Freesurfer

freesurfer@nmr.mgh.harvard.edu

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30097 discussions

Fwd: bug report
by siya sherif 07 Jun '16

07 Jun '16

FREESURFER_HOME: /usr/local/freesurfer Build stamp: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 Debian version: jessie/sid Kernel info: Linux 4.2.0-36-generic x86_64 --------------------------------------------------------------------- Please include the following additional information in your report: 1) subject name bret4 2) the entire command-line executed setenv SUBJECTS_DIR /media/brain/C60E9D2E0E9D188F/testFreesurfur recon-all -i ICBM_MNI_0101_MRI_T1-FFE_br_20050118145643139_S6730_I2233.nii -subject bert3 -all 3) the error message generated #-------------------------------------------- #@# Talairach Fri Jun 3 14:54:45 IST 2016 /media/brain/C60E9D2E0E9D188F/testFreesurfur/bert5/mri mri_nu_correct.mni --n 1 --proto-iters 1000 --distance 50 --no-rescale --i orig.mgz --o orig_nu.mgz Linux IBT-MS-7971 4.2.0-36-generic #42~14.04.1-Ubuntu SMP Fri May 13 17:27:22 UTC 2016 x86_64 x86_64 x86_64 GNU/Linux recon-all -s bert5 exited with ERRORS at Fri Jun 3 14:55:29 IST 2016 For more details, see the log file /media/brain/C60E9D2E0E9D188F/testFreesurfur/bert5/scripts/recon-all.log To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting 4) optionally include the subject's /script/recon-all.log -- Dr. Siya Sherif Ph.D Senior R & D Engineer Neuroimaging & Neurospectroscopy Lab National Brain Research Centre NH-8, Manesar, Gurgaon Haryana-122 051 India email : siya.physics(a)gmail.com , siya.sherif(a)imdea.org Tel (mob) : +91- 9447753634

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errors in wm and pial boundaries
by Corinna Bauer 07 Jun '16

07 Jun '16

Hello all, We are analyzing data from our collaborators and are running into some difficulties with the accuracy of the pial and wm boundaries. The wm.mgz appears to follow the actual WM, independent of the wm surface boundary. Attached is an example showing two types of problems. 1. the WM surface is inaccurate regardless of the number of control points used. 2. The pial surface is inaccurate, missing a bunch of the sulcal and gyral patterns of the left parietal lobe (see area around cursor). For completeness, I have also included the wm.mgz at the same slice. I should mention that these problems has been occurring in multiple subjects. Any suggestions?? Thanks Corinna

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Save REG in tkregister2
by Hao wen 07 Jun '16

07 Jun '16

Hello: I am using tkregister2 to do some manual registration, but I can not save reg with the button in the GUI

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converting Tracula outputs to Wavefront OBJ files
by David Allan Ziegler 06 Jun '16

06 Jun '16

Dear Freesurfer/Tracula team, I would like to convert some of the outputs from Tracula into wavefront objects in order to render them in Unity. Does anyone have any advice on how to do so? Based on previous threads and looking into Brainder.org's aseg2surf, I assume I need to use a combination of mri_pretess and mri_tess to generate tesselated surfaces that can then be converted into ascii files and then into .obj files using Brainder's surf2obj. My problem is in figuring out how to generate the surface meshes from the Tracula outputs. If anyone can point me to documentation on how to do this or provide any advice, I'd appreciate it. Cheers, David

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CORRECTING DEFECT
by maryam koochaki 06 Jun '16

06 Jun '16

Hi Bruce,I am wondering if you saw my last email, about uploading my subject in your ftp server.I uploaded the subject "test_emc_039.tar.gz".I appreciate any help. Thank you, Maryam

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CORRECTING DEFECT
by maryam koochaki 06 Jun '16

06 Jun '16

Dear freesurfer experts,I have a subject ending up with this error after recon-all.I tried to edit the aseg and run it, but it stuck at topological step. CORRECTING DEFECT 79 (vertices=54196, convex hull=8490) error in the retessellation normal vector of length zero at vertex 97187 with 0 faces vertex 97187 has 0 face No such file or directory Linux cs-cbl-03 2.6.32-573.22.1.el6.x86_64 #1 SMP Wed Mar 23 03:35:39 UTC 2016 x86_64 x86_64 x86_64 GNU/Linux recon-all -s test_emc_039 exited with ERRORS ..... Could you guide me how I can correct it.Thank you,Maryam Regards,Maryam Kouchakidivkolaei

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volumetric difference between 1.5 T and 3.0 T...
by Gonzalo Rojas Costa 06 Jun '16

06 Jun '16

Hi: There exist any difference between the volumetric values obtained using 1.5T and 3.0T images ? Any paper about it ? Sincerely, Gonzalo Rojas Costa Laboratory for Advanced Medical Image Processing Department of Radiology Clínica las Condes Lo Fontecilla 441, Las Condes, Santiago, Chile. Tel: 56-2-2105170 Cel: 56-9-97771785 www.clc.cl

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Build fsaverage
by shi yao wang 06 Jun '16

06 Jun '16

Hello, Thank you very much for the reply! 1. I copied calculated data into a new computer and I cannot find "fsaverage". 2. Bruce, thank you! I used make_average_subject command. However, it shows that error message: "lack of memory". I am wondering how can I do that. Thank you for helps again! Lawrence

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SOLVED: Re: convert FSL atlas label to individual freesurfer T1 space
by Jacobs H (NP) 05 Jun '16

05 Jun '16

I figured it out :) From: H Jacobs <h.jacobs(a)maastrichtuniversity.nl<mailto:h.jacobs@maastrichtuniversity.nl>> Reply-To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>> Date: Saturday, June 4, 2016 at 7:48 AM To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>> Subject: [Freesurfer] convert FSL atlas label to individual freesurfer T1 space Hello! I have a fsl label (from the JHU atlas) and want to overlay this on my T1 from FreeSurfer (native space) to create models in 3DSlicer. What is the best way to get these labels (one ROI with intensity 1 in a nifti) to fit the individual T1. I tried the following: Flirt -in MNI15_T1_1mm.nii.gz -ref brainmask.nii -out converted.nii -omat convertedmatrix.mat -bins 256 -cost corratio -searchx -90 90 -searchy -90 90 -searchz -90 90 -dof 12 -interp trillinear Flirt -in JHUlabel.niig.gz -ref brainmask.nii -applyxfm -init convertedmatrix.mat -out newlabel.nii.gz (brainmask.nii is the brainmask.mgz converted to nii using mri_convert) Unfortunately this did not work, the label is still in the wrong position. Any idea what I am doing wrong or how I can solve this? Thanks! Heidi

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selxavg3-sess error with phase-encoded data
by Francesca Strappini 05 Jun '16

05 Jun '16

Hi Freesurfer experts, I'm trying to analyze some phase-encoded data with the eccentricity protocol for retinotopic data and I'm having troubles with selxavg3-sess. I run the following commands: mkanalysis-sess -analysis OrderDisorder.idsubj.lh -surface idsubj lh -TR 2 -retinotopy 24 -paradigm rtopy.par -fwhm 0 -per-run -nskip 5 -fsd bold selxavg3-sess -a OrderDisorder.idsubj.lh -s idsubj_OrderDisorder_continous and I got this error message: Found 122573/130829 (93.7) voxels in mask Creating Design Matrix ... creation time = 0.019 sec DoMCFit = 1 ntptot = 875, nX = 80, DOF = 795 Saving X matrix to /usr/local/freesurfer/fsfast/OrderDisorder_new/MK_OrderDisorder_continous/bold/OrderDisorder.MishaK.lh/Xtmp.mat Error using svd Input to SVD must not contain NaN or Inf. Error in cond (line 35) s = svd(A); Error in fast_selxavg3 (line 279) XCond = cond(XtX); I attached the Xtmp.mat file from the output folder in case is needed. Thank you! Best Francesca -- Francesca Strappini, Ph.D. Neurobiology Department Weizmann Institute of Science 234 Herzl Street, Rehovot 7610001 Israel Tel.: +972 58 444 2584 E-mail: francesca.strappini(a)weizmann.ac.il

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