Freesurfer January 2019

freesurfer@nmr.mgh.harvard.edu

119 participants
167 discussions

Re: [Freesurfer] Trouble Installing FreeSurfer {Disarmed}
by fsbuild 01 Feb '19

01 Feb '19

External Email - Use Caution … Correction - with the v switch “tar -xzvf” it is going to list every fileit expands and then return to the “$” prompt. - R. On , at 18:11  1/28/2019, fsbuild <fsbuild(a)contbay.com> wrote:        External Email - Use Caution        Hello Rodrigo,Did you download the tar file freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0.tar.gz from this page, and attempt to follow the steps below ?https://surfer.nmr.mgh.harvard.edu/fswiki/DownloadAndInstallIf you do not have permission to untar (write files) into /usr/local, you could try using another path. But usually if the tar command has a problem it will echo some error/text to the terminal, e.g., "Permission denied", or say there was an error.If the command simply returns to the prompt than it should have succeeded, e.g., success with "$" bash shell prompt.$ tar -C /usr/local -xzvf freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0.tar.gz$Please try and point out the step that does not work for you.- R.On , at 17:47  1/28/2019, Rodrigo Montenegro <rmontenegro11(a)gmail.com> wrote:        External Email - Use Caution        Dear FreeSurfer Team, I’m a Medicine student at Oxford University and I have just registered to FreeSurfer. I just went through the registration process so I'm very new to FreeSurfer but have only run to problems so far and would like to ask for your help: 1.       I have register with FreeSurferWiki but can’t login: it gives me one of the following errors:i.                      “Error 403 Login/Edit allowed only on https/SSL connections Login/Edit allowed only on https/SSL connections Guru Meditation: XID: 1153030795 Varnish cache serve”.ii.                   Or that it is an “Invalid username or password” (not sure if  2.       More importantly I have also tried to install FreeSurfer in Virtual Box (4096 MB Memory; 32 MD Video Memory; Ubuntu 64 Bits) without any success. The Ubuntu system works fine and I have the “freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0.tar.gz” to install FreeSurfer but the being totally new to Linux I have not had success to install it:i.                     I’m not sure if at all the files are unzipped from the .gz file.ii.                   And I have been unable to create the Bash files to define the environment for it. 3.        Finally, I notice that you do have an installation for Virtual Disk Image but the download for it (ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/5.3.0/freesurfer-Virtu…) is a gz file not a .vdi file as it should be (see picture below): <image002.jpg> So either way I wasn’t able to get through with the installation and any help is appreciated. Could you please provide some advice? Many thanks, Rodrigo Montenegro+44(0)7503070807 _______________________________________________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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Pb testing the FreeSurfer Installation
by Lise_A 01 Feb '19

01 Feb '19

External Email - Use Caution Dear Sir or Madam, I've just installed the last version of FreeSurfer for Linux ( freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0.tar.gz <https://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/6.0.0/freesurfer-Lin…>), but I got some troubles testing it: When trying to follow Example 2 ( https://surfer.nmr.mgh.harvard.edu/fswiki/DownloadAndInstall#Download) I get a "syntax error message": lise.aujoulat@ICM-COHEN-LF001 ~ $ *export SUBJECTS_DIR=/home/lise.aujoulat/Bureau/SUBJECTS_DATA* lise.aujoulat@ICM-COHEN-LF001 ~ $ * bash recon-all -i sample-001.nii.gz -s bert -all/usr/local/freesurfer/bin/recon-all: recon-all: ligne 31: erreur de syntaxe près du symbole inattendu « ( »/usr/local/freesurfer/bin/recon-all: recon-all: ligne 31: `set inputargs = ($argv);'* You can find a screen shot attached to this email. It seems that no one encountered this problem so far. I had installed the macOS version some months ago on my personal computer and encountered no problem at that time. How could I fix this? Thanks for your help, Lise -- Lise AUJOULAT MSc student in Integrative Biology and Physiology, Sorbonne University, Paris, France. Phone number: + 33 6 87 97 30 32 Mail: aujoulat.lise(a)gmail.com / lise.aujoulat(a)etu.upmc.fr

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Error with trac-all -path
by Seider, Nicole 31 Jan '19

31 Jan '19

External Email - Use Caution Dear all, I am having an error with the final step of TRACULA, trac-all -path. For a single subject (of a set of 38), when processing pathway 2 of 18, I will get the following error message: Segmentation fault (core dumped). For all other subjects, all the pathways are tracked successfully. I have double checked that all the paths are correct, that all the necessary files from previous steps exist (as suggested on other error mailing lists). Looking through the error file, I can't find anything in particular that seems to have failed. Any suggestions? Three files are attached: trac-all.error, trac-all.log, and trac-all_cluster-bedp.log. We ran the second step (trac-all -bedp) on our cluster, so it's log file is seperate. Thank you, Nicole Seider Neuroscience Graduate Student Washington University in St Louis nicole.seider(a)wustl.edu

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problems with Freeview
by Laboratorio de Neurociencia Funcional 31 Jan '19

31 Jan '19

External Email - Use Caution Dear Freesurfers, we have installed the updated Freeview version in the development version of Freesurfer (Centos 6, 18 january build), but Bert images appear displaced when they are loaded with this version of Freeview. The same displacement occurs when other dataset is used. Please find attached a screenshot to display the issue. Would you please help me to solve the problem? Thank you in advance. Best, Jose

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small volume correction in native space
by Loeffler, Martin 31 Jan '19

31 Jan '19

External Email - Use Caution Dear experts, I'm running an analysis on sensory mapping. It's a simple event-related design and my analysis stream seems to work fine. I need to analyze all the data in single subject space, because I'd like to calculate surface distances later (using mris_pmake), which must not be in standard space. I'd like to run my analysis for each single subject, but limit the analysis to a specific area (e.g. BA3b). Is this possible using FS? If yes, could you show me a way how this can be done? Thanks a lot for your help! Best, Martin

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LME
by Getaneh Bayu 31 Jan '19

31 Jan '19

External Email - Use Caution Dear Freesurfer Experts, I have a question about how to interpret cortical thickness difference between groups using LME MATLAB tools. I have three groups(g0, g1, and g2) and five time points(t= 0,0.5, 1,2,3). I am trying to use LME model with random effects y-int and time from the base line. Based on the LME tutorial and the questions and answers from Freesurfer support list: Y=B1+B2*t+B3*g1+B4*g1*t+B5*g2+B6*g2*t+ .... To see the difference between group g0 and group g1, I constructed the following contrast matrix using the tutorial provided in LME MATLAB tools C = [zeros(1,3) [1 0 0] zeros(1,4)]; CM.C=[zeros(1,3) [1 0 0] zeros(1,4)]; Based on the tutorial I run the following functions. rhstats = lme_mass_fit_Rgw(X,[1 2],rhY,ni,rhTh0,rhRgs,rhsphere); F_rhstats = lme_mass_F(rhstats,CM); fs_write_fstats(F_rhstats,rhmri,'/backup/cross/rh_AB_cross_sig.mgh','sig'); nv=length(rhstats); Beta2 = zeros(1,nv); for i=1:nv if ~isempty(rhstats(i).Bhat) Beta2(i) = rhstats(i).Bhat(2); end; end; rhmri1 = rhmri; rhmri1.volsz(4) = 1; fs_write_Y(Beta2,rhmri1,'rhBeta2.mgh'); [detvtx,sided_pval,pth] = lme_mass_FDR2(F_rhstats.pval,F_rhstats.sgn,rhcortex,0.05,0); fs_write_Y(sided_pval,rhmri1,'spval.mgh'); When I view sig.mgh using tksurfer I see regions with red and blue color. 1) Does the result shows the oveall change for all the five time points? 2) How do I know the difference between the two groups for each 5 time points? 3) Does red means thickness of group A is lgreater than thickness of group B? 4) what does rhBeta2.mgh and spval.mgh tell us? How can I extract the information from the file? With regards Getaneh -- --

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Fwd: Re: mri_glmfit-sim error correcting for MC for LGI analysis
by C.P.E. Rollins 31 Jan '19

31 Jan '19

External Email - Use Caution Dear Douglas, I was wondering if you might be able to take another look at my request below. Unfortunately, I still haven't been able to resolve the issue when I try to run mri_glmfit-sim. The error seems to be with mri_surfcluster.bin. I was wondering if you might have any advice. Please see the error message below. Thank you again, Colleen Starting simulation sim over 1000 trials mri_glmfit simulation done 63.5672 Thu Jan 31 10:34:16 GMT 2019 mri_surfcluster --in lh.lgi_300119.glmdir/NH-H/sig.mgh --mask lh.lgi_300119.glmdir/mask.mgh --cwsig lh.lgi_300119.glmdir/NH-H/perm.th20.abs.sig.cluster.mgh --sum lh.lgi_300119.glmdir/NH-H/perm.th20.abs.sig.cluster.summary --ocn lh.lgi_300119.glmdir/NH-H/perm.th20.abs.sig.ocn.mgh --annot aparc --cwpvalthresh 0.05 --o lh.lgi_300119.glmdir/NH-H/perm.th20.abs.sig.masked.mgh --no-fixmni --csd lh.lgi_300119.glmdir/csd/perm.th20.abs.j001-NH-H.csd --csdpdf lh.lgi_300119.glmdir/NH-H/perm.th20.abs.pdf.dat --vwsig lh.lgi_300119.glmdir/NH-H/perm.th20.abs.sig.voxel.mgh --vwsigmax lh.lgi_300119.glmdir/NH-H/perm.th20.abs.sig.voxel.max.dat --oannot lh.lgi_300119.glmdir/NH-H/perm.th20.abs.sig.ocn.annot --bonferroni 2 --surf white Creating CDFs from CSD files csd->threshsign = 0 thsign = abs, id = 0 version $Id: mri_surfcluster.c,v 1.60 2016/11/01 19:49:22 greve Exp $ hemi = lh srcid = lh.lgi_300119.glmdir/NH-H/sig.mgh srcsubjid = fsaverage srcsurf = white srcframe = 0 thsign = abs thmin = 2 thmax = -1 fdr = -1 minarea = 0 Bonferroni = 2 xfmfile = talairach.xfm nth = -1 outid = lh.lgi_300119.glmdir/NH-H/perm.th20.abs.sig.masked.mgh MGH ocnid = lh.lgi_300119.glmdir/NH-H/perm.th20.abs.sig.ocn.mgh MGH sumfile = lh.lgi_300119.glmdir/NH-H/perm.th20.abs.sig.cluster.summary subjectsdir = /home/cper2/scratch/Freesurfer/Beijing FixMNI = 0 Found 148421 vertices in mask Found 148421 vertices in mask Found 148421 points in clabel. ------------- XFM matrix (RAS2RAS) --------------- /home/cper2/scratch/Freesurfer/Beijing/fsaverage/mri/transforms/talairach.xfm 1.00000 0.00000 0.00000 0.00000; 0.00000 1.00000 0.00000 0.00000; 0.00000 0.00000 1.00000 0.00000; 0.00000 0.00000 0.00000 1.00000; MRISread(\ufffd\ufffd\ufffd): could not open file No such file or directory ---------------------------------------------------- Reading source surface /home/cper2/scratch/Freesurfer/Beijing/fsaverage/surf/lh.white mri_surfcluster.bin: could not read surface /home/cper2/scratch/Freesurfer/Beijing/fsaverage/surf/lh.white No such file or directory -------- Original Message -------- Subject: Re: mri_glmfit-sim error correcting for MC for LGI analysis Date: 2018-11-27 11:46 From: "C.P.E. Rollins" <cper2(a)cam.ac.uk> To: Freesurfer <freesurfer(a)nmr.mgh.harvard.edu> Hi Douglas, Thanks a lot for your answers. 1) For the permutations, would you recommend using this for controlling for MC in cortical thickness analyses too? Why is it recommended to use permutation simulation as opposed to Z Monte Carlo simulation for an LGI analysis? 2) I've attached here the output from ls -Rl $FREESURFER_HOME/subjects/fsaverage. Thanks again, Colleen On 2018-11-23 16:26, C.P.E. Rollins wrote: > Dear Freesurfer Developers, > I have a 2-part question: > 1) I was advised to use permutation to control for multiple > comparisons in an LGI analysis, would you mind elaborating how to do > this in command line (in terms of command and parameters)? > 2) In running "mri_glmfit-sim --glmdir lh.5.lgi_MAN_new.glmdir --cache > 1.3 pos --cwp 0.05 --2spaces --debug", I receive the following error > (attached). I was wondering if you might have any advice? The file > /home/cper2/BeneMin/Freesurfer/fsaverage/surf/lh.white exists and I can > view it in freeview. > > Many thanks, > Colleen

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Re: [Freesurfer] Smoothing before or after PALM (and results conversion for Surf Ice)
by Daniel Leopold 30 Jan '19

30 Jan '19

External Email - Use Caution Hi Bruce, Chris Rorden informed me that Surfice previously assumed that MGZ/MGH files were voxelwise images used to surface-paint a mesh. Anderson's palm, however, uses the format as a one-to-one correspondence with the vertices (i.e., data-per-vertex). Chris' newest/upcoming version of Surfice automatically detects this data-per-vertex format and can load the files appropriately. The main feature that freeview lacks is the ability to display multiple overlays/sets of palm results at once. My initial approach was to convert the .mgz palm outputs into .nii so that I could use fslmaths to combine results, but (apparently) NIFTI handles a maximum of 65,535 voxels in any one dimension, which is why Chris thought Anderson used MGH, which allows billions of vertices (32-bit). So, Surfice can now load the palm .mgz outputs onto ?h.inflated, .pial, and .curv surfaces, but I'm now wondering if mgh/mgz overlays be be loaded on top of other background meshes (such as BrainMesh_ICBM152 or mni2fs meshes that are provided with Surfice). I've emailed Darren Price because I'm essentially looking for the inverse transform of his mni2fs package (i.e., fs2mni), but I was wondering if you or Doug have encountered this question or similar requests to convert freesurfer to mni surfaces/meshes before? I'm familiar with the Freesurfer Coordinate Systems info, but I don't know how I might generalize the RAS to MNI152 point conversion to an entire surface. Thank you again for your suggestions and help! Dan

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Average-subject space
by Sofia Rodriguez Penuela 30 Jan '19

30 Jan '19

External Email - Use Caution Hi Freesurfer team! How can I export the volumes of each subject to .nii in the space of the average subject? Thank you. Sofía Rodríguez Peñuela.

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Re: [Freesurfer] Thalamic segmentation questions
by Iglesias Gonzalez, Eugenio 29 Jan '19

29 Jan '19

External Email - Use Caution Dear Manoj, First question: The one without the suffix is defined at higher resolution, on a voxel grid that does not correspond to the standard FS space (where norm.mgz, aseg.mgz, etc. live). The one with the suffix lives on the voxel grid of norm.mgz, aseg.mgz, etc Both of them live in the physical RAS coordinates or the other volumes, that’s why they look similar when you open them of FreeView. But if you zoom in enough, you’ll notice that the one without the suffix has higher resolution. Second question: Yes, you first need to register, manually or (preferably) automatically, e.g., with BBregister, mri_robust_register, etc. Then, you can run: mri_convert moving.nii.gz deformed.nii.gz -rl nu.mgz -at [YOURTRANSFORMFILE.LTA] -rt nearest I hope this helps. /Eugenio -- Juan Eugenio Iglesias ERC Senior Research Fellow Centre for Medical Image Computing (CMIC) University College London Research staff Martinos Center for Biomedical Imaging Massachusetts General Hospital Research Affiliate Computer Science and Artificial Intelligence Laboratory (CSAIL) Massachusetts Institute of Technology Lecturer on Radiology Harvard Medical School http://www.jeiglesias.com From: <freesurfer-bounces(a)nmr.mgh.harvard.edu> on behalf of Manoj Saranathan <manojsar(a)radiology.arizona.edu> Reply-To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> Date: Tuesday, 29 January 2019 at 19:15 To: "freesurfer(a)nmr.mgh.harvard.edu" <freesurfer(a)nmr.mgh.harvard.edu> Subject: [Freesurfer] Thalamic segmentation questions External Email - Use Caution The thalamic nuclei segmentation produces 2 mgz files. One has the FS suffix and other does not. Is the latter without the FS in the native space? If I import and view in freeview, they look same. I want it in native space so I can do some Dice calculations. My manual segmentations are on a different data set very close to but not necessarily perfectly aligned to the T1 data set used in recon-all. I can use the mri_conver -rl 'reslice like' option but it does not do any registrations does it? It just reslices it in the orientation of the file argument to -rl right. I assume have to manually affine register and propagate the warps if they are not aligned? Thanks, manoj ________________________________ From: Manoj Saranathan Sent: Tuesday, January 29, 2019 5:11 PM To: freesurfer(a)nmr.mgh.harvard.edu Subject: Thalamic segmentation questions The thalamic nuclei segmentation produces 2 mgz files. One has the FS suffix and other does not. Is the latter without the FS in the native space? If I import and view in freeview, they look same. I want it in native space so I can do some Dice calculations. My manual segmentations are on a different data set very close to but not necessarily perfectly aligned to the T1 data set used in recon-all. I can use the mri_conver -rl 'reslice like' option but it does not do any registrations does it? It just reslices it in the orientation of the file argument to -rl right. I assume have to manually affine register and propagate the warps if they are not aligned? Thanks, manoj ________________________________ From: Manoj Saranathan Sent: Tuesday, January 29, 2019 5:06 PM To: freesurfer(a)nmr.mgh.harvard.edu Subject: Thalamic segmentation questions The thalamic registration produces 2 mgz files. One has the FS suffix and other does not. Is the latter without the FS in the native space? If I import and view in freeview, they look same. I want it in native space so I can do some Dice with manual segmentation. The 'reslice like' option of mri_convert does not do any registrations does it? It just reslices it in the orientation of the file argument to -rl right. I assume have to manually register and propagate the warps if they are not aligned. Thanks, manoj Manoj Saranathan Associate Professor, Dept. of Medical Imaging University of Arizona Ph: 520-626-6531

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Freesurfer January 2019