Freesurfer

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30132 discussions

Re: [Freesurfer] Fwd: (no subject)
by Bruce Fischl 29 Nov '12

29 Nov '12

Hi Hugh how far is the closest visible white matter? Do you have any other image types (e.g. a FLAIR)? Bruce On Wed, 28 Nov 2012, Hugh Pemberton wrote: > Hi freesurfers, > Just want to ask how I might go about including parts of the temporal lobes > that have been left out of the the surfaces due to severe atrophy but where > there's no white matter so control points are of no use? I have attached a > jpg few screen shots as examples.. > > Cheers, > Hugh > > > On 21 November 2012 11:29, Hugh Pemberton <hughpemberton1(a)gmail.com> wrote: > Hi Bruce, > Just to let you know the new mris_topo_fixer worked and there was no > error with the recon. > > I also meant to ask how I might go about including parts of the > temporal lobes that have been left out of the the surfaces due to > severe atrophy but where there's no white matter so control points are > of no use? I have attached a jpg few screen shots as examples.. > > Cheers, > Hugh > > > On 16 November 2012 14:44, Hugh Pemberton <hughpemberton1(a)gmail.com> > wrote: > Hi Bruce, > I also meant to ask how I might go about including parts of the > temporal lobes that have been left out of the the surfaces due > to severe atrophy but where there's no white matter so control > points are of no use? I have attached a few screen shots as > examples.. > > Cheers, > Hugh > > > On 16 November 2012 11:14, Bruce Fischl > <fischl(a)nmr.mgh.harvard.edu> wrote: > this is a bug in the topology fixer. Maybe Zeke or > Nick can post a new version of it? Was it > mris_topo_fixer that was runing or > mris_fix_topology? > On Fri, 16 Nov 2012, Hugh Pemberton wrote: > > Hi Bruce, > Thanks for getting back to me. In > terminal window it says > "freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0" > but recon-all -version > give me "$Id: recon-all,v 1.379.2.17 > 2011/05/20 22:48:18 nicks Exp $" > > Hugh > > > On 16 November 2012 11:05, Bruce Fischl > <fischl(a)nmr.mgh.harvard.edu> wrote: > Hi Hugh > This is fixed in the newest version. > What version are you running? > Bruce > > > > On Nov 15, 2012, at 6:48 PM, Hugh > Pemberton <hughpemberton1(a)gmail.com> > wrote: > > Hi, > I have just received this error after a > recon-all subjid- ___ > all : > > ERROR: _FindFacePath: could not find > path! > /home/hughp/freesurfer/subjects/B______________/scripts > > mris_remove_intersection > ../surf/lh.orig ../surf/lh.orig > > intersection removal took 0.00 hours > removing intersecting faces > writing corrected surface to > ../surf/lh.orig > > rm ../surf/lh.inflated > > > cp ../surf/lh.orig_corrected > ../surf/lh.orig > > Linux naoshi-WS 3.2.0-32-generic > #51-Ubuntu SMP Wed Sep 26 > 21:33:09 UTC 2012 x86_64 x86_64 x86_64 > GNU/Linux > > recon-all -s B______________ exited with > ERRORS at Thu Nov 15 > 11:40:44 EST 2012 > > To report a problem, see > http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > > Many thanks in advance, > Best, > Hugh > > > _______________________________________________ > 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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Re: [Freesurfer] Retinotopy Maps
by Zhou, Wei 29 Nov '12

29 Nov '12

I see. Yes. Thanks a lot. Best Wei Those values are radians. Does that help? doug On 11/29/2012 06:09 PM, Zhou, Wei wrote: > Hi Doug, > > Thank you for your patient. I wanted to see how the polar angle > correlates with the map and I expect a wheel bar which distinguish > different polar angles. > I typed: > > rtview --s SUBJ1 --lh --polar --real > SUBJ01/bold/rtopy.self.lh/polar/real.nii.gz --imag > SUBJ01/bold/rtopy.self.lh/polar/imag.nii.gz --fsig > SUBJ01/bold/rtopy.self.lh/polar/fsig.nii.gz > > I could see some blue, red and green region in the cortex. Then i > click "show the color scale bar" and I get a all-blue and vertical bar > ranging from -1.18 to -0.4 and 0.4 to 1.18. I do not know how to > interpret the image with this bar. > > I am asking if wheel bar is still supported in freesurfer5. If so, how > can I get it to interpret the maps? > > Thank you. > >

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Re: [Freesurfer] Retinotopy Maps
by Zhou, Wei 29 Nov '12

29 Nov '12

Hi Doug, Thank you for your patient. I wanted to see how the polar angle correlates with the map and I expect a wheel bar which distinguish different polar angles. I typed: rtview --s SUBJ1 --lh --polar --real SUBJ01/bold/rtopy.self.lh/polar/real.nii.gz --imag SUBJ01/bold/rtopy.self.lh/polar/imag.nii.gz --fsig SUBJ01/bold/rtopy.self.lh/polar/fsig.nii.gz I could see some blue, red and green region in the cortex. Then i click "show the color scale bar" and I get a all-blue and vertical bar ranging from -1.18 to -0.4 and 0.4 to 1.18. I do not know how to interpret the image with this bar. I am asking if wheel bar is still supported in freesurfer5. If so, how can I get it to interpret the maps? Thank you. _________________ Hi Wei, I don't think I understand your question. Can you elaborate? doug On 11/29/2012 04:06 PM, Zhou, Wei wrote: > Hi Doug, > > Thank you very much. I have thrown all the fixation sessions and run > the analysis again. So in rtview how can i get the color scale bar > which indicates the corresponding time points of polar or eccen? Is it > still supported in free surfer 5? > > Best > Wei > --------------------------- > Hi Wei, the argument to -retinotopy should be the period of stimuluation > (ie, how long it takes the wedge to go around 360 degrees), not the > duration of your run. Also, it is not set up to handle fixation at the > beginning or the end, so you might want to cut those frames out. > doug > On 11/29/2012 12:30 PM, Zhou, Wei wrote: > > Dear freesurfers, > > > > I am doing retinotopy analysis using freesurfer 5 with > >http://surfer.nmr.mgh.harvard.edu/fswiki/FsFastIndividualRetinotopyAnalysis > >. > > I have four runs, two eccen and two polar. For each run I have 15 > > seconds fixation, 300 seconds stimuli and 15s fixation at the end > > (total 330s and 300s for stimuli). > > > > 1) For -retinotopy option in mkanalysis-sess I typed "300". Do you > > think this setting is fine? > > > > 2) After finishing running, I use tksurfer-sess to display the result. > > When I typed "tksurfer-sess -s SUBJ01 -analysis rtopy.self.lh -map > > angle" with "-c polar" or "-c eccen'" I got two maps with -4.0 to 4.0 > > color range. I learn from mail list, the two maps do not represent > > time course of retinotopy, right? So what are these two maps tell us? > > > > 3) I tried rtview cmd and the maps look strange. Color scale is from > > -1.185 to -0.4 and 0.4 to 1.185 and it does not include all the colors > > in display. > > > > 4) I tried to use -run-wise in selxavg3-sess, it fails with: > > "/analysis/retinotopy/SUBJ01/bold/rtopy.self.lh/pr001/Xtmp.mat > > Error using svd > > Input to SVD must not contain NaN or Inf." > > > > Could you please give me some idea? Thank you very much in advance.

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Re: [Freesurfer] Subgroup analysis
by Mahinda Yogarajah 29 Nov '12

29 Nov '12

Hi - sorry probably being slow - not sure i follow - treating them as one group (with appropriate covariate scale for level of endogenous factor/severity of disease) and using scaled age scores how would i look for an interaction between age and severity of disease across the group as both are treated as continuous covariates as opposed to discrete fixed factors. Thanks M

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Re: [Freesurfer] Retinotopy Maps
by Zhou, Wei 29 Nov '12

29 Nov '12

Hi Doug, Thank you very much. I have thrown all the fixation sessions and run the analysis again. So in rtview how can i get the color scale bar which indicates the corresponding time points of polar or eccen? Is it still supported in free surfer 5? Best Wei --------------------------- Hi Wei, the argument to -retinotopy should be the period of stimuluation (ie, how long it takes the wedge to go around 360 degrees), not the duration of your run. Also, it is not set up to handle fixation at the beginning or the end, so you might want to cut those frames out. doug On 11/29/2012 12:30 PM, Zhou, Wei wrote: > Dear freesurfers, > > I am doing retinotopy analysis using freesurfer 5 with > http://surfer.nmr.mgh.harvard.edu/fswiki/FsFastIndividualRetinotopyAnalysis . > I have four runs, two eccen and two polar. For each run I have 15 > seconds fixation, 300 seconds stimuli and 15s fixation at the end > (total 330s and 300s for stimuli). > > 1) For -retinotopy option in mkanalysis-sess I typed "300". Do you > think this setting is fine? > > 2) After finishing running, I use tksurfer-sess to display the result. > When I typed "tksurfer-sess -s SUBJ01 -analysis rtopy.self.lh -map > angle" with "-c polar" or "-c eccen'" I got two maps with -4.0 to 4.0 > color range. I learn from mail list, the two maps do not represent > time course of retinotopy, right? So what are these two maps tell us? > > 3) I tried rtview cmd and the maps look strange. Color scale is from > -1.185 to -0.4 and 0.4 to 1.185 and it does not include all the colors > in display. > > 4) I tried to use -run-wise in selxavg3-sess, it fails with: > "/analysis/retinotopy/SUBJ01/bold/rtopy.self.lh/pr001/Xtmp.mat > Error using svd > Input to SVD must not contain NaN or Inf." > > Could you please give me some idea? Thank you very much in advance. >

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Reference for clusterwise correction for multiple comparisons
by Ed Gronenschild 29 Nov '12

29 Nov '12

Hi, Can you give me a reference to the method used for the clusterwise correction for multiple comparisons (CSD)? Is it Hagler et al, NeuroImage 2006, vol 33, 1093-1103? Cheers, Ed

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Problem with Xubuntu VM on Windows 7
by Negar Memarian 29 Nov '12

29 Nov '12

Hi all, I've installd FreeSurfer through Xubuntu virtual machine on Windows 7, 64 bit according to the installation instructions the FreeSurfer Beginner's Guide. Unfortunately I'm facing an error in the recon-all process (as described below), which I think has to do with the VM, because the error does not occur if run on a real Linux machine. Would someone please advise if I'm missing something? Are there specific VM setup steps in terms of sharing drives or copying certain files into a specific folder that I'm not aware of? (I have just followed the steps on the installation guide, nothing more). The problem I'm facing is: recon-all -autorecon1 crashes for me in one of the steps before skull stripping with an error like this: Done spline_smooth: posixio.c:210: px_pgin: Assertion `*posp == ((off_t)(-1)) || *posp == lseek(nciop->fd, 0, 1)' failed. nu_estimate_np_and_em: crashed while running spline_smooth (termination status=6) nu_correct: crashed while running nu_estimate_np_and_em (termination status=65280) ERROR: nu_correct Linux FreeSurfer 2.6.28-11-generic #42-Ubuntu SMP Fri Apr 17 01:57:59 UTC2009 i686GNU/Linux recon-all -s BT501_FS exited with ERRORS at Mon Nov 26 15:26:10 EST 2012 I made sure that I have the newest version of FreeSurfer, the environment variables MNI_DATAPATH and MNI_PERL5LIB and PERL5LIB exist and I ran $FREESURFER_HOME/bin/fixup_mni_paths as well. But unfortunately I still face the same problem. I also tried the process for a different subject, but the same error. Does anyone have any idea how I can fix this? I have attached the recon-all.log file. I'd really appreciate your help. Negar Negar Memarian, MASc, PhD NSERC Postdoctoral Fellow Department of Neurology David Geffen School of Medicine at UCLA

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Re: [Freesurfer] Subgroup analysis
by Mahinda Yogarajah 29 Nov '12

29 Nov '12

Hi - thanks - I was thinking about doing it the other way (3 separate groups) because as well as looking to see whether there is a linear change in dependent measures (eg area) across groups I also want to see if there is a linear change in the slope of dependent measure against age across the 3 groups. I can' t see how to do that with the single group method against 1,2,3 covariates. Is there a way of doing it ? Also why do you recommend the 1 group method ? Better powered Thanks. Mahinda

2 1

Retinotopy Maps
by Zhou, Wei 29 Nov '12

29 Nov '12

Dear freesurfers, I am doing retinotopy analysis using freesurfer 5 with http://surfer.nmr.mgh.harvard.edu/fswiki/FsFastIndividualRetinotopyAnalysis . I have four runs, two eccen and two polar. For each run I have 15 seconds fixation, 300 seconds stimuli and 15s fixation at the end (total 330s and 300s for stimuli). 1) For -retinotopy option in mkanalysis-sess I typed "300". Do you think this setting is fine? 2) After finishing running, I use tksurfer-sess to display the result. When I typed "tksurfer-sess -s SUBJ01 -analysis rtopy.self.lh -map angle" with "-c polar" or "-c eccen'" I got two maps with -4.0 to 4.0 color range. I learn from mail list, the two maps do not represent time course of retinotopy, right? So what are these two maps tell us? 3) I tried rtview cmd and the maps look strange. Color scale is from -1.185 to -0.4 and 0.4 to 1.185 and it does not include all the colors in display. 4) I tried to use -run-wise in selxavg3-sess, it fails with: "/analysis/retinotopy/SUBJ01/bold/rtopy.self.lh/pr001/Xtmp.mat Error using svd Input to SVD must not contain NaN or Inf." Could you please give me some idea? Thank you very much in advance. Best Wei Zhou Medical Physics Ph.D. Student

2 1

correcting for discrete variables in Qdec
by Berg, S.F. van den 29 Nov '12

29 Nov '12

Hi Freesurfer Experts, In my design i want to use a general linear model tot relate cognitive performance and cortical thickness. I want to control for age, total gray matter, gender and education. I have two discrete variables, including gender (0,1) and Education (1-7). The problem is that the discrete variables do not appear in the nuisance screen in qdec. How can i control for this discrete variables? Can i put these variables in the nuisance screen? Or should i remove the gender.levels and education.levels file? Just highlighting the two variables gender and age result in an error in analyze: command failed: mri_glmfit --y In the qdec screen. When i just highlight gender and education in the discrete screen, highlight cogitive_performance in the continous screen, and Age and Total_gray in the nuisance screen. Analysing gives a error. But when i highlight only cognitive_performance in the continuous screen and nuisance factors age and total_gray in the nuisance screet. It work very well. And a vertex-wise cluster analyses can be done. Thanks, Stan

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