Freesurfer

freesurfer@nmr.mgh.harvard.edu

30132 discussions

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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ERROR: fast_selxavg3() failed\n
by mahdiyeh khanbagi 02 Mar '20

02 Mar '20

External Email - Use Caution Dear FreeSurfer Developers, I am trying to do FSFAST analysis on Mac OS Catalina 10.15.3, and I have completed the preprocessing (preproc-sess, mkanalysis-sess and mkcontrast-sess) with no problem. When I ran the function selxavg3-sess, it proceeded somehow (-->preproc-sess done--> MATLAB opened and then was closed), but when it started running fast_selxavg3b it stopped after a while (fast_selxavg3() failed\n) with the following errors: Extension format = nii.gz INFO: key nSliceGroups unrecognized, line 12, skipping 1 AnimalvsNonAnimal.mat Excluding 4 points Subscript indices must either be real positive integers or logicals. Error in fast_st2fir (line 118) Xfirss(ind,nthd) = wstim; Error in flac_desmat (line 58) flacnew.ev(nthev).Xfir = fast_st2fir(st,ntpssr,TER,ev.psdwin,useweight); Error in flac_customize (line 357) flacnew = flac_desmat(flacnew); Error in fast_selxavg3b (line 129) flac0 = flac_customize(flac0); Could anyone help me with this problem, please? Best Regards, Mahdiyeh

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make_average_subject
by Benjamin Ineichen 02 Mar '20

02 Mar '20

External Email - Use Caution Dear Freesurfer experts, I want to create a new standard template from my study population. For this, I thought about using make_average_subject. Thus, I run: make_average_subject --out avgsubject --subjects REMY001 REMY002 REMY003 I get an error message - ERROR: make_average_surface. Please find attached the error.log. Would be very thankful for 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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