Freesurfer November 2012

freesurfer@nmr.mgh.harvard.edu

105 participants
177 discussions

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

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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

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

29 Nov '12

Hi, I think (hope) i am finally getting to grips with how to analyse things but wanted to check one last thing. Say I have 1 factor with 3 levels (3 groups of subjects) and 2 covariates (age and icv). My design matrix would include: Regressor 1 - ones for subject in Gp 1, 0 otherwise, codes intercept/mean for gp 1 Regressor 2 - ones for subject in Gp 2, 0 otherwise, codes intercept/mean for gp 2 Regressor 3 - ones for subject in Gp 3, 0 otherwise, codes intercept/mean for gp 3 Regressor 4 - age for subjects in Gp 1, 0 otherwise, codes age slope for gp 1 Regressor 5- age for subjects in Gp 2, 0 otherwise, codes age slope for gp 2 Regressor 6 - age for subjects in Gp 3, 0 otherwise, codes age slope for gp 3 Regressor 7 - icv for subjects in Gp 1, 0 otherwise, codes icv slope for gp 1 Regressor 8 - icv for subjects in Gp 2, 0 otherwise, codes icv slope for gp 2 Regressor 9 - icv for subjects in Gp 3, 0 otherwise, codes icv slope for gp 3 In terms of contrast would the following be correct: 1.5 0.5 -1.5 0 0 0 0 0 0 - to look for linear change in dependent variable across groups after correcting for age and icv 0 0 0 1.5 0.5 -1.5 0 0 0 - to look for linear change in age slope against dependent variable across groups while correcting for icv ie whether age-dependent measure correlations get stronger/weaker across gps Thanks Mahinda

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functional ROI analysis
by Susan Alice McLaughlin 29 Nov '12

29 Nov '12

Hi, I am hoping do a surface-based functional ROI analysis on subject-specific ROIs that are both defined structurally and are masked by an all/nothing functional contrast. func2roi-sess seems perfect for this except that my data are not in an FS-FAST data/analysis structure, but are instead pre-processed and preliminarily analyzed using FSL and mapped to the surface using reg-feat2anat. Is there any way to pass my original analysis into func2roi-sess? I tried using: func2roi-sess -roidef LH_ant_STG_soundthresh2 -analysis 1012_Run4_featFULLrev.feat/stats/zstat4.nii.gz -anatlabel lh_ant_STG -maskcontrast 1012_Run4_featFULLrev/stats/zstat16.nii.gz -maskthreshold 2 -s 1012 -d but get "ERROR: cannot find any sessions." Or is there another tool more appropriate for what I am trying to do? I am looking at mri_segstats, but my hand-drawn ROIs (drawn on fsaverage in tksurfer and morphed to each subject using label_2_label) are in .label format and are on the surface. Thanks in advance for and advice or suggestions. Susan McLaughlin Doctoral Candidate SPACE Lab (Stimulus-Parametric Imaging of Auditory Cortex) Dept. of Speech and Hearing Sciences University of Washington

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Re: [Freesurfer] fieldsign-sess problem in retinotopy
by Zhou, Wei 29 Nov '12

29 Nov '12

Hi Doug, Thank you for reply. yes all 4 are in bold separately. I tried -run-wise with selxavg3-sess, but it failed with the following msg: Saving X matrix to /media/local_home/zhouw4/EM0220/analysis/retinotopy/SUBJ01/bold/rtopy.self.lh/pr001/Xtmp.mat Error using svd Input to SVD must not contain NaN or Inf. Error in cond (line 39) s = svd(A); Error in fast_selxavg3 (line 254) XCond = cond(XtX); I attach the mat file in the email. I am thinking that the error is similar as that I only put polar or eccen session in bold folder. Thank you for looking into it. Best Wei ________________ But all four runs into a single bold folder, then try running selxavg3-sess with the -run-wise option. This will create separate run analysis in the output directory. I have not tried it with retinotopy before, so get back to me if it fails. doug On 11/26/2012 05:53 PM, Zhou, Wei wrote: > Hi Doug, > I think I didnt explain clearly last time. > Here's the thing: > I have four runs: 2 eccen and 2 polars. I followed the > processhttp://surfer.nmr.mgh.harvard.edu/fswiki/FsFastIndividualRetinotopyA… > and I hope to view the result of an individual session, e.g. one polar, > which could display the activations with different angles. What should I do > after all the analysis is done? Or I should run a retinotopy analysis > different from the link above. > Thank you in advance. > Best > Wei > ---- > Hi Wei, do you have both polar and eccentricity? It looks like you only > have polar. > doug > On 11/19/2012 01:39 PM, Zhou, Wei wrote: > > Please find the Xtmp.mat in the attachment.Thank you, Doug. > > Best > > Wei > > ---- > > Can you send me the Xtmp.mat file? > > dloug > > > > On 11/16/2012 01:01 PM, Zhou, Wei wrote: > > > Hi Doug, > > > > > > It seems the previous fieldsign-sess problem is due to that I stored > > > data on one server while freesurfer is on the other server. > > > But when I put the data and freesurfer on the same server and run the > > > retinotopy analysis again, it reported fail msg for "selxavg3-ses" : > > > -- > > > ntptot = 80, nX = 27, DOF = 53 > > > Saving X matrix to > > > > > > > > /media/local_home/zhouw4/testf/retinotopy/SUBJ01/bold/rtopy.self.lh/Xtmp.mat > > > Error using svd > > > Input to SVD must not contain NaN or Inf. > > > > > > Error in cond (line 39) > > > s = svd(A); > > > > > > Error in fast_selxavg3 (line 254) > > > XCond = cond(XtX); > > > --- > > > I checked Xtmp.mat. There is NaN in Xn and XtX. > > > My rtopy par is: eccen and pos. > > > > > > Would you please give me some idea about this error? > > > > > > Best > > > Wei > > > > > > >> > > > Try using this version > > > > > > > > > > > ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/fieldsign-sess > > > > > > doug > > > > > > On 11/01/2012 11:47 AM, Zhou, Wei wrote: > > > > Hi Doug, > > > > > > > > The subject name for structural is "SUBJ1" when I did recon-all, > > which > > > > is also the content of file "subjectname". My dir structures of > > > > "structural" and "retinotopy" are the same as > > > > http://www.alivelearn.net/?p=65 . "SUBJ1" is stored under > > > > "structural". if I set SUBJECTS_DIR as "....../structural", > > > > $SUBJECT_DIR/SUBJ1 does exist, then still I get the same error > > msg. > > > > > > > > The following is the log file: > > > > > > > > fieldsign-sess log file $Id: fieldsign-sess,v 1.2 2010/05/04 > > 22:00:18 > > > > greve Exp $ Thu Nov 1 10:36:52 CDT 2012 Linux rii-appserv-02 > > > > 2.6.32-279.11.1.el6.x86_64 #1 SMP Sat Sep 22 07:10:26 EDT 2012 > > x86_64 > > > > x86_64 x86_64 GNU/Linux /media/users/zhouw4/testf/retinotopy > > > > /usr/local/freesurfer/fsfast/bin/fieldsign-sess -a rtopy.self.lh > > > > -occip -s SUBJ1 uid=20120(zhouw4) gid=22000(rii_users) > > > > groups=22000(rii_users),21100(rii_appservers),23000(domain^users) > > > > context=unconfined_u:unconfined_r:unconfined_t:s0-s0:c0.c1023 > > > > > > > > Best > > > > Wei > > > > > > > > > > > > >What is the name of FreeSurfer subject? This is not necessarily > > the > > > > same>> > > > > >as SUBJ01 in your command line below. That is the session (which > > may > > > or > > > > >may not be the same as the "subject name"). What ever the > > subjectname > > > > is, does SUBJECT_DIR/subject exist? > > > > On 10/31/2012 03:07 PM, Zhou, Wei wrote: > > > > > > > > > > Hi, Doug > > > > > > > > > > Thank you for your reply. I have tried exporting > > SUBJECTS_DIR to > > > the > > > > > directory of upper fold, retinotopy or SUBJ01 But none of > > them > > > works. > > > > > Still the same error msg. > > > > > > > > > > So what should SUBJECTS_DIR be exported to for this > > analysis? > > > > > > > > > > Best > > > > > > > > > > Wei > > > > > > > > > > > > > > > > > > > > >Hi Wei, this is a bug in the error msg. It is trying to > > say that > > > your > > > > > >source subject is not in the $SUBJECTS_DIR. > > > > > >doug > > > > > > > > > > >On 10/27/2012 02:27 PM, Zhou, Wei wrote: > > > > > > Dear freesurfers, > > > > > > > > > > > > I am trying retinotopy analysis in freesurfer. For > > > > "fieldsign-sess", I > > > > > > encounter the following problem when I type > > "fieldsign-sess > > > -a > > > > > > rtopy.self.lh -occip -s SUBJ01" or "fieldsign-sess > > -a > > > > rtopy.self.lh > > > > > > -occip -sf sessid": > > > > > > > > > > > > > > > > > > */media/users/zhouw4/testf/retinotopy/SUBJ01/log/fieldsign-sess.log* > > > > > > *subject: Undefined variable.* > > > > > > > > > > > > my structure of retinotopy fold is : > > > > > > retinotopy > > > > > > | |--sessid > > > > > > |--SUBJ01 > > > > > > |--subjectname > > > > > > > > > > > > |--bold > > > > > > |--001 > > > > > > |--f.nii > > > > > > |--rtopy.par| > > > > > > > > > > > > I really appreciate it if you could give me some > > idea about > > > that > > > > > > problem. Thanks a lot in advance. > > > > > > > > > > > > Best > > > > > > Wei Zhou > > > > > > Medical Physics Ph.D. Student > > > > > > Diagnostic Imaging Track > > > > > > cgxz...(a)gmail.com<mailto:cgxz...@gmail.com> > > > > > > > > > zho...(a)livemail.uthscsa.edu<mailto:zho...@livemail.uthscsa.edu> > > > > > > > > > > > > > > > > > > _______________________________________________ > > > > > > Freesurfer mailing list > > > > > > Freesurfer(a)nmr.mgh.harvard.edu > > > > > > > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > > > > > > -- > > > > > Douglas N. Greve, Ph.D. > > > > > MGH-NMR Center > > > > > gr...(a)nmr.mgh.harvard.edu > > > > > Phone Number: 617-724-2358 > > > > > Fax: 617-726-7422 > > > > > > > > > > > > > > > > > > > > _______________________________________________ > > > > > Freesurfer mailing list > > > > > Freesurfer(a)nmr.mgh.harvard.edu > > > > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > > > > Best > > > > Wei Zhou > > > > Medical Physics Ph.D. Student > > > > cgxz...(a)gmail.com<mailto:cgxz...@gmail.com> > > > > zho...(a)livemail.uthscsa.edu<mailto:zho...@livemail.uthscsa.edu> > > > > > > > > > > > > _______________________________________________ > > > > Freesurfer mailing list > > > > Freesurfer(a)nmr.mgh.harvard.edu > > > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > > Best > > > Wei Zhou > > > > > > > > > > > > _______________________________________________ > > > Freesurfer mailing list > > > Freesurfer(a)nmr.mgh.harvard.edu > > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > -- > > Douglas N. Greve, Ph.D. > > MGH-NMR Center > > gr...(a)nmr.mgh.harvard.edu > > Phone Number: 617-724-2358 > > Fax: 617-726-7422 > > > > Best > > Wei Zhou

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Re: [Freesurfer] spline_smooth (please reply, no answer from email-list)
by Douglas N Greve 29 Nov '12

29 Nov '12

Hi Negar, I cannot reproduce this error. I'm not sure how to proceed, but here are three possibilities: 1. Is this a virtual machine? If so, do you have a real machine you can run it on? 2. You only have 2G of memory on your machine. Can you increase that or run it on a machine with more? 3. There is an outside chance it could be an MNI version issue. Run nu_estimate_np_and_em and look at the version (should be 1.10) doug On 11/27/2012 03:31 PM, Negar Memarian wrote: > Hi Doug, > > Thanks very much for your reply. I checked the org.mgz and it looks > okay, so as you advised I uploaded the subject to FileDrop for you to > see. I also uploaded the recon-all log file so you can see where > exactly the error occurs. > > Many thanks and looking forward to hear from you, > Negar > > On Tue, Nov 27, 2012 at 9:42 AM, Douglas N Greve > <greve(a)nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> wrote: > > > Hi Negar, sorry about the delay. The first thing to do is to look > at the orig.mgz to see if there is anything funny going on, maybe > most of the image is dark with one very bright spot or some other > distortion. If that looks ok, please tar up the subject and drop > it to me at our file drop (url at thenend of this email). > doug > > > On 11/26/2012 09:10 PM, Negar Memarian wrote: > > Hello Dr. Greve, > I'm not sure if my questions actually get posted on the > FreeSurfer email list or not, as I have never received a > reply. I really need help with the following issue and would > appreciate if you or your colleagues please advise: > **I've checked similar posts on the email-list and still could > not find an answer to my question. I'd really appreciate your > attention and feedback: > 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 FreeSurfer2.6.28-11-generic #42-UbuntuSMPFri Apr 17 > 01:57:59 UTC2009 i686GNU/Linux > recon-all -s BT501_FSexited with ERRORS at Mon Nov 26 15:26:10 > EST2012 > 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 > > > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > greve(a)nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> > Phone Number: 617-724-2358 <tel:617-724-2358> > Fax: 617-726-7422 <tel:617-726-7422> > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > Outgoing: > ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ > > > > 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. > > -- Douglas N. Greve, Ph.D. MGH-NMR Center greve(a)nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/

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Freesurfer November 2012