Freesurfer

freesurfer@nmr.mgh.harvard.edu

30132 discussions

Stuck in "CORRECTING DEFECT"
by Rosalia Dacosta Aguayo 03 Nov '18

03 Nov '18

External Email - Use Caution Dear FreeSurfer team, I Have run -autorecon1 in my sample and the report.log was "finished without errors" Now, running recon-all -all I have seen that a participant is stuck in CORRECTING DEFECT 0 (vertices=31977, convex hull=5359, v0=0) for more than an hour. I wonder if this is normal or if I should be worried because recon-all takes 4.5 hours approximately for every participant but for this one, it seems that is not moving from this step. Anyone could help me with this? Best regards, Rosaila

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Qdec table
by Miguel Ángel Rivas Fernández 03 Nov '18

03 Nov '18

External Email - Use Caution Hi Freesurfer devs, How can I create a qdec.table.dat file? I tried using a txt file but it doesn´t works. I attached the qdec.table.dat file that I have created. Sorry for this absurd question and thanks in advance. Cheers, -- *Miguel Ángel Rivas Fernández*

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myelination and freesurfer segmentation...
by Gonzalo Rojas Costa 02 Nov '18

02 Nov '18

External Email - Use Caution Hi: Could you please tell me if Is there is a paper on myelination and segmentation? Sincerely, Gonzalo Rojas Costa Laboratory for Advanced Medical Image Processing Department of Radiology Clínica las Condes Lo Fontecilla 441, Las Condes, Santiago, Chile. Tel: 56-2-2105170 Cel: 56-9-97771785 www.clc.cl http://www.aribrain.info https://scholar.google.com/citations?user=LO7LZ3oAAAAJ https://www.researchgate.net/profile/Gonzalo_Rojas2 https://cl.linkedin.com/in/gonzalorojascosta

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automating custom color map
by Nillo, Ryan Michael R 02 Nov '18

02 Nov '18

External Email - Use Caution Hi Freesurfer Users, I used linear regression to map regional beta values on the fsaverage surface. I want to use a colormap that goes from blue to gray or gray to red (no cyan and yellow). I've been using a custom colormap shown in example.tiff. I've been making this by going into freeview and adjusting the parameters from the GUI. Is there a way to load this and create a snapshot from the command line? I know you can adjust certain parameters like overlay threshold and change the colormap, but I don't see an option for "custom". The end goal is to make multiple regression models and automate the screenshot process. Best, Ryan M Nillo Staff Research Associate I UCSF Department of Radiology and Biomedical Imaging

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Re: [Freesurfer] Lacunes
by Antonin Skoch 02 Nov '18

02 Nov '18

External Email - Use Caution Dear Emily, similar errors I usually try to correct by editing wm.mgz (fill the spots by intensity 255). But it does not work always (mainly when the hypointensities are of large extent, it often does not help either). Antonin Hi Emily it's going to be tough to get it past the gray matter lesions. If you have labels we could implement something to fill them in with surrounding tissue intensities I suppose, but we don't have anything at the moment sorry Bruce On Wed, 31 Oct 2018, Emily Schwartz wrote: External Email - Use Caution Hi Freesurfer team, I was wondering if there is a way to edit incorrect surfaces due to lacunes? As you can see in the image the surfaces are incorrect. I tried editing the aseg, but this did not work. I have attached both images in the coronal and axial view as well as FLAIR (obviously there are other errors that need to be fixed in this subject as well). I am using version 6.0 (freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c). Any guidance is appreciated. Thank you, Emily Emily Schwartz, B.A. Research Assistant Department of Neurology -- Cognitive and Motor Aging Albert Einstein College of Medicine

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Export stats
by Miguel Ángel Rivas Fernández 02 Nov '18

02 Nov '18

External Email - Use Caution Hi Freesurfer devs, Is there any way to export all the stats using an unique command? For example, export the mean area, volume, thickness, thicknessstd, meancurv values of the Desikian-Killiany atlas using an unique command or is only possible export it using separate commands? Thanks in advance, Cheers -- *Miguel Ángel Rivas Fernández*

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Freeview xcb error
by Emily Levin 02 Nov '18

02 Nov '18

External Email - Use Caution Hi Freesurfer experts, I'm using redhat 7 so I installed the development centos7 version of freesurfer: *https://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/dev/ <https://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/dev/>* I followed the installation instructions and it is having issues with xcb from qt when I try and run freeview: *freeview* *This application failed to start because it could not find or load the Qt platform plugin "xcb"* *in "".* *Reinstalling the application may fix this problem.* *Aborted (core dumped)* I have a previously installed version of freesurfer (6.0) that is statically linked to qt and it runs freeview fine. I already tried setting the QT_QPA_PLATFORM_PLUGIN_PATH environment variable for my qt/5.10.1 plugins directory that contains xcb. Also see the attached output of ldd on freeview. Do you have any other thoughts or actions I can take? Thank you, Emily -- Emily J. Levin Lab Manager Attention & Perception Neuroimaging Lab Boston University Lab: 617-358-1737

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Lacunes
by Emily Schwartz 02 Nov '18

02 Nov '18

External Email - Use Caution Hi Freesurfer team, I was wondering if there is a way to edit incorrect surfaces due to lacunes? As you can see in the image the surfaces are incorrect. I tried editing the aseg, but this did not work. I have attached both images in the coronal and axial view as well as FLAIR (obviously there are other errors that need to be fixed in this subject as well). I am using version 6.0 (freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c). Any guidance is appreciated. Thank you, Emily Emily Schwartz, B.A. Research Assistant Department of Neurology -- Cognitive and Motor Aging Albert Einstein College of Medicine

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Re: [Freesurfer] Third party dependencies directory not found when building from source
by fsbuild 01 Nov '18

01 Nov '18

External Email - Use Caution Hello Christian, To build Freesurfer e.g., on CentOS7, we use rev 4.8.5 of gcc, g++ and gfortran.  You can tell cmake what compilers to use on the command line with CC=<path>/gcc  CXX=<path>/g++  FC=<path>/gfortran  If you need to specify the gfortran library to use, you can set it with -DGFORTRAN_LIBRARIES=<path to gfortran's lib>/libgfortran.a On Ubuntu 16, the native /usr/bin/gcc is rev 5.4.0, so I installed the gcc 4.9 compilers, and set the above to CC=/usr/bin/gcc-4.9, CXX=/usr/bin/g++-4.9, FC=/usr/bin/gfortran-4.9.  You could try doing the same on Ubuntu 18 as the native gcc may be rev 5.4 or newer, and I don't believe gcc rev 5 will work to build freesurfer. On Oct 31, 2018, at 23:13, Christian Lee Mcdaniel <clm121(a)uga.edu> wrote:        External Email - Use Caution        Hi there,Thank you for directing me to the CMake fswiki. I was able to install the third party packages and execute the command `cmake . -DFS_PACKAGES_DIR="path/to/pkgs"`. However, when I run `make -j4` (after adjusting a few bash files in various libraries to find (#include) other libraries) I am met with numerous similarly-worded link error lines under the step "Linking Fortran executable t4imgs_4dfp" with the general schema:/usr/bin/ld: path/to/fortran-related/filename: relocation R_X86_64_32 against `some.variable.or.file.name` can not be used when making a PIE object; recompile with -fPICwhere path/to/fortran-related/filename is either CMakeFiles/t4imgs_4dfp.dir/some-file.c.o or /usr/lib/gcc/x86_64-linux-gnu/4.8/libgfortran.a(some-function.o)I tried finding a solution online and found the suggestion to add a global -fPIC flag via export CXXFLAGS="$CXXFLAGS -fPIC" (https://stackoverflow.com/questions/13812185/how-to-recompile-with-fpic). I tried this by starting completely over with a new clone of the freesurfer repo and calling cmake . -DFS_PACKAGES_DIR="path/to/pkgs" and the make still failed at the same point. Other suggestions (e.g., to add --enable-shared at ./configure(in that same thread linked above)) suggest adding arguments when configuring, but since this is all part of the make process I'm not sure whether that's possible. Any advice? I did not find any similar issues in the archive. Thank you very much,Christian McDaniel On Oct 31, 2018, at 23:13, Christian Lee Mcdaniel <clm121(a)uga.edu> wrote:        External Email - Use Caution        Hi there,Thank you for directing me to the CMake fswiki. I was able to install the third party packages and execute the command `cmake . -DFS_PACKAGES_DIR="path/to/pkgs"`. However, when I run `make -j4` (after adjusting a few bash files in various libraries to find (#include) other libraries) I am met with numerous similarly-worded link error lines under the step "Linking Fortran executable t4imgs_4dfp" with the general schema:/usr/bin/ld: path/to/fortran-related/filename: relocation R_X86_64_32 against `some..variable.or.file.name` can not be used when making a PIE object; recompile with -fPICwhere path/to/fortran-related/filename is either CMakeFiles/t4imgs_4dfp.dir/some-file.c.o or /usr/lib/gcc/x86_64-linux-gnu/4.8/libgfortran.a(some-function.o)I tried finding a solution online and found the suggestion to add a global -fPIC flag via export CXXFLAGS="$CXXFLAGS -fPIC" (https://stackoverflow.com/questions/13812185/how-to-recompile-with-fpic). I tried this by starting completely over with a new clone of the freesurfer repo and calling cmake . -DFS_PACKAGES_DIR="path/to/pkgs" and the make still failed at the same point. Other suggestions (e.g., to add --enable-shared at ./configure(in that same thread linked above)) suggest adding arguments when configuring, but since this is all part of the make process I'm not sure whether that's possible. Any advice? I did not find any similar issues in the archive. Thank you very much,Christian McDaniel

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Re: [Freesurfer] Third party dependencies directory not found when building from source
by fsbuild 01 Nov '18

01 Nov '18

External Email - Use Caution Hello Christian, Allow me to suggest that you try following the instructions for the Fresrufer cmake build located here, http://freesurfer.net/fswiki/CMake Besides the option to build the 3rd party packages with build_packages.py script, you can also download an archive of the prebuilt packages from http://surfer.nmr.mgh.harvard.edu/pub/data/fspackages/prebuilt/ Another option would be to install the equivalent of the CentOS 7 packages on the Ubuntu system you are using, i.e., you may need to install at least cmake, so you will likely need sudo/admin privileges. Christian Lee Mcdaniel wrote October 30, 2018 at 21:43 via Postbox         External Email - Use Caution         Hello Developers, I am attempting to build Freesurfer from source on my Ubuntu 18.04.1 LTS machine. I have followed the instructions on the freesurfer_linux_developers wiki, and have successfully gotten through steps 1 and 2. However, when trying to install the third party dependencies at step 3 via wget ftp://surfer.nmr.mgh.harvard.edu/pub/dist/fs_supportlibs/prebuilt/centos6_x…, I get the following response: 

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