Freesurfer February 2018

freesurfer@nmr.mgh.harvard.edu

119 participants
170 discussions

thresh definition
by Ashley Cole 07 Feb '18

07 Feb '18

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 0.00001, does this mean that I need to assign threshold of 5? Thanks

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Re: [Freesurfer] recommendation for T1 and T2-based sequences use with FreeSurfer
by Matt Glasser 06 Feb '18

06 Feb '18

I think the HCP CCF protocol is a good start: http://protocols.humanconnectome.org/ Peace, Matt. From: <freesurfer-bounces(a)nmr.mgh.harvard.edu> on behalf of Colm Connolly <cconnolly(a)fsu.edu> Reply-To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> Date: Tuesday, February 6, 2018 at 10:41 AM To: "freesurfer(a)nmr.mgh.harvard.edu" <freesurfer(a)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 _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.

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Using subject specific template, atlas, & TPM
by Ramesh Babu 06 Feb '18

06 Feb '18

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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PROGRAMMER/ DATA ANALYST II
by Arpana Gupta 06 Feb '18

06 Feb '18

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 10000 lines of MySQL stored procedures and standard SQL for triggers, views, etc. The front-end consists of ~10000 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. Graphic or Web design skills are considered a plus, but not required for consideration. Additional Information: Applications must be sent by email to Dr. Arpana Gupta (AGupta(a)mednet.ucla.edu <mailto:AGupta@mednet.ucla.edu>) CCing Melenie Rosales (MRosales(a)mednet.ucla.edu <mailto:MRosales@mednet.ucla.edu>) and Cathy Liu (clliu(a)ucla.edu <mailto:clliu@ucla.edu>) Please include a CV, cover letter and names of three references. Arpana Gupta, Ph.D. Arpana Gupta, Ph.D. Assistant Professor Director, Neuroimaging Operations Core G. Oppenheimer Center for Neurobiology of Stress and Resilience Ingestive Behavior and Obesity Program Vatche and Tamar Manoukin Division of Digestive Diseases David Geffen School of Medicine UCLA CHS 42-210 10833 Le Conte Avenue Los Angeles, CA 90095-7378 http://uclacns.org/ Email: aagupta9(a)gmail.com OR AGupta(a)mednet.ucla.edu

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fast_selxavg3.m error/analysis.info file
by Yagmur Ozdemir 19 06 Feb '18

06 Feb '18

Hello FreeSurfer experts, I am getting this strange error when running selxavg3-sess. (in selxavg3 command I am calling the analysis file with: -a rtopyTR2.rh) When the system enters fast_selxavg3, it cannot read analysis.info, thus produces the following output: #@# Sess05 ############################### /home/vm01/local/freesurfer/Project_bold/Sess05 ------------------------- $Id: fast_selxavg3b.m,v 1.4 2016/05/04 22:16:47 greve Exp $ ------------------------- outtop = /home/vm01/local/freesurfer/Project_bold Extension format = nii.gz ERROR: could not open rtopyTR2.rh/analysis.info else else echo "------------------------------------------" | tee -a $LF echo ------------------------------------------ tee -a /home/vm01/local/freesurfer/Project_bold/log/selxavg3-sess-bold-rtopyTR2.rh-180130082919.log ------------------------------------------ rm $MLF rm /tmp/selxavg3-sess-10173.m if ( ! -e $okfile ) then if ( ! -e /tmp/selxavg3-sess-10173.ok ) then echo "ERROR: fast_selxavg3() failed\n" ; echo ERROR: fast_selxavg3() failed\n ERROR: fast_selxavg3() failed\n exit 1 ; exit 1 The analysis folder it is referring to( rtopyTR2.rh) is in the directory from which I am calling selxavg3-sess. It has the analysis.info file in which doesn't have any restrictions. To troubleshoot, I moved the folder to inside the session's functional directory and inside the session folder and these didn't create any changes. I looked at the script and tried to debug there but didn't give any results. It gave a similar error when trying to open the config file of contrast in mkcontrast-sess. (I also don't have root access)Any help is appreciated! Best, Idil

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recommendation for T1 and T2-based sequences use with FreeSurfer
by Colm Connolly 06 Feb '18

06 Feb '18

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&… [2] https://surfer.nmr.mgh.harvard.edu/fswiki/recon-all#UsingT2orFLAIRdatatoimp… 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] How to compile FreeSurfer with CUDA?
by Markus.Mertens＠evkb.de 06 Feb '18

06 Feb '18

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 +0000 From: Melvin Robinson <mrobinson(a)uttyler.edu> Subject: Re: [Freesurfer] How to compile FreeSurfer with CUDA? To: "freesurfer(a)nmr.mgh.harvard.edu" <freesurfer(a)nmr.mgh.harvard.edu> Message-ID: <0ec7e124a71744d9b2f1892744986933(a)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-bounces(a)nmr.mgh.harvard.edu <freesurfer-bounces(a)nmr.mgh.harvard.edu> on behalf of Markus.Mertens(a)evkb.de <Markus.Mertens(a)evkb.de> Sent: Monday, February 5, 2018 7:41 AM To: freesurfer(a)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 _______________________________________________________________ Evangelisches Klinikum Bethel gGmbH Akademisches Lehrkrankenhaus der Universität Münster Sitz der Gesellschaft Kantensiek 11 | 33617 Bielefeld Amtsgericht Bielefeld HRB 30169 Geschäftsführer Dr. Rainer Norden (Vorsitz) Dr. Matthias Ernst Dr. Maren Thäter Vorsitzender des Aufsichtsrates Pastor Ulrich Pohl

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monte-carlo error in longitudinal pipeline
by miracle ozzoude 05 Feb '18

05 Feb '18

Hello Experts, I am running a paired t-test cortical thickness analysis based on the instruction on the wiki page ( https://surfer.nmr.mgh.harvard.edu/fswiki/PairedAnalysis) However, the monte carlo files weren't not created when i corrected for multiple comparisons. Below are my script, fsgd files, mc-z log file, and a screenshot of contrast folder missing mc.z maps. Please can you help me figure out why the error is happening. Thank you. Best, Paul *Script*: pairs=pairs.fsgd paired=paired_diff.fsgd martrix1=mean.mtx martrix2=age.mtx #resample each subjects's left and right hemisphere data to fsavarage. mris_preproc --target fsaverage --hemi lh --meas thickness --out lh.paired-diff.thickness.mgh --fsgd $pairs --paired-diff mris_preproc --target fsaverage --hemi rh --meas thickness --out rh.paired-diff.thickness.mgh --fsgd $pairs --paired-diff # #smoothen the concatenated file by 5mm FWHM. --cortex means only smooth areas in the cortex. N:B. FWHM changes based on study type. mri_surf2surf --hemi lh --s fsaverage --sval lh.paired-diff.thickness.mgh --fwhm 5 --cortex --tval lh.paired-diff.thickness.sm05.mgh mri_surf2surf --hemi rh --s fsaverage --sval rh.paired-diff.thickness.mgh --fwhm 5 --cortex --tval rh.paired-diff.thickness.sm05.mgh # #Run GLM analysis mri_glmfit --y lh.paired-diff.thickness.sm05.mgh --fsgd $paired --C $martrix1 --C $martrix2 --surf fsaverage lh --cortex --glmdir lh.paired-diff.glmdirir mri_glmfit --y rh.paired-diff.thickness.sm05.mgh --fsgd $paired --C $martrix1 --C $martrix2 --surf fsaverage rh --cortex --glmdir rh.paired-diff.glmdir # # #Run Clusterwise correction for multiple comparisons using MONTE CARLO. First create a table for of simulations mri_glmfit-sim --glmdir lh.paired-diff.glmdir --sim mc-z 10000 2 mc-z.abs.2 --sim-sign abs --cwpvalthresh 0.05 --2spaces --overwrite mri_glmfit-sim --glmdir rh.paired-diff.glmdir --sim mc-z 10000 2 mc-z.abs.2 --sim-sign abs --cwpvalthresh 0.05 --2spaces --overwrite *Fsgd file 1:pairs.fsgd* GroupDescriptorFile 1 Class ADEX Input 1000_1 ADEX Input 1000_2 ADEX Input 1001_1 ADEX Input 1001_2 ADEX Input 1003_1 ADEX Input 1003_2 ADEX Input 1005_1 ADEX Input 1005_2 ADEX Input 1008_1 ADEX Input 1008_2 ADEX Input 1013_1 ADEX Input 1013_2 ADEX Input 1014_1 ADEX Input 1014_2 ADEX *Fsgd file 2: paired_diff.fsgd* GroupDescriptorFile 1 Class ADEX Variables Age Input 1000 ADEX 72 Input 1001 ADEX 76 Input 1003 ADEX 72 Input 1005 ADEX 80 Input 1008 ADEX 72 Input 1013 ADEX 80 Input 1014 ADEX 80

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correlation between the FC (obtained by FS-FAST) and cortical thickness
by stdp82＠virgilio.it 05 Feb '18

05 Feb '18

Hi list, Is there a way to obtain a map that report the "vertex by vertex" correlation between the FC (obtained by FS-FAST) and cortical thickness? Thanks Stefano

2 5

Curvature Index and Folding Index
by Ting Li 05 Feb '18

05 Feb '18

Dear FreeSurfer Expert, Could you explain me what does the curvature index and folding index mean in the Parcellation Stats File? In which way they are calculated? or you can give me some related documents. Thanks a lot. Ting

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Freesurfer February 2018