Freesurfer

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Re: [Freesurfer] Freesurfer installation on Ubuntu virtual machine
by fsbuild 03 Mar '20

03 Mar '20

External Email - Use Caution I should have said at the end for installation under $HOME to set, $ export FREESURFER_HOME=$HOME/freesurfer - R. fsbuild March 3, 2020 at 15:39         External Email - Use Caution         Hello Ben, For packages to install, see the following wiki page, https://surfer.nmr.mgh.harvard.edu/fswiki/BuildRequirements Usually to expand the freesurfer *.tar.gz archive under /usr/local, you would need sudo/root privileges, e.g. $ cd /usr/local$ sudo tar zxpf freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0.tar.gz…... output deleted - and you would end up with /usr/local/freesurfer and in turn do $ export FREESURFER_HOME=/usr/local/freesurfer But if you don’t have sudo privileges, e.g., it does not work to do$ sudo touch /usr/local/foo$ sudo rm /usr/local/foo - then you may want to consider putting freesurfer under your $HOME directory or somewhere you have permission to write files w/o needing to use sudo, e.g., $ cd $HOME$ tar zxpf freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0.tar.gz$ export FREESURFER_HOME=$HOME - R. _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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LGI help
by Nillo, Ryan Michael R 03 Mar '20

03 Mar '20

Hello Freesurfer users/developers, I want to run recon-all localGI on a subject who has been processed with Freesurfer 5.3. Whenever I run recon-all -localGI, I always get an error on “make_roi_paths”. There error can be found at the end of this email. I looked at the 5.3 release notes and found the that one issue with localGI was fixed by substituting a line of code. The current SearchProjectionOnPial.m that I am using uses this fix. LGI: issue when using Matlab 2013. the fix is to edit the file $FREESURFER_HOME/matlab/SearchProjectionOnPial.m and make these changes: find this line: < for t=1:step:size(perim,2) and change to: > si=max(size(perim)); > for t=1:step:si make_roi_paths('lh.pial','lh.pial-outer-smoothed',25,100,'/working/ABCD/FS/NDAR_INV021N0FLH/surf/tmp-mris_compute_lgi-lh.pial','/tmp/mrp_58433_.m'); exit ================= < M A T L A B (R) > Copyright 1984-2015 The MathWorks, Inc. R2015b (8.6.0.267246) 64-bit (glnxa64) August 20, 2015 For online documentation, see http://www.mathworks.com/support For product information, visit www.mathworks.com. Academic License >> loading datas ... FREESURFER_READ_SURF [v 1.2 ] ...reading surface file: lh.pial ...reading triangle file ...adding 1 to face indices for matlab compatibility. ...done ( 0.04 sec) FREESURFER_READ_SURF [v 1.2 ] ...reading surface file: lh.pial-outer-smoothed ...reading triangle file ...adding 1 to face indices for matlab compatibility. ...done ( 0.02 sec) preparing outer mesh structure ... face 5000 / 130188 face 10000 / 130188 face 15000 / 130188 face 20000 / 130188 face 25000 / 130188 face 30000 / 130188 face 35000 / 130188 face 40000 / 130188 face 45000 / 130188 face 50000 / 130188 face 55000 / 130188 face 60000 / 130188 face 65000 / 130188 face 70000 / 130188 face 75000 / 130188 face 80000 / 130188 face 85000 / 130188 face 90000 / 130188 face 95000 / 130188 face 100000 / 130188 face 105000 / 130188 face 110000 / 130188 face 115000 / 130188 face 120000 / 130188 face 125000 / 130188 face 130000 / 130188 mesh_outer = vertices: [65096x3 double] faces: [130188x3 double] facesOfVertex: [65096x1 struct] preparing pial mesh structure ... ...searching for mesh edges...done (134.42 sec). ... creating path file for vertex 1 / 65096 area file for outer ROIs saved at 1 In an assignment A(:) = B, the number of elements in A and B must be the same. Error in dsearchn (line 79) [d(i),t(i)] = min(sum((x-yi).^2,2)); Error in mesh_vertex_nearest (line 29) nearestIndex = dsearchn(vertices,points); Error in reorganize_verticeslist (line 28) [nextindex,nextvalue]=mesh_vertex_nearest(mesh_total.vertices(remaininglist,:),mesh_total.vertices(verticeslist(start_vertex),:)); Error in make_roi_paths (line 93) reorglist = reorganize_verticeslist (mesh_total, A, mesh_outer, perim, verticeslist, step); >> ERROR: make_roi_paths did not complete successfully! Linux jamestown.radiology.ucsf.edu 3.10.0-1062.1.2.el7.x86_64 #1 SMP Mon Sep 16 14:19:51 EDT 2019 x86_64 x86_64 x86_64 GNU/Linux recon-all -s NDAR_INV021N0FLH exited with ERRORS at Tue Mar 3 11:09:41 PST 2020 For more details, see the log file /working/ABCD/FS/NDAR_INV021N0FLH/scripts/recon-all.log To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting Thank you for your time, Ryan Michael Nillo Staff Research Associate I University of California San Francisco Department of Radiology and Biomedical Imaging External Email - Use Caution

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Re: [Freesurfer] Freesurfer installation on Ubuntu virtual machine
by fsbuild 03 Mar '20

03 Mar '20

External Email - Use Caution Hello Ben, For packages to install, see the following wiki page, https://surfer.nmr.mgh.harvard.edu/fswiki/BuildRequirements Usually to expand the freesurfer *.tar.gz archive under /usr/local, you would need sudo/root privileges, e.g. $ cd /usr/local$ sudo tar zxpf freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0.tar.gz…... output deleted - and you would end up with /usr/local/freesurfer and in turn do $ export FREESURFER_HOME=/usr/local/freesurfer But if you don’t have sudo privileges, e.g., it does not work to do$ sudo touch /usr/local/foo$ sudo rm /usr/local/foo - then you may want to consider putting freesurfer under your $HOME directory or somewhere you have permission to write files w/o needing to use sudo, e.g., $ cd $HOME$ tar zxpf freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0.tar.gz$ export FREESURFER_HOME=$HOME - R. On Mar 3, 2020, at 12:53, Benjamin Ineichen <bv.ineichen(a)gmail.com> wrote:        External Email - Use Caution        Dear Freesurfer experts,Even though this problem has been raised in the archives, I was not able to find a specific solution to my problem.I installed Freesurfer on a virtual machine which runs Ubuntu 18.04.4 (Host system: Windows 10). But it seems that Freesurfer is not installed properly. Upon running the installation test, I get the following errors:1.) command line: cp $FREESURFER_HOME/subjects/sample-001.mgz .Error: cp: cannot create regular file './sample-001.mgz': Permission denied2.) command line: mri_convert sample-001.mgz sample-001.nii.gzError: mri_convert..bin sample-001.mgz sample-001.nii.gz$Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 reuter Exp $reading from sample-001.mgz...mghRead(/usr/local/sample-001.mgz, -1): could not open file3.) command line: freeviewError: freeview.bin: error while loading shared libraries: libpng12.so.0: cannot open shared object file: No such file or directory.My permissions are: drwxrwsr-x for freesurfer.Any advice?Many thanks!/Ben-- ____________________________________Benjamin Victor Ineichen, MD PhDKarolinska InstitutetCenter for Molecular MedicineStockholm, Swedenineichen(a)protonmail.ch+41 76 391 04 01Dr. med. et Dr. rer. nat. ETH Benjamin Victor IneichenKarolinska InstitutetCenter for Molecular MedicineStockholm, Swedenineichen(a)protonmail.ch+41 76 391 04 01_______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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Freesurfer installation on Ubuntu virtual machine
by Benjamin Ineichen 03 Mar '20

03 Mar '20

External Email - Use Caution Dear Freesurfer experts, Even though this problem has been raised in the archives, I was not able to find a specific solution to my problem. I installed Freesurfer on a virtual machine which runs Ubuntu 18.04.4 (Host system: Windows 10). But it seems that Freesurfer is not installed properly. Upon running the installation test, I get the following errors: 1.) command line: cp $FREESURFER_HOME/subjects/sample-001.mgz . Error: cp: cannot create regular file './sample-001.mgz': Permission denied 2.) command line: mri_convert sample-001.mgz sample-001.nii.gz Error: mri_convert.bin sample-001.mgz sample-001.nii.gz $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 reuter Exp $ reading from sample-001.mgz... mghRead(/usr/local/sample-001.mgz, -1): could not open file 3.) command line: freeview Error: freeview.bin: error while loading shared libraries: libpng12.so.0: cannot open shared object file: No such file or directory. My permissions are: drwxrwsr-x for freesurfer. Any advice? Many thanks! /Ben -- ____________________________________ Benjamin Victor Ineichen, MD PhD Karolinska Institutet Center for Molecular Medicine Stockholm, Sweden ineichen(a)protonmail.ch +41 76 391 04 01 Dr. med. et Dr. rer. nat. ETH Benjamin Victor Ineichen Karolinska Institutet Center for Molecular Medicine Stockholm, Sweden ineichen(a)protonmail.ch +41 76 391 04 01

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segmentation issue
by Laboratorio de Neurociencia Funcional 03 Mar '20

03 Mar '20

External Email - Use Caution External Email - Use Caution Dear Freesurfeer experts, After running the recon-all in one of my subjets, part of the temporal lobe was partially excluded. Then, I tried to use the watershed algorithm to be less agressive in the skull stripping as follows: recon-all -skullstrip -wsthresh 35 -clean-bm -no-wsgcaatlas -subjid sub_001 The problem was solved in the brainmask.mgz but not in the cortical surfaces. To handle this issue, I edited the white matter and run the recon-all -autorecon2-wm -autorecon3 without success. I also placed control points but the following error appeared after running the recon-all -autorecon2-cp -autorecon3: recon-all -s sub_001 existed with errors I noted that white matter of this part of the temporal lobe has high values (up to 132). What can I do to solve the problem with this subject? Thank you in advance. Best regards, Marina

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Control Points
by Meike Hettwer 03 Mar '20

03 Mar '20

External Email - Use Caution Dear Freesurfer Team, I am currently performing manual edits using freesurfer v. 6.0.1. (on Debian /Linux 7). While brainmask edits work perfectly, the control points i set (mainly in temporal and frontopolar regions, running recon-all -autorecon2-cp -autorecon3) either have no effect at all or even make the situation worse (see screenshots attached). Do you have any idea why that might be and how I could fix that? I also tried editing the wm.mgz, but it didn't improve the segmentation. Thanks a lot, Doro

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comparison within same subjects for different conditions
by Marco Ninghetto 03 Mar '20

03 Mar '20

External Email - Use Caution Dear Freesurfers, sorry for the additional message but I really need your help. I'm running the retinotopy analysis to study population receptive fields on healthy subjects. Structurals have been reconstructed using "recon-all -qcache". The stimuli I used for retinotopy are: rotating wedge (45deg, counter-clockwise) for polar angle and expanding ring (out) for eccentricity. Each subject underwent retinotopy stimuli in two conditions: free normal sight and narrowed sight. So, each subject has 1 structural and 2 pairs of functionals for each condition (1 rot wedge + 1 expanding ring for each condition). I successfully computed the 1st level analysis for each subject for each condition. Now, I'd like to check the differences in cortical activation between the two conditions to understand if we have significant effects in activations when we narrow the sight (or simply make the subtraction analysis on the 2 conditions in such a way that we can check if we really narrow the sight). I checked on FREESURFER tutorials but I cannot find anything similar. The group analysis <https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis> is for comparison between 2 different subject populations. I opted for paired analysis <https://surfer.nmr.mgh.harvard.edu/fswiki/PairedAnalysis> but I'm stuck with the FSGD files (I understand two FSGD files are requested) *1)* > GroupDescriptorFile 1 > Class Main > Input subject6ng Main > Input subject6 Main > Input subject7ng Main > Input subject7 Main > Input subject8ng Main > Input subject8 Main > Input subject9ng Main > Input subject9 Main > Input subject10ng Main > Input subject10 Main > Input subject11ng Main > Input subject11 Main > Input subject12ng Main > Input subject12 Main > Input subject13ng Main > Input subject13 Main > *2)* > GroupDescriptorFile 1 > Class Main > Variables Goggles > Input subject6pair Main normal > Input subject7pair Main normal > Input subject8pair Main normal > Input subject9pair Main normal > Input subject10pair Main normal > Input subject11pair Main normal > Input subject12pair Main normal > Input subject13pair Main normal Where the "normal" variable means in free view conditions (not narrowed). Is it well done or am I making something wrong? - I have 1 main folder for structurals, storing all subject structural folders; - 1 main folder for functionals, storing all subjects two times (normal and narrowed conditions). Are there any other ways to compare activations on the same subjects in different conditions? Thank you for your patience and your help, Marco -- --------------------------------------------------- Marco Ninghetto, PhD candidate Laboratory of Neuroplasticity Nencki Institute of Experimental Biology Polish Academy of Sciences 3 Pasteur Street, 02-093 Warsaw, Poland

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Question about de-meaning the covariates and variables
by Hengameh Marzbani 02 Mar '20

02 Mar '20

External Email - Use Caution Hi Freesurfers, I'm stuck with the centering (de-meaning) issue. I have two discrete variables,gender and patient-control, and 2 continuous variables which are memory and age.I want to look for group differences as well as differences in relation to the behavior,controlling for age and sex and the relevant covariates (i.e. eTIV, mean thickness, surface area ...). I want to do vertex-wise analyses by QDEC. I have this questions: 1- Should I demean all the covariates (age, eTIV, mean thickness,surface area)? How about the variables of interest (e.g Left- hippocampus) and the relevant covariates? 2-As I want to control for sex. should I consider 0 for male and 1 for female (as discrete variable)? 3- For demeaning, should I subtract each value (i.e. each age) by the mean of all participant's ages of both patient and control groups? or I should consider each group separately (subtracting the patient's age by the mean of patient's ages and the control age by the mean of control's ages)? 3- How about the FSGD? Is it the same for FSGD? Any suggestion is very welcome, thanks in advance for your answer. Hengameh

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timeseries question
by Nasiriavanaki, Zahra 02 Mar '20

02 Mar '20

Hi Freesurferes I have extracted timeseries from a task fMRI using the command below: mri_segstats --i fmcpr.sm0.self.rh.nii.gz --slabel $subj rh rh.label --id 1 --avgwf-remove-mean --avgwf ./rh.txt My question is: Is the temporal drift being counted in considering that I used preprocessed data as the input? Thanks Mona Zahra (Mona) Nasiriavanaki Postdoctoral Research Fellow Martinos Center for Biomedical Imaging Massachusetts General Hospital 149 13th Street, 149-2615 Charlestown, MA, USA, 02129

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recon-all failure
by Ian 02 Mar '20

02 Mar '20

External Email - Use Caution Hi all. I have a T1 scan which I run through recon-all with: recon-all -all -parallel -subjid freesurfer (after mksubjdirs etc) On my office machine, recon-all completes successfully. On a cloud machine (16GB of ram), it fails after about 4 hours. I have attached the logs - the only immediate error I can see is "Cannot find rh.white.H". Any advice would be much appreciated, thank you. Ian -- *Ian Hardingham*

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