Freesurfer

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30089 discussions

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

1 0

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

1 0

FSFAST
by Ashley Cole 05 Feb '18

05 Feb '18

Hello, I have several nifti files. I have preprocessed some of them before. I used this command: preproc-sess -s sess01 -fsd bold -stc odd -surface self lhrh -mni305 -fwhm 5 -per-session -force The output files contained fmc.odd.sm5.self.lh.nii.gz, fmc.odd.sm5.self.rh.nii.gz, fmc.odd.sm5.mni305.2mm.nii.gz, and *fmc.odd.sm5.nii.gz*. Which this last one (fmc.odd.sm5.nii.gz) was the file that I needed for my further analyses. However, when I run the same command on another nifti file which was obtained from the same scanner and the same session, the output doesn't have the fmc.odd.sm5.nii.gz. I ran it several times but it never gave me that file. Also, it doesn't give me any errors. I appreciate any help. Ash

2 3

One Group (One Factor), Two Covariates
by stdp82＠virgilio.it 05 Feb '18

05 Feb '18

Hi list, in reference to One Group (One Factor), Two Covariates https://surfer.nmr.mgh.harvard.edu/fswiki/Fsgdf1G2V#Contrast2age.mtx that has been applied on FS-FAST fcMRI data I obtain three folder, respectively, for "main", "covariate 1", "covariate 2". What's meaning the sig.nii.gz that it is produced by mri_glmfit in each folder? Please correct my conclusions if they are wrong. 1 - In the "Main" folder, the sig.nii.gz contains the results of One-sample t test regressing out the effect of the two covariates. 2 - In the "Covariate 1" folder, the sig.nii.gz contains the significant cluster that are associated with the covariate 1 regressing out the effect for the covariate 2. 3 - In the "Covariate 2" folder, the sig.nii.gz contains the significant cluster that are associated with the covariate 2 regressing out the effect for the covariate 1. Thanks Stefano

3 5

Fwd: Re: One Group (One Factor), Two Covariates
by stdp82＠virgilio.it 05 Feb '18

05 Feb '18

2 1

How to compile FreeSurfer with CUDA?
by Markus.Mertens＠evkb.de 05 Feb '18

05 Feb '18

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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Freesurfer