Freesurfer November 2012

freesurfer@nmr.mgh.harvard.edu

105 participants
177 discussions

Re: [Freesurfer] Subgroup analysis
by MAHINDA YOGARAJAH 27 Nov '12

27 Nov '12

Hi Doug, Sorry the previous suggestion referred to a suggestion from Donald earlier in the thread as follows: "You might consider the contrast [0 1.5 .5 -.5 -1.5] across all 5 groups showing a linear effect of disease severity. The first column being controls." I will try that suggestion out, but I have also grouped all the patients and controls together in 1 group (as opposed to 5 different groups), and given that controls contains no endogenous factor giving them a covariate of 1, and then P1 a value of 2, P2 a value of 3, P3 a values of 4 and P4 a value of 5. There are good biological grounds to suspect that that the endogenous factor will increase linearly from P1 to P5, though the values 1 to 5 I have chosen are arbitrary. When I then run the GLM looking for correlation between dependent measure and this covariate, I see significant results in a similar (though more widespread) location compared to when I simply look for a difference between all controls and all patients (C v combined P1 to P4). Thus, I think (hope) the model has shown that Hopefully this is one valid way in which to show that it is the changes in the level of the endogenous factor contribute to the overall group differences (C v combined P1 to P4). Do you agree ? I will however try Donald's method as I also want to show that the interaction between age-thickness (that I see in C v combined P1 to P4) shows a linear effect across P1 to P4. Any suggestions for how I do that ? Thanks, M

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Re: [Freesurfer] Subgroup analysis
by Mahinda Yogarajah 27 Nov '12

27 Nov '12

Hi, Thanks for the reference and explanation of the subtle statistical inferences. It was very useful. You are right in what i am trying to show (c- controls, p1 to p4 patients with varying levels of endogenous factor) which is that when patients are subdivided into levels of endogenous factor there is correlation with the changes seen in dependent variables compared to controls. So far, C v whole P gp - differences seen in plausible areas. C v P1 (greatest endo factor) subgp - no differences C v P4 subgp (lowest endo factor) - differences seen in plausible areas. Given that it is not valid to compare c v p1 and c v p4 (and p1 v p4 shows nothing) is the following valid - perhaps it is similar to what you proposed: Consider c and p1 to p4 as one group of subjects (theoretically the only difference between subjects being level of endogenous factor) but assign each subject a variable which represents level of endoenous factor (c - 1 p1 - 2 p3 - 4 p4 - 5) - then run glm looking for correlation between endogenous factor and dependent variable. Is this very different to what you suggested and any less valid ? Thanks. M

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Regarding freesurfer segmentations for longitudinal data
by Prasanna M 27 Nov '12

27 Nov '12

Hi, I work in the area of longitudinal shape analysis, and have used the longitudinal OASIS data in the past. I was trying to find freesurfer segmentations of structures for the OASIS data, but could only find them for cross-sectional ones. I write to you to ask if you're aware of segmentations made available for the longitudinal OASIS data, specifically the hippocampus regions? If not, could you point me to the best way possible to segment these for the longitudinal OASIS data? Thanks, Prasanna -- -- Let there be peace on earth... And let it begin with me.

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Re: [Freesurfer] spline_smooth (please reply, no answer from email-list)
by Douglas N Greve 27 Nov '12

27 Nov '12

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 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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Distance between ROIs on inflated brain
by Trietsch, Rayna 27 Nov '12

27 Nov '12

Hi, Is there a way to create and save multiple ROIs given there RAS coordinates in tkmedit and then plot them and measure the distance between them onto an inflated brain surface? Thanks! ~Rayna~

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Re: [Freesurfer] fieldsign-sess problem in retinotopy
by Zhou, Wei 26 Nov '12

26 Nov '12

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 process http://surfer.nmr.mgh.harvard.edu/fswiki/FsFastIndividualRetinotopyAnalysis 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 > > > > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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How to design the contrast matrix with 12 regressors?
by 李仕广 26 Nov '12

26 Nov '12

Dear FreeSurfers: I hope you can help me out with a problem in disgning my .mtx file. I want to examine the difference among three groups (HC group, EX group and PT group). Considing gender, I have six groups as similar as the example described inhttp://surfer.nmr.mgh.harvard.edu/fswiki/Fsgdf6G0V. But I want to correct for age. Then, I have 6 classes (two factors/three levels) and one covariate (age). How can I compare the difference among three groups (HC group, EX group, and PT group)? Could you please tall me how to design the contrast matrix with 12 regressors? Thanks a zillion times! Best wishes shiguangli

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registration Fail
by Gabriel Gonzalez Escamilla 26 Nov '12

26 Nov '12

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Re: [Freesurfer] fieldsign-sess problem in retinotopy
by Zhou, Wei 26 Nov '12

26 Nov '12

Hi Doug, Thank you for reply. As in rtopy.par the stimtype is either polar or eccen, I get separate f.nii files for eccen and polar and do one of the two at one time. Do you mean I should combine polar and eccen sessions into one f.nii? e.g. i want to do polar analysis whose rtopy.par file is polar, but I still need to put eccen session into f.nii with polar and then do the analysis? 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 > > > > _______________________________________________ > 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

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spline_smooth crash (NEW problem)
by Negar Memarian 26 Nov '12

26 Nov '12

Dear FreesSurfers, **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 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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Freesurfer November 2012