Re: [Freesurfer] How to compile FreeSurfer with CUDA?

[Markus.Mertens]

I am using Mageia 6 with CUDA and gcc installed from official 
Mageia-repositories:

[mer@thalamus ~]$ uname -a
Linux thalamus 4.14.16-server-1.mga6 #1 SMP Wed Jan 31 21:02:35 UTC 2018 x86_64 
x86_64 x86_64 GNU/Linux
[mer@thalamus ~]$ nvcc --version
nvcc: NVIDIA (R) Cuda compiler driver
Copyright (c) 2005-2016 NVIDIA Corporation
Built on Tue_Jan_10_13:22:03_CST_2017
Cuda compilation tools, release 8.0, V8.0.61
[mer@thalamus ~]$ gcc -v
Es werden eingebaute Spezifikationen verwendet.
COLLECT_GCC=gcc
COLLECT_LTO_WRAPPER=/usr/lib/gcc/x86_64-mageia-linux-gnu/5.4.0/lto-wrapper
Ziel: x86_64-mageia-linux-gnu
Konfiguriert mit: ../configure --prefix=/usr --libexecdir=/usr/lib 
--with-slibdir=/lib64 --with-pkgversion='Mageia 5.4.0-5.mga6' 
--with-bugurl=https://bugs.mageia.org/ --mandir=/usr/share/man 
--infodir=/usr/share/info --enable-checking=release 
--enable-languages=c,c++,ada,fortran,objc,obj-c++,java --enable-linker-build-id 
--build=x86_64-mageia-linux-gnu --host=x86_64-mageia-linux-gnu 
--with-cpu=generic --with-system-zlib --enable-threads=posix --enable-shared 
--enable-objc-gc --enable-long-long --enable-__cxa_atexit 
--disable-libunwind-exceptions --enable-clocale=gnu --enable-java-awt=gtk 
--with-java-home=/usr/lib/jvm/java-1.5.0-gcj-1.5.0.0/jre 
--with-ecj-jar=/usr/share/java/eclipse-ecj.jar --enable-gtk-cairo 
--disable-libjava-multilib --enable-ssp --disable-libssp --disable-werror 
--with-isl --with-python-dir=/lib/python2.7/site-packages --enable-lto
Thread-Modell: posix
gcc-Version 5.4.0 (Mageia 5.4.0-5.mga6)
[mer@thalamus ~]$

GPU: Nvidia Quadro K4200.

Unfortunately, I cannot uninstall mesaGLU because my desktop environment (KDE) 
does depends on it.



Date: Mon, 5 Feb 2018 16:18:05 +
From: Melvin Robinson 
Subject: Re: [Freesurfer] How to compile FreeSurfer with CUDA?
To: "freesurfer@nmr.mgh.harvard.edu" 
Message-ID: <0ec7e124a71744d9b2f1892744986...@uttyler.edu>
Content-Type: text/plain; charset="iso-8859-1"

Once upon a time I had many problems with OpenGL/GLU problems in my FreeSurfer 
build.  Ultimately the problem was that the version of GLU installed with Mesa 
package was not really compatible with the compiler that I was using.   After 
straightening this problem out using the configure option --with-cuda allowed 
me to build with CUDA 9.1 with no problems.


What is your setup?  Compilers?  GPU?


From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of markus.mert...@evkb.de 

Sent: Monday, February 5, 2018 7:41 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] How to compile FreeSurfer with CUDA?

Hello Freesurfer experts,

I am trying to compile FreeSurfer to make use of its CUDA capabilities. The 
precompiled version does not run on my system. But when I try to compile 
FreeSurfer I get the following error:

# ./configure --with-pkgs-dir=/usr/local/centos6-x86_64-packages 
--enable-fermi-gpu
...
configure: Getting OpenGL info...
checking GL directory... gl directory is /usr/include
checking windows.h usability... no
checking windows.h presence... no
checking for windows.h... no
checking for OpenGL library... no
configure: error: FATAL: GL not found, but needed for  tcltkapps XawPlusapps 
kwwapps wxwapps. Use --with-gl-dir=... to specify


But OpenGL is installed:

# ll /usr/lib64/libGL.so*
lrwxrwxrwx 1 root root 14 Jan 15 23:35 /usr/lib64/libGL.so -> 
libGL.so.1.2.0*
lrwxrwxrwx 1 root root 14 Jan 15 23:35 /usr/lib64/libGL.so.1 -> 
libGL.so.1.2.0*
-rwxr-xr-x 1 root root 452752 Jan 15 23:37 /usr/lib64/libGL.so.1.2.0*
# ll /usr/include/GL/gl.h
-rw-r--r-- 1 root root 80615 Jan 15 23:35 /usr/include/GL/gl.h
#


The configure script did not ask for CUDA, yet. But CUDA is also installed in 
/usr/lib64:

# ll /usr/lib64/libcuda*
-rw-r--r-- 1 root root 556000 Jan 13  2017 /usr/lib64/libcudadevrt.a
lrwxrwxrwx 1 root root 16 Jan 13  2017 /usr/lib64/libcudart.so -> 
libcudart.so.8.0*
lrwxrwxrwx 1 root root 19 Jan 13  2017 /usr/lib64/libcudart.so.8.0 -> 
libcudart.so.8.0.61*
-rwxr-xr-x 1 root root 415432 Jan 13  2017 /usr/lib64/libcudart.so.8.0.61*
-rw-r--r-- 1 root root 775162 Jan 13  2017 /usr/lib64/libcudart_static.a
#


Adding the option  "--with-gl-dir=/usr/lib64" to the configure script does not 
help. What else could I try?

Regards,

Markus

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Re: [Freesurfer] fast_selxavg3.m error/analysis.info file

[Yagmur Ozdemir 19]

That works, thank you!

Best
Idil 

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: Monday, February 05, 2018 9:21 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] fast_selxavg3.m error/analysis.info file

Try running selxavg3-sess with -monly sxa3.m

Then start matlab and run sxa3.m


On 02/05/2018 02:02 PM, Yagmur Ozdemir 19 wrote:
> Dr. Greve,
>
> I tried with root access and it still gave the same error. I am using a 
> virtual machine from our server that I connect with VCN, and it has 
> freesurfer and matlab installed and setup in its shell. The VM has Ubuntu 
> 16.04 (Xenial), Freesurfer v.6, and Matlab R2016b. I appreciate your help.
>
> Best
> Idil
> 
> 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: Monday, February 05, 2018 8:34 PM
> To: freesurfer@nmr.mgh.harvard.edu
> Subject: Re: [Freesurfer] fast_selxavg3.m error/analysis.info file
>
> I don't know, it is all very weird. What platform are you using?
>
>
> On 02/05/2018 01:27 PM, Yagmur Ozdemir 19 wrote:
>> Dr. Greve,
>>
>> Yes I have tried making new files. (I also gave the previous files and 
>> folders full permission with chmod which again didn't work) Mkanalysis-sess 
>> did not have any problems as expected, but mkcontrast-sess failed for the 
>> same reason of not being able to open the .config file that it should be 
>> creating under the analysis folder.
>>
>> I am not the root user of the system, but maybe getting sudo access would be 
>> helpful? I can look into this.
>>
>> Best
>> Idil
>> 
>> From: freesurfer-boun...@nmr.mgh.harvard.edu 
>> [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas Greve 
>> [gr...@nmr.mgh.harvard.edu]
>> Sent: Monday, February 05, 2018 6:53 PM
>> To: freesurfer@nmr.mgh.harvard.edu
>> Subject: Re: [Freesurfer] fast_selxavg3.m error/analysis.info file
>>
>> I cannot replicate this. There must be some strange permission error.
>> Can you try to make a new analysis with a different name and just see if
>> fails?
>>
>>
>> On 2/4/18 12:50 PM, Yagmur Ozdemir 19 wrote:
>>> Hello Dr. Greve,
>>>
>>> The analysis.info file is below. I should also say that, when I am trying 
>>> to create new analysis and contrast files, while creating the .config file 
>>> for contrast, th system gives the same error saying that it cannot enter 
>>> the file.
>>>
>>> # FSBUILD freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c
>>> # MKAVERSION $Id: mkanalysis-sess,v 1.78 2015/12/10 22:51:30 zkaufman Exp $
>>> # MKACMD /home/vm01/local/freesurfer/fsfast/bin/mkanalysis-sess -surface 
>>> self lh -analysis rtopyTR2.lh -paradigm rtopy.par -TR 2 -nconditions 1 
>>> -event-related -fwhm 5 -per-run -fsd bold -refeventdur 10 -gammafit 2.25 
>>> 1.25 -force
>>> # DATE Tue Jan 30 07:14:05 EST 2018
>>>
>>> analysis rtopyTR2.lh
>>> mcstem fmcpr
>>> fsd bold
>>> TR 2
>>> RegDOF 6
>>> PerSession 0
>>> RawSpace surface self lh
>>> mask brain
>>> RawFWHM 5
>>> RawSTC none
>>> nSliceGroups 1
>>> UseB0DC 0
>>> ApplySubCortMask 1
>>> inorm 100
>>> acfbins 30
>>> fixacf  1
>>> acffwhm 20
>>> acfsvd  0
>>> designtype event-related
>>> nskip 0
>>> polyfit 2
>>> HPFCutoffHz 0
>>> HeteroGCor 0
>>> nconditions 1
>>> parname rtopy.par
>>> RefEventDur 10
>>> timewindow 40.00
>>> prestim 0
>>> TER 0.05
>>> gamma 2.25 1.25 2 0
>>> stimulusdelay -1.
>>> Condition 1 Condition01
>>>
>>> Best,
>>> Idil
>>> 
>>> From: freesurfer-boun...@nmr.mgh.harvard.edu 
>>> [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas Greve 
>>> [gr...@nmr.mgh.harvard.edu]
>>> Sent: Saturday, February 03, 2018 9:21 PM
>>> To: freesurfer@nmr.mgh.harvard.edu
>>> Subject: Re: [Freesurfer] fast_selxavg3.m error/analysis.info file
>>>
>>> Strange. Can you send me the analysis.info file?
>>>
>>>
>>> On 1/31/18 9:26 AM, Yagmur Ozdemir 19 wrote:
 Hello Dr. Greve,

 Yes it exists. The output below was with debug option.

 Best
 Idil
 
 From: freesurfer-boun...@nmr.mgh.harvard.edu 
 [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas Greve 
 [gr...@nmr.mgh.harvard.edu]
 Sent: Tuesday, January 30, 2018 8:40 PM
 To: freesurfer@nmr.mgh.harvard.edu
 Subject: Re: [Freesurfer] fast_selxavg3.m error/analysis.info file

 Does the file 
 /home/vm01/local/freesurfer/Project_bold/rtopyTR2.rh/analysis.info exist? 
 If so, can you run it with -debug as the first option and send the 
 terminal output?

 On 1/30/18 8:51 AM, Yagmur Ozdemir 19 wrote:


 Hello FreeSurfer experts,

 I am getting this strange error when running selxav

[Freesurfer] Gray matter mask

[Hanna Vasilevskaya]

Hello FS team,


I am new to FS and using version 5.3 on a Mac. I have minimal programming 
background and this might be a very easy question, however I was not able to 
find a similar one in the archive.


I have T1 MRI images from multiple subjects and I need to extract the brain 
gray matter mask (just cortical regions, without cerebellum). I will then use 
this mask as an ROI to extract PET activity.


Would you happen to know a way for this?


Thank you greatly,

Anna
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[Freesurfer] recommendation for T1 and T2-based sequences use with FreeSurfer

[Colm Connolly]

Hi everybody,

I’m endeavoring to help a researcher come up with a protocol which might be 
“optimal” (in some sense) for use with FreeSurfer. I’ve not really used 
FreeSurfer much hence my lack of familiarity with what the recommended 
sequences are for use with FreeSurfer.

Having searched around, I’ve found [1]. Do the recommendations in [1] still 
apply?

I’d like the researcher to get good pial surface estimate so would like to be 
able to recommend that he perform a T2 scan as well. Having read through [2], 
it makes mention of T2 and FLAIR images for improving pial surface estimation. 
Is the FLASH image recommended in [1] appropriate for use with the -T2 or 
-FLAIR args to recon-all?

We’ll be running these scans on a 3T Siemens Prisma running V11c software. Are 
there particular scans that you recommend for this particular scanner or again 
does [1] apply?

[1] 
https://surfer.nmr.mgh.harvard.edu/fswiki/FreeSurferWiki?action=AttachFile&do=get&target=FreeSurfer_Suggested_Morphometry_Protocols.pdf
[2] 
https://surfer.nmr.mgh.harvard.edu/fswiki/recon-all#UsingT2orFLAIRdatatoimprovepialsurfaces

Thanks in advance for you time,

Regards,
--
Colm G. Connolly, PhD
Dept of Biomedical Sciences
Florida State University
Tallahassee, FL 32306
Tel: +1-850-644-2105
https://www.researchgate.net/profile/Colm_Connolly2

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Re: [Freesurfer] fast_selxavg3.m error/analysis.info file

[Douglas Greve]

good, but that is not a long-term solution. I don't know why that is 
working but it does not work when you run it from the shell. There must 
be some kind of permission or id change when you run it from the shell. 
I don't know.


On 2/6/18 8:55 AM, Yagmur Ozdemir 19 wrote:
> That works, thank you!
>
> Best
> Idil
> 
> 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: Monday, February 05, 2018 9:21 PM
> To: freesurfer@nmr.mgh.harvard.edu
> Subject: Re: [Freesurfer] fast_selxavg3.m error/analysis.info file
>
> Try running selxavg3-sess with -monly sxa3.m
>
> Then start matlab and run sxa3.m
>
>
> On 02/05/2018 02:02 PM, Yagmur Ozdemir 19 wrote:
>> Dr. Greve,
>>
>> I tried with root access and it still gave the same error. I am using a 
>> virtual machine from our server that I connect with VCN, and it has 
>> freesurfer and matlab installed and setup in its shell. The VM has Ubuntu 
>> 16.04 (Xenial), Freesurfer v.6, and Matlab R2016b. I appreciate your help.
>>
>> Best
>> Idil
>> 
>> 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: Monday, February 05, 2018 8:34 PM
>> To: freesurfer@nmr.mgh.harvard.edu
>> Subject: Re: [Freesurfer] fast_selxavg3.m error/analysis.info file
>>
>> I don't know, it is all very weird. What platform are you using?
>>
>>
>> On 02/05/2018 01:27 PM, Yagmur Ozdemir 19 wrote:
>>> Dr. Greve,
>>>
>>> Yes I have tried making new files. (I also gave the previous files and 
>>> folders full permission with chmod which again didn't work) Mkanalysis-sess 
>>> did not have any problems as expected, but mkcontrast-sess failed for the 
>>> same reason of not being able to open the .config file that it should be 
>>> creating under the analysis folder.
>>>
>>> I am not the root user of the system, but maybe getting sudo access would 
>>> be helpful? I can look into this.
>>>
>>> Best
>>> Idil
>>> 
>>> From: freesurfer-boun...@nmr.mgh.harvard.edu 
>>> [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas Greve 
>>> [gr...@nmr.mgh.harvard.edu]
>>> Sent: Monday, February 05, 2018 6:53 PM
>>> To: freesurfer@nmr.mgh.harvard.edu
>>> Subject: Re: [Freesurfer] fast_selxavg3.m error/analysis.info file
>>>
>>> I cannot replicate this. There must be some strange permission error.
>>> Can you try to make a new analysis with a different name and just see if
>>> fails?
>>>
>>>
>>> On 2/4/18 12:50 PM, Yagmur Ozdemir 19 wrote:
 Hello Dr. Greve,

 The analysis.info file is below. I should also say that, when I am trying 
 to create new analysis and contrast files, while creating the .config file 
 for contrast, th system gives the same error saying that it cannot enter 
 the file.

 # FSBUILD freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c
 # MKAVERSION $Id: mkanalysis-sess,v 1.78 2015/12/10 22:51:30 zkaufman Exp $
 # MKACMD /home/vm01/local/freesurfer/fsfast/bin/mkanalysis-sess -surface 
 self lh -analysis rtopyTR2.lh -paradigm rtopy.par -TR 2 -nconditions 1 
 -event-related -fwhm 5 -per-run -fsd bold -refeventdur 10 -gammafit 2.25 
 1.25 -force
 # DATE Tue Jan 30 07:14:05 EST 2018

 analysis rtopyTR2.lh
 mcstem fmcpr
 fsd bold
 TR 2
 RegDOF 6
 PerSession 0
 RawSpace surface self lh
 mask brain
 RawFWHM 5
 RawSTC none
 nSliceGroups 1
 UseB0DC 0
 ApplySubCortMask 1
 inorm 100
 acfbins 30
 fixacf  1
 acffwhm 20
 acfsvd  0
 designtype event-related
 nskip 0
 polyfit 2
 HPFCutoffHz 0
 HeteroGCor 0
 nconditions 1
 parname rtopy.par
 RefEventDur 10
 timewindow 40.00
 prestim 0
 TER 0.05
 gamma 2.25 1.25 2 0
 stimulusdelay -1.
 Condition 1 Condition01

 Best,
 Idil
 
 From: freesurfer-boun...@nmr.mgh.harvard.edu 
 [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas Greve 
 [gr...@nmr.mgh.harvard.edu]
 Sent: Saturday, February 03, 2018 9:21 PM
 To: freesurfer@nmr.mgh.harvard.edu
 Subject: Re: [Freesurfer] fast_selxavg3.m error/analysis.info file

 Strange. Can you send me the analysis.info file?


 On 1/31/18 9:26 AM, Yagmur Ozdemir 19 wrote:
> Hello Dr. Greve,
>
> Yes it exists. The output below was with debug option.
>
> Best
> Idil
> 
> From: freesurfer-boun...@nmr.mgh.harvard.edu 
> [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas Greve 
> [gr...@nmr.mgh.harvard.edu]
> Sent: Tuesday, January 30, 2018 8:40 PM
> To: freesurfer@nmr.mgh.harvard.edu
>

[Freesurfer] Multiple regression FreeSurfer

[Martin Juneja]

Hi,

I am interested in correlating cortical volume measures with behavioral
data X1, after regressing out the effect of age and sex. For that I ran
following commands:

mri_glmfit --y lh.X1.CV.15.mgh --fsgd X1.fsgd dods --C Corr-X1-cor.mtx
--surf fsaverage lh --cortex --glmdir lh.X1_CV.glmdir

mri_glmfit-sim --glmdir lh.X1_CV.glmdir --cache 2 abs --cwp 0.05 --2spaces

where X1.fsgd is following:

GroupDescriptorFile 1
Class Male
Class Female
Variables X1 Age
Input S001 Male 127 36
 so on

and Corr-X1-cor.mtx is 0 0 0 0 1

I was wondering how can I use  multiple regression approach e.g. how can I
correlate CV and X1 after accounting for thickness and area or how can I
correlate gyrification and X1 after accounting for CV and thickness etc.

I am not sure what will be my commands for that and what will be fsgd and
mtx files?

Thanks for your help.
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[Freesurfer] PROGRAMMER/ DATA ANALYST II

[Arpana Gupta]

PROGRAMMER/ANALYST II
G. OPPENHEIMER CENTER FOR NEUROBIOLOGY OF STRESS AND RESILIENCE 
UNIVERSITY OF CALIFORNIA, LOS ANGELES
 
Background:
The G. Oppenheimer Center for Neurobiology of Stress and Resilience (Mayer Lab) 
in the Vatche and Tamar Manoukian Division of Digestive Diseases, David Geffen 
School of Medicine at the University of California, Los Angeles is seeking a 
full time Programmer/Analyst  for a multi-site funded translational research 
group studying brain-gut microbiome interactions in obesity and functional pain 
disorders including irritable bowel syndrome (IBS), chronic pelvic pain and 
interstitial cystitis, and vulvodynia.
 
This position will use multimodal MRI sequences to study structural and 
functional circuit dynamics cross sectionally and longitudinally within a 
dimensional systems biology approach. The programmer’s main responsibilities 
include: programming and optimizing automated data quality control, 
preprocessing, computational, and analyses pipelines for large scale multimodal 
brain imaging and biological data. The candidate should have a strong 
programming background in one or more of the following areas: bioengineering  
engineering, computer science, statistics, physics, and/or neuroscience. There 
will be opportunities to address basic and pathophysiological systems  
questions, in addition to work in an environment that emphasizes translational 
and clinical research skills (e.g. target discovery, individualized treatment 
development and biomarker/predictor development).
 
The G. Oppenheimer Center of Neurobiology of Stress and resilience is a dynamic 
multidisciplinary group directed by Emeran A. Mayer, MD, PhD  conducting 
clinical, translational and basic neuroscience research. You will work directly 
with him and an array of principle investigators, collaborators and 
co-investigators.


Duties and Responsibilities:
The Scientific Programmer and Data Analyst responsibilities will include, but 
are not limited to:
1. Maintain and continue to develop a full-stack application for managing and 
analyzing neuroimaging data <>.  The back-end consists of ~9000 lines of Matlab 
code for processing data and over 1 lines of MySQL stored procedures and 
standard SQL for triggers, views, etc.  The front-end consists of ~1 lines 
of Javascript/JQuery and PHP code that allows for data entry and reporting.  
This application is in production and stable. 
2. Programming and optimizing automated data quality control, preprocessing, 
computational and analyses pipelines for large-scale multimodal brain imaging, 
including resting‐state and task-based fMRI, DTI and volumetric data.
3. Implement and support statistical analyses and scripts for biological (e.g. 
microbiome, genetic, etc.), behavioral, clinical and neuroscience data. This 
will include performing mathematical calculations/statistical analyses needed 
for scientific research
4. Implementation of iCloud processing and analyses pipelines such as the Human 
Connectome Project.
5. Implementation of data visualization programs on MRI and biological data
6. Process and analyze fMRI data: 1st level analysis
7. Work closely with data management specialist on data requests and system 
upgrades This would include assisting in the creation of databases, query tools 
for data mining, and documentation on their effective use.
8. Create and update ‘standard operating protocol’ (SOP) documents for various 
CNSR lab studies and/or procedures
9. Coordinate data integration from multiple ongoing studies
10. Train students and create learning tutorials for basic quality control and 
preprocessing of neuroimaging data. 
11. Maintain detailed logs of work flow, generated codes and scripts, and 
documentation of processes
12. Communicate issues and concerns as they arise to PIs, nurses and other 
relevant research staff
 
Required Qualifications: 
B.A., B.S. Masters or equivalent with background in bioengineering  
engineering, computer science, statistics, physics, and/or neuroscience.  
Quantitative and extremely proficient with multiple neuroimaging analysis 
platforms (HCP Pipeline, FreeSurfer, SPM, FSL, AFNI, GIFT, TrackVis, CONN, 
etc.).
Strong programming skills and comfort with diverse computing environments 
required (Matlab, UNIX/BASH language, MySQL, PHP, Javascript/JQuery are 
essential).
Strong background in statistics and statistical software scripting (e.g. R, 
Python, QIIME).
Experience with data visualization (d3.js or other is a plus)
Strong interpersonal skills and a high level of organization with careful 
attention to detail are absolutely required. This position requires a high 
degree of motivation, organization, and self‐sufficiency, although some 
training and supervision will be provided. 

Additional Qualifications:
Experience with neuroimaging, biological, and behavioral databases is an 
advantage.
Experience with network analyses, machine learning and modeling confer a 
significant advantage.
Graph

Re: [Freesurfer] Using subject specific template, atlas, & TPM

[Saturne Fox]

Hey !

Is it possible not to receive the mails anymore ?

Best regards,
Antoine

Le 11 janv. 2018 18:27, "Ramesh Babu"  a écrit :

> Dear experts,
>
> I have analysed T1 data using Freesurfer. Now we have created atlas,
> template & tissue probability map using different methods and softwares. I
> need your help to use template in freesufer, so that we can compare with
> default template and our template. Please help me to put these images in
> appropriate folders in Freesurfer.
>
>
> Thank you
> RB
>
>
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Re: [Freesurfer] Using subject specific template, atlas, & TPM

[Ricardo Valle]

Take a look at the bottom of this page: 
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer 

> On Feb 6, 2018, at 2:04 PM, Saturne Fox  wrote:
> 
> Hey !  
> 
> Is it possible not to receive the mails anymore ?
> 
> Best regards,
> Antoine 
> 
> Le 11 janv. 2018 18:27, "Ramesh Babu"  > a écrit :
> Dear experts, 
> 
> I have analysed T1 data using Freesurfer. Now we have created atlas, template 
> & tissue probability map using different methods and softwares. I need your 
> help to use template in freesufer, so that we can compare with default 
> template and our template. Please help me to put these images in appropriate 
> folders in Freesurfer.
> 
> 
> Thank you 
> RB
> 
> 
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Re: [Freesurfer] Removing labels after extending parcellation into white matter

[Michiko H.]

Hi Doug,

That's very helpful, thank you! I have 2 follow-up questions though:

1. Is it possible to merge the cortical label (e.g. label 1001
ctx-lh-bankssts) with its corresponding label that extends into the WM
(e.g. label 3001 wm-lh-bankssts)? I'm not completely sure but this may/may
not give better results when tracking between labels as nodes.

2. Is it possible to include the subcortical structures in the final masked
image?

Thank you so much!
Michiko

On Mon, Feb 5, 2018 at 12:30 PM, Douglas Greve 
wrote:

> You mean you want to remove everything but the WM labels? You can do it in
> two steps:
>
> 1. Create a mask of the wm labels:
>
> mri_binarize --i aparc+aseg+2mm.nii.gz --min 2999.5 --max 4035.5 --o
> wm.mask.nii.gz
>
> 2. Mask the wmparc:
>
> mri_mask aparc+aseg+2mm.nii.gz wm.mask.nii.gz aparc+aseg+2mm.masked.nii.gz
>
>
>
>
> On 2/4/18 5:28 PM, Michiko H. wrote:
>
> Hi Freesurfer experts,
>
> I am wondering if it is possible to remove the original labels after
> extending the parcellation by 2mm into the WM for tractography? I don't
> wish to have tractography run on both sets of labels considering the
> algorithm would take into account the streamlines terminating at nodes
> defined by the labels so it doesn't quite make sense to count streamlines
> terminating at both the original label separately from the new label
> extending into the WM.
>
> I used the following command for growing the parcellation into WM:
>
> mri_aparc2aseg --s subj --annot aparc --wmparc-dmax 2 --labelwm
> --hypo-as-wm --o $SUBJECTS_DIR/$subj/mri/aparc+aseg+2mm.nii.gz
>
>
> Would appreciate help and suggestions!
>
>
> Thanks,
>
> Michiko.
>
>
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Re: [Freesurfer] recommendation for T1 and T2-based sequences use with FreeSurfer

[Matt Glasser]

I think the HCP CCF protocol is a good start:

http://protocols.humanconnectome.org/

Peace,

Matt.

From:   on behalf of Colm Connolly

Reply-To:  Freesurfer support list 
Date:  Tuesday, February 6, 2018 at 10:41 AM
To:  "freesurfer@nmr.mgh.harvard.edu" 
Subject:  [Freesurfer] recommendation for T1 and T2-based sequences use with
FreeSurfer

Hi everybody, 

I¹m endeavoring to help a researcher come up with a protocol which might be
³optimal² (in some sense) for use with FreeSurfer. I¹ve not really used
FreeSurfer much hence my lack of familiarity with what the recommended
sequences are for use with FreeSurfer.

Having searched around, I¹ve found [1]. Do the recommendations in [1] still
apply?

I¹d like the researcher to get good pial surface estimate so would like to
be able to recommend that he perform a T2 scan as well. Having read through
[2], it makes mention of T2 and FLAIR images for improving pial surface
estimation. Is the FLASH image recommended in [1] appropriate for use with
the -T2 or -FLAIR args to recon-all?

We¹ll be running these scans on a 3T Siemens Prisma running V11c software.
Are there particular scans that you recommend for this particular scanner or
again does [1] apply?

[1] 
https://surfer.nmr.mgh.harvard.edu/fswiki/FreeSurferWiki?action=AttachFile&d
o=get&target=FreeSurfer_Suggested_Morphometry_Protocols.pdf
[2] 
https://surfer.nmr.mgh.harvard.edu/fswiki/recon-all#UsingT2orFLAIRdatatoimpr
ovepialsurfaces

Thanks in advance for you time,

Regards,
--
Colm G. Connolly, PhD
Dept of Biomedical Sciences
Florida State University
Tallahassee, FL 32306
Tel: +1-850-644-2105
https://www.researchgate.net/profile/Colm_Connolly2

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[Freesurfer] brainGraph (graph theory analysis in R) major release: v2.0.0

[Chris Watson]

Dear Freesurfer users,

I am pleased to announce the 2nd major release of my R package for graph
theory analysis of brain MRI data, "brainGraph".
The main page on CRAN is at: https://cran.r-project.org/
web/packages/brainGraph/index.html
The GitHub repository is at: https://github.com/cwatson/brainGraph


*Installation*
The latest version is already on CRAN for Linux distributions, and should
be for Windows and Mac OS X soon (but there may be issues on non-Linux
systems; see Chapter 1 of the User Guide).

To install directly from CRAN:
> install.packages('brainGraph')

In the meantime (and for development versions), you may install from GitHub
using the R package "devtools":
> devtools::install_github('cwatson/brainGraph')


*Getting help*
The new User Guide has been completely overhauled, and now has a permanent
link at: my GitHub Pages site (PDF warning)
. Please start at
the "Preface".

You may also get help by opening an Issue
 on the GitHub
repository, or join
the Google Group
.


*New features*
You can find the release notes/changelog in NEWS.md, at:
https://github.com/cwatson/brainGraph/blob/master/NEWS.md

Major additions (since v1.0.0) that should be of interest include:

   - Vertex- and graph-level *mediation analysis* (chapter 11 of the Guide)
   - Multi-threshold permutation correction (MTPC) for GLM analyses
   (chapter 9)
   - Extension of GLM-based functions (including the *network-based
   statistic [NBS]* and MTPC) to allow for multiple contrasts in a single
   function call, and to allow for both T- and F-contrasts
   - Permutation/randomization is now done using the *Freedman-Lane
   algorithm* (as in *randomise* and *PALM*), although models are limited
   to simple GLM's
   - Introduction of R's *S3 classes* to simplify plotting and summarizing
   results
   - Calculation of a network's *s-core* membership
   - Calculation of network *communicability* and vertex *communicability
   betweenness centrality*

Please let me know if you have any issues, bug reports, feature requests,
etc.
Chris Watson
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[Freesurfer] thresh definition

[Ashley Cole]

Dear experts,

Could you please let me know what "thresh" means in funcroi-config.
Like in general, sig=2, does this refer to the number of decimal points,
here p<0.01?

And I want the p-value less than 0.1, does this mean that I need to
assign threshold of 5?


Thanks
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Re: [Freesurfer] thresh definition

[Douglas Greve]

thresh = -log10(p-value threshold), so it kind of means the number of 
decimal points but is more general



On 2/6/18 9:13 PM, Ashley Cole wrote:

Dear experts,

Could you please let me know what "thresh" means in funcroi-config.
Like in general, sig=2, does this refer to the number of decimal 
points, here p<0.01?


And I want the p-value less than 0.1, does this mean that I need 
to assign threshold of 5?



Thanks


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Re: [Freesurfer] thresh definition

[Ashley Cole]

Thank you so much, Dr. Greve.

My last question, are these t-tests corrected or uncorrected?



On Tue, Feb 6, 2018 at 9:03 PM, Douglas Greve 
wrote:

> thresh = -log10(p-value threshold), so it kind of means the number of
> decimal points but is more general
>
> On 2/6/18 9:13 PM, Ashley Cole wrote:
>
> Dear experts,
>
> Could you please let me know what "thresh" means in funcroi-config.
> Like in general, sig=2, does this refer to the number of decimal points,
> here p<0.01?
>
> And I want the p-value less than 0.1, does this mean that I need to
> assign threshold of 5?
>
>
> Thanks
>
>
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Re: [Freesurfer] [freesurfer] Extracting values of cortical thickness in each vertex.

[박경일]

Thanks, Bruce.
>From that, I got thickness data (vertex#, location x/y/z, thickness value).
But, amount and location of vertex are different among subjects.
As far as i understand, it is the subject space, not common space. is that
right?
If so, how can i get the thickness values in common space to compare the
vertex data between subjects?

(I'd already run recon-all and qcache process.)

Kyung


2018-02-03 0:33 GMT+09:00 Bruce Fischl :

> Hi Kyung
>
> you should look at the mris_convert help. It has an example of how to
> convert a scalar overlay like a curv file to ascii:
>
>
> Convert a scalar overlay file to ascii:
>   mris_convert -c lh.thickness lh.white lh.thickness.asc
>
>
> it needs the surface as an input to do the conversion properly.
>
> cheers
> Bruce
>
>
> On Fri, 2 Feb 2018, 박경일 wrote:
>
> Hi Bruce
>> I found a directory having a file with ".curv", open terminal and run
>> following command.
>>
>> [root@localhost surf]# mris_convert rh.curv rh.curv.asc
>> nquads=4587523,  nvertices=476
>> ERROR: MRISread: file 'rh.curv' has many more faces than vertices!
>> Probably trying to use a scalar data file as a surface!
>> No such file or directory
>>
>> what is wrong?
>>
>> Thanks as always.
>>
>> Kyung
>>
>> 2018-01-31 0:04 GMT+09:00 Bruce Fischl :
>>   Hi Kyung
>>
>>   the thickness values are stored as "curvature" file format that you
>> can load into matlab
>>   with read_curv.m. Alternatively, you can convert them to ascii with
>> mris_convert and do
>>   what you want with them. For each index, you can look up its
>> location on the white or
>>   pial (or whatever surface). That is, for the 2nd thickness value
>> (index 1), you would go
>>   find vertex #1 on the other surface and read its location that way
>>
>>   cheers
>>   Bruce
>>   On Tue, 30 Jan 2018, 박경일 wrote:
>>
>> Hi Bruce, I am very new for FS, so did not understand you
>> comments
>> completely. sorry..
>>
>> For cortical thickness from each vertex in one subject, which
>> scripts should
>> follow "mris_convert"?
>> And another question is how to recognize the location of each
>> vertex in
>> brain finally.
>>
>> thank you so much
>>
>> Kyung
>>
>>
>> 2017-11-13 10:06 GMT+09:00 Bruce Fischl <
>> fis...@nmr.mgh.harvard.edu>:
>>   p.s. if you want the vertices to correspond, first run
>> recon-all
>> -qcache for each
>>   subject. That will generate a set of thickness maps in
>> fsaverage space
>> at predefined
>>   smoothing levels (so that the vertex numbers correspond
>> across
>> subjects)
>>
>>   On Mon, 13 Nov 2017, 박경일 wrote:
>>
>> Hi Bruce,What I want is the values of cortical
>> thickness in each
>> vertex in
>> each subject. Is that
>> possible?
>> Thanks so much.
>>
>> Kyung
>>
>>
>>
>> 2017-11-13 0:43 GMT+09:00 Bruce Fischl
>> :
>>   Hi Kyung
>>
>>   you can load them into matlab or convert
>> them to ascii if
>> you want
>>   Bruce
>>   On Sun, 12 Nov 2017, 박경일 wrote:
>>
>> Dear FS experts,
>> I could get QDEC image comparing two
>> groups.
>> However, is there a way to get
>> numerical values of
>> cortical
>> thickness in
>> each vertex?
>>
>> Thank you
>>
>> Best,
>> Kyung
>>
>>
>>
>>
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>> du/mailman/listinfo/freesurfer
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>> for the person
>> to whom it is
>> addressed. If you believe this e-mail was sent to
>> you in error
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>> e-mail
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>> Compliance
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>> sender and
>> properly
>> disp

[Freesurfer] shift to account for hemodynamic response

[Ashley Cole]

Dear experts,

I just have switched from SPM to Freesurfer. I am wondering if in FSFAST
analysis, we require to shift the regressors in time to account for the
delay in hemodynamic response?

Thanks
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