[Freesurfer] Visualizing GLM analysis error

[Myers, Peter]

Hello all,



I am trying to visualize the results of my GLM analysis. Unfortunately, I keep on running into errors.





I run the command:


freeview -f

$SUBJECTS_DIR/fsaverage/surf/lh.inflated:annot=aparc.annot:annot_outline=1overlay=lh.Cog_Trial1.glmdir/lh-Avg-thickness-Cog_Trial1/sig.mgh:overlay_threshold=4,5 -viewport 3d



When I do that command, I get the error:


Unrecognized sub-option flag 'annot_outline'



I tried to remove this from the command, and freeview opens. But then I get an error saying that freeview cannot open the 'lh.Cog_Trial1.glmdir/lh-Avg-thickness-Cog_Trial1/sig.mgh'


"has many more faces than vertices! Probably trying to use a scalar data file as a surface!"





I tried to open the sig.mgh file through the GUI, but then freesurfer completely crashes with the following error:
[0]PETSC ERROR: 
[0]PETSC ERROR: Caught signal number 11 SEGV: Segmentation Violation, probably memory access out of range
[0]PETSC ERROR: Try option -start_in_debugger or -on_error_attach_debugger
[0]PETSC ERROR: or see http://www.mcs.anl.gov/petsc/petsc-as/documentation/troubleshooting.html#Signal[0]PETSC ERROR: or try http://valgrind.org on linux or man libgmalloc on Apple to find memory corruption errors
[0]PETSC ERROR: configure using --with-debugging=yes, recompile, link, and run
[0]PETSC ERROR: to get more information on the crash.
[0]PETSC ERROR: - Error Message 
[0]PETSC ERROR: Signal received!
[0]PETSC ERROR: 
[0]PETSC ERROR: Petsc Release Version 2.3.3, Patch 13, Thu May 15 17:29:26 CDT 2008 HG revision: 4466c6289a0922df26e20626fd4a0b4dd03c8124
[0]PETSC ERROR: See docs/changes/index.html for recent updates.
[0]PETSC ERROR: See docs/faq.html for hints about trouble shooting.
[0]PETSC ERROR: See docs/index.html for manual pages.
[0]PETSC ERROR: 
[0]PETSC ERROR: Unknown Name on a linux-gnu named sunshine by myerp Thu Jan 14 11:14:53 2016
[0]PETSC ERROR: Libraries linked from /autofs/space/lyon_006/pubsw/Linux2-2.3-x86_64/packages/petsc/2.3.3-p13/src/petsc-2.3.3-p13/lib/linux-gnu-c-opt
[0]PETSC ERROR: Configure run at Tue Aug 10 15:01:59 2010
[0]PETSC ERROR: Configure options --with-debugging=no --with-cc=gcc --with-fc=g77 --download-f-blas-lapack=0 --download-mpich=1 --with-mpi=1 --with-x=0 --with-gnu-copyright-code=0 --with-shared=0 COPTFLAGS=-O3 CXXOPTFLAGS=-O3 FOPTFLAGS=-O3
[0]PETSC ERROR: 
[0]PETSC ERROR: User provided function() line 0 in unknown directory unknown file
[unset]: aborting job:
application called MPI_Abort(MPI_COMM_WORLD, 59) - process 0
Segmentation fault (core dumped)


Any help is greatly appreciated!



Thanks,

peter







 



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 recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone
 or return mail.


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Re: [Freesurfer] Visualizing GLM analysis error

[Bruce Fischl]

Hi Peter

you need a colon to separate each of the modifiers you are using, not a 
space. So


freeview -f lh.inflated:annot=aparc.annot:outline=1:overlay=

cheers
Bruce

On Thu, 14 Jan 2016, Myers, Peter wrote:


Hello all,

I am trying to visualize the results of my GLM analysis. Unfortunately, I
keep on running into errors.

I run the command:
freeview -f
$SUBJECTS_DIR/fsaverage/surf/lh.inflated:annot=aparc.annot:annot_outline=1o
verlay=lh.Cog_Trial1.glmdir/lh-Avg-thickness-Cog_Trial1/sig.mgh:overlay_thr
eshold=4,5 -viewport 3d

When I do that command, I get the error:
Unrecognized sub-option flag 'annot_outline'

I tried to remove this from the command, and freeview opens. But then I get
an error saying that freeview cannot open
the 'lh.Cog_Trial1.glmdir/lh-Avg-thickness-Cog_Trial1/sig.mgh'
"has many more faces than vertices! Probably trying to use a scalar data
file as a surface!"

I tried to open the sig.mgh file through the GUI, but then freesurfer
completely crashes with the following error:
[0]PETSC ERROR:

[0]PETSC ERROR: Caught signal number 11 SEGV: Segmentation Violation,
probably memory access out of range
[0]PETSC ERROR: Try option -start_in_debugger or -on_error_attach_debugger
[0]PETSC ERROR: or 
seehttp://www.mcs.anl.gov/petsc/petsc-as/documentation/troubleshooting.html#Si
gnal[0]PETSC ERROR: or try http://valgrind.org on linux or man libgmalloc on
Apple to find memory corruption errors
[0]PETSC ERROR: configure using --with-debugging=yes, recompile, link, and
run
[0]PETSC ERROR: to get more information on the crash.
[0]PETSC ERROR: - Error Message

[0]PETSC ERROR: Signal received!
[0]PETSC ERROR:

[0]PETSC ERROR: Petsc Release Version 2.3.3, Patch 13, Thu May 15 17:29:26
CDT 2008 HG revision: 4466c6289a0922df26e20626fd4a0b4dd03c8124
[0]PETSC ERROR: See docs/changes/index.html for recent updates.
[0]PETSC ERROR: See docs/faq.html for hints about trouble shooting.
[0]PETSC ERROR: See docs/index.html for manual pages.
[0]PETSC ERROR:

[0]PETSC ERROR: Unknown Name on a linux-gnu named sunshine by myerp Thu Jan
14 11:14:53 2016
[0]PETSC ERROR: Libraries linked 
from/autofs/space/lyon_006/pubsw/Linux2-2.3-x86_64/packages/petsc/2.3.3-p13/src
/petsc-2.3.3-p13/lib/linux-gnu-c-opt
[0]PETSC ERROR: Configure run at Tue Aug 10 15:01:59 2010
[0]PETSC ERROR: Configure options --with-debugging=no --with-cc=gcc
--with-fc=g77 --download-f-blas-lapack=0 --download-mpich=1 --with-mpi=1
--with-x=0 --with-gnu-copyright-code=0 --with-shared=0 COPTFLAGS=-O3
CXXOPTFLAGS=-O3 FOPTFLAGS=-O3
[0]PETSC ERROR:

[0]PETSC ERROR: User provided function() line 0 in unknown directory unknown
file
[unset]: aborting job:
application called MPI_Abort(MPI_COMM_WORLD, 59) - process 0
Segmentation fault (core dumped)

Any help is greatly appreciated!

Thanks,
peter


 





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Healthcare Information or other information of a sensitive nature. If you
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of this information is strictly prohibited. If you have received this email
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Re: [Freesurfer] Visualizing GLM analysis error

[Douglas Greve]

also, I think that the annot_outline is a version 6 feature.

On 1/14/16 1:01 PM, Bruce Fischl wrote:

Hi Peter

you need a colon to separate each of the modifiers you are using, not 
a space. So


freeview -f lh.inflated:annot=aparc.annot:outline=1:overlay=

cheers
Bruce

On Thu, 14 Jan 2016, Myers, Peter wrote:


Hello all,

I am trying to visualize the results of my GLM analysis. 
Unfortunately, I

keep on running into errors.

I run the command:
freeview -f
$SUBJECTS_DIR/fsaverage/surf/lh.inflated:annot=aparc.annot:annot_outline=1o 

verlay=lh.Cog_Trial1.glmdir/lh-Avg-thickness-Cog_Trial1/sig.mgh:overlay_thr 


eshold=4,5 -viewport 3d

When I do that command, I get the error:
Unrecognized sub-option flag 'annot_outline'

I tried to remove this from the command, and freeview opens. But then 
I get

an error saying that freeview cannot open
the 'lh.Cog_Trial1.glmdir/lh-Avg-thickness-Cog_Trial1/sig.mgh'
"has many more faces than vertices! Probably trying to use a scalar data
file as a surface!"

I tried to open the sig.mgh file through the GUI, but then freesurfer
completely crashes with the following error:
[0]PETSC ERROR:

[0]PETSC ERROR: Caught signal number 11 SEGV: Segmentation Violation,
probably memory access out of range
[0]PETSC ERROR: Try option -start_in_debugger or 
-on_error_attach_debugger
[0]PETSC ERROR: or 
seehttp://www.mcs.anl.gov/petsc/petsc-as/documentation/troubleshooting.html#Si
gnal[0]PETSC ERROR: or try http://valgrind.org on linux or man 
libgmalloc on

Apple to find memory corruption errors
[0]PETSC ERROR: configure using --with-debugging=yes, recompile, 
link, and

run
[0]PETSC ERROR: to get more information on the crash.
[0]PETSC ERROR: - Error Message

[0]PETSC ERROR: Signal received!
[0]PETSC ERROR:

[0]PETSC ERROR: Petsc Release Version 2.3.3, Patch 13, Thu May 15 
17:29:26

CDT 2008 HG revision: 4466c6289a0922df26e20626fd4a0b4dd03c8124
[0]PETSC ERROR: See docs/changes/index.html for recent updates.
[0]PETSC ERROR: See docs/faq.html for hints about trouble shooting.
[0]PETSC ERROR: See docs/index.html for manual pages.
[0]PETSC ERROR:

[0]PETSC ERROR: Unknown Name on a linux-gnu named sunshine by myerp 
Thu Jan

14 11:14:53 2016
[0]PETSC ERROR: Libraries linked 
from/autofs/space/lyon_006/pubsw/Linux2-2.3-x86_64/packages/petsc/2.3.3-p13/src

/petsc-2.3.3-p13/lib/linux-gnu-c-opt
[0]PETSC ERROR: Configure run at Tue Aug 10 15:01:59 2010
[0]PETSC ERROR: Configure options --with-debugging=no --with-cc=gcc
--with-fc=g77 --download-f-blas-lapack=0 --download-mpich=1 --with-mpi=1
--with-x=0 --with-gnu-copyright-code=0 --with-shared=0 COPTFLAGS=-O3
CXXOPTFLAGS=-O3 FOPTFLAGS=-O3
[0]PETSC ERROR:

[0]PETSC ERROR: User provided function() line 0 in unknown directory 
unknown

file
[unset]: aborting job:
application called MPI_Abort(MPI_COMM_WORLD, 59) - process 0
Segmentation fault (core dumped)

Any help is greatly appreciated!

Thanks,
peter





 




The materials in this message are private and may contain Protected
Healthcare Information or other information of a sensitive nature. If 
you

are not the intended recipient, be advised that any unauthorized use,
disclosure, copying or the taking of any action in reliance on the 
contents
of this information is strictly prohibited. If you have received this 
email
in error, please immediately notify the sender via telephone or 
return mail.







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[Freesurfer] Postdoctoral position available, Paderborn (Germany)

[Claus Reinsberger]

The Institute of Sports Medicine at the University of Paderborn invites 
applications for a full-time
 
Postdoctoral Position

to conduct, process and analyze EEG and other neuroimaging data in the context 
of sports and exercise. The primary responsibility of this position includes 
developing novel processing and statistical analysis methods, specifically for 
analyzing properties and dynamics of resting state networks, in dependence of 
various demands and states of fatigue in sports and exercise.
The start date can be immediate and the position is scheduled for three years. 
Applicants are expected to have finished their PhD in biomedical engineering, 
Computer Science, Medical Physics, Neuroscience or related disciplines with a 
track record of relevant publications. The project requires experience with 
mathematical modeling and strong programming skills in C/C++ and Matlab/Python. 
Proficiency with EEG analyses is essential, experience with image registration 
and other statistical methods for neuroimaging are welcome. We are looking for 
a personality with the ability to think independently and work collaboratively, 
paired with high communication skills and high proficiency with English 
language. Postdocs will have the opportunity to strengthen their scientific and 
professional qualifications. The teaching responsibilities amount four semester 
periods per week.

The Institute of Sports Medicine at the University of Paderborn is the first 
sports medicine program in Germany under neurological leadership with a strong 
focus on neurophysiology in health and elite level sports. The posted position 
will further the unique neurophysiological profile within the new field of 
applied neurosciences in sports and exercise.
 
Applications from women are particularly welcome and, in case of equal 
qualifications and experiences, will receive preferential treatment according 
to the North Rhine-Westphalian Equal Opportunities Act (LGG), unless there are 
preponderant reasons to give preference to another applicant. Applications from 
disabled people with appropriate suitability are explicitly welcome. This also 
applies to people with equal opportunities in accordance with the German social 
law SGB IX.
To apply, please submit a single PDF file containing the following: 1) Cover 
letter describing research interests and relevant background; 2) CV with list 
of publications; 3) The names of three individuals who could provide reference 
letters. All files or inquiries should be submitted electronically to: 
reinsber...@sportmed.upb.de 



Claus Reinsberger, MD PhD
Department of Exercise and Health
Institute of Sports Medicine
University of Paderborn
Warburger Str. 100
33098 Paderborn, Germany___
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dispose of the e-mail.

Re: [Freesurfer] Cortical reconstruction

[Mohamed Ali Bahri]

Dear Bruce,

Many thanks for your answer.

All the best,

Mohamed

On 11/01/16 14:40, Bruce Fischl wrote:
> Hi Mohamed
>
> you can use mri_synthesize to create a flash image with good T1 contrast
> from quantitative maps and run it through recon-all.
>
> cheers
> Bruce
> On Mon, 11 Jan 2016,
> Mohamed Ali Bahri wrote:
>
>> Dear Freesurfer Experts,
>>
>> I am wondering if the cortical reconstruction is possible for the
>> quantitative mri images (R1, MT, PD...) obtained with the multiparameter
>> sequences .
>> If yes which image should i use?
>>
>> Many thanks in advance,
>>
>> Mohamed
>>
>>
> ___
> 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.
>

-- 
Dr. Mohamed Ali Bahri,
1er Logisticien de Recherche,
Cyclotron Research Centre,
University of Liège, Belgium
m.ba...@ulg.ac.be

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[Freesurfer] QDEC. Error in Analyze: command failed: mri_glmfit

[BAUTISTA-PERPINYA Maximilià]

Hi there experts,

I'm runing qdec to analyze my subject data. I am able to import the 
qdec.table.dat, but the problem comes in the Design step. I select 
'Volume-based' measure, 'Diagnosis' as my discrete independent variable and 
'LeftAmygdala' as the continuous variable. I don't select any nuisance factor. 
I then set my Design Name: 'LAmyDiagnosis' and click Analyze, but gives me the 
following error: 

---

ERROR: QdecGlmDesign::GenerateContrasts: factor 1 must have 2 levels
ninputs = 137
Checking inputs
nframestot = 137
Allocing output
Done allocing
nframes = 137
Writing to /home/freesurfer/Desktop/test005/subjects/qdec/LAmyDiagnosis/y.mgh
gdfReadHeader: reading 
/home/freesurfer/Desktop/test005/subjects/qdec/LAmyDiagnosis/qdec.fsgd
INFO: DeMeanFlag keyword not found, DeMeaning will NOT be done.
Continuous Variable Means (all subjects)
0 LeftAmygdala 1502.65 189.974
Class Means of each Continuous Variable
1 diagnosisBPD 1497.7548 
2 diagnosisCCP 1540.8923 
3 diagnosisNPC 1488.5490 
INFO: gd2mtx_method is dods
Reading source surface 
/home/freesurfer/Desktop/test005/subjects/fsaverage/surf/lh.white
ERROR: no contrasts specified.
Error in Analyze: command failed: mri_glmfit --y 
/home/freesurfer/Desktop/test005/subjects/qdec/LAmyDiagnosis/y.mgh --fsgd 
/home/freesurfer/Desktop/test005/subjects/qdec/LAmyDiagnosis/qdec.fsgd dods 
--glmdir /home/freesurfer/Desktop/test005/subjects/qdec/LAmyDiagnosis --surf 
fsaverage lh

---

Any recommendations? Any help is much appreciated :)


Best,

Max

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dispose of the e-mail.

[Freesurfer] Visualizing GLM analysis error

[Myers, Peter]

Thanks for these comments/suggestions. Still having troubles unfortunately.



I ran the command: 

freeview -f $SUBJECTS_DIR/fsaverage/surf/lh.inflated:annot=aparc.annot:overlay=lh.Cog_Trial1.glmdir/lh-Avg-thickness-Cog_Trial1/sig.mgh:overlay_threshold=4,5 -viewport 3d



I don't think there are any spaces, only colons as suggested. And I removed the 'annot_outline' part as it does not seem to be in my  5.3 version.



I still get this error message:

mghRead(/data/jsp/human2/fcMRI/PickettK/Data/FreeSurfer5.3/fsaverage/surf/lh.Cog_Trial1.glmdir/lh-Avg-thickness-Cog_Trial1/sig.mgh, -1): could not open file
mghRead(/data/jsp/human2/fcMRI/PickettK/Data/FreeSurfer5.3/fsaverage/surf/lh.Cog_Trial1.glmdir/lh-Avg-thickness-Cog_Trial1/sig.mgh, -1): could not open file
could not read overlay data from /data/jsp/human2/fcMRI/PickettK/Data/FreeSurfer5.3/fsaverage/surf/lh.Cog_Trial1.glmdir/lh-Avg-thickness-Cog_Trial1/sig.mgh
mghRead(/data/jsp/human2/fcMRI/PickettK/Data/FreeSurfer5.3/fsaverage/surf/lh.Cog_Trial1.glmdir/lh-Avg-thickness-Cog_Trial1/sig.mgh, -1): could not open file
^C
  

as well as a message from freeview that says 'failed to load surface overlay'

I've double checked and the sig.mgh file exists in the directory, but for some reason, it seems unable to be loaded?



Thanks much,

peter





From: freesurfer-boun...@nmr.mgh.harvard.edu  on behalf of Douglas Greve 
Sent: Thursday, January 14, 2016 12:06 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] Visualizing GLM analysis error
 

also, I think that the annot_outline is a version 6 feature.

On 1/14/16 1:01 PM, Bruce Fischl wrote:

Hi Peter 

you need a colon to separate each of the modifiers you are using, not a space. So


freeview -f lh.inflated:annot=aparc.annot:outline=1:overlay= 

cheers 
Bruce 

On Thu, 14 Jan 2016, Myers, Peter wrote: 

Hello all, 

I am trying to visualize the results of my GLM analysis. Unfortunately, I 
keep on running into errors. 

I run the command: 
freeview -f 
$SUBJECTS_DIR/fsaverage/surf/lh.inflated:annot=aparc.annot:annot_outline=1o 
verlay=lh.Cog_Trial1.glmdir/lh-Avg-thickness-Cog_Trial1/sig.mgh:overlay_thr 
eshold=4,5 -viewport 3d 

When I do that command, I get the error: 
Unrecognized sub-option flag 'annot_outline' 

I tried to remove this from the command, and freeview opens. But then I get 
an error saying that freeview cannot open 
the 'lh.Cog_Trial1.glmdir/lh-Avg-thickness-Cog_Trial1/sig.mgh' 
"has many more faces than vertices! Probably trying to use a scalar data 
file as a surface!" 

I tried to open the sig.mgh file through the GUI, but then freesurfer 
completely crashes with the following error: 
[0]PETSC ERROR: 
 
[0]PETSC ERROR: Caught signal number 11 SEGV: Segmentation Violation, 
probably memory access out of range 
[0]PETSC ERROR: Try option -start_in_debugger or -on_error_attach_debugger 
[0]PETSC ERROR: or seehttp://www.mcs.anl.gov/petsc/petsc-as/documentation/troubleshooting.html#Si
gnal[0]PETSC ERROR: or try 
http://valgrind.org on linux or man libgmalloc on 
Apple to find memory corruption errors 
[0]PETSC ERROR: configure using --with-debugging=yes, recompile, link, and 
run 
[0]PETSC ERROR: to get more information on the crash. 
[0]PETSC ERROR: - Error Message 
 
[0]PETSC ERROR: Signal received! 
[0]PETSC ERROR: 
 
[0]PETSC ERROR: Petsc Release Version 2.3.3, Patch 13, Thu May 15 17:29:26 
CDT 2008 HG revision: 4466c6289a0922df26e20626fd4a0b4dd03c8124 
[0]PETSC ERROR: See docs/changes/index.html for recent updates. 
[0]PETSC ERROR: See docs/faq.html for hints about trouble shooting. 
[0]PETSC ERROR: See docs/index.html for manual pages. 
[0]PETSC ERROR: 
 
[0]PETSC ERROR: Unknown Name on a linux-gnu named sunshine by myerp Thu Jan 
14 11:14:53 2016 
[0]PETSC ERROR: Libraries linked from/autofs/space/lyon_006/pubsw/Linux2-2.3-x86_64/packages/petsc/2.3.3-p13/src
/petsc-2.3.3-p13/lib/linux-gnu-c-opt 
[0]PETSC ERROR: Configure run at Tue Aug 10 15:01:59 2010 
[0]PETSC ERROR: Configure options --with-debugging=no --with-cc=gcc 
--with-fc=g77 --download-f-blas-lapack=0 --download-mpich=1 --with-mpi=1 
--with-x=0 --with-gnu-copyright-code=0 --with-shared=0 COPTFLAGS=-O3 
CXXOPTFLAGS=-O3 FOPTFLAGS=-O3 
[0]PETSC ERROR: 
 
[0]PETSC ERROR: User provided function() line 0 in unknown directory unknown 
file 
[unset]: aborting job: 
application called MPI_Abort(MPI_COMM_WORLD, 59) - process 0 
Segmentation fault (core dumped) 

Any help is greatly appreciated! 

Thanks, 
peter 


  


 


The materials 

[Freesurfer] FW: FW: problem with hard coded directory (/scratch)

[Fengji Geng]

Hi FS's experts,
I sent out a couple of emails to seek for help on an error from running 
recon-all using freesurfer 6.0 beta. Could anyone help with the question?
Thank you!



-
Fengji


From: Fengji Geng
Sent: Thursday, January 07, 2016 8:15 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] FW: problem with hard coded directory (/scratch)

Hi Douglas,
You asked us to give you an example of the problem program. I will try to do it 
here, but if it is not what you want, please let me know.

we  ran recon-all -all -s  -hippocampal-subfields-T1T2  . We saw the program tried  to create 
/scratch/$subject_hippoSF_T1_v10_right directory and failing with (Read-only 
file system) because the user does not have permission to write to /scratch.

I can also send you the strace output if needed.

Thank you!

-
Message: 4
Date: Mon, 4 Jan 2016 13:37:48 -0500
From: Douglas N Greve 
Subject: Re: [Freesurfer] FW: problem with hard coded directory
(/scratch)
To: freesurfer@nmr.mgh.harvard.edu
Message-ID: <568abbfc.5000...@nmr.mgh.harvard.edu>
Content-Type: text/plain; charset=windows-1252; format=flowed

Can you give us specific examples of problem programs?

On 01/04/2016 09:54 AM, Fengji Geng wrote:
> Hello Bruce,
>
> Happy New Year!
>
> After we reported the error related to '/scratch' several weeks ago
> (see the email attached below), we tested the newest version of
> freesurfer 6.0 recently, it looks likes that a lot of "if (-e
> /scratch)" have been changed to "if (-dw /scratch)". However, there
> are still a lot of binaries in the bin directory that match the string
> "scratch", which cause the same error that I encountered before. I am
> wondering if it is possible for you to fix '/scratch' in the bin
> directory.
>
> Thank you!

-
Fengji

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Re: [Freesurfer] FW: FW: problem with hard coded directory (/scratch)

[Eugenio Iglesias]

Hi Fengji, 
Sorry for the late reply; I was on vacation and totally missed your question. 
The hippocampal subfield module uses /scratch to create temporary files if 
available. If not, it creates a directory under the tmp directory inside the 
subject directory. It was coded this way because in our system, because of the 
way the cluster is setup, writing to /scratch is way more efficient. 
For now, the only thing you can do is to enable writing permissions on 
/scratch, or deleting /scratch. 
For the future: maybe we should remove the /scratch check and go to the 
subject's tmp directory directly (Zeke, Nick, what do you think?) 
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 


From: "Fengji Geng"  
To: "Freesurfer support list"  
Sent: Thursday, January 14, 2016 7:46:44 PM 
Subject: [Freesurfer] FW: FW: problem with hard coded directory (/scratch) 

Hi FS's experts, 
I sent out a couple of emails to seek for help on an error from running 
recon-all using freesurfer 6.0 beta. Could anyone help with the question? 
Thank you! 



- 
Fengji 


From: Fengji Geng 
Sent: Thursday, January 07, 2016 8:15 AM 
To: freesurfer@nmr.mgh.harvard.edu 
Subject: Re: [Freesurfer] FW: problem with hard coded directory (/scratch) 

Hi Douglas, 
You asked us to give you an example of the problem program. I will try to do it 
here, but if it is not what you want, please let me know. 

we ran recon-all -all -s  -hippocampal-subfields-T1T2  . We saw the program tried to create 
/scratch/$subject_hippoSF_T1_v10_right directory and failing with (Read-only 
file system) because the user does not have permission to write to /scratch. 

I can also send you the strace output if needed. 

Thank you! 

-
 
Message: 4 
Date: Mon, 4 Jan 2016 13:37:48 -0500 
From: Douglas N Greve  
Subject: Re: [Freesurfer] FW: problem with hard coded directory 
(/scratch) 
To: freesurfer@nmr.mgh.harvard.edu 
Message-ID: <568abbfc.5000...@nmr.mgh.harvard.edu> 
Content-Type: text/plain; charset=windows-1252; format=flowed 

Can you give us specific examples of problem programs? 

On 01/04/2016 09:54 AM, Fengji Geng wrote: 
> Hello Bruce, 
> 
> Happy New Year! 
> 
> After we reported the error related to '/scratch' several weeks ago 
> (see the email attached below), we tested the newest version of 
> freesurfer 6.0 recently, it looks likes that a lot of "if (-e 
> /scratch)" have been changed to "if (-dw /scratch)". However, there 
> are still a lot of binaries in the bin directory that match the string 
> "scratch", which cause the same error that I encountered before. I am 
> wondering if it is possible for you to fix '/scratch' in the bin 
> directory. 
> 
> Thank you! 

- 
Fengji 


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[Freesurfer] Register surface ROI across hemisphere and into volume

[Martha Shiell]

Hi freesurfer list.

I have a surface label for a region-of-interest in the right hemisphere,
which I generated from a cortical thickness analysis. I am now doing an
analysis on the white matter below this roi, by moving the label into
volume space with mri_label2vol, and sampling below the surface with the
--proj option. I want to repeat this white matter analysis in the
homologous region-of-interest in the left hemisphere, as accurately as
possible. I found the documentation for xhemi, and an earlier post about
interhemispheric registration of rois (
https://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/2012-July/024821.html),
but I'm not clear on what the xhemi option does, nor what the outputs are,
nor what fsaverage_sym is, and so I haven't been able to figure out how to
use it for my purpose. Is there more info available somewhere on
interhemispheric registration with freesurfer tools, and/or does anyone
have suggestions for how I should proceed?

Thank you,
Martha

-- 
Martha M. Shiell, PhD
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Re: [Freesurfer] FW: FW: problem with hard coded directory (/scratch)

[Douglas N Greve]

Hi Fengji, you have sent several emails. I keep asking you to give us a 
specific binary that has the problem, but you seem to ignore my request, 
wait a couple of weeks, then post the question back to the list. I'm 
happy to take look, but please send me something more specific!
thanks
doug



On 01/14/2016 01:46 PM, Fengji Geng wrote:
> Hi FS's experts,
> I sent out a couple of emails to seek for help on an error from 
> running recon-all using freesurfer 6.0 beta. Could anyone help with 
> the question?
> Thank you!
>
>
>
> -
> Fengji
>
> 
> *From:* Fengji Geng
> *Sent:* Thursday, January 07, 2016 8:15 AM
> *To:* freesurfer@nmr.mgh.harvard.edu
> *Subject:* Re: [Freesurfer] FW: problem with hard coded directory 
> (/scratch)
>
> Hi Douglas,
> You asked us to give you an example of the problem program. I will try 
> to do it here, but if it is not what you want, please let me know.
>
> we  ran recon-all -all -s  -hippocampal-subfields-T1T2 
>  . We saw the program tried 
>  to create /scratch/$subject_hippoSF_T1_v10_right directory 
> and failing with (Read-only file system) because the user does not 
> have permission to write to /scratch.
>
> I can also send you the strace output if needed.
>
> Thank you!
>
> -
> Message: 4
> Date: Mon, 4 Jan 2016 13:37:48 -0500
> From: Douglas N Greve 
> Subject: Re: [Freesurfer] FW: problem with hard coded directory
> (/scratch)
> To: freesurfer@nmr.mgh.harvard.edu
> Message-ID: <568abbfc.5000...@nmr.mgh.harvard.edu>
> Content-Type: text/plain; charset=windows-1252; format=flowed
>
> Can you give us specific examples of problem programs?
>
> On 01/04/2016 09:54 AM, Fengji Geng wrote:
> > Hello Bruce,
> >
> > Happy New Year!
> >
> > After we reported the error related to '/scratch' several weeks ago
> > (see the email attached below), we tested the newest version of
> > freesurfer 6.0 recently, it looks likes that a lot of "if (-e
> > /scratch)" have been changed to "if (-dw /scratch)". However, there
> > are still a lot of binaries in the bin directory that match the string
> > "scratch", which cause the same error that I encountered before. I am
> > wondering if it is possible for you to fix '/scratch' in the bin
> > directory.
> >
> > Thank you!
>
> -
> Fengji
>
>
>
> ___
> 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
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Re: [Freesurfer] (no subject)

[Jasmin Alves]

Yes I did. I was on the last step, the testing freesurfer when I discovered
the commands do not work

On Thu, Jan 14, 2016 at 2:14 PM, dgw  wrote:

> Jasmin,
>
> Did you follow the instructions from the wiki:
>
> https://surfer.nmr.mgh.harvard.edu/fswiki/QuickInstall
> which links to this mac specific page.
> https://surfer.nmr.mgh.harvard.edu/fswiki/MacOsInstall
>
> ?
>
> hth
> d
>
> On Thu, Jan 14, 2016 at 5:10 PM, Jasmin Alves  wrote:
> > Jasmins-MacBook-Pro:freesurfer jasminalves$ ls -l
> > $FREESURFER_HOME/bin/tksurfer
> >
> > -rwxr-xr-x  1 root  wheel  103 May 14  2013
> > /Applications/freesurfer/bin/tksurfer
> >
> >
> > Jasmins-MacBook-Pro:freesurfer jasminalves$ $> 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
> >
> > -bash: freeview: Permission denied
> >
> >
> > On Thu, Jan 14, 2016 at 2:04 PM, Douglas N Greve <
> gr...@nmr.mgh.harvard.edu>
> > wrote:
> >>
> >> Jasmin, can you just cut and paste it into the email?
> >>
> >> On 01/14/2016 04:59 PM, Jasmin Alves wrote:
> >> > Here is the output to the ls command
> >> >
> >> > On Thu, Jan 14, 2016 at 1:55 PM, Jasmin Alves  >> > > wrote:
> >> >
> >> > Hi Dr. Greve,
> >> >
> >> > I am still receiving the same message that I am denied access to
> >> > freeview. Is there anything I can do?
> >> >
> >> > Thanks,
> >> > Jasmin
> >> >
> >> > On Thu, Jan 14, 2016 at 1:22 PM, Douglas N Greve
> >> > >
> >> > wrote:
> >> >
> >> > Hi Jasmin, do you have permission to execute FS commands? What
> >> > is the
> >> > result of
> >> > ls -l $FREESURFER_HOME/bin/tksurfer
> >> >
> >> >
> >> >
> >> > On 01/14/2016 04:16 PM, Jasmin Alves wrote:
> >> > > Hello,
> >> > >
> >> > > I recently downloaded freesurfer on my mac with a Yosemite
> >> > operating
> >> > > system. The application itself appears to work, however I am
> >> > not able
> >> > > to use the command line to do any of the testing free surfer
> >> > commands,
> >> > > as I keep getting a access denied. I have attached a
> >> > screenshot. Your
> >> > > help would be very useful.
> >> > >
> >> > > Thank you,
> >> > > Jasmin
> >> > >
> >> > > --
> >> > > Jasmin Alves
> >> > > Predoctoral Student
> >> > > Medical Biology Graduate Program
> >> > > University of Southern California
> >> > > jal...@usc.edu 
> >> > >
> >> > >
> >> > >
> >> > >
> >> > > ___
> >> > > 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.
> >> >
> >> >
> >> >
> >> >
> >> > --
> >> > 

[Freesurfer] (no subject)

[Jasmin Alves]

-- 
Jasmin Alves
Predoctoral Student
Medical Biology Graduate Program
University of Southern California
jal...@usc.edu
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[Freesurfer] (no subject)

[Jasmin Alves]

Hello,

I recently downloaded freesurfer on my mac with a Yosemite operating
system. The application itself appears to work, however I am not able to
use the command line to do any of the testing free surfer commands, as I
keep getting a access denied. I have attached a screenshot. Your help would
be very useful.

Thank you,
Jasmin

-- 
Jasmin Alves
Predoctoral Student
Medical Biology Graduate Program
University of Southern California
jal...@usc.edu
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Re: [Freesurfer] QDEC. Error in Analyze: command failed: mri_glmfit

[Douglas N Greve]

how many levels does factor 1 have? How did you make the factor file?

On 01/14/2016 05:30 AM, BAUTISTA-PERPINYA Maximilià wrote:
> Hi there experts,
>
> I'm runing qdec to analyze my subject data. I am able to import the 
> qdec.table.dat, but the problem comes in the Design step. I select 
> 'Volume-based' measure, 'Diagnosis' as my discrete independent variable and 
> 'LeftAmygdala' as the continuous variable. I don't select any nuisance 
> factor. I then set my Design Name: 'LAmyDiagnosis' and click Analyze, but 
> gives me the following error:
>
> ---
>
> ERROR: QdecGlmDesign::GenerateContrasts: factor 1 must have 2 levels
> ninputs = 137
> Checking inputs
> nframestot = 137
> Allocing output
> Done allocing
> nframes = 137
> Writing to /home/freesurfer/Desktop/test005/subjects/qdec/LAmyDiagnosis/y.mgh
> gdfReadHeader: reading 
> /home/freesurfer/Desktop/test005/subjects/qdec/LAmyDiagnosis/qdec.fsgd
> INFO: DeMeanFlag keyword not found, DeMeaning will NOT be done.
> Continuous Variable Means (all subjects)
> 0 LeftAmygdala 1502.65 189.974
> Class Means of each Continuous Variable
> 1 diagnosisBPD 1497.7548
> 2 diagnosisCCP 1540.8923
> 3 diagnosisNPC 1488.5490
> INFO: gd2mtx_method is dods
> Reading source surface 
> /home/freesurfer/Desktop/test005/subjects/fsaverage/surf/lh.white
> ERROR: no contrasts specified.
> Error in Analyze: command failed: mri_glmfit --y 
> /home/freesurfer/Desktop/test005/subjects/qdec/LAmyDiagnosis/y.mgh --fsgd 
> /home/freesurfer/Desktop/test005/subjects/qdec/LAmyDiagnosis/qdec.fsgd dods 
> --glmdir /home/freesurfer/Desktop/test005/subjects/qdec/LAmyDiagnosis --surf 
> fsaverage lh
>
> ---
>
> Any recommendations? Any help is much appreciated :)
>
>
> Best,
>
> Max
>
> ___
> 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/

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but does not contain patient information, please contact the sender and properly
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Re: [Freesurfer] (no subject)

[Douglas N Greve]

Hi Jasmin, do you have permission to execute FS commands? What is the 
result of
ls -l $FREESURFER_HOME/bin/tksurfer



On 01/14/2016 04:16 PM, Jasmin Alves wrote:
> Hello,
>
> I recently downloaded freesurfer on my mac with a Yosemite operating 
> system. The application itself appears to work, however I am not able 
> to use the command line to do any of the testing free surfer commands, 
> as I keep getting a access denied. I have attached a screenshot. Your 
> help would be very useful.
>
> Thank you,
> Jasmin
>
> -- 
> Jasmin Alves
> Predoctoral Student
> Medical Biology Graduate Program
> University of Southern California
> jal...@usc.edu 
>
>
>
> ___
> 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/

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Re: [Freesurfer] Interpreting white matter regressor dat file

[Afzal, Afsana]

Hi Doug, 

These are the first few lines of the wm.dat.pca-stats.dat file:

  1   143481216.00 143481216.00 4.064.06 
  2   77359288.00 220840504.00 2.196.25 
  3   42542944.00 263383448.00 1.207.46 
  4   26329902.00 289713350.00 0.758.20 
  5   21830372.00 311543722.00 0.628.82 
  6   19145688.00 330689410.00 0.549.36 
  7   18512178.00 349201588.00 0.529.89

According to the functional connectivity tutorial 
(http://surfer.nmr.mgh.harvard.edu/fswiki/FsFastFunctionalConnectivityWalkthrough),
 usually only the first 5 components are used for white matter regression. 
However, if I understand correctly, it looks like the first five components 
only remove ~8.82% cumulative variance, is that correct? If so, how should I go 
about choosing components for white matter regression? 

Thanks, 

Afsana


__
Afsana Afzal
Clinical Research Coordinator
Massachusetts General Hospital
Division of Neurotherapeutics
Department of Psychiatry: Neurosciences
149 13th St, Room 2612
Charlestown, MA 02129
Phone: 617-643-5129
Fax: 617-726-4078


From: freesurfer-boun...@nmr.mgh.harvard.edu 
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve 
[gr...@nmr.mgh.harvard.edu]
Sent: Wednesday, January 13, 2016 12:36 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] Interpreting white matter regressor dat file

here you go
   (1) component number
   (2) variance spanned by that component
   (3) cumulative variance spanned up to that component
   (4) percent variance spanned by that component
   (5) cumulative percent variance spanned up to that component


On 01/13/2016 09:56 AM, Afzal, Afsana wrote:
> Hi,
>
> I have generated white matter regressor files for resting state
> analysis using fcseed-config and fcseed-sess. The resulting files
> include: wm.dat, wm.dat.pca-stats.dat and wm.dat.log.
>
> How do I interpret the wm.dat.pca-stats.dat file? There are 388
> numbered rows (I'm guessing one per acquisition since # of
> acquisitions is 388?) and five columns. What do the columns represent?
>
>
> Thanks for your help!
>
> - Afsana
>
> __
> *Afsana Afzal*
> Clinical Research Coordinator
> Massachusetts General Hospital
> Division of Neurotherapeutics
> Department of Psychiatry: Neurosciences
> 149 13th St, Room 2612
> Charlestown, MA 02129
> Phone: 617-643-5129
> Fax: 617-726-4078
>
>
> ___
> 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

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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
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Re: [Freesurfer] Visualizing GLM analysis error

[Bruce Fischl]

can you run mri_info on that file? Is it in fact a surface overlay?
On Thu, 
14 Jan 2016, Myers, Peter wrote:




Thanks for these comments/suggestions. Still having troubles unfortunately.


I ran the command: 

freeview 
-f$SUBJECTS_DIR/fsaverage/surf/lh.inflated:annot=aparc.annot:overlay=lh.Cog_T
rial1.glmdir/lh-Avg-thickness-Cog_Trial1/sig.mgh:overlay_threshold=4,5
-viewport 3d


I don't think there are any spaces, only colons as suggested. And I removed
the 'annot_outline' part as it does not seem to be in my  5.3 version.


I still get this error message:

mghRead(/data/jsp/human2/fcMRI/PickettK/Data/FreeSurfer5.3/fsaverage/surf/l
h.Cog_Trial1.glmdir/lh-Avg-thickness-Cog_Trial1/sig.mgh, -1): could not open
file
mghRead(/data/jsp/human2/fcMRI/PickettK/Data/FreeSurfer5.3/fsaverage/surf/l
h.Cog_Trial1.glmdir/lh-Avg-thickness-Cog_Trial1/sig.mgh, -1): could not open
file
could not read overlay data 
from/data/jsp/human2/fcMRI/PickettK/Data/FreeSurfer5.3/fsaverage/surf/lh.Cog_Tr
ial1.glmdir/lh-Avg-thickness-Cog_Trial1/sig.mgh
mghRead(/data/jsp/human2/fcMRI/PickettK/Data/FreeSurfer5.3/fsaverage/surf/l
h.Cog_Trial1.glmdir/lh-Avg-thickness-Cog_Trial1/sig.mgh, -1): could not open
file
^C
  
as well as a message from freeview that says 'failed to load surface
overlay'

I've double checked and the sig.mgh file exists in the directory, but for
some reason, it seems unable to be loaded?


Thanks much,

peter



From: freesurfer-boun...@nmr.mgh.harvard.edu
 on behalf of Douglas Greve

Sent: Thursday, January 14, 2016 12:06 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] Visualizing GLM analysis error  
also, I think that the annot_outline is a version 6 feature.

On 1/14/16 1:01 PM, Bruce Fischl wrote:
  Hi Peter

  you need a colon to separate each of the modifiers you are
  using, not a space. So

  freeview -f lh.inflated:annot=aparc.annot:outline=1:overlay=

  cheers
  Bruce

  On Thu, 14 Jan 2016, Myers, Peter wrote:

Hello all,

I am trying to visualize the results of my
GLM analysis. Unfortunately, I
keep on running into errors.

I run the command:
freeview -f
$SUBJECTS_DIR/fsaverage/surf/lh.inflated:annot=aparc.annot:annot_outline=1o

verlay=lh.Cog_Trial1.glmdir/lh-Avg-thickness-Cog_Trial1/sig.mgh:overlay_thr

eshold=4,5 -viewport 3d

When I do that command, I get the error:
Unrecognized sub-option flag 'annot_outline'

I tried to remove this from the command, and
freeview opens. But then I get
an error saying that freeview cannot open
the 'lh.Cog_Trial1.glmdir/lh-Avg-thickness-Cog_Trial1/sig.mgh'
"has many more faces than vertices! Probably trying
to use a scalar data
file as a surface!"

I tried to open the sig.mgh file through the GUI,
but then freesurfer
completely crashes with the following error:
[0]PETSC ERROR:


[0]PETSC ERROR: Caught signal number 11 SEGV:
Segmentation Violation,
probably memory access out of range
[0]PETSC ERROR: Try option -start_in_debugger or
-on_error_attach_debugger
[0]PETSC ERROR: 
orseehttp://www.mcs.anl.gov/petsc/petsc-as/documentation/troubleshooting.html
#Si
gnal[0]PETSC ERROR: or try http://valgrind.org on
linux or man libgmalloc on
Apple to find memory corruption errors
[0]PETSC ERROR: configure using
--with-debugging=yes, recompile, link, and
run
[0]PETSC ERROR: to get more information on the
crash.
[0]PETSC ERROR: - Error Message

[0]PETSC ERROR: Signal received!
[0]PETSC ERROR:


[0]PETSC ERROR: Petsc Release Version 2.3.3, Patch
13, Thu May 15 17:29:26
CDT 2008 HG revision:
4466c6289a0922df26e20626fd4a0b4dd03c8124
[0]PETSC ERROR: See docs/changes/index.html for
recent updates.
[0]PETSC ERROR: See docs/faq.html for hints about
trouble shooting.
[0]PETSC ERROR: See docs/index.html for manual
pages.
[0]PETSC ERROR:


[0]PETSC ERROR: Unknown Name on a linux-gnu named
sunshine by myerp Thu Jan
14 11:14:53 2016
[0]PETSC ERROR: Libraries 

Re: [Freesurfer] Visualizing GLM analysis error

[Myers, Peter]

It's working now!
Thank you everyone for your help.
Some settings in the GUI seemed off for some reason.

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Bruce Fischl 

Sent: Thursday, January 14, 2016 12:39 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] Visualizing GLM analysis error

can you run mri_info on that file? Is it in fact a surface overlay?
On Thu,
14 Jan 2016, Myers, Peter wrote:

>
> Thanks for these comments/suggestions. Still having troubles unfortunately.
>
>
> I ran the command:
>
> freeview 
> -f$SUBJECTS_DIR/fsaverage/surf/lh.inflated:annot=aparc.annot:overlay=lh.Cog_T
> rial1.glmdir/lh-Avg-thickness-Cog_Trial1/sig.mgh:overlay_threshold=4,5
> -viewport 3d
>
>
> I don't think there are any spaces, only colons as suggested. And I removed
> the 'annot_outline' part as it does not seem to be in my  5.3 version.
>
>
> I still get this error message:
>
> mghRead(/data/jsp/human2/fcMRI/PickettK/Data/FreeSurfer5.3/fsaverage/surf/l
> h.Cog_Trial1.glmdir/lh-Avg-thickness-Cog_Trial1/sig.mgh, -1): could not open
> file
> mghRead(/data/jsp/human2/fcMRI/PickettK/Data/FreeSurfer5.3/fsaverage/surf/l
> h.Cog_Trial1.glmdir/lh-Avg-thickness-Cog_Trial1/sig.mgh, -1): could not open
> file
> could not read overlay data 
> from/data/jsp/human2/fcMRI/PickettK/Data/FreeSurfer5.3/fsaverage/surf/lh.Cog_Tr
> ial1.glmdir/lh-Avg-thickness-Cog_Trial1/sig.mgh
> mghRead(/data/jsp/human2/fcMRI/PickettK/Data/FreeSurfer5.3/fsaverage/surf/l
> h.Cog_Trial1.glmdir/lh-Avg-thickness-Cog_Trial1/sig.mgh, -1): could not open
> file
> ^C
>
> as well as a message from freeview that says 'failed to load surface
> overlay'
>
> I've double checked and the sig.mgh file exists in the directory, but for
> some reason, it seems unable to be loaded?
>
>
> Thanks much,
>
> peter
>
>
> 
> From: freesurfer-boun...@nmr.mgh.harvard.edu
>  on behalf of Douglas Greve
> 
> Sent: Thursday, January 14, 2016 12:06 PM
> To: freesurfer@nmr.mgh.harvard.edu
> Subject: Re: [Freesurfer] Visualizing GLM analysis error
> also, I think that the annot_outline is a version 6 feature.
>
> On 1/14/16 1:01 PM, Bruce Fischl wrote:
>   Hi Peter
>
>   you need a colon to separate each of the modifiers you are
>   using, not a space. So
>
>   freeview -f lh.inflated:annot=aparc.annot:outline=1:overlay=
>
>   cheers
>   Bruce
>
>   On Thu, 14 Jan 2016, Myers, Peter wrote:
>
> Hello all,
>
> I am trying to visualize the results of my
> GLM analysis. Unfortunately, I
> keep on running into errors.
>
> I run the command:
> freeview -f
> $SUBJECTS_DIR/fsaverage/surf/lh.inflated:annot=aparc.annot:annot_outline=1o
>
> verlay=lh.Cog_Trial1.glmdir/lh-Avg-thickness-Cog_Trial1/sig.mgh:overlay_thr
>
> eshold=4,5 -viewport 3d
>
> When I do that command, I get the error:
> Unrecognized sub-option flag 'annot_outline'
>
> I tried to remove this from the command, and
> freeview opens. But then I get
> an error saying that freeview cannot open
> the 'lh.Cog_Trial1.glmdir/lh-Avg-thickness-Cog_Trial1/sig.mgh'
> "has many more faces than vertices! Probably trying
> to use a scalar data
> file as a surface!"
>
> I tried to open the sig.mgh file through the GUI,
> but then freesurfer
> completely crashes with the following error:
> [0]PETSC ERROR:
> 
> 
> [0]PETSC ERROR: Caught signal number 11 SEGV:
> Segmentation Violation,
> probably memory access out of range
> [0]PETSC ERROR: Try option -start_in_debugger or
> -on_error_attach_debugger
> [0]PETSC ERROR: 
> orseehttp://www.mcs.anl.gov/petsc/petsc-as/documentation/troubleshooting.html
> #Si
> gnal[0]PETSC ERROR: or try http://valgrind.org on
> linux or man libgmalloc on
> Apple to find memory corruption errors
> [0]PETSC ERROR: configure using
> --with-debugging=yes, recompile, link, and
> run
> [0]PETSC ERROR: to get more information on the
> crash.
> [0]PETSC ERROR: - Error Message
> 
> [0]PETSC ERROR: Signal received!
> [0]PETSC ERROR:
> 
> 
> [0]PETSC ERROR: Petsc Release Version 2.3.3, Patch
> 13, Thu May 15 17:29:26
>

Re: [Freesurfer] Visualizing GLM analysis error

[Bruce Fischl]

glad to hear it
On Thu, 14 Jan 2016, Myers, Peter wrote:

> It's working now!
> Thank you everyone for your help.
> Some settings in the GUI seemed off for some reason.
> 
> From: freesurfer-boun...@nmr.mgh.harvard.edu 
>  on behalf of Bruce Fischl 
> 
> Sent: Thursday, January 14, 2016 12:39 PM
> To: Freesurfer support list
> Subject: Re: [Freesurfer] Visualizing GLM analysis error
>
> can you run mri_info on that file? Is it in fact a surface overlay?
> On Thu,
> 14 Jan 2016, Myers, Peter wrote:
>
>>
>> Thanks for these comments/suggestions. Still having troubles unfortunately.
>>
>>
>> I ran the command:
>>
>> freeview 
>> -f$SUBJECTS_DIR/fsaverage/surf/lh.inflated:annot=aparc.annot:overlay=lh.Cog_T
>> rial1.glmdir/lh-Avg-thickness-Cog_Trial1/sig.mgh:overlay_threshold=4,5
>> -viewport 3d
>>
>>
>> I don't think there are any spaces, only colons as suggested. And I removed
>> the 'annot_outline' part as it does not seem to be in my  5.3 version.
>>
>>
>> I still get this error message:
>>
>> mghRead(/data/jsp/human2/fcMRI/PickettK/Data/FreeSurfer5.3/fsaverage/surf/l
>> h.Cog_Trial1.glmdir/lh-Avg-thickness-Cog_Trial1/sig.mgh, -1): could not open
>> file
>> mghRead(/data/jsp/human2/fcMRI/PickettK/Data/FreeSurfer5.3/fsaverage/surf/l
>> h.Cog_Trial1.glmdir/lh-Avg-thickness-Cog_Trial1/sig.mgh, -1): could not open
>> file
>> could not read overlay data 
>> from/data/jsp/human2/fcMRI/PickettK/Data/FreeSurfer5.3/fsaverage/surf/lh.Cog_Tr
>> ial1.glmdir/lh-Avg-thickness-Cog_Trial1/sig.mgh
>> mghRead(/data/jsp/human2/fcMRI/PickettK/Data/FreeSurfer5.3/fsaverage/surf/l
>> h.Cog_Trial1.glmdir/lh-Avg-thickness-Cog_Trial1/sig.mgh, -1): could not open
>> file
>> ^C
>>
>> as well as a message from freeview that says 'failed to load surface
>> overlay'
>>
>> I've double checked and the sig.mgh file exists in the directory, but for
>> some reason, it seems unable to be loaded?
>>
>>
>> Thanks much,
>>
>> peter
>>
>>
>> 
>> From: freesurfer-boun...@nmr.mgh.harvard.edu
>>  on behalf of Douglas Greve
>> 
>> Sent: Thursday, January 14, 2016 12:06 PM
>> To: freesurfer@nmr.mgh.harvard.edu
>> Subject: Re: [Freesurfer] Visualizing GLM analysis error
>> also, I think that the annot_outline is a version 6 feature.
>>
>> On 1/14/16 1:01 PM, Bruce Fischl wrote:
>>   Hi Peter
>>
>>   you need a colon to separate each of the modifiers you are
>>   using, not a space. So
>>
>>   freeview -f lh.inflated:annot=aparc.annot:outline=1:overlay=
>>
>>   cheers
>>   Bruce
>>
>>   On Thu, 14 Jan 2016, Myers, Peter wrote:
>>
>> Hello all,
>>
>> I am trying to visualize the results of my
>> GLM analysis. Unfortunately, I
>> keep on running into errors.
>>
>> I run the command:
>> freeview -f
>> $SUBJECTS_DIR/fsaverage/surf/lh.inflated:annot=aparc.annot:annot_outline=1o
>>
>> verlay=lh.Cog_Trial1.glmdir/lh-Avg-thickness-Cog_Trial1/sig.mgh:overlay_thr
>>
>> eshold=4,5 -viewport 3d
>>
>> When I do that command, I get the error:
>> Unrecognized sub-option flag 'annot_outline'
>>
>> I tried to remove this from the command, and
>> freeview opens. But then I get
>> an error saying that freeview cannot open
>> the 'lh.Cog_Trial1.glmdir/lh-Avg-thickness-Cog_Trial1/sig.mgh'
>> "has many more faces than vertices! Probably trying
>> to use a scalar data
>> file as a surface!"
>>
>> I tried to open the sig.mgh file through the GUI,
>> but then freesurfer
>> completely crashes with the following error:
>> [0]PETSC ERROR:
>> 
>> 
>> [0]PETSC ERROR: Caught signal number 11 SEGV:
>> Segmentation Violation,
>> probably memory access out of range
>> [0]PETSC ERROR: Try option -start_in_debugger or
>> -on_error_attach_debugger
>> [0]PETSC ERROR: 
>> orseehttp://www.mcs.anl.gov/petsc/petsc-as/documentation/troubleshooting.html
>> #Si
>> gnal[0]PETSC ERROR: or try http://valgrind.org on
>> linux or man libgmalloc on
>> Apple to find memory corruption errors
>> [0]PETSC ERROR: configure using
>> --with-debugging=yes, recompile, link, and
>> run
>> [0]PETSC ERROR: to get more information on the
>> crash.
>> [0]PETSC ERROR: - Error Message
>> 
>> [0]PETSC ERROR: Signal received!
>> [0]PETSC ERROR:
>> 

Re: [Freesurfer] (no subject)

[Jasmin Alves]

Hi Dr. Greve,

I am still receiving the same message that I am denied access to freeview.
Is there anything I can do?

Thanks,
Jasmin

On Thu, Jan 14, 2016 at 1:22 PM, Douglas N Greve 
wrote:

> Hi Jasmin, do you have permission to execute FS commands? What is the
> result of
> ls -l $FREESURFER_HOME/bin/tksurfer
>
>
>
> On 01/14/2016 04:16 PM, Jasmin Alves wrote:
> > Hello,
> >
> > I recently downloaded freesurfer on my mac with a Yosemite operating
> > system. The application itself appears to work, however I am not able
> > to use the command line to do any of the testing free surfer commands,
> > as I keep getting a access denied. I have attached a screenshot. Your
> > help would be very useful.
> >
> > Thank you,
> > Jasmin
> >
> > --
> > Jasmin Alves
> > Predoctoral Student
> > Medical Biology Graduate Program
> > University of Southern California
> > jal...@usc.edu 
> >
> >
> >
> > ___
> > 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.
>
>


-- 
Jasmin Alves
Predoctoral Student
Medical Biology Graduate Program
University of Southern California
jal...@usc.edu
___
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.

Re: [Freesurfer] (no subject)

[Jasmin Alves]

Here is the output to the ls command

On Thu, Jan 14, 2016 at 1:55 PM, Jasmin Alves  wrote:

> Hi Dr. Greve,
>
> I am still receiving the same message that I am denied access to freeview.
> Is there anything I can do?
>
> Thanks,
> Jasmin
>
> On Thu, Jan 14, 2016 at 1:22 PM, Douglas N Greve <
> gr...@nmr.mgh.harvard.edu> wrote:
>
>> Hi Jasmin, do you have permission to execute FS commands? What is the
>> result of
>> ls -l $FREESURFER_HOME/bin/tksurfer
>>
>>
>>
>> On 01/14/2016 04:16 PM, Jasmin Alves wrote:
>> > Hello,
>> >
>> > I recently downloaded freesurfer on my mac with a Yosemite operating
>> > system. The application itself appears to work, however I am not able
>> > to use the command line to do any of the testing free surfer commands,
>> > as I keep getting a access denied. I have attached a screenshot. Your
>> > help would be very useful.
>> >
>> > Thank you,
>> > Jasmin
>> >
>> > --
>> > Jasmin Alves
>> > Predoctoral Student
>> > Medical Biology Graduate Program
>> > University of Southern California
>> > jal...@usc.edu 
>> >
>> >
>> >
>> > ___
>> > 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.
>>
>>
>
>
> --
> Jasmin Alves
> Predoctoral Student
> Medical Biology Graduate Program
> University of Southern California
> jal...@usc.edu
>
>


-- 
Jasmin Alves
Predoctoral Student
Medical Biology Graduate Program
University of Southern California
jal...@usc.edu
___
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.

Re: [Freesurfer] (no subject)

[Douglas N Greve]

Jasmin, can you just cut and paste it into the email?

On 01/14/2016 04:59 PM, Jasmin Alves wrote:
> Here is the output to the ls command
>
> On Thu, Jan 14, 2016 at 1:55 PM, Jasmin Alves  > wrote:
>
> Hi Dr. Greve,
>
> I am still receiving the same message that I am denied access to
> freeview. Is there anything I can do?
>
> Thanks,
> Jasmin
>
> On Thu, Jan 14, 2016 at 1:22 PM, Douglas N Greve
> > wrote:
>
> Hi Jasmin, do you have permission to execute FS commands? What
> is the
> result of
> ls -l $FREESURFER_HOME/bin/tksurfer
>
>
>
> On 01/14/2016 04:16 PM, Jasmin Alves wrote:
> > Hello,
> >
> > I recently downloaded freesurfer on my mac with a Yosemite
> operating
> > system. The application itself appears to work, however I am
> not able
> > to use the command line to do any of the testing free surfer
> commands,
> > as I keep getting a access denied. I have attached a
> screenshot. Your
> > help would be very useful.
> >
> > Thank you,
> > Jasmin
> >
> > --
> > Jasmin Alves
> > Predoctoral Student
> > Medical Biology Graduate Program
> > University of Southern California
> > jal...@usc.edu 
> >
> >
> >
> >
> > ___
> > 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.
>
>
>
>
> -- 
> Jasmin Alves
> Predoctoral Student
> Medical Biology Graduate Program
> University of Southern California
> jal...@usc.edu 
>
>
>
>
> -- 
> Jasmin Alves
> Predoctoral Student
> Medical Biology Graduate Program
> University of Southern California
> jal...@usc.edu 
>
>
>
> ___
> 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

Re: [Freesurfer] (no subject)

[Jasmin Alves]

Jasmins-MacBook-Pro:freesurfer jasminalves$ ls -l
$FREESURFER_HOME/bin/tksurfer

-rwxr-xr-x  1 root  wheel  103 May 14  2013
/Applications/freesurfer/bin/tksurfer


Jasmins-MacBook-Pro:freesurfer jasminalves$ $> 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

-bash: freeview: Permission denied

On Thu, Jan 14, 2016 at 2:04 PM, Douglas N Greve 
wrote:

> Jasmin, can you just cut and paste it into the email?
>
> On 01/14/2016 04:59 PM, Jasmin Alves wrote:
> > Here is the output to the ls command
> >
> > On Thu, Jan 14, 2016 at 1:55 PM, Jasmin Alves  > > wrote:
> >
> > Hi Dr. Greve,
> >
> > I am still receiving the same message that I am denied access to
> > freeview. Is there anything I can do?
> >
> > Thanks,
> > Jasmin
> >
> > On Thu, Jan 14, 2016 at 1:22 PM, Douglas N Greve
> > >
> wrote:
> >
> > Hi Jasmin, do you have permission to execute FS commands? What
> > is the
> > result of
> > ls -l $FREESURFER_HOME/bin/tksurfer
> >
> >
> >
> > On 01/14/2016 04:16 PM, Jasmin Alves wrote:
> > > Hello,
> > >
> > > I recently downloaded freesurfer on my mac with a Yosemite
> > operating
> > > system. The application itself appears to work, however I am
> > not able
> > > to use the command line to do any of the testing free surfer
> > commands,
> > > as I keep getting a access denied. I have attached a
> > screenshot. Your
> > > help would be very useful.
> > >
> > > Thank you,
> > > Jasmin
> > >
> > > --
> > > Jasmin Alves
> > > Predoctoral Student
> > > Medical Biology Graduate Program
> > > University of Southern California
> > > jal...@usc.edu 
> > >
> > >
> > >
> > >
> > > ___
> > > 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.
> >
> >
> >
> >
> > --
> > Jasmin Alves
> > Predoctoral Student
> > Medical Biology Graduate Program
> > University of Southern California
> > jal...@usc.edu 
> >
> >
> >
> >
> > --
> > Jasmin Alves
> > Predoctoral Student
> > Medical Biology Graduate Program
> > University of Southern California
> > jal...@usc.edu 
> >
> >
> >
> > ___
> > 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: 

Re: [Freesurfer] (no subject)

[dgw]

Jasmin,

Did you follow the instructions from the wiki:

https://surfer.nmr.mgh.harvard.edu/fswiki/QuickInstall
which links to this mac specific page.
https://surfer.nmr.mgh.harvard.edu/fswiki/MacOsInstall

?

hth
d

On Thu, Jan 14, 2016 at 5:10 PM, Jasmin Alves  wrote:
> Jasmins-MacBook-Pro:freesurfer jasminalves$ ls -l
> $FREESURFER_HOME/bin/tksurfer
>
> -rwxr-xr-x  1 root  wheel  103 May 14  2013
> /Applications/freesurfer/bin/tksurfer
>
>
> Jasmins-MacBook-Pro:freesurfer jasminalves$ $> 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
>
> -bash: freeview: Permission denied
>
>
> On Thu, Jan 14, 2016 at 2:04 PM, Douglas N Greve 
> wrote:
>>
>> Jasmin, can you just cut and paste it into the email?
>>
>> On 01/14/2016 04:59 PM, Jasmin Alves wrote:
>> > Here is the output to the ls command
>> >
>> > On Thu, Jan 14, 2016 at 1:55 PM, Jasmin Alves > > > wrote:
>> >
>> > Hi Dr. Greve,
>> >
>> > I am still receiving the same message that I am denied access to
>> > freeview. Is there anything I can do?
>> >
>> > Thanks,
>> > Jasmin
>> >
>> > On Thu, Jan 14, 2016 at 1:22 PM, Douglas N Greve
>> > >
>> > wrote:
>> >
>> > Hi Jasmin, do you have permission to execute FS commands? What
>> > is the
>> > result of
>> > ls -l $FREESURFER_HOME/bin/tksurfer
>> >
>> >
>> >
>> > On 01/14/2016 04:16 PM, Jasmin Alves wrote:
>> > > Hello,
>> > >
>> > > I recently downloaded freesurfer on my mac with a Yosemite
>> > operating
>> > > system. The application itself appears to work, however I am
>> > not able
>> > > to use the command line to do any of the testing free surfer
>> > commands,
>> > > as I keep getting a access denied. I have attached a
>> > screenshot. Your
>> > > help would be very useful.
>> > >
>> > > Thank you,
>> > > Jasmin
>> > >
>> > > --
>> > > Jasmin Alves
>> > > Predoctoral Student
>> > > Medical Biology Graduate Program
>> > > University of Southern California
>> > > jal...@usc.edu 
>> > >
>> > >
>> > >
>> > >
>> > > ___
>> > > 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.
>> >
>> >
>> >
>> >
>> > --
>> > Jasmin Alves
>> > Predoctoral Student
>> > Medical Biology Graduate Program
>> > University of Southern California
>> > jal...@usc.edu 
>> >
>> >
>> >
>> >
>> > --
>> > Jasmin Alves
>> > Predoctoral Student
>> > Medical Biology Graduate Program
>> > University of Southern California
>> > jal...@usc.edu 
>> >
>> >
>> >
>> >