Freesurfer July 2019

freesurfer@nmr.mgh.harvard.edu

104 participants
165 discussions

FLAIR data to improve pial surfaces
by Leyton Moscoso, Cristian Eduardo 18 Jul '19

18 Jul '19

Dear Freesurfer experts, I want to improve pial reconstruction by using FLAIR images in the pial reconstruction (freesurfer v6.0). Ø recon-all -subject subjectname -FLAIR /path/to/FLAIR_volume -FLAIRpial -autorecon3 T1 was acquired in a 3T Phillips scanner with a isometric voxel size of 1 mm3, whereas FLAIR images have a voxel size of 0.5 x 0.5 x 3.5 mm. Is there any issue in using different voxel sizes? Thank you Dr Cristian Leyton M Research Fellow in Neurology Department of Neurology Massachusetts General Hospital Harvard Medical School 149 13th Street Charlestown, MA 02129

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(no subject)
by 许飞飞 18 Jul '19

18 Jul '19

External Email - Use Caution Dear Freesurfer experts, I want to know how Freesufer to compute the volume and area at each vertex. Are there any references? I just found the reference which introduces the measure of thickness(MacDonald et al.2000). Any help with this would be greatly appreciated. Best regards, Feifei

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DF for Longitudinal LME
by Bronwyn Overs 18 Jul '19

18 Jul '19

External Email - Use Caution Dear Freesurfer Mailing List, I am trying to calculate the effect size of the main and interaction effect clusters that were significant in my vertex-wise LME analysis. For this I need the degrees of freedom for each contrast, but I am confused about how to derive this. My input sample has 218 subjects (153 with 2 time-points, 65 with 1 time-point). The effects for which I need the degrees of freedom are: 1) Main effect of years in the control group (n=112) 2) Main effect of years in the case group (n=106) 3) Main effect of group at baseline (group has two levels, 0 or 1) 4) Interaction between years and group Any assistance you can provide would be great. Kind regards, Bronwyn Overs Research Assistant Neuroscience Research Australia Margarete Ainsworth Building Barker Street Randwick Sydney NSW 2031 Australia M 0411 308 769 T +61 2 9399 1725 [ http://neura.edu.au/ | neura.edu.au ] [ https://twitter.com/neuraustralia | Twitter ] | [ https://www.facebook.com/NeuroscienceResearchAustralia | Facebook ] | [ http://www.neura.edu.au/help-research/subscribe | Subscribe ]

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input image for infantFS
by Mahmoud 17 Jul '19

17 Jul '19

External Email - Use Caution Hi all, I have my data organized in this way: study/sub/T1/data.nii.gz infantFS wants the input as study/sub/mprage.nii.gz. Is there a way to feed my data to infantFS without reorganizing/renaming? -i switch seems to not be recognized by infantFS. Thank you, Mahmoud

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Re: [Freesurfer] Fwd: Fwd: Fwd: Freeview {Disarmed}
by fsbuild 17 Jul '19

17 Jul '19

External Email - Use Caution Hello JC, My bad with the first command, try $ cd  /usr/local/freesurfer/bin ... try the next command w/o sudo first, $ ln -s  /usr/lib/x86_64-linux-gnu/qt5/plugins/platforms  platforms ... if that works, then try running freeview again. ... if that fails with a permission denied error, then you do not have permission to modify anything under the freesurfer install.   You can try running the command again with sudo but you may need to know the sudo password, e.g. it may prompt you for the password, $ sudo  ln -s  /usr/lib/x86_64-linux-gnu/qt5/plugins/platforms  platforms[sudo] password for JC:  If the sudo command does work, then try running freeview again. If you do not know the password, then try asking whoever setup the machine for the passowrd, or ask them to run the commands. You can also try running the script that Andrew sent you.  But if the above “ln” command failed w/o sudo, then I think you will also need sudo privileges to run the script. - R. On Jul 13, 2019, at 19:40, Juan Rivas <jcrn12(a)gmail.com> wrote:        External Email - Use Caution        Hello, this is the message I get:$ ls /usr/local/freesurfer/bin/platformsls: cannot access '/usr/local/freesurfer/bin/platforms': No such file or directory$ sudo cd /usr/local/freesurfer/bin[sudo] password for jcrn12: sudo: cd: command not found$ Thank you,JC.---------- Forwarded message ---------De: fsbuild <fsbuild@contbay.com>Date: mar., 16 jul. 2019 a las 16:25Subject: Re: [Freesurfer] Fwd: Fwd: FreeviewTo: <freesurfer(a)nmr.mgh.harvard.edu>Cc: <jcrn12(a)gmail.com>OK, please check to see if this directory exists,$ ls /usr/local/freesurfer/bin/platformsIf 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  platformsIf 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(a)nmr.mgh.harvard.eduMailScanner has detected a possible fraud attempt from "mail.nmr.mgh.harvard.edu" claiming to be https://mail...nmr.mgh.harvard.edu/mailman/listinfo/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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Error in running make_average_subject
by Renew Andrade 17 Jul '19

17 Jul '19

External Email - Use Caution Dear freesurfer experts: I have the same error as explained here https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2018-February/056008… <https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2018-February/056008…> but unfortunately I do not know how to implement the solution being given in the forum. I am a student I hope I am not asking too much of your help. Sincerely, Andrade.

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Error in analyze (Qdec)
by Abby tang 17 Jul '19

17 Jul '19

External Email - Use Caution Hello FreeSurfer Developers, I want to compare the relationship between age and thickness, which is controlled the effect about sex,education and eTIV, so QDEC was used. However I met a problem when I use it, such as picture1. I get the wrong message, Error in Analyze: command failed: mri_glmfit --y /home/abby/Desktop/qdecyoung/qdec/Untitled/y.mgh --fsgd /home/abby/Desktop/qdecyoung/qdec/Untitled/qdec.fsgd dods --glmdir /home/abby/Desktop/qdecyoung/qdec/Untitled --surf fsaverage lh --label /home/abby/Desktop/qdecyoung/fsaverage/label/lh.aparc.label --C /home/abby/Desktop/qdecyoung/qdec/Untitled/contrasts/lh-Avg-Intercept-thickness.mat --C /home/abby/Desktop/qdecyoung/qdec/Untitled/contrasts/lh-Avg-thickness-age-Cor.mat --C /home/abby/Desktop/qdecyoung/qdec/Untitled/contrasts/lh-Diff-Female-Male-Intercept-thickness.mat --C /home/abby/Desktop/qdecyoung/qdec/Untitled/contrasts/lh-Diff-Female-Male-Cor-thickness-age.mat. So I tried to put those to terminal, the feedback is: gdfRead(): reading /home/abby/Desktop/qdecyoung/qdec/Untitled/qdec.fsgd INFO: DeMeanFlag keyword not found, DeMeaning will NOT be done. Continuous Variable Means (all subjects) 0 age 80.3537 2.43637 1 education 12.189 3.6099 2 eTIV 1.33934e+06 242446 Class Means of each Continuous Variable 1 sexFemale 80.0568 11.4773 1265564.4638 2 sexMale 80.6974 13.0132 1424768.7681 INFO: gd2mtx_method is dods Reading source surface /usr/local/freesurfer/subjects/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 /home/abby/Desktop/qdecyoung/qdec cmdline mri_glmfit.bin --y /home/abby/Desktop/qdecyoung/qdec/Untitled/y.mgh --fsgd /home/abby/Desktop/qdecyoung/qdec/Untitled/qdec.fsgd dods --glmdir /home/abby/Desktop/qdecyoung/qdec/Untitled --surf fsaverage lh --label /home/abby/Desktop/qdecyoung/fsaverage/label/lh.aparc.label --C /home/abby/Desktop/qdecyoung/qdec/Untitled/contrasts/lh-Avg-Intercept-thickness.mat --C /home/abby/Desktop/qdecyoung/qdec/Untitled/contrasts/lh-Avg-thickness-age-Cor.mat --C /home/abby/Desktop/qdecyoung/qdec/Untitled/contrasts/lh-Diff-Female-Male-Intercept-thickness.mat --C /home/abby/Desktop/qdecyoung/qdec/Untitled/contrasts/lh-Diff-Female-Male-Cor-thickness-age.mat sysname Linux hostname abby-virtual-machine machine x86_64 user abby FixVertexAreaFlag = 1 UseMaskWithSmoothing 1 OneSampleGroupMean 0 y /home/abby/Desktop/qdecyoung/qdec/Untitled/y.mgh logyflag 0 usedti 0 FSGD /home/abby/Desktop/qdecyoung/qdec/Untitled/qdec.fsgd labelmask /home/abby/Desktop/qdecyoung/fsaverage/label/lh.aparc.label maskinv 0 glmdir /home/abby/Desktop/qdecyoung/qdec/Untitled IllCondOK 0 ReScaleX 1 DoFFx 0 Creating output directory /home/abby/Desktop/qdecyoung/qdec/Untitled Loading y from /home/abby/Desktop/qdecyoung/qdec/Untitled/y.mgh ... done reading. INFO: gd2mtx_method is dods Saving design matrix to /home/abby/Desktop/qdecyoung/qdec/Untitled/Xg.dat Computing normalized matrix Normalized matrix condition is 9294.65 Matrix condition is 1e+08 Found 148151 points in label. Pruning voxels by thr: 1.175494e-38 Found 139197 voxels in mask Saving mask to /home/abby/Desktop/qdecyoung/qdec/Untitled/mask.mgh Reshaping mriglm->mask... search space = 69257.619818 DOF = 156 Starting fit and test Fit completed in 0.338183 minutes Computing spatial AR1 on surface Residual: ar1mn=0.995542, ar1std=0.000996, gstd=6.054132, fwhm=14.256391 Writing results lh-Avg-Intercept-thickness maxvox sig=10.0394 F=48.3686 at index 13210 0 0 seed=1563457975 MatrixMultiplyD(): m2 is null break matrix.c:415 No such file or directory When same operations were did with other files, Qdec running normally. I don't know why. Please help me. Thank you Best regards

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Pixel values in Brainstem segmentation
by Min Zhang 16 Jul '19

16 Jul '19

External Email - Use Caution To whom it may concern I used the freesufer brainstem segmentation, and I want to calculate the area of the segmented brainstem by slices. Would you like to let me know the pixel value of all three directions. Many Thanks! Best Jackie

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Re: [Freesurfer] Freeview
by fsbuild 16 Jul '19

16 Jul '19

External Email - Use Caution Hello JC, You can try installing the following,  $ sudo apt-get install qt5-default  qtcreator  $ sudo apt-get install libqt5x11extras5-dev Are 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

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need for help
by Reza Rahmanzadeh 16 Jul '19

16 Jul '19

External Email - Use Caution Dear Freesurfer, I have a batch of myelin water image (MWI) from patients and controls, and trying to have inflated cortex registered on standard surface for GLM (Qdec). With the commandlines below i get my inflated surface of MWI map of my patients and controls. 1-using bbregister to put MWI into FS space and to calculate register.dat: bbregister --s FSP042/ --mov mwf.nii --init-fsl --reg register.dat --o mwf_FS --t1 2-using mri_vol2surf to extract inflated surface of MWI: mri_vol2surf --mov mwf.nii --reg register.dat --projfrac 0.5 --interp nearest --hemi lh --o lh.inflated_MWI.w --out_type paint --inflated (or --surf sphere) However the tksurfer could not open the inflated surface and the error message is: ERROR: MRISread: file 'inflated.lh.mwf.mgh' has 0 vertices! Probably trying to use a scalar data file as a surface! I used the commandline below for #2: mri_vol2surf --src mwf.nii --srcreg register.dat --hemi lh --o mwf-lh.w --out_type paint and i got the error: ERROR: MRISread: file '/usr/local/freesurfer/subjects/FSP010//surf/lh.mwf-lh.w' has many more faces than vertices! Probably trying to use a scalar data file as a surface! As tksurfer could not open my surfaces with errors above, i think perhaps the vol2surf procedure is not done properly. Where is the problem? i need to get the inflated cortex and then putting ob sphere (using mris_sphere) and the registering to standard surface using mris_register for GLM in Qdec, right? It is two weeks i am struggling with these commands, any helps highly appreciated. Best, Reza

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Freesurfer July 2019