Freesurfer April 2013

freesurfer@nmr.mgh.harvard.edu

131 participants
220 discussions

Problems with Saving Segmentation
by iripp＠smail.uni-koeln.de 18 Apr '13

18 Apr '13

Hello, I have troubles with saving my files, after I did some segmentation changes. I think this could be related to a problem, which I have, when I load the brainmask: libGL error: failed to load driver: nouveau libGL error: Try again with LIBGL_DEBUG=verbose for more details. This is shown, but it would still be loading and open the brainmask (aseg). Can anyone help me with this problem? Thanks a lot, Isabelle Ripp

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recon-all -autorecon2 bug?
by Jitesh Joshi 18 Apr '13

18 Apr '13

Hi, I too am facing the same problem as mentioned by Miklos Argyelan: http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg28047.html Jitesh

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Hippo-subfields
by Marcos Martins da Silva 17 Apr '13

17 Apr '13

Hi, all After running recon-all with -hippo-subfield several .mgz files are created. I could add each of those files as volumes in freeview , toggle " show as isosurface in 3D view" and select a different color for each kind of subfield and got the attached screenshots. They are very interesting but now I have some doubts. 1- How do I save the combined 3D view I got as a surface? 2-I know the hippo-subifields .mgz files are probability maps and if I guess right kvlQuantifyPosteriorProbabilityImages read these files to count how many voxels you have in each subfield. I also guess it count only the voxels with reasonable high probability to be part of each subfield. If so, what is the minimum value between 1 and 255 the program use to decide if a particular voxel is valid? 3- Is it possible to merge hippo-subfield .mgz files data and to generate a different segmentation like anterior (anterior quarter), body (the2 intermediate quarters) and posterior (posterior quarter). TY in advance

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hippo-subfields
by Marcos Martins da Silva 17 Apr '13

17 Apr '13

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Crash reports on several situations.
by Nate Lee 17 Apr '13

17 Apr '13

Hello everyone, I'm using Freesurfer from Texas Medical Center. I'm using an iMac, and am experiencing regular crashes during these several occasions: 1. Opening more than two volumes at once 2. When one volume and one surface is open and: a. switching back and forth between different exposé desktops b. opening up Internet or other files such as Excel c. right after I press "save" (the work is saved, thankfully) Is anyone else experiencing this as well? I make sure that none of the other programs or files are open when using freesurfer. Do you have any suggestions to avoid such crashes? Best regards, Nate

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Fwd: volumeROI coritcal thickness
by Jon Wieser 17 Apr '13

17 Apr '13

I want to measure the cortical thickness for an ROI. I have been following the instructions in http://surfer.nmr.mgh.harvard.edu/fswiki/VolumeRoiCorticalThickness my ROI is the PFC (pre frontal cortex) I made the ROI in AFNI and converted it to NIFTI format I confirmed that the ROI is in the expected place with : tkmedit -f T1.mgz -overlay MJ0015_PFC_ROI.nii -fthresh 0.5 i have attached a picture "PFC_ROI.jpg" then i rane fslregister to register the ROI - anatomical voul to the FSaverage subject fslregister --s fsavreage --mov /Studies/MJMRI/MJ0015/freesurfer/mri/T1.mgz --reg T1_to_fsaverage.dat i viewed the result with tkmedit fsaverage T1.mgz -overlay /Studies/MJMRI/MJ0015/freesurfer/mri/MJ0015_PFC_ROI.nii -overlay-reg T1_to_fsaverage.dat -fthresh 0.5 -surface lh.white -aux-surface rh.white i have attached a snapshot "aligned.jpg" the ROI is not aligned well. it has been rotated 90 degrees, and is in the right side of the brain, instead of the prefrontal location. how can I fix this? THanks Jon -- Jon Wieser Research Specialist UW-Milwaukee Psychology Department, Pearse Hall Rm 366 2441 East Hartford Ave Milwaukee, WI 53211 Phone: 414-229-7145 Fax: 414-229-5219 -- Jon Wieser Research Specialist UW-Milwaukee Psychology Department, Pearse Hall Rm 366 2441 East Hartford Ave Milwaukee, WI 53211 Phone: 414-229-7145 Fax: 414-229-5219

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Template from scratch
by Sophie Maingault 17 Apr '13

17 Apr '13

Hi Experts, I'm creating a template from scratch. When I run mris_make_template is it enough to run mris_make_template ?h smoothwm <subjid> my.temp0.tif ? My question is about which sphere_name I have to put for argument ? I hope I was clear. Best regards. Sophie

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Re: [Freesurfer] Template from scratch
by Bruce Fischl 17 Apr '13

17 Apr '13

Hi Sophie the surface has to be a spherical one. Internally it will use the geometry for some other surfaces like smoothwm, but the command line has to be a spherical surfaces. Usually the first time with an individual subject you can use sphere, but if you are using multiple ones it should be sphere.reg. I'll cc the list so that others who are interested can see the response. cheers Bruce On Wed, 17 Apr 2013, Sophie Maingault wrote: > But it is not really from scratch ? > > Because I run > mris_make_template ?h smoothwm sujet0 mytemp0.tif (one reference subject) > mris_make_template ?h sphere sujet0 mytemp0.tif (one reference subject) > > > mris_register -curv ?h.sphere mytemp0.tif ?h.sphere.myreg0 (for all the > subjects that I want to use in order to create my template) > > Then If i do : mris_make_template ?h sphere.myreg0 mytemp1.tif > > mytemp1.tif will represent corresponding points across subjects ? > > Sophie > > Le 17/04/13 15:42, « Bruce Fischl » <fischl(a)nmr.mgh.harvard.edu> a écrit : > >> Hi Sophie, >> >> if you want the template to represent corresponding points across your >> subjects you need to use sphere.reg >> >> cheers >> Bruce >> On Wed, 17 Apr 2013, Sophie Maingault >> wrote: >> >>> Hi Experts, >>> >>> I'm creating a template from scratch. When I run mris_make_template is >>> it enough to >>> run mris_make_template ?h smoothwm <subjid> my.temp0.tif ? My question >>> is about which >>> sphere_name I have to put for argument ? I hope I was clear. >>> >>> Best regards. >>> >>> Sophie >>> >>> >> >> >> The information in this e-mail is intended only for the person to whom it >> is >> addressed. If you believe this e-mail was sent to you in error and the >> e-mail >> contains patient information, please contact the Partners Compliance >> HelpLine at >> http://www.partners.org/complianceline . If the e-mail was sent to you in >> error >> but does not contain patient information, please contact the sender and >> properly >> dispose of the e-mail. > > > > >

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defect 0
by Varghese Chikku 17 Apr '13

17 Apr '13

Hi All, I am running recon-all on a set of Diff images since last 2 days and it looks like FS stopped working.It says correcting defect 0 since yesterday afternoon. Any way to figure whats going on? Many Thanks Chikku #@# Fix Topology lh Tue Apr 16 14:47:22 CEST 2013 \n cp ../surf/lh.orig.nofix ../surf/lh.orig \n \n cp ../surf/lh.inflated.nofix ../surf/lh.inflated \n /Applications/freesurfer/subjects/Diff1/scripts \n mris_fix_topology -mgz -sphere qsphere.nofix -ga -seed 1234 Diff1 lh \n reading spherical homeomorphism from 'qsphere.nofix' using genetic algorithm with optimized parameters setting seed for random number genererator to 1234 ************************************************************* Topology Correction Parameters retessellation mode: genetic search number of patches/generation : 10 number of generations : 10 surface mri loglikelihood coefficient : 1.0 volume mri loglikelihood coefficient : 10.0 normal dot loglikelihood coefficient : 1.0 quadratic curvature loglikelihood coefficient : 1.0 volume resolution : 2 eliminate vertices during search : 1 initial patch selection : 1 select all defect vertices : 0 ordering dependant retessellation: 0 use precomputed edge table : 0 smooth retessellated patch : 2 match retessellated patch : 1 verbose mode : 0 ************************************************************* INFO: assuming .mgz format $Id: mris_fix_topology.c,v 1.48 2011/03/02 00:04:32 nicks Exp $ $Id: mrisurf.c,v 1.693.2.4 2012/11/07 22:38:00 nicks Exp $ before topology correction, eno=-340 (nv=73648, nf=147976, ne=221964, g=171) using quasi-homeomorphic spherical map to tessellate cortical surface... Correction of the Topology Finding true center and radius of Spherical Surface...done Surface centered at (0,0,0) with radius 100.0 in 12 iterations marking ambiguous vertices... 82800 ambiguous faces found in tessellation segmenting defects... 41 defects found, arbitrating ambiguous regions... analyzing neighboring defects... -merging segment 2 into 0 -merging segment 10 into 0 -merging segment 32 into 15 -merging segment 19 into 16 -merging segment 38 into 40 36 defects to be corrected 0 vertices coincident reading input surface /Applications/freesurfer/subjects/Diff1/surf/lh.qsphere.nofix... reading brain volume from brain... reading wm segmentation from wm... Computing Initial Surface Statistics -face loglikelihood: -8.8449 (-4.4225) -vertex loglikelihood: -7.8841 (-3.9420) -normal dot loglikelihood: -3.5035 (-3.5035) -quad curv loglikelihood: -6.1723 (-3.0862) Total Loglikelihood : -26.4048 CORRECTING DEFECT 0 (vertices=30266, convex hull=4754)

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mkbrainmask error with libmeshclass.so
by Corinna Bauer 16 Apr '13

16 Apr '13

Hello all, when running preproc-sess, I got this error message: ERROR: could not determine file for /usr/local/freesurfer/subjects/symmetry/lindsay/first_test/bold/masks/brain Try running mkbrainmask-sess with -per-run I then ran the mkbrainmask-sess as follows (kbrainmask-sess -s . -d . -fsd bold m) and got the output below, which shows a problem with a shared library? Any suggestions? Corinna ------------------------------------------------ /usr/local/freesurfer/subjects/symmetry/lindsay/first_test Fri Apr 12 15:53:14 EDT 2013 mkbrainmask -i template.nii.gz -o masks/brain.nii.gz -thresh 0.1 -ndil 1 -nerode 0 FSLMATHS fslmaths.fsl Scratch Dir is /tmp/mkbrainmask_9634 /usr/local/freesurfer/subjects/symmetry/lindsay/first_test/bold mri_convert template.nii.gz /tmp/mkbrainmask_9634/in.nii mri_convert template.nii.gz /tmp/mkbrainmask_9634/in.nii $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from template.nii.gz... TR=2000.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-0.996119, -0.0108587, 0.0873391) j_ras = (0.000562893, 0.991553, 0.129698) k_ras = (0.0880098, -0.129244, 0.9877) writing to /tmp/mkbrainmask_9634/in.nii... # ---------- Using FSL's BET to Extract Brain------------------ # /usr/local/freesurfer/subjects/symmetry/lindsay/first_test/bold bet.fsl /tmp/mkbrainmask_9634/in.nii /tmp/mkbrainmask_9634/brain -m -f 0.1 /usr/share/fsl/5.0/bin/bet2: error while loading shared libraries: libmeshclass.so: cannot open shared object file: No such file or directory mri_binarize --i /tmp/mkbrainmask_9634/brain_mask.nii --min .01 --o /tmp/mkbrainmask_9634/brain_mask.nii niiRead(): error opening file /tmp/mkbrainmask_9634/brain_mask.nii $Id: mri_binarize.c,v 1.26.2.1 2011/04/08 15:40:50 greve Exp $ cwd /usr/local/freesurfer/subjects/symmetry/lindsay/first_test/bold cmdline mri_binarize --i /tmp/mkbrainmask_9634/brain_mask.nii --min .01 --o /tmp/mkbrainmask_9634/brain_mask.nii sysname Linux hostname lotfi machine x86_64 user bauer input /tmp/mkbrainmask_9634/brain_mask.nii frame 0 nErode3d 0 nErode2d 0 output /tmp/mkbrainmask_9634/brain_mask.nii Binarizing based on threshold min 0.01 max +infinity binval 1 binvalnot 0

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Freesurfer April 2013