Freesurfer

freesurfer@nmr.mgh.harvard.edu

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30088 discussions

Question about coordinates in Freesurfer
by Zhi Li 16 Jul '19

16 Jul '19

External Email - Use Caution Dear Freesurfer experts, Now I have an annotation file in fsaverage space and a MNI voxel coordinate of one subject. May I ask how could I know if this coordinate is in one parcel of the annotation file? There are many coordinates that I cannot check it one by one in Freeview. In addition, if this is a native image coordinate how could I check whether it is in a parcel then? An additional question is whether the spaces of all the files in folder "mri" generated by recon-all are native individual space? What do the files 'orig.mgz', norm.mgz'', 'brainmask.mgz', 'brain.mgz' and 'T1.mgz' refer to? They are very similar to each other, with skull-stripped or not. Is there any document on it I could reference? Looking forward to your kind suggestions, Many thanks and best regards, Lizhi

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freeview
by Juan Rivas 16 Jul '19

16 Jul '19

External Email - Use Caution I try again with fortran, uploaded it again, and now I get this message: jcrn12@jcrn12-VirtualBox:~$ 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) Best regards, JC.

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Viewing Uncorrected Significance Map in Freeview
by Marie Hill 15 Jul '19

15 Jul '19

External Email - Use Caution Hi everyone, I have just finished running glmfit. When I try to load the significance maps in freeview, they appear to load for a moment and then disappear, just showing the brain volume without any highlighted areas of significance. Does anyone have any idea why this could be? I ran the command: freeview -f $SUBJECTS_DIR/fsaverage/surf/lh.inflated:annot=aparc.annot:annot_outline=1:overlay=lh.g4v1.glmdir/bipolar-vs-schizophrenia/sig.mgh:overlay_threshold=4,5 -viewport 3d Kindest Regards, Marie

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How to Divide the Surface Parcellations of the Brain
by Mahshid Fouladivanda 15 Jul '19

15 Jul '19

External Email - Use Caution Dear Bruce, All the outputs are .nii and .gii I do not know if it is possible to convert it to the annotation! By the way, what is needed for creation of the annotation file? I mean what information, it needs? Regards Mahshid

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make_average_subject error: could not load norm volume from (null)
by Mads Jensen 15 Jul '19

15 Jul '19

External Email - Use Caution HI FreeSurfer Developers, I'm attempting to create an average subject make_average_subject but I get the error message the following error when I run the make_average_command: Loading aseg from REMOVED-PATH/avg_elder/mri/aseg.presurf.hypos.mgz ASeg Vox2RAS: ----------- -1.00000 0.00000 0.00000 128.00000; 0.00000 0.00000 1.00000 -128.00000; 0.00000 -1.00000 0.00000 128.00000; 0.00000 0.00000 0.00000 1.00000; mghRead(mri/norm.mgz, -1): could not open file ------------------------- Labeling Slice relabeling unlikely voxels in interior of white matter mri/norm.mgz: could not load norm volume from (null) Linux 4.4.0-130-generic #156-Ubuntu SMP Thu Jun 14 08:53:28 UTC 2018 x86_64 x86_64 x86_64 GNU/Linux I cannot find anything similar on the mailing list. I hope anyone have any thoughts on how to trouble-shoot this one? Also, Ive attached the recon-all.log in case it's of any use. 1) FreeSurfer version: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c 2) Platform: Ubuntu 16.04.4 LTS 3) uname -a: Linux hyades02 4.4.0-130-generic #156-Ubuntu SMP Thu Jun 14 08:53:28 UTC 2018 x86_64 x86_64 x86_64 GNU/Linux 4) recon-all.log: see attached

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A Question Regarding Topology Correction
by Maedeh Khalilian 15 Jul '19

15 Jul '19

External Email - Use Caution Dear FreeSurfer experts, I know that FreeSurfer does segmentation, surface reconstruction and topology correction through its routine pipeline using "recon-all" . However, I have some T2w brain MR images and I have done the segmentation and extracted WM, GM, and CSF with my own algorithm. Now I need to remove back to back (i.e. a part of topology correction) which is caused in sulci due to the segmentation. In other word, after doing my segmentation, I wanna open the closed concavities in CSF that were open originally. Now I wanna know if I can do the topology correction using FreeSurfer while I have done the segmentation by myself? I would be grateful if you could help me with that. Best, Maedeh

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Re: [Freesurfer] optseq2 parameters setup
by Greve, Douglas N.,Ph.D. 15 Jul '19

15 Jul '19

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 in]linkedin.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.

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Fwd: Question about Freesurfer LME analysis
by Bronwyn Overs 15 Jul '19

15 Jul '19

External Email - Use Caution Dear Freesurfer Mailing list, I have run a mass-univariate spatiotemporal model using 'lme_mass_fit_EMinit' and then applied an FDR correction across both hemispheres (syntax provided below). On completion I realised that m ost of the corrected p-values for my main and interaction effects were well above the alpha of 0.05. The corrected p-value thresholds in log base 10 format are included in the attached figure and summarised below. Summary of p-value thresholds in attached images: Figure Key Log10P P Figure 1 A1 -1.193 0.064 A2 -0.695 0.202 B1 -0.969 0.107 B2 -0.243 0.571 C1 -0.195 0.638 C2 -0.001 0.998 Figure 2 A -2.663 0.002 B -1.295 0.051 I have no idea why this has happened and would greatly appreciate any insight you can provide. I would also note that the same issue occurred in a model where we exclude all subjects with only a single time-point. However, it did not occur when we included only Caucasians in our analysis and excluded the two dummy coded ethnicity covariates. This leads me to think its something to do with the complexity of the model, but I cannot understand why the error is only occurring when we correct for multiple comparisons. I have provided the details of sample and methods below. Sample Our sample includes 112 controls subjects, and 106 at-risk subjects (individuals with a first degree relative of BD but not personal history of BD). All subjects are aged between 12 and 30 years. 153 or these subjects have 2 time-points (77 control, 76 at-risk), while the remaining 65 individuals have only 1 MRI time-point. We also have mixed ethnicites - 165 Caucasians, 23 Asians, and 30 mixed (Asians-Caucasians). Analysis Design The QDEC file contains the following 6 variables: 1. Y (years between scans) 2. A (baseline age) 3. G (group, 1=case, 0=control) 4. S (sex, 1=female, 0=male) 5. E1 (Ethnicity 1, 1=asian, 0=other) 6. E2 (Ethnicity 1, 1=mixed-asian-caucasian, 0=other) Design matrix: [ones(length(M),1) M M(:,1).*M(:,3)] i.e. main effects for each of the qdec variables + an interaction term for years X group DVs: Cortical thickness, area and volume Model: Mass-univariate spatiotemporal model using 'lme_mass_fit_EMinit' CODE: % Read in surface files [Y,mri] = fs_read_Y(mgh); % Read in qdec file Qdec = fReadQdec(qdec); % Remove fsid from qdec Qdec = rmQdecCol(Qdec,1); % Store col 1 (fsid-base) in sID variable sID = Qdec(2:end,1); % Remove col 1 (fsid-base) from Qdec array Qdec = rmQdecCol(Qdec,1); % Convert Qdec to numeric matrix M M = Qdec2num(Qdec); % Sort data and evaluate design matrix [M,Y,ni] = sortData(M,1,Y,sID); X = eval([ones(length(M),1) M M(:,1).*M(:,3)]) % Compute vertex-wise temporal covariance estimates. [Th0, Re] = lme_mass_fit_EMinit(X,[1],Y,ni,cortex,3); %Segmentation and model fitting. [Rgs, RgMeans, stats] = fit(Th0, Re, [1], sphere, cortex, X, Y, ni); %Check surfaces. surfcomp(Th0, RgMeans, sphere, fig1, fig2) Correction for multiple comparisons: FDR across both hemispheres CODE: P = [ F_lhstats.pval(lhcortex) F_rhstats.pval(rhcortex) ]; G = [ F_lhstats.sgn(lhcortex) F_rhstats.sgn(rhcortex) ]; [detvtx, sided_pval, pth] = lme_mass_FDR2(P,G,[],0.05,0); pcor = -log10(pth); thrlh(r,2) = {pcor}; thrrh(r,2) = {pcor}; [~,dc] = size(detvtx); dvtx(r,2) = {dc}; 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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Re: [Freesurfer] freeview
by fsbuild 15 Jul '19

15 Jul '19

External Email - Use Caution Did you try, $ ldd /usr/local/freesurfer/bin/freeview | grep not ? - R. On Jul 12, 2019, at 08:42, Juan Rivas <jcrn12(a)gmail.com> wrote:        External Email - Use Caution        It looks like freeview is in: jcrn12@jcrn12-VirtualBox:~$ /usr/local/freesurfer/bin/freeviewBut when I try to use it, I can not do it, because: jcrn12@jcrn12-VirtualBox:~$ ldd freeview | grep notldd: ./freeview: No such file or directory.Thank you for your help,JC.---------- Forwarded message ---------De: Juan Rivas <jcrn12(a)gmail.com>Date: vie., 12 jul. 2019 a las 6:57Subject: freeviewTo: <freesurfer(a)nmr.mgh.harvard.edu>That is what happened:$ ldd /usr/local/bin/freeview | grep notldd: /usr/local/bin/freeview: No such file or directory$ bashjcrn12@jcrn12-VirtualBox:~$ ldd /usr/local/bin/freeview | grep notldd: /usr/local/bin/freeview: No such file or directoryJC.---------- Forwarded message ---------De: fsbuild <fsbuild@contbay.com>Date: lun., 15 jul. 2019 a las 14:19Subject: Re: [Freesurfer] FreeviewTo: <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._______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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Re: [Freesurfer] Fwd: Freeview
by fsbuild 15 Jul '19

15 Jul '19

External Email - Use Caution Sorry - from your previous mail, I mistakenly thought “which freeview” returned /usr/local/bin/freeview. If you can reproduce what you did before to run freeview from the command line where it tells you that it was not finding libgfortran, then “which freeview” will likely tell you where the binary is.  You should have already set FREESURFER_HOME to point to the freesurfer  installation and then did the source of the shell init file (SetUpFreeSurfer.sh for bash or sh, SetUpFreeSurfer.csh for csh).  See the wiki page here under setup and configuration, https://surfer.nmr.mgh.harvard.edu/fswiki/DownloadAndIn… That should have put freeview in your PATH so that “which freeview” works. What you want to do is to cd into the directory where the freeview binary lives and run ldd on it.  If “which freeview” returned /usr/local/bin/freeview then you could “cd /usr/local/bin” and from there directly run “ldd freeview | grep not”. - R.  On Jul 12, 2019, at 07:32, Juan Rivas <jcrn12(a)gmail.com> wrote:        External Email - Use Caution        That is what happened:$ ldd /usr/local/bin/freeview | grep notldd: /usr/local/bin/freeview: No such file or directory$ bashjcrn12@jcrn12-VirtualBox:~$ ldd /usr/local/bin/freeview | grep notldd: /usr/local/bin/freeview: No such file or directoryJC.---------- Forwarded message ---------De: fsbuild <fsbuild@contbay.com>Date: lun., 15 jul. 2019 a las 14:19Subject: Re: [Freesurfer] FreeviewTo: <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 18This is the message I get:$ freeviewsh: 8: freeview: not found$  which freeview                  $ /usr/local/bin/freeviewsh: 10: /usr/local/bin/freeview: not found$ which ldd/usr/bin/ldd$ ldd `which freeview` | grep notldd: missing file argumentsTry `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_64For Ubuntu,$sudo apt-get install gfortranOne thing you might want to try first is to run the “ldd” command on the freeview binary to see all/any libraries that are missing....This should return the path to freeview, e.g., /usr/local/bin/freeview, though your path may differ.$ which freeview/usr/local/bin/freeview- then check you have the ldd command, $ which ldd/usr/bin/lddIf 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 notAlso 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 3:02Subject: Re: [Freesurfer] FreeviewTo: 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-devOn 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 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_______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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Freesurfer