Freesurfer

freesurfer@nmr.mgh.harvard.edu

19 participants
30088 discussions

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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Re: [Freesurfer] optseq2 parameters setup
by Greve, Douglas N.,Ph.D. 16 Jul '19

16 Jul '19

You are probably interested in the power (ie, "can I detect an effect with this many trials scheduled in this way?"). It is not possible to answer this question without an effect size. Having said that, I generally feel comfortable when the VRF is 20-40. Note that this assumes an FIR (not assuming a shape to the hemodynamic response) and dPSD=TR. If you assume a shape, you will get much more power out of it (assuming your assumed shape is close to correct:). On 7/16/19 9:51 AM, Tugce Duran wrote: > > External Email - Use Caution > > Thank you, Dr. Greve! This was helpful. > > When we look at the .sum file, what are the reference ranges for Eff > and VRF avg? > > I saw 20-40 for VRF on the help page but wasn’t fully sure. > > Thanks! > > Tugce > > *Tugce Duran* > *Graduate Student, Biomedical Sciences MS Program/ > /Neuroscience Concentration | **Section on Gerontology & Geriatric > Medicine, WFSM* > 2color > *Graduate Programs in Biomedical Sciences* > 525 Vine Street, Suite 150, Winston-Salem, NC 27101** > > *(*317-893-9100 *| ****_tduran(a)wakehealth.edu > <mailto:tduran@wakehealth.edu>_| |Image result for linked > inlinkedin.com/in/tugceduran/ <http://linkedin.com/in/janesmith/> > The information contained in this message is privileged and > confidential information intended for the sole use of the addressee. > If the reader of this message is not the intended recipient, or the > employee or agent responsible for delivering it to the intended > recipient, you are hereby notified that any dissemination, > distribution or copying of this communication is strictly prohibited. > If you have received this message in error, please notify the person > listed above immediately by e-mail, and delete the original message > and attachments. > > *From:*Greve, Douglas N.,Ph.D. <DGREVE(a)mgh.harvard.edu> > *Sent:* Monday, July 15, 2019 11:03 PM > *To:* Tugce Duran <tduran(a)wakehealth.edu>; Freesurfer support list > <freesurfer(a)nmr.mgh.harvard.edu> > *Subject:* Re: optseq2 parameters setup > > On 7/15/2019 12:50 PM, Tugce Duran wrote: > > * External Email - Use Caution * > > Hi Dr. Greve, > > I am interested in designing the Face Name Associative Memory Exam > (FNAME) fMRI task for our study. > > There are *80* face-name pairs that we will use and the duration > can be between 3.5 and 4.75 secs. I have used the following command: > > *optseq2 --ntp 200 --tr 2 --psdwin 0 32 2 --ev facename 4 80 > --nkeep 3 --o trial2 --tnullmin 0 --tnullmax 6 --nsearch 10000* > > Total scan time appx 6-7 mins. > > Q1: For NULL, why do we have only 2 sec and 4 sec jitters? Can we > change the variety amount of the jitters? Are more jitters good or > bad (instead of just having 2 secs and 4 secs, let’s say we get > 0.25, 1, 2, 3 and 4 secs) ? > > It always makes the NULL durations a integer multiple of the dPSD. You > set this to 2 (--psdwin 0 32 2). If you are assuming the shape to the > hemodyamic response (eg, the canonical SPM HRF), then it won't matter > much if you decrease it to 1 or less). The benefit of jitter in that > case depends more on the psychology than the signal processing. > > Q2: For the event design I am interested in above, what would be > the “best” parameters used? > > Usually, you set the total time for the NULL to be equal to that of a > stimulus type. In this case, you have one stimulus type presented for > a total of 320 sec (4*80), so you could set the scan duration to be > 320*2=640sec=10min 40sec. That would be optimum for testing your > stimulus against baseline, but that is probably not what you are > planning to do. > > *Trial2-001.par:* > > *0.0000 1 4.000 1.0000 facename* > > * 4.0000 1 4.000 1.0000 facename* > > * 8.0000 1 4.000 1.0000 facename* > > *12.0000 0 2.000 1.0000 NULL* > > *14.0000 1 4.000 1.0000 facename* > > *18.0000 1 4.000 1.0000 facename* > > *22.0000 1 4.000 1.0000 facename* > > *26.0000 1 4.000 1.0000 facename* > > *30.0000 1 4.000 1.0000 facename* > > *34.0000 1 4.000 1.0000 facename* > > *38.0000 1 4.000 1.0000 facename* > > *42.0000 0 4.000 1.0000 NULL* > > *46.0000 1 4.000 1.0000 facename* > > *50.0000 1 4.000 1.0000 facename* > > *54.0000 1 4.000 1.0000 facename* > > *58.0000 1 4.000 1.0000 facename* > > *62.0000 1 4.000 1.0000 facename* > > *66.0000 1 4.000 1.0000 facename* > > *70.0000 1 4.000 1.0000 facename* > > *74.0000 0 2.000 1.0000 NULL* > > *76.0000 1 4.000 1.0000 facename* > > *80.0000 0 2.000 1.0000 NULL* > > *82.0000 1 4.000 1.0000 facename* > > *.* > > *.* > > *.* > > *.* > > ** > > *372.0000 0 4.000 1.0000 NULL* > > *376.0000 1 4.000 1.0000 facename* > > *380.0000 1 4.000 1.0000 facename* > > *384.0000 1 4.000 1.0000 facename* > > *388.0000 1 4.000 1.0000 facename* > > *392.0000 1 4.000 1.0000 facename* > > *396.0000 1 4.000 1.0000 facename* > > Thank you in advance! > > Tugce > > *Tugce Duran* > *Graduate Student, Biomedical Sciences MS Program/ > /Neuroscience Concentration | Section on Gerontology & Geriatric > Medicine, WFSM* > 2color > *Graduate Programs in Biomedical Sciences* > 525 Vine Street, Suite 150, Winston-Salem, NC 27101 > > *(*317-893-9100 *| ****_tduran(a)wakehealth.edu > <mailto:tduran@wakehealth.edu>_| |Image result for linked > inlinkedin.com/in/tugceduran/ [linkedin.com] > <https://urldefense.proofpoint.com/v2/url?u=http-3A__linkedin.com_in_janesmi…> > The information contained in this message is privileged and > confidential information intended for the sole use of the > addressee. If the reader of this message is not the intended > recipient, or the employee or agent responsible for delivering it > to the intended recipient, you are hereby notified that any > dissemination, distribution or copying of this communication is > strictly prohibited. If you have received this message in error, > please notify the person listed above immediately by e-mail, and > delete the original message and attachments. >

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Problem while fix topology
by Li Ma 16 Jul '19

16 Jul '19

External Email - Use Caution Hi Everyone! I have met a problem that when I run the recon-all command, freesurfer always stuck at fix topology and dont give any files modify or terminal return for days. Could you please to help me solve this problem? Thanks!

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question for files recon-all generated
by ping cao 16 Jul '19

16 Jul '19

External Email - Use Caution Dear expert, I want to know if the *norm.mgz* is already linearly registered？ And is the *T1.mgz *not linearly registered? They are all generated from *recon-all. * Is there any file non-linearly registered? Best wishes, ping

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