Freesurfer

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30081 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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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 V6 installation: ubuntu virtual machine
by Steve Petersen 31 May '19

31 May '19

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

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