Re: [Freesurfer] Freesurfer Dev 6.0 Hippocampal Segmentation

[Eugenio Iglesias]

Hi Aarthi,
first of all, sorry for the late reply; you caught me on vacation.
Would you mind trying the following: please unset your DYLD_LIBRARY_PATH 
environment variable, and the run the hippocampal subfield module. You can do 
that as follows:

In bash:
unset DYLD_LIBRARY_PATH

In (t)csh:
unsetenv DYLD_LIBRARY_PATH

Let us know if this helps

Cheers,

Eugenio


Juan Eugenio Iglesias
Postdoctoral researcher BCBL
www.jeiglesias.com
www.bcbl.eu

Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer

- Original Message -
From: "Aarthi Padmanabhan" 
To: "Freesurfer support list" 
Sent: Saturday, September 19, 2015 9:32:55 AM
Subject: Re: [Freesurfer] Freesurfer Dev 6.0 Hippocampal Segmentation

Hi, I had posted this earlier and am still having issues. 




Thank you, 










I tried running the Hippocampal Segmentation using the Dev version, I get the 
following error (running on a mac os x Yosemite): 

I just downloaded the dev version a couple of days ago. Recon-all -all runs 
fine, but it's unable to run the hippocampals segmentation component. 






recon-all -s 15-03-07.1_3T2 -hippocampal-subfields-T1 




Subject Stamp: freesurfer-Darwin-OSX-dev-20150826 

Current Stamp: freesurfer-Darwin-OSX-dev-20150826 

INFO: SUBJECTS_DIR is /Applications/freesurfer/subjects 

Actual FREESURFER_HOME /Applications/freesurfer 

-rw-rw-r-- 1 lab wheel 605436 Sep 11 11:56 
/Applications/freesurfer/subjects/15-03-07.1_3T2/scripts/recon-all.log 

Darwin DN2m1id7p.SUNet 14.5.0 Darwin Kernel Version 14.5.0: Wed Jul 29 02:26:53 
PDT 2015; root:xnu-2782.40.9~1/RELEASE_X86_64 x86_64 

# 

#@# Hippocampal Subfields processing (T1 only) left Fri Sep 11 11:57:14 PDT 
2015 

\n /Applications/freesurfer/bin/segmentSF_T1.sh /Applications/freesurfer/MCRv80 
/Applications/freesurfer 15-03-07.1_3T2 /Applications/freesurfer/subjects left 
\n 

See log file: 
/Applications/freesurfer/subjects/15-03-07.1_3T2/scripts/hippocampal-subfields-T1.log
 

-- 

Setting up environment variables 

--- 

DYLD_LIBRARY_PATH is 
.:/Applications/freesurfer/MCRv80/runtime/maci64:/Applications/freesurfer/MCRv80/bin/maci64:/Applications/freesurfer/MCRv80/sys/os/maci64:/Applications/freesurfer/lib/gcc/lib:/Applications/freesurfer/lib/gcc/lib
 

dyld: Library not loaded: @rpath/libmwi18n.dylib 

Referenced from: 
/Applications/freesurfer/bin/segmentSubjectT1_autoEstimateAlveusML.app/Contents/MacOS/segmentSubjectT1_autoEstimateAlveusML
 

Reason: image not found 

/Applications/freesurfer/bin/run_segmentSubjectT1_autoEstimateAlveusML.sh: line 
40: 6182 Trace/BPT trap: 5 
"${exe_dir}"/segmentSubjectT1_autoEstimateAlveusML.app/Contents/MacOS/segmentSubjectT1_autoEstimateAlveusML
 $args 

# 

#@# Hippocampal Subfields processing (T1 only) right Fri Sep 11 11:57:15 PDT 
2015 

\n /Applications/freesurfer/bin/segmentSF_T1.sh /Applications/freesurfer/MCRv80 
/Applications/freesurfer 15-03-07.1_3T2 /Applications/freesurfer/subjects right 
\n 

See log file: 
/Applications/freesurfer/subjects/15-03-07.1_3T2/scripts/hippocampal-subfields-T1.log
 

-- 

Setting up environment variables 

--- 

DYLD_LIBRARY_PATH is 
.:/Applications/freesurfer/MCRv80/runtime/maci64:/Applications/freesurfer/MCRv80/bin/maci64:/Applications/freesurfer/MCRv80/sys/os/maci64:/Applications/freesurfer/lib/gcc/lib:/Applications/freesurfer/lib/gcc/lib
 

dyld: Library not loaded: @rpath/libmwi18n.dylib 

Referenced from: 
/Applications/freesurfer/bin/segmentSubjectT1_autoEstimateAlveusML.app/Contents/MacOS/segmentSubjectT1_autoEstimateAlveusML
 

Reason: image not found 

/Applications/freesurfer/bin/run_segmentSubjectT1_autoEstimateAlveusML.sh: line 
40: 6219 Trace/BPT trap: 5 
"${exe_dir}"/segmentSubjectT1_autoEstimateAlveusML.app/Contents/MacOS/segmentSubjectT1_autoEstimateAlveusML
 $args 




#-- 




Started at Fri Sep 11 11:57:12 PDT 2015 

Ended at Fri Sep 11 11:57:15 PDT 2015 

#@#%# recon-all-run-time-hours 0.001 

recon-all -s 15-03-07.1_3T2 finished without error at Fri Sep 11 11:57:15 PDT 
2015 



done 




Thank you, 




Aarthi 



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Re: [Freesurfer] Freeview.bin - error while loading shared libraries: libvtkverdict.so.5.6 cannot open sharted ...

[Felipe Picon]

Dear colleagues,
I'm installing Freesurfer-Linux-CentOS4-stable-pub-v5.3.0 on Ubuntu 14.04
LTS (updated) and I managed to make tkmedit run correctly, but when I try
QDEC and Freeview I'm getting this message:
"qdec.bin: error while loading shared libraries: libjpeg.so.62: cannot open
shared object file: No such fie or directory
and
"freeview.bin: error while loading shared libraries: libjpeg.so.62: cannot
open shared object file: No such file or directory"

Any ideas or suggestions of what I might have done wrong?
Thank you very much
Best,
Felipe Picon

2015-04-06 19:04 GMT-03:00 Johannes Kaufhold 
:

> Hi Zeke,
>
> I managed to solve this issue.
>
> I have changed the ownership of all folders and files in
> /usr/local/freesurfer to my Ubuntu user name and now Freeview is working
> with the sample data.
>
> ..Just seeing your email coming in.
>
> Best,
> jk
>
> On 06/04/15 22:34, Johannes Kaufhold wrote:
> > Hi Zeke,
> >
> > Yes, I'm attempting to open freeview in the same terminal window in
> > which I have sourced SetUpFreeSurfer.csh.
> >
> > Here's the output from ls -l
> > $FREESURFER_HOME/lib/vtk/lib/vtk-5.6/*libvtkverdict*
> >
> > lrwxrwxrwx 1 root root 22 May 13  2013
> > /usr/local/freesurfer/lib/vtk/lib/vtk-5.6/libvtkverdict.so ->
> > libvtkverdict.so.5.6.0
> > lrwxrwxrwx 1 root root 22 May 13  2013
> > /usr/local/freesurfer/lib/vtk/lib/vtk-5.6/libvtkverdict.so.5.6 ->
> > libvtkverdict.so.5.6.0
> > -rwsrwsr-t 1 root root 189017 Aug 17  2010
> > /usr/local/freesurfer/lib/vtk/lib/vtk-5.6/libvtkverdict.so.5.6.0
> >
> > Best,
> > Johannes
> >
> > On 06/04/15 21:48, Z K wrote:
> >> Hello Johannes,
> >>
> >> You are attempting to open freeview *in the same window* that you
> >> sourced SetUpFreeSurfer.csh(sh), correct? Also, can you tell me what the
> >> output of the terminal is when you type the following command:
> >>
> >> ls -l $FREESURFER_HOME/lib/vtk/lib/vtk-5.6/*libvtkverdict*
> >>
> >> -Zeke
> >>
> >> On 04/06/2015 04:32 PM, Johannes Kaufhold wrote:
> >>> Hi all,
> >>>
> >>> I'm super new to Freesurfer. I just set it up on my computer earlier
> >>> today, following the official wiki on harvard.edu/fswiki...
> >>>
> >>> My system:
> >>> - Ubuntu 14.04 LTS (up to date)
> >>> - Tcsh installed
> >>> - Freesurfer version:
> >>> freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0.tar.gz
> >>> <
> ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/5.3.0/freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0.tar.gz
> >
> >>> - Mathlab not installed
> >>>
> >>> Sourcing the SetUpFreeSurfer.csh(sh) script worked fine and license.txt
> >>> is in $FREESURFER_HOME.
> >>>
> >>> When trying to pull and view the sample data by entering the below in
> >>> the terminal (tcsh)
> >>>
> >>> freeview -v $SUBJECTS_DIR/bert/mri/brainmask.mgz -v
> >>> $SUBJECTS_DIR/bert/mri/aseg.mgz:colormap=lut:opacity=0.2 -f
> >>> $SUBJECTS_DIR/bert/surf/lh.white:edgecolor=yellow -f
> >>> $SUBJECTS_DIR/bert/surf/rh.white:edgecolor=yellow -f
> >>> $SUBJECTS_DIR/bert/surf/lh.pial:annot=aparc:edgecolor=red -f
> >>> $SUBJECTS_DIR/bert/surf/rh.pial:annot=aparc:edgecolor=red
> >>>
> >>> I'm getting the following error message*
> >>> **
> >>> **freeview.bin: error while loading shared libraries:
> >>> libvtkverdict.so.5.6: cannot open shared object file: No such file or
> >>> directory*
> >>>
> >>> I was searching for the missing file in Aptitude and on the internet,
> >>> but couldn't manage to find it.
> >>>
> >>> Any suggestions how to proceed from here?
> >>>
> >>> Thanks and best wishes!
> >>> Johannes
> >>>
> >>>
> >>> ___
> >>> 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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>
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-- 
*Felipe Picon, MD, MSc*
Child and Adolescent Psychiatrist
=
ADHD Neuroimaging Researcher at the
Adult ADHD outpatient research 

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

[Douglas Greve]

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
>
>
> ___
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> 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/

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Re: [Freesurfer] Freeview.bin - error while loading shared libraries: libvtkverdict.so.5.6 cannot open sharted ...

[zkaufman]

Hello,

This is a known when running freesurfer on Ubuntu systems. The solution is
addressed in the FAQ section on the frresurfer download page:

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

pecifically, the solution is to go into you system's lib directory and
create a symlink as follows:

  $> cd /usr/lib/x86_64 (or something similar depending upon exact version)
  $> sudo ln -s libjpeg.so.8 libjpeg.so.62
  $> sudo ln -s libtiff.so.4 libtiff.so.3

This should solve it. Best,

-Zeke



> Dear colleagues,
> I'm installing Freesurfer-Linux-CentOS4-stable-pub-v5.3.0 on Ubuntu 14.04
> LTS (updated) and I managed to make tkmedit run correctly, but when I try
> QDEC and Freeview I'm getting this message:
> "qdec.bin: error while loading shared libraries: libjpeg.so.62: cannot
> open
> shared object file: No such fie or directory
> and
> "freeview.bin: error while loading shared libraries: libjpeg.so.62: cannot
> open shared object file: No such file or directory"
>
> Any ideas or suggestions of what I might have done wrong?
> Thank you very much
> Best,
> Felipe Picon
>
> 2015-04-06 19:04 GMT-03:00 Johannes Kaufhold
> 
> :
>
>> Hi Zeke,
>>
>> I managed to solve this issue.
>>
>> I have changed the ownership of all folders and files in
>> /usr/local/freesurfer to my Ubuntu user name and now Freeview is working
>> with the sample data.
>>
>> ..Just seeing your email coming in.
>>
>> Best,
>> jk
>>
>> On 06/04/15 22:34, Johannes Kaufhold wrote:
>> > Hi Zeke,
>> >
>> > Yes, I'm attempting to open freeview in the same terminal window in
>> > which I have sourced SetUpFreeSurfer.csh.
>> >
>> > Here's the output from ls -l
>> > $FREESURFER_HOME/lib/vtk/lib/vtk-5.6/*libvtkverdict*
>> >
>> > lrwxrwxrwx 1 root root 22 May 13  2013
>> > /usr/local/freesurfer/lib/vtk/lib/vtk-5.6/libvtkverdict.so ->
>> > libvtkverdict.so.5.6.0
>> > lrwxrwxrwx 1 root root 22 May 13  2013
>> > /usr/local/freesurfer/lib/vtk/lib/vtk-5.6/libvtkverdict.so.5.6 ->
>> > libvtkverdict.so.5.6.0
>> > -rwsrwsr-t 1 root root 189017 Aug 17  2010
>> > /usr/local/freesurfer/lib/vtk/lib/vtk-5.6/libvtkverdict.so.5.6.0
>> >
>> > Best,
>> > Johannes
>> >
>> > On 06/04/15 21:48, Z K wrote:
>> >> Hello Johannes,
>> >>
>> >> You are attempting to open freeview *in the same window* that you
>> >> sourced SetUpFreeSurfer.csh(sh), correct? Also, can you tell me what
>> the
>> >> output of the terminal is when you type the following command:
>> >>
>> >> ls -l $FREESURFER_HOME/lib/vtk/lib/vtk-5.6/*libvtkverdict*
>> >>
>> >> -Zeke
>> >>
>> >> On 04/06/2015 04:32 PM, Johannes Kaufhold wrote:
>> >>> Hi all,
>> >>>
>> >>> I'm super new to Freesurfer. I just set it up on my computer earlier
>> >>> today, following the official wiki on harvard.edu/fswiki...
>> >>>
>> >>> My system:
>> >>> - Ubuntu 14.04 LTS (up to date)
>> >>> - Tcsh installed
>> >>> - Freesurfer version:
>> >>> freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0.tar.gz
>> >>> <
>> ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/5.3.0/freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0.tar.gz
>> >
>> >>> - Mathlab not installed
>> >>>
>> >>> Sourcing the SetUpFreeSurfer.csh(sh) script worked fine and
>> license.txt
>> >>> is in $FREESURFER_HOME.
>> >>>
>> >>> When trying to pull and view the sample data by entering the below
>> in
>> >>> the terminal (tcsh)
>> >>>
>> >>> freeview -v $SUBJECTS_DIR/bert/mri/brainmask.mgz -v
>> >>> $SUBJECTS_DIR/bert/mri/aseg.mgz:colormap=lut:opacity=0.2 -f
>> >>> $SUBJECTS_DIR/bert/surf/lh.white:edgecolor=yellow -f
>> >>> $SUBJECTS_DIR/bert/surf/rh.white:edgecolor=yellow -f
>> >>> $SUBJECTS_DIR/bert/surf/lh.pial:annot=aparc:edgecolor=red -f
>> >>> $SUBJECTS_DIR/bert/surf/rh.pial:annot=aparc:edgecolor=red
>> >>>
>> >>> I'm getting the following error message*
>> >>> **
>> >>> **freeview.bin: error while loading shared libraries:
>> >>> libvtkverdict.so.5.6: cannot open shared object file: No such file
>> or
>> >>> directory*
>> >>>
>> >>> I was searching for the missing file in Aptitude and on the
>> internet,
>> >>> but couldn't manage to find it.
>> >>>
>> >>> Any suggestions how to proceed from here?
>> >>>
>> >>> Thanks and best wishes!
>> >>> Johannes
>> >>>
>> >>>
>> >>> ___
>> >>> Freesurfer mailing list
>> >>> Freesurfer@nmr.mgh.harvard.edu
>> >>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>> >>>
>> >> ___
>> >> 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 

Re: [Freesurfer] PVC correction - estimation release version 6

[Mohamed Ali Bahri]

Dear All,

I am also waiting for this PVC correction. If you have/know an other 
tool for the PVC, please do not hesitate to share.


Many thanks,

Bahri

On 21/09/15 13:30, Kok, JG (neuro) wrote:

Dear Freesurfer experts,

I would be very interested in using the PVC correction software for 
PET images, that will be available within Freesurfer version 6. Would 
you be able to estimate a date for the release of the stable release 
of version 6 (I realize this may be difficult)? Depending on your 
estimation I may wait for this release, or keep using 5.3.0 for 
segmentation of the T1 image (and try to find PVC correction somewhere 
else).


Best,

Jelmer

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University of Liège, Belgium
m.ba...@ulg.ac.be

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[Freesurfer] PVC correction - estimation release version 6

[Kok, JG (neuro)]

Dear Freesurfer experts,

I would be very interested in using the PVC correction software for PET images, 
that will be available within Freesurfer version 6. Would you be able to 
estimate a date for the release of the stable release of version 6 (I realize 
this may be difficult)? Depending on your estimation I may wait for this 
release, or keep using 5.3.0 for segmentation of the T1 image (and try to find 
PVC correction somewhere else).

Best,

Jelmer

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[Freesurfer] FreeSurfer 6

[Pedro Paulo de Magalhães Oliveira Junior]

Hey Guys,

Sorry if this is a frequently asked question.

Do we have an updated ETA for version 6 of Freesurfer? We are planning on
upgrading our 1024-node cluster and version 6 is a big deal for us.

Best

Pedro Paulo Jr.
-
Pedro Paulo de Magalhães Oliveira Junior
Netfilter & SpeedComm Telecom
-- www.netfilter.com.br
-- For mobile: http://itunes.apple.com/br/artist/netfilter/id365306441
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Re: [Freesurfer] Question about the multiple comparison correction in FreeSurfer

[chenhf_uestc]

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.

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".

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 

--  
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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 
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[Freesurfer] corrupt download, 6.0 beta

[Chuck Theobald]

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

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[Freesurfer] Basal ganglia

[John Anderson]

Hi Experts,

I want to do tractography for the cortico spinal tract between two ROIs ( ROI1: precentral gyrus; ROI2: basal ganglia). I created the first ROI using mask form wmparc.mgz. How can I create mask for the basal ganglia ( there is no label for it). Do I need to segmenta the basal ganglia separatly? Is there any tool in Freesurfer that can help? Thanks for any suggestion.

 

Bests,
John Anderson

Senior Research Associate
Psychological and Brain Sciences Dept.
Dartmouth College, 419 Moore Hall, Hinman Box 6207, Hanover, NH 03755
Phone: +1 (603) 646-9834
Fax: +1 (603) 646-1419
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Re: [Freesurfer] Basal ganglia

[Bruce Fischl]

Hi John

what parts of the basal ganglia do you want? We label 
caudate/putamen/pallidum/accumbens separately. You can combine them all 
together and get one ROI if you want. They should all be in the wmparc.mgz


cheers
Bruce
On Mon, 21 Sep 2015, John Anderson 
wrote:



Hi Experts,
I want to do tractography for the cortico spinal tract between two ROIs ( ROI1: 
precentral gyrus;
ROI2: basal ganglia). I created the first ROI using mask form wmparc.mgz. How 
can I create mask for
the basal ganglia ( there is no label for it). Do I need to segmenta the basal 
ganglia separatly? Is
there any tool in Freesurfer that can help? Thanks for any suggestion.
 
Bests,
John Anderson

Senior Research Associate
Psychological and Brain Sciences Dept.
Dartmouth College, 419 Moore Hall, Hinman Box 6207, Hanover, NH 03755
Phone: +1 (603) 646-9834
Fax: +1 (603) 646-1419

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[Freesurfer] Qdec: group differences covaring for age and sex

[pablo najt]

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 DiffHC  PT  AgeHC  AgePT  SexHC SexPT 1 -10   0  
0   0
Group x Age effectHC  PT  AgeHC  AgePT  SexHC SexPT 0  0 1  -1  
   00
Group X Sex effectHC  PT  AgeHC  AgePT  SexHC SexPT 0  0 0   0  
1   -1Continues 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___
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[Freesurfer] mri_deface error.

[Andrew Schoen]

Hi all,

I have encountered some strange behavior with mri_deface.
I am working on defacing around 70 scans, and was using the mri_deface program 
to do so. To start off with, I ran them using the version of mri_deface from 
version 5.3, along with the .gca files included here:
https://surfer.nmr.mgh.harvard.edu/fswiki/mri_deface 


1: When I ran that, many of the files defaced correctly, but a sizable number 
had only the inside of the face removed (eg. nasal cavity, inside of mouth, 
etc), maintaining the outward facial structure. 
Is there a way to adjust the thresholding/settings, such that we can prevent 
this from happening, and thereby reduce the need to do hand-editing? As it is, 
they are still very much identifiable.

2: Thinking I may have an outdated version of mri_deface, I tried downloading 
and running both 32-bit and 64-bit versions from that site (v1.22), and when I 
ran them, I obtained different results from the 5.3 version. The results from 
v1.22 (both versions) actually took out large sections of brain/skull from the 
right side of the head, instead of the face. We are running on 64-bit linux. 
Any idea what may be causing this? All the gca files were downloaded directly 
from the site.

Let me know if any more information would be helpful!

Thanks!
Andrew Schoen
Center for Investigating Healthy Minds
Waisman Center
University of Wisconsin - Madison___
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Re: [Freesurfer] Question about the multiple comparison correction in FreeSurfer

[Douglas N Greve]

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

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
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Re: [Freesurfer] How could I display the tksurfer correctly

[Douglas N Greve]

You can use the methods from my previous email to do FDR correction, 
then load that into tksurfer

On 09/20/2015 10:55 PM, chenhf_uestc wrote:
> Dear Freesurfer experts,
> I use Oracle VM VirtualBox to run Freesurfer software and I want to 
> perform FDR correction in TKSurfer. However, I cannot get the whole 
> window size (attached 1.png), and thus I cannot find the FDR option. 
> Actually, there are lots of options (2.png) cannot be displayed in 1.png.
> I try to change the window resolution, but I failed because now is the 
> max resolution.
> Could anyone give me some suggestions?
> Best,
> Feng
>
>
> ___
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> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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

[Douglas N Greve]

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.
> >
> > Which should be the advised folder for  func.vmPFC_MASK.nii?
> >
> >
> > Thank you very much
> >
> >
> > Stefano
> >
> >
> > Messaggio originale
> > Da: gr...@nmr.mgh.harvard.edu
> > Data: 30-giu-2015 0.36
> > A: 
> > Ogg: Re: [Freesurfer] Import mask from FSL to FS for performing
> > seed-based FS-FAST functional connectivity
> >
> > Hi Stefano, sorry for the delay, I was traveling. It sounds like you
> > just need to run fcseed-config and specify -seg ROI_MASK.mgz and -segid
> > 1 (assuming your ROI_MASK is in $SUBJECTS_DIR/subject/mri). If the mask
> > is in the orig.mgz space, 

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

[Douglas N Greve]

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
>
>
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> 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
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www.nmr.mgh.harvard.edu/facility/filedrop/index.html
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Re: [Freesurfer] Magnitude of group difference

[Douglas N Greve]

Once you have covariates you need to decide what "percent difference" 
means. Do you want to include the covariates? If so, then you'd use 1 0 
0 0 and 0 1 0 0 (although see my warning in my previous email about 
using gender as a continuous covariate).

On 09/19/2015 05:55 AM, pablo najt wrote:
> Hello Doug,
> Thanks for the answer, my intention is to compute percent difference 
> between groups in area (and separately for area.pial). About the 
> contrast, you said that in order to compute the percent difference 
> between groups I need to specify a contrast for each group separately 
> (think would be one contrast with group1 as "1" versus "0") and same 
> for group2.
> As my glm original contrasts have four regressors: (group1, group2, 
> age, sex) I am in doubt if for these two new contrasts for percent 
> difference I still keep my covariates or should get rid of?
> Thanks!
>
> > To: freesurfer@nmr.mgh.harvard.edu
> > From: gr...@nmr.mgh.harvard.edu
> > Date: Fri, 18 Sep 2015 15:00:40 -0400
> > Subject: Re: [Freesurfer] Magnitude of group difference
> >
> >
> >
> > On 09/18/2015 02:37 PM, pablo najt wrote:
> > > Hello Doug,
> > > Below you suggested that I can calculate percent difference if I
> > > create a contrast of group1 vs 0 and same group2, for cortical
> > > thickness. Does this applies to Area and Area.Pial as well?
> > You mean to compute the percent diff between the white and pial surface
> > area? yes, that will work. or to look at percent diff between group1 
> and
> > group2 for white surface and then for pial surface as well? that will
> > work too.
> > > About my contrasts for my qdec analysis I have two levels two 
> covariates
> > > So my contrasts look: 1 -1 0 0, etc.
> > > So should I keep the two regressors corresponding to the two 
> variables
> > > (1 0 0 0)?
> > > Or it should it be like this:(1 0)?
> > what is this in reference to?
> > > Thanks,
> > > Pablo
> > >
> > > 
> 
> > > Date: Fri, 28 Aug 2015 10:41:30 -0400
> > > From: gr...@nmr.mgh.harvard.edu
> > > To: freesurfer@nmr.mgh.harvard.edu
> > > Subject: Re: [Freesurfer] Magnitude of group difference
> > >
> > > There are a couple of things you can do.
> > >
> > > You can create a contrast for each group separately, then compute the
> > > voxel-wise percent difference between the maps, eg,
> > > fscalc group1/gamma.mgh pctdiff group2/gamma.mgh -o pctdiff.mgh
> > >
> > > You can compute the percent differences from the average in the
> > > cluster. For this you'll need to load the y file for the clusters and
> > > sort the subjects (rows) into groups and compute the precentage
> > > difference.
> > >
> > >
> > >
> > > On 8/28/15 4:54 AM, pablo najt wrote:
> > >
> > > Hello FS experts and all,
> > > I would like to find out the magnitude of the group difference
> > > between a two-group comparison (e.g. percent difference on
> > > cortical thickness indicating how much one group differs from the
> > > other.) I have run analysis using both mri_glmfit and qdec, I also
> > > run cluster wise correction for multiple comparisons but in my
> > > summary tables I am not finding this information. Do I need to run
> > > any additional command to find out about this?
> > > Thank you
> > > Pablo
> > >
> > >
> > > ___
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> > > Freesurfer@nmr.mgh.harvard.edu 
> > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> > >
> > >
> > >
> > > ___ 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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> > > 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/
> >
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>
>
>