Freesurfer June 2019

freesurfer@nmr.mgh.harvard.edu

82 participants
138 discussions

Pial surface segmentation QC through recon-all
by Faezeh Vedaei 04 Jun '19

04 Jun '19

External Email - Use Caution Hello I just needed to get help from someone has experience working on correcting pial surface segmentation by recon-all. Based on FreeSurfer tutorial and some instructions I have found by googling I have found some clues that was helpful, but for the issue I have right now was not enough. As you know I need to make sure that there is no dura or blood flow included in pial surface (cortex), so need to do editing by removing extra voxels. For some of our subject's data, there are some spots or areas obviously has no barrier between dura and cortex, and in my eyes it seems dura in included in the cortex (or cortex is extended to the dura) which needs correction. But I was wondering if I want to remove them, that would be so time-consuming and hard to check and edit every spot and slice, as these are shown a lot on many spots. So do you recommend me to do editing on these areas or forget about? I really appreciate that if you clarify me about this process specifically dura removing correction. Bests Faeze

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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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Cluster-wise multiple comparison correction
by Jacobs, H (NP) 02 Jun '19

02 Jun '19

External Email - Use Caution Hi all! I would love to use the cluster-wise multiple comparison correction method in FS 6.0 for our PET data (in fsaverage space and smoothed). However, since we have some complex models, I did the statistical analyses in R and then converted this to a surface overlay map in mgh format (in log10 p-values). That means that I don’t have the typical glm output that is usually obtained in Freesurfer. I tried to run the mri_glmfit-sim function, but it does need the mri_glmfit.log file. Is there a way around this? Many thanks! Heidi

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selxavg3-sess failed
by starxifd 02 Jun '19

02 Jun '19

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fsl_rigid_register error: error opening .nii file
by Mingjian He 01 Jun '19

01 Jun '19

Hi FreeSurfer Developers, I’m using mne.bem.make_flash_bem python function to create BEM meshes, and mne.bem.make_flash_bem makes use of the FreeSurfer functions fsl_rigid_register and mri_convert. I’m running into an error reading the temporary files when using fsl_rigid_register. It looks like the FSL flirt step in fsl_rigid_register creates a compressed file outvol.fsl_rigid_register.nii.gz in the temporary folder. But in mri_convert, the uncompressed file name outvol.fsl_rigid_register.nii is passed to niiRead(), which runs into an error opening it since the compressed file from flirt has a different format suffix. Is there a way to specify the output format of FSL when sourcing Freesurfer such that it saves in .nii rather than .nii.gz formats? I tried to specify the FSF_OUTPUT_FORMAT, which doesn’t seem to impact FSL output formats. Alternatively, is there a way to flag to either mri_convert of niiRead() such that they can handle a compressed .nii.gz file? Thank you for your time and help! Best, Alex External Email - Use Caution

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Freesurfer June 2019