Re: [Freesurfer] License issue with qdec

[Lisa S. Pao]

Hi everyone,

In response to the questions:

I did not recently upgrade or reinstall.
Other things still run, despite the problem with qdec.
The .license file is valid.

Best,
Lisa

---
Lisa Pao, Ph.D.
Postdoctoral Research Fellow
Division of Child and Adolescent Psychiatry
Columbia University Medical Center
New York State Psychiatric Institute
646-774-5782



Message: 2
Date: Thu, 17 Sep 2015 12:14:14 -0400
From: Douglas N Greve 
>
Subject: Re: [Freesurfer] License issue with qdec
To: freesurfer@nmr.mgh.harvard.edu
Message-ID: 
<55fae6d6.2080...@nmr.mgh.harvard.edu>
Content-Type: text/plain; charset=windows-1252; format=flowed

did you recently upgrade or reinstall? Does anything else run since you
found this problem? Eg, mri_convert? When you created the .license file,
did you put a valid license key in it?

On 09/17/2015 12:09 PM, Lisa S. Pao wrote:
Hi everyone,

I?m having some issues using qdec. The program runs for about 30
seconds, and then quits with the following error message:

ERROR: FreeSurfer license file /Applications/freesurfer/.license not
found.
 If you are outside the NMR-Martinos Center,
 go to http://surfer.nmr.mgh.harvard.edu to
 get a valid license file (it's free).
 If you are inside the NMR-Martinos Center,
 make sure to source the standard environment.

I?ve been using Freesurfer for over a year now to run recons and use
freeview, so I?m not sure why the error is popping up now. I
definitely have a license, and have successfully used the program (but
not qdec) in the past.

I?ve tried the following fixes without any success:
-renaming the ?license.txt? file to ?license? (without the .txt
extension)
-using terminal to create a file called ?.license? (when I did this
and used ls -a to view all files, I noticed the file was actually
named ?.license.save?)

I?m running freesurfer-i386-apple-darwin11.4.2-stable5-20130514 on an
iMac, OS X Yosemite (10.10.3).

I?d greatly appreciate any suggestions for how to fix this issue.

Thanks!

Best,
Lisa

---
Lisa Pao, Ph.D.
Postdoctoral Research Fellow
Division of Child and Adolescent Psychiatry
Columbia University Medical Center
New York State Psychiatric Institute
646-774-5782





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--
Douglas N. Greve, Ph.D.
MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

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


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contains patient information, please contact the Partners Compliance HelpLine at
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dispose of the e-mail.

[Freesurfer] R: Re: R: Re: R: R: Re: Import mask from FSL to FS for performing seed-based FS-FAST functional connectivity

[stdp82]

Thanks,
the error occurred in the command line because I have used 
fcseed-config -segid 1 -seg MRS_MASK.mgz -fsd rest -mean -cfg 
mean.MRS_MASK.configfcseed-sess -sf sessid -cfg mean.MRS_MASK.config
and the correct form is MRS_MASK without mean.
fcseed-config -segid 1 -seg MRS_MASK.mgz -fsd rest -mean -cfg 
MRS_MASK.configfcseed-sess -sf sessid -cfg MRS_MASK.config

Stefano


Messaggio originale
Da: gr...@nmr.mgh.harvard.edu
Data: 21-set-2015 23.44
A: 
Ogg: Re: [Freesurfer] R: Re: R: R: Re: Import mask from FSL to FS for 
performing seed-based FS-FAST functional connectivity

Is there a file in that folder named something like "MRS_MASK"

On 09/19/2015 06:03 AM, std...@virgilio.it wrote:
> Hi listi,
>
> the following error now occur:
>
> --- matlab output 
>
>
>   < M A T L A B (R) >
>
> Copyright 1984-2014 The MathWorks, Inc.
>
> R2014a (8.3.0.532) 64-bit (maci64)
>
> February 11, 2014
>
>
> To get started, type one of these: helpwin, helpdesk, or demo.
>
> For product information, visit www.mathworks.com.
>
> Warning: Control Character '\%' is not valid. See 'doc sprintf' for 
> control
>
> characters valid in the format string.
>
> > In startup at 3
>
>   In matlabrc at 189
>
> >> >> >> >> >> >> >>
>
> sxa3pwd =
>
>
> /Applications/freesurfer/subjects/fMRI
>
>
> >>
>
> sxa3cmd =
>
>
> /Applications/freesurfer/fsfast/bin/selxavg3-sess -s Sess130 -a 
> fc.MRS_MASK.surf.lh
>
>
> >> /Applications/freesurfer/fsfast/toolbox/fast_selxavg3.m
>
> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >>
>
>
> #@# Sess130 ###
>
> /Applications/freesurfer/subjects/fMRI/Sess130
>
> -
>
> $Id: fast_selxavg3.m,v 1.100.2.2 2012/11/30 18:40:38 greve Exp $
>
> /Applications/freesurfer/fsfast/toolbox/fast_selxavg3.m
>
> /Applications/freesurfer/fsfast/toolbox/fast_ldanaflac.m
>
> /Applications/freesurfer/matlab/MRIread.m
>
> -
>
> outtop = /Applications/freesurfer/subjects/fMRI
>
> Extension format = nii.gz
>
> ERROR: cannot find volume matching 
> /Applications/freesurfer/subjects/fMRI/Sess130/rest/001/MRS_MASK
>
> ERROR: loading nonpar reg 
> /Applications/freesurfer/subjectsfMRI/Sess130/rest/001/MRS_MASK
>
> --
>
> ERROR: fast_selxavg3() failed\n
>
>
>
> Thanks
>
>
>
> Stefano
>
>
>
>
>
> My concern is whether this command line is correctfcseed-config -segid 1 -seg
> ROI_MASK. -fsd rest -mean -cfg mean.ROI_MASK.configfcseed-sess -s SessXXX -cfg
> mean.ROI_MASK.configThank youStefano
> Messaggio originale
> Da: gr...@nmr.mgh.harvard.edu
> Data: 20-lug-2015 19.17
> A: 
> Ogg: Re: [Freesurfer] R: R: Re: Import mask from FSL to FS for performing
> seed-based FS-FAST functional connectivity
>
>
>
> On 07/20/2015 02:10 AM, std...@virgilio.it wrote:
> > Hi list,
> >
> > in the previous mail you have suggested to run fcseed-config and
> > specify -seg ROI_MASK.mgz and -segid 1 (assuming my ROI_MASK is in
> > $SUBJECTS_DIR/subject/mri).
> > I have two question please.
> > A- my mask is on vmPFC, thus it include the both hemispheres. Should I
> > divide it in right and left? If yes, how can I do?
> You do not need to, just specify the appropriate index value. If they
> were divided between lh and rh and you wanted to merge them, you would
> just list the lh and rh indices.
> > B- I have difficulties to run the fcseed-conf command:
> what do you mean by "difficulties"?
>
> > fcseed-config -segid 1 -seg ROI_MASK. -fsd rest -mean -cfg
> > mean.ROI_MASK.config
> > fcseed-sess -s SessXXX -cfg mean.ROI_MASK.config
> > Is these command lines corrected?
> >
> > Thanks,
> >
> >
> > Stefano
> >
> > Messaggio originale
> > Da: std...@virgilio.it
> > Data: 13-lug-2015 10.16
> > A: 
> > Ogg: [Freesurfer] R: Re: Import mask from FSL to FS for performing
> > seed-based FS-FAST functional connectivity
> >
> > Hi list,
> >
> > When I use tkmedit the overlap between orig and ROI_MASK.nii.gz seem
> > to correspond. However, when I added the ROI_MASK.nii.gz, the orig is
> > vanished, and is remained the ROI_MASK in correct position (and in
> > white) and around all black. My concern is the correct binarization of
> > ROI_MASK which it seem correct when I use fslview.
> >
> > fslview orig.nii.gz ROI_MASK.nii.gz produce perfect outputs.
> >
> >
> >
> > After
> > mri_label2vol --seg $SUBJECTS_DIR/ROI_MASK.nii.gz --reg
> > $FUNCTIONAL_DATA/Sess102/rest/001/register.dof6.dat --temp
> > $FUNCTIONAL_DATA/Sess102/rest/001/template.nii.gz --fillthresh 0.5 --o
> > func.vmPFC_MASK.nii
> >
> > The func.vmPFC_MASK.nii (344MB) seem to be empty when I open it with
> > tkmedit and too big (a red bar which cover the whole) when I use fslview.
> > With MRIcron, is screen is irregularly divided in half in black and white.
> >
> > 

[Freesurfer] R: Re: R: Re: R: Re: R: R: Re: Import mask from FSL to FS for performing seed-based FS-FAST functional connectivity

[stdp82]

Yes, selxavg3-sess runs fine.


Stefano

Messaggio originale
Da: gr...@nmr.mgh.harvard.edu
Data: 22-set-2015 20.50
A: 
Ogg: Re: [Freesurfer] R: Re: R: Re: R: R: Re: Import mask from FSL to FS for 
performing seed-based FS-FAST functional connectivity

So it is working now?

On 09/22/2015 02:49 PM, std...@virgilio.it wrote:
> Thanks,
>
> the error occurred in the command line because I have used
>
> fcseed-config -segid 1 -seg MRS_MASK.mgz -fsd rest -mean -cfg 
> mean.MRS_MASK.config
> fcseed-sess -sf sessid -cfg mean.MRS_MASK.config
>
> and the correct form is MRS_MASK without mean.
>
> fcseed-config -segid 1 -seg MRS_MASK.mgz -fsd rest -mean -cfg 
> MRS_MASK.config
> fcseed-sess -sf sessid -cfg MRS_MASK.config
>
>
> Stefano
>
> Messaggio originale
> Da: gr...@nmr.mgh.harvard.edu
> Data: 21-set-2015 23.44
> A: 
> Ogg: Re: [Freesurfer] R: Re: R: R: Re: Import mask from FSL to FS for 
> performing seed-based FS-FAST functional connectivity
>
> Is there a file in that folder named something like "MRS_MASK"
>
> On 09/19/2015 06:03 AM, std...@virgilio.it wrote:
> > Hi listi,
> >
> > the following error now occur:
> >
> > --- matlab output 
> >
> >
> >   < M A T L A B (R) >
> >
> > Copyright 1984-2014 The MathWorks, Inc.
> >
> > R2014a (8.3.0.532) 64-bit (maci64)
> >
> > February 11, 2014
> >
> >
> > To get started, type one of these: helpwin, helpdesk, or demo.
> >
> > For product information, visit www.mathworks.com.
> >
> > Warning: Control Character '\%' is not valid. See 'doc sprintf' for
> > control
> >
> > characters valid in the format string.
> >
> > > In startup at 3
> >
> >   In matlabrc at 189
> >
> > >> >> >> >> >> >> >>
> >
> > sxa3pwd =
> >
> >
> > /Applications/freesurfer/subjects/fMRI
> >
> >
> > >>
> >
> > sxa3cmd =
> >
> >
> > /Applications/freesurfer/fsfast/bin/selxavg3-sess -s Sess130 -a
> > fc.MRS_MASK.surf.lh
> >
> >
> > >> /Applications/freesurfer/fsfast/toolbox/fast_selxavg3.m
> >
> > >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >>
> >
> >
> > #@# Sess130 ###
> >
> > /Applications/freesurfer/subjects/fMRI/Sess130
> >
> > -
> >
> > $Id: fast_selxavg3.m,v 1.100.2.2 2012/11/30 18:40:38 greve Exp $
> >
> > /Applications/freesurfer/fsfast/toolbox/fast_selxavg3.m
> >
> > /Applications/freesurfer/fsfast/toolbox/fast_ldanaflac.m
> >
> > /Applications/freesurfer/matlab/MRIread.m
> >
> > -
> >
> > outtop = /Applications/freesurfer/subjects/fMRI
> >
> > Extension format = nii.gz
> >
> > ERROR: cannot find volume matching
> > /Applications/freesurfer/subjects/fMRI/Sess130/rest/001/MRS_MASK
> >
> > ERROR: loading nonpar reg
> > /Applications/freesurfer/subjectsfMRI/Sess130/rest/001/MRS_MASK
> >
> > --
> >
> > ERROR: fast_selxavg3() failed\n
> >
> >
> >
> > Thanks
> >
> >
> >
> > Stefano
> >
> >
> >
> >
> >
> > My concern is whether this command line is correctfcseed-config 
> -segid 1 -seg
> > ROI_MASK. -fsd rest -mean -cfg mean.ROI_MASK.configfcseed-sess -s 
> SessXXX -cfg
> > mean.ROI_MASK.configThank youStefano
> > Messaggio originale
> > Da: gr...@nmr.mgh.harvard.edu
> > Data: 20-lug-2015 19.17
> > A: 
> > Ogg: Re: [Freesurfer] R: R: Re: Import mask from FSL to FS for 
> performing
> > seed-based FS-FAST functional connectivity
> >
> >
> >
> > On 07/20/2015 02:10 AM, std...@virgilio.it wrote:
> > > Hi list,
> > >
> > > in the previous mail you have suggested to run fcseed-config and
> > > specify -seg ROI_MASK.mgz and -segid 1 (assuming my ROI_MASK is in
> > > $SUBJECTS_DIR/subject/mri).
> > > I have two question please.
> > > A- my mask is on vmPFC, thus it include the both hemispheres. Should I
> > > divide it in right and left? If yes, how can I do?
> > You do not need to, just specify the appropriate index value. If they
> > were divided between lh and rh and you wanted to merge them, you would
> > just list the lh and rh indices.
> > > B- I have difficulties to run the fcseed-conf command:
> > what do you mean by "difficulties"?
> >
> > > fcseed-config -segid 1 -seg ROI_MASK. -fsd rest -mean -cfg
> > > mean.ROI_MASK.config
> > > fcseed-sess -s SessXXX -cfg mean.ROI_MASK.config
> > > Is these command lines corrected?
> > >
> > > Thanks,
> > >
> > >
> > > Stefano
> > >
> > > Messaggio originale
> > > Da: std...@virgilio.it
> > > Data: 13-lug-2015 10.16
> > > A: 
> > > Ogg: [Freesurfer] R: Re: Import mask from FSL to FS for performing
> > > seed-based FS-FAST functional connectivity
> > >
> > > Hi list,
> > >
> > > When I use tkmedit the overlap between orig and ROI_MASK.nii.gz seem
> > > to correspond. However, when I added the ROI_MASK.nii.gz, the orig is
> > > vanished, and is remained the ROI_MASK in correct 

Re: [Freesurfer] R: Re: R: Re: R: R: Re: Import mask from FSL to FS for performing seed-based FS-FAST functional connectivity

[Douglas N Greve]

So it is working now?

On 09/22/2015 02:49 PM, std...@virgilio.it wrote:
> Thanks,
>
> the error occurred in the command line because I have used
>
> fcseed-config -segid 1 -seg MRS_MASK.mgz -fsd rest -mean -cfg 
> mean.MRS_MASK.config
> fcseed-sess -sf sessid -cfg mean.MRS_MASK.config
>
> and the correct form is MRS_MASK without mean.
>
> fcseed-config -segid 1 -seg MRS_MASK.mgz -fsd rest -mean -cfg 
> MRS_MASK.config
> fcseed-sess -sf sessid -cfg MRS_MASK.config
>
>
> Stefano
>
> Messaggio originale
> Da: gr...@nmr.mgh.harvard.edu
> Data: 21-set-2015 23.44
> A: 
> Ogg: Re: [Freesurfer] R: Re: R: R: Re: Import mask from FSL to FS for 
> performing seed-based FS-FAST functional connectivity
>
> Is there a file in that folder named something like "MRS_MASK"
>
> On 09/19/2015 06:03 AM, std...@virgilio.it wrote:
> > Hi listi,
> >
> > the following error now occur:
> >
> > --- matlab output 
> >
> >
> >   < M A T L A B (R) >
> >
> > Copyright 1984-2014 The MathWorks, Inc.
> >
> > R2014a (8.3.0.532) 64-bit (maci64)
> >
> > February 11, 2014
> >
> >
> > To get started, type one of these: helpwin, helpdesk, or demo.
> >
> > For product information, visit www.mathworks.com.
> >
> > Warning: Control Character '\%' is not valid. See 'doc sprintf' for
> > control
> >
> > characters valid in the format string.
> >
> > > In startup at 3
> >
> >   In matlabrc at 189
> >
> > >> >> >> >> >> >> >>
> >
> > sxa3pwd =
> >
> >
> > /Applications/freesurfer/subjects/fMRI
> >
> >
> > >>
> >
> > sxa3cmd =
> >
> >
> > /Applications/freesurfer/fsfast/bin/selxavg3-sess -s Sess130 -a
> > fc.MRS_MASK.surf.lh
> >
> >
> > >> /Applications/freesurfer/fsfast/toolbox/fast_selxavg3.m
> >
> > >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >>
> >
> >
> > #@# Sess130 ###
> >
> > /Applications/freesurfer/subjects/fMRI/Sess130
> >
> > -
> >
> > $Id: fast_selxavg3.m,v 1.100.2.2 2012/11/30 18:40:38 greve Exp $
> >
> > /Applications/freesurfer/fsfast/toolbox/fast_selxavg3.m
> >
> > /Applications/freesurfer/fsfast/toolbox/fast_ldanaflac.m
> >
> > /Applications/freesurfer/matlab/MRIread.m
> >
> > -
> >
> > outtop = /Applications/freesurfer/subjects/fMRI
> >
> > Extension format = nii.gz
> >
> > ERROR: cannot find volume matching
> > /Applications/freesurfer/subjects/fMRI/Sess130/rest/001/MRS_MASK
> >
> > ERROR: loading nonpar reg
> > /Applications/freesurfer/subjectsfMRI/Sess130/rest/001/MRS_MASK
> >
> > --
> >
> > ERROR: fast_selxavg3() failed\n
> >
> >
> >
> > Thanks
> >
> >
> >
> > Stefano
> >
> >
> >
> >
> >
> > My concern is whether this command line is correctfcseed-config 
> -segid 1 -seg
> > ROI_MASK. -fsd rest -mean -cfg mean.ROI_MASK.configfcseed-sess -s 
> SessXXX -cfg
> > mean.ROI_MASK.configThank youStefano
> > Messaggio originale
> > Da: gr...@nmr.mgh.harvard.edu
> > Data: 20-lug-2015 19.17
> > A: 
> > Ogg: Re: [Freesurfer] R: R: Re: Import mask from FSL to FS for 
> performing
> > seed-based FS-FAST functional connectivity
> >
> >
> >
> > On 07/20/2015 02:10 AM, std...@virgilio.it wrote:
> > > Hi list,
> > >
> > > in the previous mail you have suggested to run fcseed-config and
> > > specify -seg ROI_MASK.mgz and -segid 1 (assuming my ROI_MASK is in
> > > $SUBJECTS_DIR/subject/mri).
> > > I have two question please.
> > > A- my mask is on vmPFC, thus it include the both hemispheres. Should I
> > > divide it in right and left? If yes, how can I do?
> > You do not need to, just specify the appropriate index value. If they
> > were divided between lh and rh and you wanted to merge them, you would
> > just list the lh and rh indices.
> > > B- I have difficulties to run the fcseed-conf command:
> > what do you mean by "difficulties"?
> >
> > > fcseed-config -segid 1 -seg ROI_MASK. -fsd rest -mean -cfg
> > > mean.ROI_MASK.config
> > > fcseed-sess -s SessXXX -cfg mean.ROI_MASK.config
> > > Is these command lines corrected?
> > >
> > > Thanks,
> > >
> > >
> > > Stefano
> > >
> > > Messaggio originale
> > > Da: std...@virgilio.it
> > > Data: 13-lug-2015 10.16
> > > A: 
> > > Ogg: [Freesurfer] R: Re: Import mask from FSL to FS for performing
> > > seed-based FS-FAST functional connectivity
> > >
> > > Hi list,
> > >
> > > When I use tkmedit the overlap between orig and ROI_MASK.nii.gz seem
> > > to correspond. However, when I added the ROI_MASK.nii.gz, the orig is
> > > vanished, and is remained the ROI_MASK in correct position (and in
> > > white) and around all black. My concern is the correct binarization of
> > > ROI_MASK which it seem correct when I use fslview.
> > >
> > > fslview orig.nii.gz ROI_MASK.nii.gz produce perfect outputs.
> > >
> > >
> > >
> > > After
> > > mri_label2vol --seg 

[Freesurfer] Longitudinal Two Stage Model using mri_glmfit

[Bronwyn Overs]

Dear freesurfer mailing list,

Is it possible to run a longitudinal two stage model from the command 
line using mri_glmift, instead of using the qdec gui? If so, what --y 
would you pass to use the preprocessed spc values?

--

Kind regards,

Bronwyn Overs
Research Assistant

Neuroscience Research Australia

Neuroscience Research Australia
Margarete Ainsworth Building
Barker Street Randwick Sydney NSW 2031 Australia
*M* 0411 308 769 *T* +61 2 9399 1883

neura.edu.au 

Follow @neuraustralia on twitter 
Follow NeuRA on facebook 
Subscribe to the 
NeuRA Magazine 


___
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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.

Re: [Freesurfer] Longitudinal Two Stage Model using mri_glmfit

[Bronwyn Overs]

Hi Douglas,

Sorry I don't know what you mean by the different mri_glmfit levels? 
Also how do you use two fsgd files simultaneously (I assume one file for 
time 1 and the other for time 2)?


Kind regards,

Bronwyn Overs
Research Assistant

Neuroscience Research Australia

Neuroscience Research Australia
Margarete Ainsworth Building
Barker Street Randwick Sydney NSW 2031 Australia
*M* 0411 308 769 *T* +61 2 9399 1883

neura.edu.au 

Follow @neuraustralia on twitter 
Follow NeuRA on facebook 
Subscribe to the 
NeuRA Magazine 


On 23/09/2015 12:16 am, Douglas Greve wrote:
If you intend to compute a slope for each subject (first level 
mri_glmfit),  then input the slopes to the 2nd level to test for 
effects of interest. Is this what you mean? It is probably possible to 
do this with a single FSGD file and single command line, but it is 
much easier to set up and understand if you use two.

doug


On 9/22/15 3:13 AM, Bronwyn Overs wrote:

Dear freesurfer mailing list,

Is it possible to run a longitudinal two stage model from the command 
line using mri_glmift, instead of using the qdec gui? If so, what --y 
would you pass to use the preprocessed spc values?

--

Kind regards,

Bronwyn Overs
Research Assistant

Neuroscience Research Australia

Neuroscience Research Australia
Margarete Ainsworth Building
Barker Street Randwick Sydney NSW 2031 Australia
*M* 0411 308 769 *T* +61 2 9399 1883

neura.edu.au 

Follow @neuraustralia on twitter 
Follow NeuRA on facebook 
Subscribe to 
the NeuRA Magazine 




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Re: [Freesurfer] Question about the multiple comparison correction in FreeSurfer {Disarmed}

[pablo najt]

Thank you!

Date: Mon, 21 Sep 2015 23:43:39 -0400
From: gr...@nmr.mgh.harvard.edu
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] Question about the multiple comparison correction in 
FreeSurfer


  

  
  




On 9/21/15 9:15 PM, chenhf_uestc wrote:



  
  
  
  
  Hi, Douglas
   
  Thanks for your reply. I have two further questions here.
First, I know that
--grf is gaussian random fields for the volume (not surface). Could
the Monte Carlo simulation such as "--cache 4 neg" be used for
correction on volume? Because the manual introduces this method
for the correction on surface, and thus I do not whether this
method could be used on volume.

Yes, I think that should work. If you are going to run simulations
on the surface, see
https://surfer.nmr.mgh.harvard.edu/fswiki/BuildYourOwnMonteCarlo


   
  Second, in the Monte Carlo simulation on surface 
"--cache 4 neg", I can specify the sign (neg for negative, pos,
or abs). However, in the grf correction, there are "--grf 3 pos or neg 
".  Could I
specify the sign "abs" such as "--grf
3 abs".

No, sorry


   
  Best,
  Feng
  

  
  
发件人：Douglas N Greve
  
发送时间：2015-09-22 05:35
主题：Re: [Freesurfer] Question about the
  multiple comparison correction in FreeSurfer
收件人："freesurfer"
抄送：
 

  --grf is gaussian random fields for the volume (not surface). 
   
  Re: --2spaces, your understanding is correct. 
   
  FDR: you can do it in matlab, something like 
 sig = MRIread('sig.mgh'); 
 p = 10.^-abs(sig.vol) 
 pthresh = fast_fdrthresh(p,fdr); 
 ind = find(p < pthresh); 
 sig.vol(ind) = 0; 
 MRIwrite(sig,'sig.fdr.mgh') 
   
  It is also possible with mri_surfcluster 
   
   
   
  On 09/20/2015 12:47 PM, chenhf_uestc wrote: 
  > Dear Freesurfer experts, 
  > I have some questions about the multiple comparison correction 
method  
  > for group analysis in Freesurfer. The manual stated that we could 
use  
  > the commands as follows: 
  > mri_glmfit-sim \ 
  >--glmdir lh.gender_age.glmdir \ 
  >--cache 4 neg \ 
  >--cwp  0.05\ 
  >--2spaces 
  > This is the alphasim correction, right?  When I write this command 
in  
  > terminal, there are detailed explanations about this command. In 
the  
  > above-mentioned command, I used parameter "--cache threshold sign". 
In  
  > this way, a precomputed Z Monte Carlo simulation (--cache) was 
used.  
  > Also, I can run my own simulation by using "--sim mc-z  
  > iterations threshold". 
  > However, I find an interesting parameter "--grf threshold sign". I  
  > would like to know whether this parameter could give me another  
  > correction method rather than alphasim, i.e. the gaussian random 
field  
  > correction method?  In other words, if I add the parameter "grf", 
then  
  > the mri_glmfit-sim performs the GRF correction; if I do not add 
this  
  > parameter, then mri_glmfit-sim performs alphasim correction, right? 
  > Another question is about the parameter "--2spaces: adjust p-values 
 
  > for two hemispheres", I give an example here. I want to perform  
  > cluster-level correction of *p<0.05* based on vertex-wise thershold 
of  
  > 4 (p < .0001) for the left hemisphere; and perform the same 
correction  
  > for the right hemisphere. So, I should add the parameter 
"--2spaces".  
  > Is this equal to perform cluster-level correction of *p<0.025 
(0.05/2,  
  > if I also want to examine the subcortical diferences, then the 
cluster  
  > p value should be 0.05/3)* based on vertex-wise thershold of 4 (p < 
 
  > .0001). Have I understood correctly? 
  > The third question is that could I perform False discovery rate 
(FDR)  
  > using commands rather than GUI? If not, could I load the sig.mgh 
file  
  > into MatLab and then perform FDR correction manually? 
  > In addition to the aforementioned multiple comparison correction  
  > method, is there other correction method in Freesurfer? 
  > Best, 
  > Feng 
  > 
  > 
  > ___ 
  > Freesurfer mailing list 
  > Freesurfer@nmr.mgh.harvard.edu 
  > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer 
   
  --  
  Douglas N. Greve, 

Re: [Freesurfer] Qdec: group differences covaring for age and sex {Disarmed}

[pablo najt]

Hello Douglas,
If I understand your comment about defining all discrete variables as classes 
(e.g. PT_F, PT_M, HC_F, HC_M) *only applies* to glm command line stream not 
qdec. If I am using qdec I can have discrete variables defined separately (e.g. 
Sex, Diagnosis) specified in the qdec.table text file as I am not required to 
specify classes as in the FS descriptor file.  I am following here the 
instructions as shown below. Do I understand correct?
Thanks,
Pablo

qdec.table example from FSpage
  


> To: freesurfer@nmr.mgh.harvard.edu
> From: gr...@nmr.mgh.harvard.edu
> Date: Mon, 21 Sep 2015 17:39:14 -0400
> Subject: Re: [Freesurfer] Qdec: group differences covaring for age and sex
> 
> Yes, it is addressing that question. The contrast should be the same as 
> your Group Diff below. Although I'm not sure you're using the proper 
> design. It looks like you are using Sex as a continuous covariate? That 
> is not correct. It should be discrete. So you should have 4 classes 
> (HC-M, HC-F, PT-M, PT-F)
> 
> On 09/21/2015 09:31 AM, pablo najt wrote:
> > Hello FS experts,
> > I would like to understand the results from qdec in a GLM model with 
> > Group (PT/HC), and two covariates (Age, gender).
> > I set up my contrast as follow:
> >
> > Group Diff
> > HC  PT  AgeHC  AgePT  SexHC SexPT
> >  1 -10   0  0   0
> >
> > Group x Age effect
> > HC  PT  AgeHC  AgePT  SexHC SexPT
> >  0  0 1  -1 00
> >
> > Group X Sex effect
> > HC  PT  AgeHC  AgePT  SexHC SexPT
> >  0  0 0   0  1   -1
> > Continues just as indicated in the "2 Groups 2 Covariates example"
> >
> > What I would like to find out: /If there are group differences while 
> > controlling for age and sex/.
> >
> > In Qdec I selected Group, Gender, and Age. (Age as normal variable, 
> > not as nuisance)
> > However, when I open my results with Qdec I am not quite sure it is 
> > answering my question.
> >
> > From all the questions listed I thought that the following was 
> > addressing what I need, but would like to clarify.
> > "/Does the thickness, --Age correlation, accounting for Gender, differ 
> > between HC and PT?"/
> > Would you mind confirming this for me?
> > Thanks!!
> > Pablo
> >
> >
> > ___
> > Freesurfer mailing list
> > Freesurfer@nmr.mgh.harvard.edu
> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> 
> -- 
> Douglas N. Greve, Ph.D.
> MGH-NMR Center
> gr...@nmr.mgh.harvard.edu
> Phone Number: 617-724-2358
> Fax: 617-726-7422
> 
> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
> www.nmr.mgh.harvard.edu/facility/filedrop/index.html
> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
> 
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> 
> 
> The information in this e-mail is intended only for the person to whom it is
> addressed. If you believe this e-mail was sent to you in error and the e-mail
> contains patient information, please contact the Partners Compliance HelpLine 
> at
> http://www.partners.org/complianceline . If the e-mail was sent to you in 
> error
> but does not contain patient information, please contact the sender and 
> properly
> dispose of the e-mail.
> 
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Re: [Freesurfer] corrupt download, 6.0 beta

[Z K]

Is this still an issue for you? Because I just ran a test and was able 
to download to completion.

-Zeke

On 09/21/2015 06:03 PM, Chuck Theobald wrote:
> I've tried downloading the 6.0 beta from
> ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/6.0.0-beta/freesurfer-Linux-centos6_x86_64-stable-v6-beta-20150724.tar.gz
> but it keeps arriving corrupt. Any suggestions on how to proceed?
>
> Thank you,
>
> --
> Chuck Theobald
> System Administrator
> The Robert and Beverly Lewis Center for Neuroimaging
> University of Oregon
> P: 541-346-0343
> F: 541-346-0345
>
>
>
> ___
> 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
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Re: [Freesurfer] Qdec: group differences covaring for age and sex {Disarmed}

[Douglas Greve]

Yes, that is fine as long as they are listed as discrete variables (as 
is the case below).

doug

On 9/22/15 7:59 AM, pablo najt wrote:

Hello Douglas,
If I understand your comment about defining all discrete variables as 
classes (e.g. PT_F, PT_M, HC_F, HC_M) *only applies* to glm command 
line stream not qdec. If I am using qdec I can have discrete variables 
defined separately (e.g. Sex, Diagnosis) specified in the qdec.table 
text file as I am not required to specify classes as in the FS 
descriptor file.  I am following here the instructions as shown below. 
Do I understand correct?

Thanks,
Pablo

qdec.table example from FSpage



> To: freesurfer@nmr.mgh.harvard.edu
> From: gr...@nmr.mgh.harvard.edu
> Date: Mon, 21 Sep 2015 17:39:14 -0400
> Subject: Re: [Freesurfer] Qdec: group differences covaring for age 
and sex

>
> Yes, it is addressing that question. The contrast should be the same as
> your Group Diff below. Although I'm not sure you're using the proper
> design. It looks like you are using Sex as a continuous covariate? That
> is not correct. It should be discrete. So you should have 4 classes
> (HC-M, HC-F, PT-M, PT-F)
>
> On 09/21/2015 09:31 AM, pablo najt wrote:
> > Hello FS experts,
> > I would like to understand the results from qdec in a GLM model with
> > Group (PT/HC), and two covariates (Age, gender).
> > I set up my contrast as follow:
> >
> > Group Diff
> > HC PT AgeHC AgePT SexHC SexPT
> > 1 -1 0 0 0 0
> >
> > Group x Age effect
> > HC PT AgeHC AgePT SexHC SexPT
> > 0 0 1 -1 0 0
> >
> > Group X Sex effect
> > HC PT AgeHC AgePT SexHC SexPT
> > 0 0 0 0 1 -1
> > Continues just as indicated in the "2 Groups 2 Covariates example"
> >
> > What I would like to find out: /If there are group differences while
> > controlling for age and sex/.
> >
> > In Qdec I selected Group, Gender, and Age. (Age as normal variable,
> > not as nuisance)
> > However, when I open my results with Qdec I am not quite sure it is
> > answering my question.
> >
> > From all the questions listed I thought that the following was
> > addressing what I need, but would like to clarify.
> > "/Does the thickness, --Age correlation, accounting for Gender, 
differ

> > between HC and PT?"/
> > Would you mind confirming this for me?
> > Thanks!!
> > Pablo
> >
> >
> > ___
> > Freesurfer mailing list
> > Freesurfer@nmr.mgh.harvard.edu
> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
> --
> Douglas N. Greve, Ph.D.
> MGH-NMR Center
> gr...@nmr.mgh.harvard.edu
> Phone Number: 617-724-2358
> Fax: 617-726-7422
>
> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
> www.nmr.mgh.harvard.edu/facility/filedrop/index.html
> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
> The information in this e-mail is intended only for the person to 
whom it is
> addressed. If you believe this e-mail was sent to you in error and 
the e-mail
> contains patient information, please contact the Partners Compliance 
HelpLine at
> http://www.partners.org/complianceline . If the e-mail was sent to 
you in error
> but does not contain patient information, please contact the sender 
and properly

> dispose of the e-mail.
>


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Re: [Freesurfer] Non-matching ROI areal measures using mri_segstats and mris_anatomical_stats (2nd post)

[Douglas Greve]

Sorry, I thought I had answered this (or something like it) recently. 
When transforming area (or volume) with mri_surf2surf you have to turn 
on jacobian correction with --jac. Try that and see if the results are 
similar
doug


On 9/22/15 8:58 AM, julienbesle wrote:
> I am reposting this message, as I didn't get any answer so far:
> -
>
> Dear Freesurfer experts
>
> I have run a group ROI analysis comparing cortical thickness and area
> between two groups of subject. I did this in two different ways: (1)
> using mri_segstats after transforming each subject's data to fsaverage
> space, AND (2) using mris_anatomical_stats after transforming the ROI
> from fsaverage space to the space of each subjects. I get very similar
> results for cortical thickness, but completely different results for
> area. Does anyone have any idea why that could be happening ?
>
> Details:
>
> I have an ROI that I obtained from an atlas in MNI space and projected
> to the fsaverage surface (into say ROI_lh.mgh file). The aim of the ROI
> analysis was to find whether there are differences in cortical thickness
> and area between two groups of subjects in this ROI.
>
> I tested this in two ways:
>
> Method 1:
> a) I transformed the cortical thickness and area data of each subject
> into fsaverage space
>
> mri_surf2surf --s subj --trgsubject fsaverage --hemi lh --sval area
> --tval subj_area_fsaverage.mgh
>
> mri_surf2surf --s subj --trgsubject fsaverage --hemi lh --sval thickness
> --tval subj_thickness_fsaverage.mgh
>
> b) I averaged the thickness or area data within the ROI in fsaverage
> space for each subject using mri _segstats
>
> mri_segstats --seg ROI_lh.mgh --in subj_area_fsaverage.mgh --sum
> output_area_subj.stats
>
> mri_segstats --seg ROI_lh.mgh --in subj_area_fsaverage.mgh --sum
> output_thickness_subj.stats
>
> c) I used a 2-sample T test to compare the area or thickness output
> between my two groups of subjects.
>
>
> Method 2:
> a) I transformed ROI.mgh into a label file ROI.label
>
> mri_cor2label --i ROI_lh.mgh --id 1 --l ROI_lh.label --surf fsaverage lh
>
> b) I transformed the label file from fsaverage space to each subject's space
>
> mri_label2label --srcsubject fsaverage --srclabel ROI_lh.label
> --trgsubject subj --trglabel ROI_lh_subj.label --hemi lh --regmethod surface
>
> c) I averaged the thickness and area data within the ROI in each
> subject's space using mris_anatomicalstats
>
> mris_anatomical_stats -l ROI_lh_subj.label -f output_subj.stats subj lh
>
> d) I used a 2 sample T test to compare the area or thickness data (from
> the output_subj.stats files) between my two groups of subjects.
>
>
> For cortical thickness, i obtain very similar results (not identical,
> but similar to a hundredth of a mm), but for area, I get completely
> different results, sometimes opposite direction of effect between the
> two groups. I have 10 ROIs, and across ROIs, group differences are much
> more significant in the first than the second method. The areal results
> are in different units, which is expected (in the first method, they are
> in mm2/vertex and in the second they are in mm2 because they express the
> total area of the ROI). But despite that, shouldn't I get similar
> patterns of results ? I would have assumed that the vertexwise areal
> values averaged in the first method should somehow reflect differences
> in area betwen subjects and therefore should give similar result to the
> total area approach (2nd method). Or is it that, in the first method,
> mri_surf2surf interpolates the vertexwise areal values without taking
> into account the stretching/deformation from the subject's space to
> fsaverage space (in contrast with a vertexwise analysis using
> mris_preproc) ?
>
> This is suggested by the fact that when I divide the total ROI area data
> obtained in the second method by the number of vertices in the ROI (in
> each subject's space), I end up with results that are very similar to
> the first method. The absolute values are different (around 0.7
> mm2/vertex in the first method and around 0.6 mm2/vertex for the second
> method), but the group effects are in the same direction (across the 10
> ROIs, all the effect sizes and p-values are similar so it can't be a
> coincidence). This suggests that the vertexwise areal values obtained in
> both methods simply reflect the ROI-average vertexwise areal values of
> each subject's mesh (and therefore do not include potential areal
> differences between subjects, assuming similar vertex spacing betwen
> subjects, and so shouldn't be used to compare areas between groups).
> However, if this is correct, isn't it strange that I should find
> significant differences in these vertexwise areal values between groups?
>
>
> So I guess I have three main questions:
>
> 1) Why is there a difference between the 2 methods for area but not
> thickness ?
>
> 2) What is the 'correct' 

Re: [Freesurfer] Longitudinal Two Stage Model using mri_glmfit

[Martin Reuter]

Hi Bronwyn,

yes that is possible, you would pass the SPC values stack as y. See

https://surfer.nmr.mgh.harvard.edu/fswiki/LongitudinalTwoStageModel

for an example (that one uses percent change with respect to baseline, 
pc1, but you can do the same with symmetrized percent change (spc)).


Best, Martin

On 09/22/2015 03:13 AM, Bronwyn Overs wrote:

Dear freesurfer mailing list,

Is it possible to run a longitudinal two stage model from the command 
line using mri_glmift, instead of using the qdec gui? If so, what --y 
would you pass to use the preprocessed spc values?

--

Kind regards,

Bronwyn Overs
Research Assistant

Neuroscience Research Australia

Neuroscience Research Australia
Margarete Ainsworth Building
Barker Street Randwick Sydney NSW 2031 Australia
*M* 0411 308 769 *T* +61 2 9399 1883

neura.edu.au 

Follow @neuraustralia on twitter 
Follow NeuRA on facebook 
Subscribe to 
the NeuRA Magazine 




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

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[Freesurfer] Non-matching ROI areal measures using mri_segstats and mris_anatomical_stats (2nd post)

[julienbesle]

I am reposting this message, as I didn't get any answer so far:
-

Dear Freesurfer experts

I have run a group ROI analysis comparing cortical thickness and area 
between two groups of subject. I did this in two different ways: (1) 
using mri_segstats after transforming each subject's data to fsaverage 
space, AND (2) using mris_anatomical_stats after transforming the ROI 
from fsaverage space to the space of each subjects. I get very similar 
results for cortical thickness, but completely different results for 
area. Does anyone have any idea why that could be happening ?

Details:

I have an ROI that I obtained from an atlas in MNI space and projected 
to the fsaverage surface (into say ROI_lh.mgh file). The aim of the ROI 
analysis was to find whether there are differences in cortical thickness 
and area between two groups of subjects in this ROI.

I tested this in two ways:

Method 1:
a) I transformed the cortical thickness and area data of each subject 
into fsaverage space

mri_surf2surf --s subj --trgsubject fsaverage --hemi lh --sval area 
--tval subj_area_fsaverage.mgh

mri_surf2surf --s subj --trgsubject fsaverage --hemi lh --sval thickness 
--tval subj_thickness_fsaverage.mgh

b) I averaged the thickness or area data within the ROI in fsaverage 
space for each subject using mri _segstats

mri_segstats --seg ROI_lh.mgh --in subj_area_fsaverage.mgh --sum 
output_area_subj.stats

mri_segstats --seg ROI_lh.mgh --in subj_area_fsaverage.mgh --sum 
output_thickness_subj.stats

c) I used a 2-sample T test to compare the area or thickness output 
between my two groups of subjects.


Method 2:
a) I transformed ROI.mgh into a label file ROI.label

mri_cor2label --i ROI_lh.mgh --id 1 --l ROI_lh.label --surf fsaverage lh

b) I transformed the label file from fsaverage space to each subject's space

mri_label2label --srcsubject fsaverage --srclabel ROI_lh.label 
--trgsubject subj --trglabel ROI_lh_subj.label --hemi lh --regmethod surface

c) I averaged the thickness and area data within the ROI in each 
subject's space using mris_anatomicalstats

mris_anatomical_stats -l ROI_lh_subj.label -f output_subj.stats subj lh

d) I used a 2 sample T test to compare the area or thickness data (from 
the output_subj.stats files) between my two groups of subjects.


For cortical thickness, i obtain very similar results (not identical, 
but similar to a hundredth of a mm), but for area, I get completely 
different results, sometimes opposite direction of effect between the 
two groups. I have 10 ROIs, and across ROIs, group differences are much 
more significant in the first than the second method. The areal results 
are in different units, which is expected (in the first method, they are 
in mm2/vertex and in the second they are in mm2 because they express the 
total area of the ROI). But despite that, shouldn't I get similar 
patterns of results ? I would have assumed that the vertexwise areal 
values averaged in the first method should somehow reflect differences 
in area betwen subjects and therefore should give similar result to the 
total area approach (2nd method). Or is it that, in the first method, 
mri_surf2surf interpolates the vertexwise areal values without taking 
into account the stretching/deformation from the subject's space to 
fsaverage space (in contrast with a vertexwise analysis using 
mris_preproc) ?

This is suggested by the fact that when I divide the total ROI area data 
obtained in the second method by the number of vertices in the ROI (in 
each subject's space), I end up with results that are very similar to 
the first method. The absolute values are different (around 0.7 
mm2/vertex in the first method and around 0.6 mm2/vertex for the second 
method), but the group effects are in the same direction (across the 10 
ROIs, all the effect sizes and p-values are similar so it can't be a 
coincidence). This suggests that the vertexwise areal values obtained in 
both methods simply reflect the ROI-average vertexwise areal values of 
each subject's mesh (and therefore do not include potential areal 
differences between subjects, assuming similar vertex spacing betwen 
subjects, and so shouldn't be used to compare areas between groups). 
However, if this is correct, isn't it strange that I should find 
significant differences in these vertexwise areal values between groups?


So I guess I have three main questions:

1) Why is there a difference between the 2 methods for area but not 
thickness ?

2) What is the 'correct' method for area (if any) ? Or is there a better 
method for an ROI analysis of area?

3) Why are there even significant differences between vertexwise area 
values in the first and second method ?


I am using Freesurfer v 5.3.0 (although the first analysis was 
potentially run using 5.0.0, not sure!)

Thanks in advance

Julien



-- 
-
Julien Besle
Senior 

Re: [Freesurfer] Longitudinal Two Stage Model using mri_glmfit

[Douglas Greve]

If you intend to compute a slope for each subject (first level 
mri_glmfit),  then input the slopes to the 2nd level to test for effects 
of interest. Is this what you mean? It is probably possible to do this 
with a single FSGD file and single command line, but it is much easier 
to set up and understand if you use two.

doug


On 9/22/15 3:13 AM, Bronwyn Overs wrote:

Dear freesurfer mailing list,

Is it possible to run a longitudinal two stage model from the command 
line using mri_glmift, instead of using the qdec gui? If so, what --y 
would you pass to use the preprocessed spc values?

--

Kind regards,

Bronwyn Overs
Research Assistant

Neuroscience Research Australia

Neuroscience Research Australia
Margarete Ainsworth Building
Barker Street Randwick Sydney NSW 2031 Australia
*M* 0411 308 769 *T* +61 2 9399 1883

neura.edu.au 

Follow @neuraustralia on twitter 
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the NeuRA Magazine 




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[Freesurfer] GRF correction in mri_glmfit-sim

[Meiling Li]

Dear FS experts
I do GRF correction using mri_glmfit-sim --grf in volume. I find --grf pos and 
--grf neg, but not --grf abs. 
My first question is, is the --grf just used for ONE-side correction? For 
instance,  we can test, are the FCs of patients larger than that of healthy 
controls or smaller than the healthy controls? If I want to test the difference 
of FCs between patients and healthy controls, how do i do that? Please help me 
to check the following commands i used to do the TWO-sides correction (for 
example. voxel-wise p: 0.05, cluster-wise p: 0.05):
  mri_glmfit-sim --glmdir g2v0 --grf 1.3 pos --cwp .05
  mri_glmfit-sim --glmdir g2v0 --grf 1.3 neg --cwp .05
Then  i use the following commands to combine the 'pos' and 'neg' results 
together
mri_convert grf.th1.3.neg.sig.cluster.mgh grf.th1.3.neg.sig.cluster.nii.gz
mri_convert grf.th1.3.pos.sig.cluster.mgh grf.th1.3.pos.sig.cluster.nii.gz
fslmaths grf.th1.3.pos.sig.cluster.nii.gz -add grf.th1.3.neg.sig.cluster.nii.gz 
grf.th1.3.sig.cluster.nii.gz 
Finally, i think the result  grf.th1.3.sig.cluster.nii.gz is what i want, which 
is the difference between patients and healthy controls with GRF corrected, 
with vertex-wise p< 0.05 and cluster-wise p<0.05. Is it right?


2. The other question is, If i  do the two-sides GRF correction(vertex-wise 
p<0.05 and cluster-wise p<0.05) with 'pos' or 'neg', should the vertex-wise or 
cluster-wise be 0.05/2 and 0.05/2? or 0.05 and 0.05?
for example, we should write like this
  mri_glmfit-sim --glmdir g2v0 --grf -log10(0.05/2) pos --cwp 0.05/2
  mri_glmfit-sim --glmdir g2v0 --grf -log10(0.05/2) neg --cwp 0.05/2


3. If i want to do cluster-based FDR correction, is there any FS command to do 
it? is it right if i load the statistic p map into MATLAB and do the FDR 
correction, then i use 'mri_volcluster --minsizevox'  to threshold it to remove 
voxels smaller than the cluster size i set. 


Thank you very much for any help!


All the best,
Meiling








 







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