Freesurfer

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30090 discussions

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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pial surface with FLAIR
by Popescu, Veronica 16 Apr '13

16 Apr '13

Dear all, I have already run the FreeSurfer 5.2 -all, and I would like to improve the pial surface recongition using the FLAIR. From the $SUBJECTS_DIR (where I have also placed the FLAIR file) I use the following syntax: recon-all -autorecon3 -subjid ${SUBJ_ID} -FLAIR $FLAIRFILE -FLAIRpial It starts running but then it hangs, I never get an output. The FLAIR file is in nifti format. I am not sure what I am doing wrong: it is the syntax? Should I first convert the FLAIR file to .mgz? Thank you in advance for the help! Veronica Popescu, MD, MSc Department of Radiology & Nuclear Medicine VU University Medical Center Amsterdam, The Netherlands

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recon-all -autorecon2 bug?
by Miklos Argyelan 16 Apr '13

16 Apr '13

Hi, I have recently installed Freesurfer on a new computer, and downloaded the latest version of Freesurfer (centos 64 bit) and when ran: recon-all -subject test001 -autorecon2 I got the following error message: $Id: mri_segstats.c,v 1.75.2.9 2013/02/16 00:09:33 greve Exp $ cwd cmdline mri_segstats --seg mri/aseg.mgz --sum stats/aseg.stats --pv mri/norm.mgz --empty --brainmask mri/brainmask.mgz --brain-vol-from-seg --excludeid 0 --excl-ctxgmwm --subcortgray --in mri/norm.mgz --in-intensity-name norm --in-intensity-units MR --etiv --surf-wm-vol --surf-ctx-vol --totalgray --euler --ctab /usr/local/freesurfer/ASegStatsLUT.txt --subject test001 sysname Linux hostname mikbox machine x86_64 user amiklos UseRobust 0 atlas_icv (eTIV) = 1444225 mm^3 (det: 1.348893 ) *mghRead(/home/amiklos/nethome/work/METHODS/FS/subjects/test001/mri/ribbon.mgz, -1): could not open file* I am not sure but the bug seems that autorecon2 tries to run SegStats too early (supposed to be in autorecon3). Maybe this is the error in recon-all: case "-autorecon2": set DoGCAReg = 1; set DoCARegInv = 1; set DoRemoveNeck = 1; set DoSkullLTA = 1; set DoCANormalize = 1; set DoCAReg = 1; set DoCALabel = 1; * set DoSegStats = 1;* set DoNormalization2 = 1; set DoMaskBFS = 1; set DoSegmentation = 1; set DoFill = 1; set DoTessellate = 1; set DoSmooth1 = 1; set DoInflate1 = 1; set DoQSphere = 1; set DoFix = 1; set DoSmooth2 = 1; set DoInflate2 = 1; set DoWhiteSurfs = 1; set DoCurvStats = 1; breaksw Could some expert verify please that this is indeed the problem and I can change the 1 to zero, or am I completely off? Miklos

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Re: [Freesurfer] A problem while doing retinotopy by freesurfer
by Douglas Greve 16 Apr '13

16 Apr '13

Hi Yufeng, it cannot handle only a single run. You must have both polar and eccen. You can "fool" it by copying your polar run into another run and calling it eccen. doug ps. Please remember to send email to the list and not to me personally. Thanks! On 4/16/13 11:02 AM, yufeng(a)mail.ustc.edu.cn wrote: > Hi Doug, > Thank you for your patient. I am doing retinotopy analysis by using freesurfer 5.1 with the help of the webside http://surfer.nmr.mgh.harvard.edu/fswiki/FsFastIndividualRetinotopyAnalysis . And my problem is as followed while doing > selxavg3-sess -s Sess01 -a fmcpr.sm5.self.lh.nii.gz > My mmkanalysis-sess code is as followed: > mmkanalysis-sess -fsd bold -stc odd -surface self lh -fwhm 5 -retinotopy 32 -paradigm rtopy.par -analysis fmcpr.sm5.self.lh.nii.gz -TR 2 > > Error information > Saving X matrix to /usr/local/freesurfer/stable5/retinotopy_002/Sess01/bold/fmcpr.odd.sm5.fsaverage.lh.nii.gz/Xtmp.mat > ??? Error using ==> svd > Input to SVD must not contain NaN or Inf. > > Error in ==> cond at 40 > s = svd(A); > > Error in ==> fast_selxavg3 at 254 > XCond = cond(XtX); > >>> ------------------------------------------ > ERROR: fast_selxavg3() failed\n > > I just have one run and the rtopy.par is > stimtype polar > > direction neg > > I attach the analysis.info and Xtmp.mat on the email. Thanks very much. > Yours Yufeng >

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Re: [Freesurfer] 5.2 pial surfaces
by Yang, Daniel 16 Apr '13

16 Apr '13

Thanks so much for the improvement! I ran the new mris_make_surfaces and the pial surfaces look much better in FS 5.2! Here is the comparison slice if you're interested. https://yalesurvey.qualtrics.com/SE/?SID=SV_ddwW7I9yMQuCtPn Best, Daniel -- Yung-Jui "Daniel" Yang, PhD Postdoctoral Researcher Yale Child Study Center New Haven, CT (203) 737-5454 > >Date: Sat, 13 Apr 2013 22:36:32 -0400 (EDT) >From: Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> >Subject: [Freesurfer] 5.2 pial surfaces >To: freesurfer(a)nmr.mgh.harvard.edu > > >Hi All > >we've tracked down the problem with 5.2 pial surfaces that affects some >types of acquisitions. We will be testing the fixed version this week and >hope to release a corrected mris_make_surfaces in the near future. You >should just be able to rerun autorecon2 I believe to update your surfaces >and not the whole recon pipeline, but we'll make a more detailed >announcement when we are ready with it. Anyone who has had problems with >the 5.2 pial surfaces (or anyone else for that matter) is welcome to try >it >out. Just let us know your hardware/software environment and we'll send >you >a version. > >Sorry for the problems. > >cheers >Bruce > >

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recon-all for multiple subjects using "for" loop
by Anupa AV 16 Apr '13

16 Apr '13

Dear FS experts, I'd like to know about the for loop command for running recon-all for multiple subjects. I went thru this link, https://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/2006-November/004083.… But didn't get much info. Can anyone please tell me how to run recon-all for multiple subjects? Thanks in advance.

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