Freesurfer

freesurfer@nmr.mgh.harvard.edu

19 participants
30088 discussions

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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Individual surface
by Alex Peng 12 Jul '19

12 Jul '19

External Email - Use Caution Hi FreeSurfer experts, I am having trouble with making individual surface as template. 1. I reconstructed a macaque T1 to his individual surface and I want to make it as my macaque template. However the vertices number of left hemi and right hemi are different. How can I revise them to have same vertices just like fsaverage template? 2. Since subcortical mask draw by myself, the generated medial wall regions on the surfaces are not smooth. Is there any way that allows me to smooth the medial wall region on surface space? 3. Currently, the generated surface have about 10k vertices on each hemi. How can I downsample them and get the transform matrix between them because I also want to project bold data to the downsampled surface. I have tried mris_decimate, it only gives me a downsampled surface without transform matrix. Thanks for your help. Appreciate it! X. Peng

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freeview
by Juan Rivas 12 Jul '19

12 Jul '19

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Fwd: Freeview
by Juan Rivas 12 Jul '19

12 Jul '19

External Email - Use Caution That is what happened: $ ldd /usr/local/bin/freeview | grep not ldd: /usr/local/bin/freeview: No such file or directory $ bash jcrn12@jcrn12-VirtualBox:~$ ldd /usr/local/bin/freeview | grep not ldd: /usr/local/bin/freeview: No such file or directory JC. ---------- Forwarded message --------- De: fsbuild <fsbuild(a)contbay.com> Date: lun., 15 jul. 2019 a las 14:19 Subject: Re: [Freesurfer] Freeview To: <freesurfer(a)nmr.mgh.harvard.edu> Cc: <jcrn12(a)gmail.com> Hello JC, Try this to see what libs are missing, $ ldd /usr/local/bin/freeview | grep not - R. On Jul 12, 2019, at 06:19, Juan Rivas <jcrn12(a)gmail.com> wrote: External Email - Use Caution Hi, thank you for your help. I tried again and once again it did not work. I am using Ubuntu 18 This is the message I get: $ freeview sh: 8: freeview: not found $ which freeview $ /usr/local/bin/freeview sh: 10: /usr/local/bin/freeview: not found $ which ldd /usr/bin/ldd $ ldd `which freeview` | grep not ldd: missing file arguments Try `ldd --help' for more information. Thank you very much, JC. El lun., 15 jul. 2019 a las 12:50, fsbuild (<fsbuild(a)contbay.com>) escribió: > Hello Juan, > > For CentOS try: > $ sudo yum install gcc-gfortran.x86_64 > … if that does not work then, > $ sudo yum install libgfortran.x86_64 > > For Ubuntu, > $sudo apt-get install gfortran > > One thing you might want to try first is to run the “ldd” command on the > freeview binary to see all/any libraries that are missing.... > > This should return the path to freeview, e.g., /usr/local/bin/freeview, > though your path may differ. > $ which freeview > /usr/local/bin/freeview > > - then check you have the ldd command, > $ which ldd > /usr/bin/ldd > > If the above returned paths for freeview and ldd, then run the ldd command > followed by the grep command to see what libraries are missing. Prior to > doing the install of libgfortran above, it should list libgfortran is > missing. > > $ ldd `which freeview` | grep not > > Also it would be good to know what linux you are running, e.g., CentOS 7, > Ubuntu 18, etc. > > - R. > > On Jul 15, 2019, at 12:39, Juan Rivas <jcrn12(a)gmail.com> wrote: > > External Email - Use Caution > > > > ---------- Forwarded message --------- > De: Juan Rivas <jcrn12(a)gmail.com> > Date: vie., 12 jul. 2019 a las 3:02 > Subject: Re: [Freesurfer] Freeview > To: fsbuild <fsbuild(a)contbay.com> > > > Hi, thank you for your answer. > I did what you recommended to me, and I get this message: > freeview: error while loading shared libraries: libgfortran.so.3: cannot > open shared object file: No such file or directory. > What could be the next step? > JC. > > El lun., 15 jul. 2019 a las 9:57, fsbuild (<fsbuild(a)contbay.com>) > escribió: > >> Hello JC, >> >> Your machine could be missing the qt5 libraries/files. >> >> On Ubuntu linux you can try installing them with, >> $ sudo apt-get install qt5-default qtcreator libqt5x11extras5-dev >> >> On CentOS linux, >> $ sudo yum install qt-create qt-config.x86_64 >> $ sudo yum install qt5-qtx11extras.x86_64 qt5-qtx11extras-devel..x86_64 >> >> - R. >> >> On Jul 12, 2019, at 02:28, Juan Rivas <jcrn12(a)gmail.com> wrote: >> >> External Email - Use Caution >> >> Hello, I am trying to use freeview, but everytime I try I get this >> message: >> freeview: error while loading shared libraries: libQt5Widgets.so.5: >> cannot open shared object file: No such file or directory. >> How can I fix it? >> Thanks a lot, >> JC. >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer(a)nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> >> _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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