Freesurfer

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30087 discussions

mri_vol2surf produces invalid surface
by Shuntaro Aoki 05 Mar '20

05 Mar '20

External Email - Use Caution Dear mailing list, I was trying to convert a volume image to a freesurfer surface (as gii) with `mri_vol2surf` for visualization, but ended up with invalid surface data (i.e., a file not loadable by freeview). What I did was: --- % mri_vol2surf --version stable5 % mri_vol2surf --src ./sample_volume.nii.gz --regheader sample-sub --hemi lh --out ./sample_vol2surf_lh.gii --- Here, `sample_volume.nii.gz` is a volume image (such as a statistical map) registered to an individual reference T1w image of subject `sample-sub`, which was the input of recon-all for the subject. The command completed without errors: --- srcvol = ./sample_volume.nii.gz srcreg unspecified srcregold = 0 srcwarp unspecified surf = white hemi = lh reshape = 0 interp = nearest float2int = round GetProjMax = 0 INFO: float2int code = 0 Done loading volume Computing registration from header. Using /home/share/data/fmri/freesurfer/subjects/sample-sub/mri/orig.mgz as target reference. Reading surface /home/share/data/fmri/freesurfer/subjects/sample-sub/surf/lh.white Done reading source surface Mapping Source Volume onto Source Subject Surface 1 0 0 0 using old Done mapping volume to surface Number of source voxels hit = 31055 Writing to ./sample_vol2surf_lh.gii Dim: 155685 1 1 --- Then I tried to open the resulting surface `sample_vol2surf_lh.gii` with freeview (ver 1.0 build 2013-05-13) but it failed, saying "Failed to load Surface". I also got the following shell output: --- mriseadGIFTIfile: mris is NULL! found when parsing file /home/mu/aoki/work/surf_sphere/sample_vol2surf_lh.gii MRISread failed mriseadGIFTIfile: mris is NULL! found when parsing file /home/mu/aoki/work/surf_sphere/sample_vol2surf_lh.gii --- The output of `mris_info` is: --- % mris_info sample_vol2surf_lh.gii ================================================== gifti_image struct version = 1.0 numDA = 1 gim->meta nvpairs struct, len = 3 : nvpair: 'UserName' = 'aoki' nvpair: 'Date' = 'Thu Feb 27 17:32:40 2020' nvpair: 'gifticlib-version' = 'gifti library version 1.09, 28 June, 2010' gim->labeltable giiLabelTable struct, len = 0 : -------------------------------------------------- gim->darray[0] giiDataArray struct intent 0 = NIFTI_INTENT_NONE datatype 16 = NIFTI_TYPE_FLOAT32 ind_ord 1 = RowMajorOrder num_dim = 1 dims = 155685, 0, 0, 0, 0, 0 encoding 3 = GZipBase64Binary endian 2 = LittleEndian ext_fname = ext_offset = 0 darray->meta nvpairs struct, len = 0 : data = <set> nvals = 155685 nbyper = 4 numCS = 0 darray->ex_atrs nvpairs struct, len = 0 : -------------------------------------------------- gifti_image struct swapped = 0 compressed = 1 -- darray totals: 1 MB gim->ex_atrs nvpairs struct, len = 0 : ================================================== --- I checked matching between voxels in the input volume and the surface with the output of --srchit option and found the registration was fine. I also tried mgh output but got another invalid file. --- % mris_info sample_vol2surf_lh.mgh ERROR: MRISread: file 'sample_vol2surf_lh.mgh' has 0 vertices! Probably trying to use a scalar data file as a surface! No such file or directory --- I would appreciate any advice on this. Regards, Shuntaro -- ---------------------------------------- Shuntaro C. Aoki, Ph.D. Program-specific Researcher Neuroinformatics group Graduate School of Informatics Kyoto University s_aoki(a)i.kyoto-u.ac.jp ----------------------------------------

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(no subject)
by Laboratorio de Neurociencia Funcional 04 Mar '20

04 Mar '20

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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CBF data for mri_glmfit processing
by Beata Brzeska 04 Mar '20

04 Mar '20

External Email - Use Caution Hello everyone, I am using Freesurfer 6.0 on linux cluster. We are analyzing CBF data (ASL derived) coupled with fMRI task in longitudinal design. The fMRI data was analyzed in FS-FAST (with paired-diff) and now we want to repeat the group analyses on CBF maps. So far I registered the ASL data to individual anatomy and successfully transformed into fsaverage surface space (and smoothed afterwards). The data looks good so far - I can overlay it on inflated fsaverage surface. My question is: how to stack the data for further mri_glmfit processing? I suppose I should use mris_preproc for this purpose, but I am at loss with which flags are appropriate and hoe to use CBF maps as an input here. So far I did as follows for all the subjects, timepoints and hemispheres: bbregister --s Sub01_I --mov Sub01_I_CBF.nii.gz --t2 --reg Sub01_I_reg.dat ; mri_vol2surf --src Sub01_I_CBF.nii.gz --trgsubject fsaverage --out Sub01_I_CBF_to_surf_lh.nii.gz --srcreg Sub01_I_reg.dat --hemi lh mris_fwhm --s fsaverage --hemi lh --fwhm 5 --smooth-only --i Sub01_I_CBF_to_surf_lh.nii.gz --o Sub01_I_CBF_to_surf_lh_smooth.nii.gz; I would really appreciate your help. Thanks, Beata -- Beata Brzeska Medical University of Gdansk, Poland Radiology Department -- Beata Brzeska Zakład Radiologii Uniwersyteckie Centrum Kliniczne w Gdańsku

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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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