD from
a lower-res (diffusion) space to a higher-res (T1) space, so it should be
smooth already, relatively to measure derived from the T1. And MD varies
pretty smoothly (it¹s a mean of 3 things, after all).

On 8/11/17, 1:11 PM, "Bruce Fischl"  wrote:

>Hi Shane
>
>not really - it totally depends on the size of the effect you are looking
>for. I would be *very* careful about partial volume effects though
>
>cheers
>Bruce
>On Fri, 
>11 Aug 2017, Shane Schofield wrote:
>
>> Appreciate it Dr Bruce. Do you have guidelines for smoothing MD?
>> 
>> Dr Yendiki, I am trying to investigate whether cortical MD can be a
>>marker
>> of neurodegeneration. The idea is that during the early stages of a
>>disease,
>> cellular microstructure may breakdown before cortical thinning occurs.
>>This
>> results in "less" barriers against diffusion resulting in an increase of
>> MD. 
>> 
>> 
>> On Friday, August 11, 2017, 5:49:40 PM GMT+1, Bruce Fischl
>>  wrote:
>> 
>> 
>> Hi Shane
>> 
>> you probably don't need cvs as it is more to extend the surface-based
>> registration to the entire volume. Here you just need the surface-based
>> registration I believe. Use mri_vol2surf to sample the FA onto the
>>surface.
>> After that it is identical to a thickness study
>> 
>> cheers
>> Bruce
>> 
>> 
>> 
>> On Fri, 11 Aug 2017, Shane Schofield
>> wrote:
>> 
>> > Thanks Dr Yendiki.
>> >
>> > I am more interested to compare MD in grey matter regions by putting
>>the
>> MD on the surface, and then do a glmfit type of comparisons. Is that OK?
>> Would you recommend me
>> > to smooth the data after spatial normalisation? I have also used the
>> mri_cvs_register as described on the tutorial.
>> >
>> >
>> > On Friday, August 11, 2017, 7:03:49 AM GMT+1, Shane Schofield
>>  wrote:
>> >
>> >
>> > Hi DTI Experts,
>> >
>> > Is it sensible to do comparisons of MD on the cortex surface like a
>>normal
>> cortical thickness comparisons between group? If the answer is yes, are
>> there recommended on
>> > smoothing ?
>> >
>> > DT_RECON has been completed in Freesurfer.
>> >
>> > Thank you.
>> >
>> >
>> >
>> ___
>> Freesurfer mailing list
>> Freesurfer@nmr.mgh.harvard.edu
>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>> 
>> 
>> The information in this e-mail is intended only for the person to whom
>>it is
>> addressed. If you believe this e-mail was sent to you in error and the
>> e-mail
>> contains patient information, please contact the Partners Compliance
>> HelpLine at
>> http://www.partners.org/complianceline . If the e-mail was sent to you
>>in
>> error
>> but does not contain patient information, please contact the sender and
>> properly
>> dispose of the e-mail.
>> 


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Re: [Freesurfer] mri_glmfit-sim output

[Douglas N Greve]

that is experimental to look at the "weight" of the cluster (ie, 
size*intensity)


On 08/11/2017 11:50 AM, Van Der Deijl, Rosanne wrote:
> Thanks for the link, I hadn't seen that one indeed!
> However, the variable WghtVtx is not explained on this page. What is 
> this variable?
>
> Thank you!
>
> Message: 8
> Date: Mon, 7 Aug 2017 15:01:46 -0400
> From: Douglas N Greve 
> Subject: Re: [Freesurfer] mri_glmfit-sim output
> To: freesurfer@nmr.mgh.harvard.edu
> Message-ID: <0b5fc464-a5ed-cee5-e3fa-3603b99e8...@nmr.mgh.harvard.edu>
> Content-Type: text/plain; charset=windows-1252; format=flowed
>
> see here
> https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysisClusterSummary
>
>
> On 08/07/2017 02:40 PM, Van Der Deijl, Rosanne wrote:
> > Dear Freesurfer team,
> >
> > In the mri_glmfit-sim summary output file, I get a number of output
> > variables, and I'm not sure what some of them are. Could you explain
> > the ones in bold to me?
> >
> > # ClusterNo  Max   VtxMax   Size(mm^2)  MNIX   MNIY MNIZ *CWP
> > CWPLow   CWPH * NVtxs *WghtVtx*   Annot
> >12.015  134872355.89 -36.3 -9.7   -1.4
> >0.96620  0.96390 0.96850841 1298.68 insula
> >21.652   71259154.25 -49.4 -52.7   39.2
> > 1.0  -0.00010 1.0363  526.18 supramarginal
> >3   -1.521   91550 39.92 -37.1 -26.5  -23.3
> > 1.0  -0.00010 1.0 90 -125.33 fusiform
> >41.322  139141  0.76 -36.4 3.5 -10.7
> >   1.0  -0.00010 1.0  2 2.62  insula
> >51.312   73658  0.47 -36.0 -4.4   9.6
> >1.0  -0.00010 1.0  1 1.31  insula
> >61.387  133422  0.44 -5.1 -17.251.7
> >  1.0  -0.00010 1.0  1 1.39  paracentral
> >
> > I know CWP stands for Cluster-wise P-value. But what is the low and
> > the high number, a confidence interval? And isn't it odd that my
> > p-values are (almost) 1?
> >
> > Thank you in advance.
> >
> > Kind regards,
> >
> > Rose
> >
>
>
> ___
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-- 
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MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

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

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Re: [Freesurfer] Mean diffusivity on cortex?

[Bruce Fischl]

Hi Shane

not really - it totally depends on the size of the effect you are looking 
for. I would be *very* careful about partial volume effects though


cheers
Bruce
On Fri, 
11 Aug 2017, Shane Schofield wrote:



Appreciate it Dr Bruce. Do you have guidelines for smoothing MD? 

Dr Yendiki, I am trying to investigate whether cortical MD can be a marker
of neurodegeneration. The idea is that during the early stages of a disease,
cellular microstructure may breakdown before cortical thinning occurs. This
results in "less" barriers against diffusion resulting in an increase of
MD. 


On Friday, August 11, 2017, 5:49:40 PM GMT+1, Bruce Fischl
 wrote:


Hi Shane

you probably don't need cvs as it is more to extend the surface-based
registration to the entire volume. Here you just need the surface-based
registration I believe. Use mri_vol2surf to sample the FA onto the surface.
After that it is identical to a thickness study

cheers
Bruce



On Fri, 11 Aug 2017, Shane Schofield
wrote:

> Thanks Dr Yendiki. 
>
> I am more interested to compare MD in grey matter regions by putting the
MD on the surface, and then do a glmfit type of comparisons. Is that OK?
Would you recommend me
> to smooth the data after spatial normalisation? I have also used the
mri_cvs_register as described on the tutorial.
>
>
> On Friday, August 11, 2017, 7:03:49 AM GMT+1, Shane Schofield
 wrote:
>
>
> Hi DTI Experts,
>
> Is it sensible to do comparisons of MD on the cortex surface like a normal
cortical thickness comparisons between group? If the answer is yes, are
there recommended on
> smoothing ?
>
> DT_RECON has been completed in Freesurfer.
>
> Thank you.
>
>
>
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e-mail
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HelpLine at
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Re: [Freesurfer] Mean diffusivity on cortex?

[Shane Schofield]

Appreciate it Dr Bruce. Do you have guidelines for smoothing MD? 
Dr Yendiki, I am trying to investigate whether cortical MD can be a marker of 
neurodegeneration. The idea is that during the early stages of a disease, 
cellular microstructure may breakdown before cortical thinning occurs. This 
results in "less" barriers against diffusion resulting in an increase of MD. 

On Friday, August 11, 2017, 5:49:40 PM GMT+1, Bruce Fischl 
 wrote:

Hi Shane

you probably don't need cvs as it is more to extend the surface-based 
registration to the entire volume. Here you just need the surface-based 
registration I believe. Use mri_vol2surf to sample the FA onto the surface. 
After that it is identical to a thickness study

cheers
Bruce



On Fri, 11 Aug 2017, Shane Schofield 
wrote:

> Thanks Dr Yendiki. 
> 
> I am more interested to compare MD in grey matter regions by putting the MD 
> on the surface, and then do a glmfit type of comparisons. Is that OK? Would 
> you recommend me
> to smooth the data after spatial normalisation? I have also used the 
> mri_cvs_register as described on the tutorial.
> 
> 
> On Friday, August 11, 2017, 7:03:49 AM GMT+1, Shane Schofield 
>  wrote:
> 
> 
> Hi DTI Experts,
> 
> Is it sensible to do comparisons of MD on the cortex surface like a normal 
> cortical thickness comparisons between group? If the answer is yes, are there 
> recommended on
> smoothing ?
> 
> DT_RECON has been completed in Freesurfer.
> 
> Thank you.
> 
> 
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Re: [Freesurfer] Mean diffusivity on cortex?

[Bruce Fischl]

Hi Shane

you probably don't need cvs as it is more to extend the surface-based 
registration to the entire volume. Here you just need the surface-based 
registration I believe. Use mri_vol2surf to sample the FA onto the surface. 
After that it is identical to a thickness study


cheers
Bruce



On Fri, 11 Aug 2017, Shane Schofield 
wrote:



Thanks Dr Yendiki. 

I am more interested to compare MD in grey matter regions by putting the MD on 
the surface, and then do a glmfit type of comparisons. Is that OK? Would you 
recommend me
to smooth the data after spatial normalisation? I have also used the 
mri_cvs_register as described on the tutorial.


On Friday, August 11, 2017, 7:03:49 AM GMT+1, Shane Schofield 
 wrote:


Hi DTI Experts,

Is it sensible to do comparisons of MD on the cortex surface like a normal 
cortical thickness comparisons between group? If the answer is yes, are there 
recommended on
smoothing ?

DT_RECON has been completed in Freesurfer.

Thank you.


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Re: [Freesurfer] Test-retest reliability small subcortical regions

[Bruce Fischl]

Hi Rose

do you mean cross-sectional or longitudinal analysis?

cheers
Bruce

On Fri, 11 Aug 2017, 
Van Der Deijl, Rosanne wrote:

> Dear Freesurfer team,
> 
> I was wondering what the test-retest reliability is of comparing small
> regions in the subcortical volume, e.g. the amygdala. Has this improved with
> the 6.0 version?
> 
> Thank you!
> 
> Kind regards,
> 
> Rose
> 
>
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[Freesurfer] Test-retest reliability small subcortical regions

[Van Der Deijl, Rosanne]

Dear Freesurfer team,

I was wondering what the test-retest reliability is of comparing small regions 
in the subcortical volume, e.g. the amygdala. Has this improved with the 6.0 
version?

Thank you!

Kind regards,

Rose
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Re: [Freesurfer] mri_glmfit-sim output

[Van Der Deijl, Rosanne]

Thanks for the link, I hadn't seen that one indeed!
However, the variable WghtVtx is not explained on this page. What is this 
variable?

Thank you!

Message: 8
Date: Mon, 7 Aug 2017 15:01:46 -0400
From: Douglas N Greve 
Subject: Re: [Freesurfer] mri_glmfit-sim output
To: freesurfer@nmr.mgh.harvard.edu
Message-ID: <0b5fc464-a5ed-cee5-e3fa-3603b99e8...@nmr.mgh.harvard.edu>
Content-Type: text/plain; charset=windows-1252; format=flowed

see here
https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysisClusterSummary


On 08/07/2017 02:40 PM, Van Der Deijl, Rosanne wrote:
> Dear Freesurfer team,
>
> In the mri_glmfit-sim summary output file, I get a number of output
> variables, and I'm not sure what some of them are. Could you explain
> the ones in bold to me?
>
> # ClusterNo  Max   VtxMax   Size(mm^2)  MNIX   MNIY MNIZ *CWP
> CWPLow   CWPH * NVtxs *WghtVtx*   Annot
>12.015  134872355.89 -36.3   -9.7   -1.4
>0.96620  0.96390 0.96850841 1298.68  insula
>21.652   71259154.25 -49.4-52.7   39.2
> 1.0  -0.00010 1.0363  526.18  supramarginal
>3   -1.521   91550 39.92 -37.1  -26.5  -23.3
> 1.0  -0.00010 1.0 90 -125.33   fusiform
>41.322  139141  0.76 -36.43.5 -10.7
>   1.0  -0.00010 1.0  22.62  insula
>51.312   73658  0.47 -36.0   -4.4   9.6
>1.0  -0.00010 1.0  11.31  insula
>61.387  133422  0.44 -5.1  -17.251.7
>  1.0  -0.00010 1.0  11.39  paracentral
>
> I know CWP stands for Cluster-wise P-value. But what is the low and
> the high number, a confidence interval? And isn't it odd that my
> p-values are (almost) 1?
>
> Thank you in advance.
>
> Kind regards,
>
> Rose
>
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Re: [Freesurfer] Generating Surfaces from Labels

[Zach Humphrey]

Hello Dr. Fischl,

Thanks for the feedback. Can the flattened patches be "re-inflated" into
surface files again after being flattened?

I am also continuing to run into the issue with the label2vol function
where I end up with a volume that is completely filled. The steps I have
been following to reach this point are
1: Run mri_annotation2label --subject subjectname --hemi lh --outdir out
2: mri_label2vol --label $labelgeneratedfromstep1 --temp rawavg.mgz
--subject subjectname --hemi lh --o outputdirectory --fillthresh .3 --reg
register.dat --proj frac 0 1 .1
Honestly I am not sure what the --proj field actually means and so I have
been just using the 0 1 .1 that I found in examples of mri_label2vol. Could
this be the problem?

Thanks,
Zachary Humphrey

On Tue, Aug 8, 2017 at 3:51 PM, Bruce Fischl 
wrote:

> Hi Zach
>
> I think if you cut and flatten the cortical part of the surfaces, convert
> tha .annot files to separate label files, you can then use label2flat on
> each label to generate a flattened patch that is just taht label. I haven't
> used it in years (decades?), but I think it should work
>
> cheers
> Bruce
>
>  On Tue, 8 Aug 2017, Zach Humphrey wrote:
>
> Hello All,
>> I have been attempting to convert Label files generated using
>> mri_annotation2label into surface files for use in external programs. In
>> order to do this I first need to convert the label files into freesurfer
>> binary. I have attempted to use the mri_label2vol function to generate an
>> mgz file which could then be converted into freesurfer binary but this has
>> resulted in mgz files which depict a solid cube rather than any brain
>> structure. Any ideas as to why this could be?
>>
>> I would also prefer to avoid ever converting the label files to a volume
>> as
>> converting the volume file to a surface file results in a lower quality
>> than
>> if the file has been maintained as a surface file throughout. Is there any
>> way to use the Desikan Atlas to "divide" say the lh.pial surface file and
>> generate a number of .pial files each consisting of one of the regions
>> described by the Desikan Atlas?
>>
>> Thanks,
>> Zachary Humphrey
>>
>>
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>
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Re: [Freesurfer] PET surfer

[John Anderson]

Hi Dr Greve,

Thanks again for the great explanation and for clarifying how smoothing  may 
exacerbate the partial volume effects.

I have additional question and I appreciate your answer:

In the literature of the voxel-wise analysis using FSL/randomise to study the 
difference between two groups (e.g. TBSS, VBM, ASL, PET,  etc). The authors 
used to register their maps (FA, PET, ASL, ...etc) to a standard template 
MNI152 then merge all the images using fslmerge and then run voxel-wise 
comparison using randomise with a number of permutations and a method to 
correct for multiple comparison.

In  this type of analyses, the authors of these studies didn't applying any 
kind of PVE on the data like how we do in PET surfer. Is this something related 
to registration? meaning all the maps are in the standard space, so PVE has 
trivial/no effect? While in PET surfer we feed to the analysis images in the 
native space then we re sample the images to the brain surface that's why we 
apply PVE? Is the registration to standard template exacerbates PVE?

On 08/10/2017 11:35 AM, John Anderson wrote:

>

> Dear Dr Greve,

>

> Thank you very much for the great explanation. I will definitely

> correct for PVC using PET surfer.

>

> Kindly I have one follow-up question and I highly appreciate your input.

>

> I have PET data for two groups. I studied the difference in PET signal

> using  voxel-wise ( FSL/randomise) and surface-based using PET surfer.

>

> My question is about PVC. We correct for PVC in surface based because

> we re-sample PET data to the brain surface which is an output of

> segmentation process, meaning we expect partial volume effects between

> the grey/white  for a possible contamination between them during

> segmentation.

>

> We don't do PVE in voxel-wise because we don't worry about the

> contamination meaning there are no segmentation lines to separate

> between brain regions.

>

> Kindly is my understanding for this fact correct ( i.e. why we correct

> in surface based and we don't correct in voxel-wise).

It is not correct. You do PVC to remove interactions between the anatomy and 
the PET through PVEs. Those will be there in both surface-based and 
volume-based analysis.  If you perform smoothing in volume-based analysis, you 
will make the PVEs worse. Doing MG PVC then volume-based smoothing will result 
in a disaster. In my opinion, the only way to do PVC in a map-based analysis 
(vs ROI) is to do it on the surface. For subcortical, you can do volume-based 
smoothing within a GM mask.

> By the way, I ran voxel-wise using randomise with TFCE and 5000

> permutations.

For the surface, you can use mri_glmfit with the --perm option.

>

> Thank you again for any clarification

> John

>

>

>

>

> The PET signalcan change with a lot of anatomical changes in the brain

> including thickness, surface area, and gyrification. There is no known

> regressor that will account for this. Right right way to account for

> it is with partialvolume correction (PVC). It is best to do PVC

> simultaneously with the recon, but software is not available to

> perform this. You can do it on a post-hoc basis in PETsurfer using the

> PVC options in mri_gtmpvc. See the wiki.

>

>

>

> On 08/10/2017 04:11 AM, John Anderson wrote:

>

> >

>

> > Hi Dr Greve,

>

> >

>

> > I have PET data for two groups and I used PET surfer in FSV 6.0 to

> > run

>

> > the analyses. The pipeline is straightforward and the analysis ran

>

> > smoothly without any issues.

>

> >

>

> > Is it correct procedure to adjust PET signal to differences in gray

>

> > matter volume or cortical thinness between two groups?

>

> >

>

> > In other words, is it correct if gray matter volume or cortical

>

> > thickness for subjects be included as EVs in GLM or a nausiance

> > factor

>

> > in QDEC?

>

> >

>

> > Specifically, is the PET signal changeable depending ondifferences

>

> > in cortical thickness.

>

> > or differences in gray matter volume?

>

> >

>

> > Thank youfor any clarification

>

> >

>

> >> Thank you !

>

> >> Jon

>

> >>

>

> >

>

> >

>

> >

>

> > ___

>

> > Freesurfer mailing list

>

> > Freesurfer@nmr.mgh.harvard.edu

> > 

>

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

>

>

> --

>

> Douglas N. Greve, Ph.D.

>

> MGH-NMR Center

>

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

>

> Phone Number: 617-724-2358

>

> Fax: 617-726-7422

>

>

> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting

> 

>

> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2

>

> www.nmr.mgh.harvard.edu/facility/filedrop/index.html

> 

>

> Outgoing:

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

>

>

> 

Re: [Freesurfer] Mean diffusivity on cortex?

[Yendiki, Anastasia]

Sorry, my question wasn't very clear. I meant to ask what sort of biological 
effect you're hoping to measure using MD.


From: freesurfer-boun...@nmr.mgh.harvard.edu 
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Shane Schofield 
[shane.schofi...@yahoo.com]
Sent: Friday, August 11, 2017 6:42 AM
To: Freesurfer support list
Subject: Re: [Freesurfer] Mean diffusivity on cortex?

Hi Dr Yendiki, I am studying a group of people with APOE4 and I want to see 
whether cortical MD increases can be detected relative to non-carriers, and if 
so, is the effect size bigger than changes in cortical thickness.



On Friday, August 11, 2017, 11:19:32 AM GMT+1, Yendiki, Anastasia 
 wrote:


What effect are you trying to measure with MD on the cortex?


From: Shane Schofield [shane.schofi...@yahoo.com]
Sent: Friday, August 11, 2017 3:12 AM
To: Freesurfer Support List; Yendiki, Anastasia
Subject: Re: Mean diffusivity on cortex?

Thanks Dr Yendiki.

I am more interested to compare MD in grey matter regions by putting the MD on 
the surface, and then do a glmfit type of comparisons. Is that OK? Would you 
recommend me to smooth the data after spatial normalisation? I have also used 
the mri_cvs_register as described on the tutorial.


On Friday, August 11, 2017, 7:03:49 AM GMT+1, Shane Schofield 
 wrote:


Hi DTI Experts,

Is it sensible to do comparisons of MD on the cortex surface like a normal 
cortical thickness comparisons between group? If the answer is yes, are there 
recommended on smoothing ?

DT_RECON has been completed in Freesurfer.

Thank you.

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Re: [Freesurfer] Skullstriping problems

[Boyd, Emma]

Hi Mateus,


Please attach the recon-all.log file for your subject and I will take a look.


Best,

Emma



From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of MATEUS ROZALEM ARANHA 

Sent: Friday, August 11, 2017 9:56 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] Skullstriping problems

Hi,

I had problems with skullstriping. I ran recon-all and part of the skull is 
being considered as cortex in the segmentation. I tried to fix this using:

recon-all -skullstrip -wsthresh 50 -clean-bm -subjid 

and than

recon-all -autorecon-pial -subjid 

But nothing changed.

Do I need to run recon-all all over?

Thanks,
Mateus
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[Freesurfer] Skullstriping problems

[MATEUS ROZALEM ARANHA]

Hi,

I had problems with skullstriping. I ran recon-all and part of the skull is
being considered as cortex in the segmentation. I tried to fix this using:

*recon-all -skullstrip -wsthresh 50 -clean-bm -subjid *

and than

*recon-all -autorecon-pial -subjid *

But nothing changed.

Do I need to run recon-all all over?

Thanks,
Mateus
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Re: [Freesurfer] Mean diffusivity on cortex?

[Shane Schofield]

Hi Dr Yendiki, I am studying a group of people with APOE4 and I want to see 
whether cortical MD increases can be detected relative to non-carriers, and if 
so, is the effect size bigger than changes in cortical thickness.


On Friday, August 11, 2017, 11:19:32 AM GMT+1, Yendiki, Anastasia 
 wrote:

#yiv9314780658 P {margin-top:0;margin-bottom:0;}What effect are you trying to 
measure with MD on the cortex?

From: Shane Schofield [shane.schofi...@yahoo.com]
Sent: Friday, August 11, 2017 3:12 AM
To: Freesurfer Support List; Yendiki, Anastasia
Subject: Re: Mean diffusivity on cortex?

Thanks Dr Yendiki. 
I am more interested to compare MD in grey matter regions by putting the MD on 
the surface, and then do a glmfit type of comparisons. Is that OK? Would you 
recommend me to smooth the data after spatial normalisation? I have also used 
the mri_cvs_register as described on the tutorial.

On Friday, August 11, 2017, 7:03:49 AM GMT+1, Shane Schofield 
 wrote:

Hi DTI Experts,
Is it sensible to do comparisons of MD on the cortex surface like a normal 
cortical thickness comparisons between group? If the answer is yes, are there 
recommended on smoothing ?
DT_RECON has been completed in Freesurfer.

Thank you.
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Re: [Freesurfer] Mean diffusivity on cortex?

[Yendiki, Anastasia]

What effect are you trying to measure with MD on the cortex?


From: Shane Schofield [shane.schofi...@yahoo.com]
Sent: Friday, August 11, 2017 3:12 AM
To: Freesurfer Support List; Yendiki, Anastasia
Subject: Re: Mean diffusivity on cortex?

Thanks Dr Yendiki.

I am more interested to compare MD in grey matter regions by putting the MD on 
the surface, and then do a glmfit type of comparisons. Is that OK? Would you 
recommend me to smooth the data after spatial normalisation? I have also used 
the mri_cvs_register as described on the tutorial.


On Friday, August 11, 2017, 7:03:49 AM GMT+1, Shane Schofield 
 wrote:


Hi DTI Experts,

Is it sensible to do comparisons of MD on the cortex surface like a normal 
cortical thickness comparisons between group? If the answer is yes, are there 
recommended on smoothing ?

DT_RECON has been completed in Freesurfer.

Thank you.

___
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[Freesurfer] mri_glmfit long_stats_slopes with group

[Kasper Jessen]

Dear Freesurfer,

I would like to test  if the percentage change (two time points) of cortical 
thickness is different between two groups.

What i have done:

FIRST: long_stats_slopes --qdec ./qdec/long.qdec.table.dat --stats 
lh.aparc.stats --meas thickness --sd $SUBJECTS_DIR --do-spc --generic-time 
--stack-spc ./qdec/long.lh.aparc.stats.stack.txt

SECOND: mri_glmfit --osgm --glmdir lh_thickness.aparc-spc --table 
long.lh.aparc_thickness.stats.stack.txt

 THIRD: cat lh_thickness.aparc-spc/sig.table.dat

Qesteions:
1. How do i test if there is a significant difference between the two groups?
2. How do i visualise this difference in FreeView?

Best regards
Kasper Jessen___
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Re: [Freesurfer] Mean diffusivity on cortex?

[Shane Schofield]

Thanks Dr Yendiki. 
I am more interested to compare MD in grey matter regions by putting the MD on 
the surface, and then do a glmfit type of comparisons. Is that OK? Would you 
recommend me to smooth the data after spatial normalisation? I have also used 
the mri_cvs_register as described on the tutorial.

On Friday, August 11, 2017, 7:03:49 AM GMT+1, Shane Schofield 
 wrote:

Hi DTI Experts,
Is it sensible to do comparisons of MD on the cortex surface like a normal 
cortical thickness comparisons between group? If the answer is yes, are there 
recommended on smoothing ?
DT_RECON has been completed in Freesurfer.

Thank you.
___
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Re: [Freesurfer] Mean diffusivity on cortex?

[Yendiki, Anastasia]

You can use the wmparc, which includes ROIs of the WM underlying each cortical 
area, right below the grey-white boundary surface. These are the relevant 
tutorials:

https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/DiffusionV6.0
https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/AnatomicalROIV6.0


From: freesurfer-boun...@nmr.mgh.harvard.edu 
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Shane Schofield 
[shane.schofi...@yahoo.com]
Sent: Friday, August 11, 2017 2:03 AM
To: Freesurfer Support List
Subject: [Freesurfer] Mean diffusivity on cortex?

Hi DTI Experts,

Is it sensible to do comparisons of MD on the cortex surface like a normal 
cortical thickness comparisons between group? If the answer is yes, are there 
recommended on smoothing ?

DT_RECON has been completed in Freesurfer.

Thank you.

___
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Re: [Freesurfer] Freesurfer PIB PET image processing

[M Janani]

Thanks for your support Douglas. 

I have processed my PIB PET images using PETSURFER. It works fine.

I have one more query. Could you please help in computing the PiB mean value 
and intensity value for the ROIs.

Regards,
Janani


-Original Message-
From: freesurfer-boun...@nmr.mgh.harvard.edu 
[mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Douglas N Greve
Sent: 10 August 2017 20:06
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] Freesurfer PIB PET image processing

do you mean to run the anatomical analysis on them? No.


On 08/10/2017 05:23 AM, M Janani wrote:
> Is it correct to process the PiB images using Freesurfer ?
>
>
> -Original Message-
> From: freesurfer-boun...@nmr.mgh.harvard.edu 
> [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Douglas N 
> Greve
> Sent: 10 August 2017 03:41
> To: freesurfer@nmr.mgh.harvard.edu
> Subject: Re: [Freesurfer] Freesurfer PIB PET image processing
>
> We do not have any thing to specifically analyze PiB. You can look at 
> the PETsurfer page for more general instructions
>
>
> On 08/09/2017 02:15 AM, M Janani wrote:
>> Hi Team,
>>
>> I apologize, I am new to Freesurfer.
>>
>> Currently we are processing PIB PET images.
>>
>>  When we compare the SPM data along with FREESURFER 
>> outputs. We were able to see a large variation in the values.
>>
>>  Could you please guide us in processing PIB PET 
>> images in Freesurfer?
>>
>>  Since the signal of a PET image is very weak, we 
>> used MRI image as a guide to map it to Standard brain.
>>
>>  How does Freesurfer process in this case?
>>
>>  Your help would be grateful.
>>
>> Regards,
>>
>> Janani
>>
>>
>>
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--
Douglas N. Greve, Ph.D.
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[Freesurfer] Mean diffusivity on cortex?

[Shane Schofield]

Hi DTI Experts,
Is it sensible to do comparisons of MD on the cortex surface like a normal 
cortical thickness comparisons between group? If the answer is yes, are there 
recommended on smoothing ?
DT_RECON has been completed in Freesurfer.

Thank you.
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