Freesurfer April 2013

freesurfer@nmr.mgh.harvard.edu

131 participants
220 discussions

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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recon-all problems [solved]
by Marcos Martins da Silva 15 Apr '13

15 Apr '13

I had several problems testing freesurfer 5.2 installation, as previously posted. Now it is all OK and I would like to share what I could learn: 1- It does not work on Fedora 18 (segfaults with all tests with tkmedit, tksurfer and recon-all) that is due to a restriction imposed by glibc (only newest version). Only freeview works under Fedora 18 but, even here, I got a misalignment problem among surfaces and volumes. More details at https://bugzilla.redhat.com/show_bug.cgi?id=905638 2- I got partial functionality using VirtualBox (4.2.8 and 4.2.10). I cannot say about previous versions and the latest one (4.2.12 was released on Apriil, 12th). But I had problems with both virtual machines I tried: CentOS6 (fresh install) and the Xubuntu + FreeSurfer 5.1 vdi file I downloaded from FreeSurfer website. Tkmedit, tksurfer and freeview all worked but recon-all failed all time. 3- Fedora 17 and CentOS 6 work flawlessly out of box if you do not use virtualbox. Probably, other distros will work too, except if they are using the latest glibc (2.16-30). So my final setup is a dual boot machine: Fedora 18 (day-by-day tasks) and CentOS6 (freesurfer tasks). You can do it with only one disk but it is a lot easier with two. I hope it can help people with similar problems.

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Re: [Freesurfer] setting thresholds in qdec
by Michael Harms 15 Apr '13

15 Apr '13

I just transferred all the data to a different system running CentOS 5.5 and I'm able to set the display thresholds in qdec on that system. It also uses a different FS version (5.1) but I think it is an OS issue, and not a FS version issue, since I have the same problem on the original RHEL 5.9 system using the qdec in FS 5.1 as well. So, must be something about the libraries qdec uses not quite playing nice in RHEL 5.9 ? thanks, -MH -- Michael Harms, Ph.D. ----------------------------------------------------------- Conte Center for the Neuroscience of Mental Disorders Washington University School of Medicine Department of Psychiatry, Box 8134 660 South Euclid Ave. Tel: 314-747-6173 St. Louis, MO 63110 Email: mharms(a)wustl.edu From: Michael Harms <mharms(a)conte.wustl.edu> Date: Friday, April 12, 2013 11:32 AM To: "freesurfer(a)nmr.mgh.harvard.edu" <freesurfer(a)nmr.mgh.harvard.edu> Subject: [Freesurfer] setting thresholds in qdec Hello, Is it no longer possible to set the Min, Mid, and Max thresholds directly on the Qdec display tab? The only way I seem to be able to change them is via the sliders in the histogram at the bottom, which I don't recall previously being the case. This is Qdec 1.4 (FS 5.2) on a RHEL 5.9 system using freesurfer-Linux-centos4_x86_64-stable-pub-v5.2.0 distribution. I can't change the FDR "Rate" either. thanks, -MH -- Michael Harms, Ph.D. ----------------------------------------------------------- Conte Center for the Neuroscience of Mental Disorders Washington University School of Medicine Department of Psychiatry, Box 8134 660 South Euclid Ave. Tel: 314-747-6173 St. Louis, MO 63110 Email: mharms(a)wustl.edu _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer 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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unit of corpus callosum segmentation
by Marie Schaer 15 Apr '13

15 Apr '13

Hi all, I have a quick question related to the corpus callosum segmentation: I read in previous posts that the reference explaining more about the CC subdivision in 5 segments was the one by Rosas et al, Neuroimage 2010. But in this publication, you show thickness of the corpus callosum as the main outcome variable, with average values ranging from ~4 to 9 mm. And when I extract the values from the aseg.stats, in my dataset I rather get average values that are ranging between ~400 and 900 depending on the segment. Do these values correspond to thickness in mm/100, or to area, or to something else? Is that a thickness measurement, or a surface area measurement? Many thanks in advance for your reply, Marie

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Re: [Freesurfer] using volume label mask in mri_vol2surf
by Fred Dick 15 Apr '13

15 Apr '13

Hi Doug I've actually tried both inclusive and exclusive and have failed - just checked again in tkmedit that the label was coming up correctly and it was. Just to double-check - the label should be in the space of the --mov, right? Thanks! Fred Hi Fred, that mask is an inclusive mask, not an exclusive mask. Try inverting you mask. doug On 4/14/13 4:31 PM, Fred Dick wrote: Dear all I am painting some higher-res anatomical data from a volume to a surface, and want to use a mask that excludes the vessels. (The same data but 1x1x1 conformed were used to create the surface). I've created a binary label in the same space >> mri_cor2label --i ./R2Mask.nii.gz --l ./R2s.label --id 1 made sure that it looks ok when I read in hi-res to tkmedit and display label, then ran mri_vol2surf >> mri_vol2surf --mov ./sPQ07082012-0009-00001-000208-01_R1.nii --regregister.dat --surf-fwhm 4 --hemi $hemi --projfrac $frac --interp trilinear --out_type w --mask R2s.label --o ./dancar-0.5-lh.w And got the output (pasted below), showing that the output is all zero. Output is fine without label, or with -cortex. I've also tried this with a conformed version of the label (also verified in tkmedit) and have had the same thing. (I thought maybe it was applying it to orig vol, which I admit would be strange). (I noticed someone had a similar issue a couple of years ago, but it involved a surface rather than volume label, and looked like it had been resolved). Am running current stable version on Mountain Lion. Thanks for any pointers, best, Fred ########################################################## masking output with label R2s.label INFO: output format is paint srcvol = ./sPQ07082012-0009-00001-000208-01_R1.nii srcreg = register.dat srcregold = 0 srcwarp unspecified surf = white hemi = lh ProjFrac = 0.5 thickness = thickness reshape = 0 interp = trilinear float2int = round GetProjMax = 0 INFO: float2int code = 0 Done loading volume Loading label R2s.label Reading surface /Applications/freesurfer/subjects/dancar-synth-handnorm/surf/lh.white Done reading source surface Reading thickness /Applications/freesurfer/subjects/dancar-synth-handnorm/surf/lh.thickness Done Mapping Source Volume onto Source Subject Surface 1 0.5 0.5 0.5 using old Done mapping volume to surface Number of source voxels hit = 108676 Surface smoothing by fwhm = 4 (n=10) Masking with R2s.label Warning: all vertex values are zero

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Job: Postdoc in Cognitive Neuroscience at Haskins Laboratories
by Peter J. Molfese 15 Apr '13

15 Apr '13

Postdoctoral position in Cognitive Neuroscience at Haskins Laboratories Applications are solicited for a postdoctoral fellowship in Cognitive Neuroscience at Haskins Laboratories. Applicants should have a Ph.D. in psychology, linguistics, cognitive neuroscience, or a related field. The selected candidate will contribute to multiple funded NIH studies of speech perception, reading, word acquisition, and language processing. Prior experience in research using MRI/fMRI is required. Responsibilities will include assistance with design and execution of fMRI and behavioral experiments; fMRI data analysis; formulating and participating in writing of scientific papers as part of the research team; participating in grant writing towards the eventual goal of independent funding; and developing independent projects in the areas of speech, reading, and language. Position requirements include: - Experience with MRI/fMRI data acquisition and analysis - Strong analytical and statistical skills - Strong computer and data management skills Additional desirable qualifications include: - Experience with MRI/fMRI data analysis using AFNI and/or FreeSurfer - Experience with EEG/ERP analysis - Experience with modeling, broadly construed - Programming skills, e.g., Python, R, Matlab The successful applicant will join Haskins Laboratories (www.haskins.yale.edu) a private, non-profit research institute located in downtown New Haven, CT. Founded in 1935, our primary focus is on speech, language, reading, and their biological bases. Haskins Laboratories has long-standing, formal affiliations with the University of Connecticut and Yale University. We are also actively engaged in research collaborations and partnerships with institutions, groups, and individuals around the world. We house facilities for conducting eye tracking, including 3 Eyelink 1000 eye-trackers, EEG/ERP (both Biosemi and EGI systems), ultrasound and NIRS technology, and a mock fMRI scanner, which replicates the 3T scanner used for fMRI research at Yale University. Interested applicants should direct application materials to Dr. W. Einar Mencl, Director of Neuroimaging Research (einar(a)haskins.yale.edu) including cover letter, statement of research interests, CV, and three letters of recommendation. Please reference Job Posting #5001. This position is initially for a one-year duration, with potential of an additional 1-2 years contingent on performance and continued funding. Applications should be submitted by 15 May 2013; the application process will continue until the position is filled. International applicants are welcome. Haskins Laboratories is an Equal Opportunity Employer.

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Freesurfer April 2013