Freesurfer May 2019

freesurfer@nmr.mgh.harvard.edu

95 participants
141 discussions

"MATLAB: Undefined variable" error, FSFAST Tutorial, using Octave
by Zacharie Saint-Georges 02 Jul '19

02 Jul '19

External Email - Use Caution Dear Freesurfer Developers, I am running into a "MATLAB: Undefined variable" error while doing the FSFAST tutorial, using Ubuntu 18.04, Freesurfer v6, and Octave***. I did try a few solutions posted already (please see links below), but I still cannot successfully run the tutorial command line. .basrc additions for Octave environment variables (Ref: https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg21241.html) export FS_OCTAVE_LIB=/usr/bin/octave export FS_OCTAVE_LIB=/usr/bin/octave additional command line: export FS_USE_OCTAVE=1 Ref: https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg60448.html main command line: mkcontrast-sess -analysis my-workmem.sm05.lh -contrast encode-v-base -a 1 (tutorial page: https://surfer.nmr.mgh.harvard.edu/fswiki/FsFastTutorialV6.0/FsFastFirstLev… ) error output: INFO: Found 5 Non-Null Conditions INFO: Found 1 Delays Condition Weights: 1.00000000000000000000 0 0 0 0 mkcontrast2 -config my-workmem.sm05.lh/encode-v-base.config -anadir my-workmem.sm05.lh -wcond 1.00000000000000000000 0 0 0 0 -sumconds -o my-workmem.sm05.lh/encode-v-base.mat -wdelay 1 -octave $Id: mkcontrast2,v 1.3 2016/03/11 23:46:48 greve Exp $ cmtxfile my-workmem.sm05.lh/encode-v-base.mat nconds 5, wcond 1.00000000000000000000 0 0 0 0 ndelays 1, wdelay 1 ndelays 1, wpsa sumconds 1 sumdelays 0 nircorr 0 TER 0.050000 rdelta rtau cmtxfile my-workmem.sm05.lh/encode-v-base.mat monly 0 NCond 5 WCond 1.00000000000000000000 0 0 0 0 NDelay 1 WDelay 1 TER 0.050000 sumconds 1 sumdelays 0 nircorr 0 TPreStim 0 RmPreStim 0 rdelta 0 0 rtau 0 0 ndelays 1 CNorm 1 setwdelay 0 setwcond 0 Matlab file is /tmp/mkcontrast2.18977.m MATLAB: Undefined variable. ERROR running mkcontrast mkcontrast2 -config my-workmem.sm05.lh/encode-v-base.config -anadir my-workmem.sm05.lh -wcond 1.00000000000000000000 0 0 0 0 -sumconds -o my-workmem.sm05.lh/encode-v-base.mat -wdelay 1 -octave Tue May 28 16:51:41 EDT 2019 I also modified the mkcontrast freesurfer file according to this post: Ref: https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg58758.html Thank you for your assistance! Regards, Zach Zacharie Saint-Georges Research Assistant Royal Ottawa Institute for Mental Health Research Zacharie.Saint-Georges(a)TheRoyal.ca

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Labelling SurfStat p-value surface map
by Loïc Daumail 27 Jun '19

27 Jun '19

External Email - Use Caution Dear Freesurfer community, I obtained score matrices of surfaces after performing diffusion embedding map on fMRI data. I am now using the SurfStat toolbox(Matlab) in order to obtain p-value maps to compare between two groups. After obtaining the p-value map, I would like to label the surface in order to identify the regions of significant difference between both groups. Would it be possible to use Freview in order to do it? If so, which format should I use for my SurfStatP output p-value map? How would you do it, (tools to convert into a specific format, surfaces and atlas to load on Freeview, which format for those ones)? I would be very grateful if you could detail a bit, as I am new to these tools! Thanks in advance, Loïc Daumail

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T2 seq. for hippocampus ??
by Anik Dar 25 Jun '19

25 Jun '19

External Email - Use Caution Hi All, I have 1x1x3 cubic mm T2 and 1x1x1 cubic mm FLAIR, in addition to 1x1x1 cubic mm MPRAGE. Can you please let me know whether I should use only T1 or should I use one of the additional seq. for hippocampal subfield segmentation ? cheers Nik

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Segmenting internal capsule
by Chinappen, Dhinakaran Maheswaran 16 Jun '19

16 Jun '19

Dear Freesurfer community experts, We're looking to segment the internal capsule using T1 data. We found documentation in the FreeSurfer white matter segmentation atlas that states that the right and left anterior and posterior portions of the internal capsule are segmented as regions 155-158, but they don't actually appear in any of the output parcellations. We've seen this question appear in previous email threads, <https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2016-August/047133.h…>, but can't find the script "intcapseg" that Doug mentioned here: <https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2011-October/020985.…>. If anyone could send us this script it would be much appreciated. Thanks! Lauren and Dhinakaran.

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4 optseq2 questions
by Katarina Bendtz 04 Jun '19

04 Jun '19

External Email - Use Caution Dear experts: I'm using the optseq2 version 2.15 2009/05/26. I have three questions: 1. How does the [PSDmin, PSDmax] relate to the jittered intertrial intervals? 2. I have stimuli of between 12 and 20 seconds, where the part of my stimulus that I want to measure is in the last 5 seconds or so. What should I put my dPSD window to? It's both a matter of that the signal starts later than the stimulus presentation, so I guess I would have a PSDmin of a couple of seconds, but how do I handle the variation in stimuli lengths? 3. As mentioned above I have quite a large variation between my stimuli. When I try to specify them individually (about 25) I always get that all schedules are ill-conditioned. Is this because such schedules are generally hard to optimize? 4. I quite often get that all schedules are ill-conditioned, but there is no information in the log file that tells me what is wrong. Example: ./optseq2 --ntp 1500 --tr 1.86 --psdwin 0 22.32 0.93 --nkeep 3 --nsearch 1000 --o test --ev control_trial_1 16.74 1 --ev control_trial_3 18.6 1 --ev control_trial_7 18.6 1 --ev test_trial_11 16.74 1 I get: NFO: searched 1000 iterations for 0.010556 hours INFO: 26.3158 iterations per second INFO: 1000/1000 schedules were ill-conditioned ERROR: all schedules found were ill-conditioned. This probably means that you need more scan time (ie, a greater number of time points) or fewer repetitions. (I'm running on a macOS Mojave version 10.14.3. ) But it's obviously not the ntp that is the problem since I put an extra long time there that cover the event durations by far. Is there any way I can troubleshoot more efficiently myself? The log file doesn't tell me anything. Very happy for any advice, All the best, Katarina Katarina Bendtz, Ph.D. (particle physics) Postdoctoral researcher in cognitive neuroscience Department of Psychology, Stockholm University

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Re: [Freesurfer] Freesurfer V6 installation: ubuntu virtual machine
by fsbuild 03 Jun '19

03 Jun '19

External Email - Use Caution Hello Steve, We have run the freesurfer 6.0.0 release on Ubuntu 16 and 18 which should also work in a VM. You may have to install some packages in order to run freesurfer, especially for the freeview program which uses various graphics packages, etc.  After downloading the freesurfer 6.0.0 binaries from, https://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/6.0.0/freesurfer-Lin… - I would first try to run the freeview binary as that is a good test to help determine what packages may be missing. I needed to both build and run freesurfer on Ubuntu, so I will list below the packages I installed for both purposes.  You should not need for example the gcc compiler packages just to run the 6.0.0 release binaries, but I have not tried to identify a set of packages to only run the binaries. You will likely also need sudo privileges to install packages. - R.      $ sudo apt-get install build-essential     $ sudo apt-get install libgl1-mesa-dev freeglut3-dev mesa-common-dev     $ sudo apt-get install libblas-dev liblapack-dev     $ sudo apt-get install ocl-icd-opencl-dev     $ sudo apt-get install libxmu-dev libxi-dev     $ sudo apt-get install libopencv-dev      Ubuntu 16:  $ sudo apt-get install gcc-4.9 g++-4.9 gfortran-4.9     Ubuntu 18:  $ sudo apt-get install gcc-4.8 g++-4.8 gfortran-4.8     $ sudo apt-get install xorg xorg-dev libx11-dev     $ sudo apt-get install tcl tcl-dev tk tk-dev     $ sudo apt-get install qt5-default qtcreator     $ sudo apt-get install libqt5x11extras5-dev     $ sudo apt-get install git-annex      $ sudo apt-get install python3-dev     … you will need a libpng, which I got from the archives,     http://se.archive.ubuntu.com/ubuntu/pool/main/libp/libpng/libpng12-0_1.2.54-1ubuntu1_amd64.deb     $ curl -O  http://se.archive.ubuntu.com/ubuntu/pool/main/libp/libpng/libpng12-0_1.2.54-1ubuntu1_amd64..deb    - then install the gdebi tool,      $ sudo  apt install gdebi     - change directories to where you downloaded the libpng12 package, and use gdebi to install it,     $ sudo  gdebi  libpng12-0_1.2.54-1ubuntu1_amd64.deb On May 31, 2019, at 02:57, Steve Petersen <marfneuro(a)GMAIL.COM> wrote:        External Email - Use Caution        Dear Freesurfer experts, Just a simple question, is possible to install the Freesurfer (Version 6) in a virtual machine of ubuntu?Thanks in advance,Best regards,Steve_______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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Problem with lme_mass_fit_vw
by Hua, Jessica 03 Jun '19

03 Jun '19

External Email - Use Caution Dear FreeSurfer Experts, Just reposting this since I did not see it on the forum. I am trying to run longitudinal gyrification analyses following the FreeSurfer Linear Mixed Effects Models instructions, and I ran into a problem using lme_mass_fit_vw. I have 49 participants, and each participant has 2 timepoints. My model is: Yij = ß1 + ß2*tij +ß3*adjBACi + ß4*adjBACi *tij + ß5*sexi + ß6*ICVi + b1i + b2i*tij + eij lhcortex 1x149955 uint32 lhsphere 1x1 struct M 98x4 double mri 1x1 struct ni 49x1 double Qdec 99x4 cell sID 98x1 cell X 98x6 double Y 98x163842 double X Column 1 = column of 1s X Column 2 = column of alternating 0s and 1s (corresponding to either time 1 or time 2) X Column 3 = adjBAC X Column 4 = adjBAC * column 2 X Column 5 = participant's sex X Column 6 = participant's ICV After following the steps in the FreeSurfer instructions, I ran this code: lhstats = lme_mass_fit_vw(X,[1],Y,ni,lhcortex); And I got the following errors: Error using parfor_progress (line 17) Do you have write permissions for /Applications/freesurfer/matlab/lme/mass_univariate? Error in lme_mass_fit (line 155) fn = parfor_progress('init',nv); Error in lme_mass_fit_vw (line 73) [stats1,st1] = lme_mass_fit(X,[],Xrows,Zcols,Y,ni,prs,e); Do you know what I am doing wrong? I am using Matlab R2018b (with parallel computing) and FreeSurfer v.6.0. Please let me know if you need me to provide you with any additional information. Thank you! Jessica Hua

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units for tracula output
by Alexopoulos, Dimitrios 03 Jun '19

03 Jun '19

External Email - Use Caution What units are the diffusion measures generated by tracula that are found in the files named "pathstats.overall.txt". For example, as 10^-3 Jim ________________________________ The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail.

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Tracula error -path
by Lorenzo Pini 03 Jun '19

03 Jun '19

External Email - Use Caution Hi list, Im using TRACULA in a dataset of 60 subjects. for 56 subjects everything is fine, but for 4 subjects I had the following error: >> ncpts: Subscript out of range. For these subjects TRACULA does not reconstruct the file dpath/merged_avg33_mni_bbr.mgz and the statistics of the tracts (i.e. pathstats.* files) Freesurfer parcellations look fine Do you have any suggestions? Thank you Lorenzo

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Fw: mri_aparc2aseg increases number of parcels? {Disarmed}
by Winkelbeiner, Stephanie A 31 May '19

31 May '19

External Email - Use Caution Hi Freesurfers, the number of my parcels increases after extending them into the WM with mri_aparc2aseg \ --s s001 \ --annot 500.aparc \ --wmparc-dmax 2 \ --labelwm \ --hypo-as-wm \ --o mri/aparc.500+2mm.nii.gz Could that really be the case? And if so, what can I do to keep the original number of parcels? (See more detailed description of my approach below) I would be very grateful for some suggestions! Thanks a lot, Stephanie Winkelbeiner ----------------------------------------------- Stephanie Winkelbeiner, PhD Psychiatry Research Zucker Hillside Hospital 75-59 263 Street Glen Oaks, NY 11004 Tel: (718) 470-8267 Email: swinkelbei(a)northwell.edu<mailto:swinkelbei@northwell.edu> ________________________________ From: freesurfer-bounces(a)nmr.mgh.harvard.edu <freesurfer-bounces(a)nmr.mgh.harvard.edu> on behalf of Winkelbeiner, Stephanie A <Swinkelbei(a)northwell.edu> Sent: Friday, 24 May 2019 6:08 PM To: Freesurfer support list Subject: Re: [Freesurfer] [EXTERNAL] Re: Checking number of parcels after transformation of an annotation file into a .nii.gz file External Email. Use Caution. External Email - Use Caution Hi Doug, thanks again for the great tip with MRIread - worked perfectly (after gunzipping the parc300.nii.gz). So, this means I have the next problem now: instead of 300 parcels this image contains 638 parcels... How I created parc300.nii.gz: 1. MATLAB script to create annotation file with 150 parcels/hemisphere 2. extending the parcels 2mm into the WM with mri_aparc2aseg (see 1st email) 3. coregistering to the T1 to get the transformation matrix (bbregister) 4. coregistering to DWI space (mri_vol2vol) I found in an earlier answer of yours that the extention into the WM might duplicate the parcels/labels (https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2018-February/055952…<https://urldefense.proofpoint.com/v2/url?u=https-3A__mail.nmr.mgh.harvard.e…>) Following your suggestions in that email exchange, I did the following: ## 1. Create a mask of the wm labels: mri_binarize \ --i aparc.500+2mm.nii.gz \ --min 2999.5 \ --max 4035.5 \ --o wm.mask.500.nii.gz ## 2. Mask the wmparc: mri_mask \ aparc.500+2mm.nii.gz \ wm.mask.500.nii.gz \ aparc.500+2mm.masked.nii.gz This results in only two parcels... What am I doing wrong or overlooking here? Thanks a lot for your help (as always)! Cheers, Stephanie ________________________________ From: freesurfer-bounces(a)nmr.mgh.harvard.edu <freesurfer-bounces(a)nmr.mgh.harvard.edu> on behalf of Winkelbeiner, Stephanie A <Swinkelbei(a)northwell.edu> Sent: Wednesday, 22 May 2019 6:23 PM To: Freesurfer support list Subject: Re: [Freesurfer] [EXTERNAL] Re: Checking number of parcels after transformation of an annotation file into a .nii.gz file External Email. Use Caution. External Email - Use Caution That sounds like a perfect plan! I gonna try that immediately! Thanks so much, Doug! ________________________________ From: freesurfer-bounces(a)nmr.mgh.harvard.edu <freesurfer-bounces(a)nmr.mgh.harvard.edu> on behalf of Greve, Douglas N.,Ph.D. <DGREVE(a)mgh.harvard.edu> Sent: Wednesday, 22 May 2019 6:19 PM To: freesurfer(a)nmr.mgh.harvard.edu Subject: [EXTERNAL] Re: [Freesurfer] Checking number of parcels after transformation of an annotation file into a .nii.gz file External Email. Use Caution. the way that pops to mind is to use matlab a = MRIread('aparc.250+2mm.nii.gz'); u = unique(a.vol(:)); length(u) will give you the number of unique segmentation number (including 0) On 5/22/19 5:54 PM, Winkelbeiner, Stephanie A wrote: > > External Email - Use Caution > > Hi Freesurfers, > > I'm struggling to find out if the number of parcels during a process > of transformations from annot -> nii.gz has changed. > > I extended the parcels from 500.annot 2mm into the WM with > mri_aparc2aseg \ > --s s001 \ > --annot 500.aparc \ > --wmparc-dmax 2 \ > --labelwm \ > --hypo-as-wm \ > --o mri/aparc.250+2mm.nii.gz > and coregistered the resulting file to the DWI image using bbregister > and mri_vol2vol. > > Using afni's probilistic tractography pipeline, I end up with more > parcels than I thought I had. > > Is there a way to check the number of parcels after extension into the > WM (mri_aparc2aseg)? > > I would be extremely grateful for some insight! > Thanks, > Stephanie > > The information contained in this electronic e-mail transmission and > any attachments are intended only for the use of the individual or > entity to whom or to which it is addressed, and may contain > information that is privileged, confidential and exempt from > disclosure under applicable law. If the reader of this communication > is not the intended recipient, or the employee or agent responsible > for delivering this communication to the intended recipient, you are > hereby notified that any dissemination, distribution, copying or > disclosure of this communication and any attachment is strictly > prohibited. If you have received this transmission in error, please > notify the sender immediately by telephone and electronic mail, and > delete the original communication and any attachment from any > computer, server or other electronic recording or storage device or > medium. Receipt by anyone other than the intended recipient is not a > waiver of any attorney-client, physician-patient or other privilege. > > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu > https://urldefense.proofpoint.com/v2/url?u=https-3A__mail.nmr.mgh.harvard.e… _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://urldefense.proofpoint.com/v2/url?u=https-3A__mail.nmr.mgh.harvard.e… The information contained in this electronic e-mail transmission and any attachments are intended only for the use of the individual or entity to whom or to which it is addressed, and may contain information that is privileged, confidential and exempt from disclosure under applicable law. If the reader of this communication is not the intended recipient, or the employee or agent responsible for delivering this communication to the intended recipient, you are hereby notified that any dissemination, distribution, copying or disclosure of this communication and any attachment is strictly prohibited. If you have received this transmission in error, please notify the sender immediately by telephone and electronic mail, and delete the original communication and any attachment from any computer, server or other electronic recording or storage device or medium. Receipt by anyone other than the intended recipient is not a waiver of any attorney-client, physician-patient or other privilege. The information contained in this electronic e-mail transmission and any attachments are intended only for the use of the individual or entity to whom or to which it is addressed, and may contain information that is privileged, confidential and exempt from disclosure under applicable law. If the reader of this communication is not the intended recipient, or the employee or agent responsible for delivering this communication to the intended recipient, you are hereby notified that any dissemination, distribution, copying or disclosure of this communication and any attachment is strictly prohibited. If you have received this transmission in error, please notify the sender immediately by telephone and electronic mail, and delete the original communication and any attachment from any computer, server or other electronic recording or storage device or medium. Receipt by anyone other than the intended recipient is not a waiver of any attorney-client, physician-patient or other privilege. The information contained in this electronic e-mail transmission and any attachments are intended only for the use of the individual or entity to whom or to which it is addressed, and may contain information that is privileged, confidential and exempt from disclosure under applicable law. If the reader of this communication is not the intended recipient, or the employee or agent responsible for delivering this communication to the intended recipient, you are hereby notified that any dissemination, distribution, copying or disclosure of this communication and any attachment is strictly prohibited. If you have received this transmission in error, please notify the sender immediately by telephone and electronic mail, and delete the original communication and any attachment from any computer, server or other electronic recording or storage device or medium. Receipt by anyone other than the intended recipient is not a waiver of any attorney-client, physician-patient or other privilege.

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Freesurfer May 2019