Freesurfer July 2019

freesurfer@nmr.mgh.harvard.edu

104 participants
165 discussions

Create no-skull brain with gray matter mask
by Marina Fernández 15 Jul '19

15 Jul '19

External Email - Use Caution Dear experts, I need to get a no-skull brain. The automated no-skull brain has many errors and I was thinking that I could create it taking into account the gray matter mask (we segment manually, so the mask is accurate) in such a way that everything outside the gray matter mask is eliminated and everything inside is maintained. Do you know how can I create it? Any idea will be welcome. Thank you very much. Best regards, Marina.

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CSF mask
by Laboratorio de Neurociencia Funcional 15 Jul '19

15 Jul '19

External Email - Use Caution Dear Freesurfer experts, Is there any way to obtain a CSF mask in Freesurfer similar to that obtained with the SPM segmentation (see attached file)? I would need that the CSF mask contains not only the cerebral ventricles but also the extracerebral CSF. Any help with this would be greatly appreciated. Best regards, Jose

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general installation and configuration questions (new user!)
by Robin Warne 15 Jul '19

15 Jul '19

External Email - Use Caution Hi folks, I am new to the Freesurfer world and I have a couple of questions about installing the application, specifically around the 10Gb "footprint" of data, after unpacking the archive file. So I have run through the installation and configuration steps outlined on the Wiki page, which is great, by the way! Running through the steps first time around went without a hitch but the conversion of the sample data took many hours. If I have to run that conversion again, I will try the recon-all with " -openmp { some appropriate value } " to try and speed it up. I'm guessing that the sample data is occupying a large part of the 10Gb disk space "footprint" so is it appropriate to remove it, without breaking anything? If we wanted to install Freesurfer on to a server, for multiple users to access, is that possible? Somewhere like '/usr/local', as described in the Wiki? Thanks in advance, for any guidance anyone can offer. Robin Warne, University of Kent (U.K.)

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Petsurfer: PET -> MNI305 problem
by Eckbo, Ryan 15 Jul '19

15 Jul '19

Hi Doug and experts, We're interested in running a voxel wise test-retest reliability analysis on a set of PBR28 PET images that we have. Following the petsurfer wiki page (https://surfer.nmr.mgh.harvard.edu/fswiki/PetSurfer) I ran this command to get one of the images into 2mm MNI305 space: mri_vol2vol --mov mgx.gm.nii.gz --reg aux/bbpet2anat.lta --tal --talres 2 --o gm.mni305.2mm.sm00.nii.gz However, the resulting image has 2 problems (see attached): 1) it is cutoff at the edges 2) the axes are switched, suggesting there's something wrong with the voxel ordering. I tested the correctness of aux/bbpet2anat.lta by applying it to mgx.gm.nii.gz and it gives the correct result, i.e., it is aligned with orig.mgz. Any ideas on what may be going wrong or suggestions on how to fix this? Thanks! Ryan

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mri_glmfit residualized data after motion correction
by Mcnorgan, Christopher 15 Jul '19

15 Jul '19

Hello FreeSurfers, I have an existing pipeline that computes the residualized time series after removing any linear trends using mri_glmfit: mri_glmfit --y ${source_dir}/${r}/${filepat}.${surf}.${hemi}.nii.gz \ --glmdir ${source_dir}/${r}/${hemi}.detrend \ --qa --save-yhat --eres-save \ --surf ${SURFTOUSE} ${hemi} This saves the detrended eres.mgh data in *h.detrend/ I would like to additionally include motion correction values as regressors in this step, but I am not completely clear how to do this. My best guess is that this will entail a fixed effects analysis using the values in mcprextreg, but I cannot find any examples of this in the mailing list archives nor on the wiki, so any help would be greatly appreciated! Thanks, Chris /********************************************** * Chris McNorgan * Assistant Professor * Department of Psychology * University at Buffalo, * The State University of New York * http://ccnlab.buffalo.edu/ <http://ccnlab.buffalo.edu/> * Office: 716.645.0236 * Lab: 716.645.0222 **********************************************/ External Email - Use Caution

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Re: [Freesurfer] Fwd: Fwd: Freeview {Disarmed}
by fsbuild 13 Jul '19

13 Jul '19

External Email - Use Caution OK, please check to see if this directory exists, $ ls /usr/local/freesurfer/bin/platforms If it does exist, then please let us know what is there with a repply email. But I expect that it does not exist and ls will report there is no such platforms directory. If the directory does not exist, then go to the freesurfer bin directory and create a soft link to point to the Qt platforms subdirectory, $ sudo cd /usr/local/freesurfer/bin$ sudo ln -s  /usr/lib/x86_64-linux-gnu/qt5/plugins/platforms  platforms If you create the link, then try running freeview again. - R. On Jul 13, 2019, at 03:33, Juan Rivas <jcrn12(a)gmail.com> wrote:        External Email - Use Caution        That was the systemś answer:jcrn12@jcrn12-VirtualBox:~$ ls /usr/lib/x86_64-linux-gnu/qt5/plugins/platformslibqeglfs.so libqminimalegl.so  libqoffscreen.so  libqxcb.solibqlinuxfb.so libqminimal.so   libqvnc.sojcrn12@jcrn12-VirtualBox:~$ export QT_DEBUG_PLUGINS=1jcrn12@jcrn12-VirtualBox:~$ freeviewQFactoryLoader::QFactoryLoader() checking directory path "/usr/local/freesurfer/bin/platforms" ...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)---------- Forwarded message ---------De: fsbuild <fsbuild@contbay.com>Date: mar., 16 jul. 2019 a las 14:07Subject: Re: [Freesurfer] Fwd: FreeviewTo: <freesurfer(a)nmr.mgh.harvard.edu>Cc: <jcrn12(a)gmail.com>See if you have the following directory with the plugins libraries,$ ls /usr/lib/x86_64-linux-gnu/qt5/plugins/platformsThere should be a libqxcb.so listed in that directory if you have them.Also try setting the following in your environment$ export QT_DEBUG_PLUGINS=1- then try running freeview again and see what it reports.- R.On Jul 16, 2019, at 11:55, Juan Rivas <jcrn12(a)gmail.com> wrote:        External Email - Use Caution        Hello, I am working with Ubuntu 18.I did what you asked to me, but the results are the same:jcrn12@jcrn12-VirtualBox:~$ sudo apt-get install qt5-default  qtcreatorReading package lists... DoneBuilding dependency tree       Reading state information.... Doneqtcreator is already the newest version (4.5.2-3ubuntu2).qt5-default is already the newest version (5.9.5+dfsg-0ubuntu2.1).0 upgraded, 0 newly installed, 0 to remove and 64 not upgraded.jcrn12@jcrn12-VirtualBox:~$ sudo apt-get install libqt5x11extras5-devReading package lists... DoneBuilding dependency tree       Reading state information... Donelibqt5x11extras5-dev is already the newest version (5.9.5-0ubuntu1).0 upgraded, 0 newly installed, 0 to remove and 64 not upgraded..jcrn12@jcrn12-VirtualBox:~$ freeviewThis 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)Then, I tried:jcrn12@jcrn12-VirtualBox:~$ libxcb.so.1 => /lib64/libxcb.so.1 bash: /lib64/libxcb.so.1: Permission deniedWhat could be the next step?Thanks a lot,JC.---------- Forwarded message ---------De: fsbuild <fsbuild@contbay.com>Date: mar., 16 jul. 2019 a las 10:38Subject: Re: [Freesurfer] FreeviewTo: <freesurfer(a)nmr.mgh.harvard.edu>Cc: <jcrn12(a)gmail.com>Hello JC,You can try installing the following, $ sudo apt-get install qt5-default  qtcreator $ sudo apt-get install libqt5x11extras5-devAre you working on Ubuntu 18 ?- R.On Jul 12, 2019, at 22:29, Juan Rivas <jcrn12(a)gmail.com> wrote:        External Email - Use Caution        Hello, since yesterday i am trying to run freeview. I have followed the steps you asked to me, and today I updated freeview. I get this message again:jcrn12@jcrn12-VirtualBox:~$ freeviewThis 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 installed fortran and update libx11, then I tried freeview and I get this message:jcrn12@jcrn12-VirtualBox:~$ sudo apt-get install libx11-xcb1[sudo] password for jcrn12: Reading package lists... DoneBuilding dependency tree       Reading state information... Donelibx11-xcb1 is already the newest version (2:1.6.4-3ubuntu0.2).0 upgraded, 0 newly installed, 0 to remove and 64 not upgraded.jcrn12@jcrn12-VirtualBox:~$ freeviewThis 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)Could you please help me?Thanks,JC._______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer_______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer_______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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Paired Analysis Questions
by FAST Study 13 Jul '19

13 Jul '19

External Email - Use Caution Dear Dr. Greve: Hooray! All has run successfully for the Paired Analysis ( https://surfer.nmr.mgh.harvard.edu/fswiki/PairedAnalysis) I used the [1 0] contrast to examine whether there are different within-group changes in brain structure for an Intervention (PA) and Control (C) group.. After running — *mri_glmfit --glmdir lh.paired-diff --y lh.paired-diff.thickness.sm05.mgh --fsgd paired-diff.fsgd --C mean.mtx --surface fsaverage lh* (Full terminal output below) *Will you help me read the output of mri_glmfit?* I am not sure what to check for results. Are the results corrected for multiple comparisons? THANKS. *mri_glmfit --glmdir lh.paired-diff --y lh.paired-diff.thickness.sm05.mgh --fsgd paired-diff.fsgd --C mean.mtx --surface fsaverage lh* gdfRead(): reading paired-diff.fsgd INFO: ignoring tag subs INFO: gd2mtx_method is dods Reading source surface /Volumes/HealthDevelopment/FITKIDS2/FREESURFER/Pairedt/fsaverage/surf/lh.white Number of vertices 163842 Number of faces 327680 Total area 65416.984375 AvgVtxArea 0.399269 AvgVtxDist 0.721953 StdVtxDist 0.195470 $Id: mri_glmfit.c,v 1.241.2.4 2016/12/08 22:02:40 zkaufman Exp $ cwd /Volumes/HealthDevelopment/FITKIDS2/FREESURFER/Pairedt cmdline mri_glmfit.bin --glmdir lh.paired-diff --y lh.paired-diff.thickness.sm05.mgh --fsgd paired-diff.fsgd --C mean.mtx --surface fsaverage lh sysname Darwin hostname laurachaddock.vp.illinois.edu machine x86_64 user laurachaddock FixVertexAreaFlag = 1 UseMaskWithSmoothing 1 OneSampleGroupMean 0 y /Volumes/HealthDevelopment/FITKIDS2/FREESURFER/Pairedt/lh.paired-diff.thickness.sm05.mgh logyflag 0 usedti 0 FSGD paired-diff.fsgd labelmask /Volumes/HealthDevelopment/FITKIDS2/FREESURFER/Pairedt/fsaverage/label/lh.cortex.label maskinv 0 glmdir lh.paired-diff IllCondOK 0 ReScaleX 1 DoFFx 0 Creating output directory lh.paired-diff Loading y from /Volumes/HealthDevelopment/FITKIDS2/FREESURFER/Pairedt/lh.paired-diff.thickness.sm05.mgh ... done reading. INFO: gd2mtx_method is dods Saving design matrix to lh.paired-diff/Xg.dat Computing normalized matrix Normalized matrix condition is 1 Matrix condition is 1.29787 Found 149955 points in label. Pruning voxels by thr: 1.175494e-38 Found 149946 voxels in mask Saving mask to lh.paired-diff/mask.mgh Reshaping mriglm->mask... search space = 74607.309418 DOF = 106 Starting fit and test Fit completed in 0.0936 minutes Computing spatial AR1 on surface Residual: ar1mn=0.984663, ar1std=0.005741, gstd=3.255205, fwhm=7.665423 Writing results mean maxvox sig=3.95093 F=16.1054 at index 115412 0 0 seed=1563757270 mri_glmfit done bash-3.2$

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Re: [Freesurfer] Fwd: Freeview
by fsbuild 13 Jul '19

13 Jul '19

External Email - Use Caution See if you have the following directory with the plugins libraries, $ ls /usr/lib/x86_64-linux-gnu/qt5/plugins/platforms There should be a libqxcb.so listed in that directory if you have them. Also try setting the following in your environment $ export QT_DEBUG_PLUGINS=1 - then try running freeview again and see what it reports.. - R. On Jul 16, 2019, at 11:55, Juan Rivas <jcrn12(a)gmail.com> wrote:        External Email - Use Caution        Hello, I am working with Ubuntu 18.I did what you asked to me, but the results are the same:jcrn12@jcrn12-VirtualBox:~$ sudo apt-get install qt5-default  qtcreatorReading package lists... DoneBuilding dependency tree       Reading state information... Doneqtcreator is already the newest version (4.5.2-3ubuntu2).qt5-default is already the newest version (5.9.5+dfsg-0ubuntu2.1).0 upgraded, 0 newly installed, 0 to remove and 64 not upgraded.jcrn12@jcrn12-VirtualBox:~$ sudo apt-get install libqt5x11extras5-devReading package lists... DoneBuilding dependency tree       Reading state information... Donelibqt5x11extras5-dev is already the newest version (5.9.5-0ubuntu1)..0 upgraded, 0 newly installed, 0 to remove and 64 not upgraded.jcrn12@jcrn12-VirtualBox:~$ freeviewThis 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)Then, I tried:jcrn12@jcrn12-VirtualBox:~$ libxcb.so.1 => /lib64/libxcb.so.1 bash: /lib64/libxcb.so.1: Permission deniedWhat could be the next step?Thanks a lot,JC.---------- Forwarded message ---------De: fsbuild <fsbuild@contbay.com>Date: mar., 16 jul. 2019 a las 10:38Subject: Re: [Freesurfer] FreeviewTo: <freesurfer(a)nmr.mgh.harvard.edu>Cc: <jcrn12(a)gmail.com>Hello JC,You can try installing the following, $ sudo apt-get install qt5-default  qtcreator $ sudo apt-get install libqt5x11extras5-devAre you working on Ubuntu 18 ?- R.On Jul 12, 2019, at 22:29, Juan Rivas <jcrn12(a)gmail.com> wrote:        External Email - Use Caution        Hello, since yesterday i am trying to run freeview. I have followed the steps you asked to me, and today I updated freeview. I get this message again:jcrn12@jcrn12-VirtualBox:~$ freeviewThis 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 installed fortran and update libx11, then I tried freeview and I get this message:jcrn12@jcrn12-VirtualBox:~$ sudo apt-get install libx11-xcb1[sudo] password for jcrn12: Reading package lists... DoneBuilding dependency tree       Reading state information... Donelibx11-xcb1 is already the newest version (2:1.6.4-3ubuntu0.2).0 upgraded, 0 newly installed, 0 to remove and 64 not upgraded.jcrn12@jcrn12-VirtualBox:~$ freeviewThis 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)Could you please help me?Thanks,JC._______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer_______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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Freeview
by Juan Rivas 12 Jul '19

12 Jul '19

External Email - Use Caution Hello, since yesterday i am trying to run freeview. I have followed the steps you asked to me, and today I updated freeview. I get this message again: *jcrn12@jcrn12-VirtualBox:~$ freeviewThis 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 installed fortran and update libx11, then I tried freeview and I get this message: *jcrn12@jcrn12-VirtualBox:~$ sudo apt-get install libx11-xcb1[sudo] password for jcrn12: Reading package lists... DoneBuilding dependency tree Reading state information... Donelibx11-xcb1 is already the newest version (2:1.6.4-3ubuntu0.2).0 upgraded, 0 newly installed, 0 to remove and 64 not upgraded.jcrn12@jcrn12-VirtualBox:~$ freeviewThis 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)* Could you please help me? Thanks, JC.

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Research Specialist position at the Center for Healthy Minds
by CHM Recruiting 12 Jul '19

12 Jul '19

External Email - Use Caution The Center for Healthy Minds (CHM) is hiring a Research Specialist! Founded and led by world-renowned neuroscientist, Dr. Richard J. Davidson, CHM's mission is to cultivate well-being and relieve suffering through a scientific understanding of the mind. CHM is a leader in rigorous, interdisciplinary basic and translational research aimed at understanding the mind and how to nurture well-being in ourselves and others. CHM communicates these findings to the world, inspires scientists to conduct further research and engages influencers to shift the culture to embrace well-being. The Research Specialist will be responsible for scientific integrity of data collection, data processing, and participant recruitment, screening, and scheduling for research at the CHM. This individual may work on several research projects examining the import of individual differences in the time course of emotional responses for varied domains including cognition, health, and well-being, while elucidating the critical functional and structural brain substrates underlying these relationships. Please view the attached position description for more information and instructions on how to apply.

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Freesurfer July 2019