Freesurfer December 2013

freesurfer@nmr.mgh.harvard.edu

107 participants
197 discussions

R: Re: R: Re: Linear regression
by stdp82＠virgilio.it 04 Dec '13

04 Dec '13

Dear Douglas, thank you very much for you kind reply.In the paper I have 3 groups (2 diseases and 1 controls).I have performed cortical thickness analysis among groups, individuating relevant difference in the posterior regions. Next, for one group, I have used qdec to individuate statistically significant regions where NPS test scores and thickness were correlated. 3 nuisance factors was also added to regressor. All results were corrected for multiple comparisons by using a pre-cached cluster-wise Monte-Carlo Simulation.qdec analysis results have individuated a "composite region" (superior parietal cortex and precuneus) where NPS correlated with thinning. Now, if I understand, I should extract the mean thickness from superior parietal cortex and precuneus and I should perform a linear regression (and partial correlation) with an other statistical program (SPSS for example).Is there a better way to perform a regression the most possible similar to qdec computation? Stefano ----Messaggio originale---- Da: greve(a)nmr.mgh.harvard.edu Data: 4-dic-2013 17.35 A: <stdp82(a)virgilio.it>, <freesurfer(a)nmr.mgh.harvard.edu> Ogg: Re: R: Re: [Freesurfer] Linear regression On 12/02/2013 03:14 PM, stdp82(a)virgilio.it wrote: > Tank you very much. > > A-Do you mean the partial correlation coeff (PCC) at each voxel > averaged over region? > Finally a linear regression is done between cortical thickness of a > composite region and NPS. However the authors discuss every individual > region as related to disease. So a table with partials correlations of > individuals ROIs with NPS seems useful to support the discussion. What did you do in the paper? The reviewer mentions a "composite region". Did you average the thickness over that region and then do the regression with NPS? > > B- I'd like to obtain the covariance matrix of the regression made > between cortical thickness, group and covariates. How can I do it? > I'm not sure what you mean. Would this be a different matrix for each > vertex? > I cite the referee: "The authors must provide the covariance matrix of > the regression made between cortical thickness, group and covariates > as supplementary information in order to increase the value of the > results." Sorry, I don't understand what the reviewer is asking for. doug > > I don't have Matlab for mri_glmfit_pcc matlab. > > Stefano > > > > > ----Messaggio originale---- > Da: greve(a)nmr.mgh.harvard.edu > Data: 2-dic-2013 20.47 > A: <freesurfer(a)nmr.mgh.harvard.edu> > Ogg: Re: [Freesurfer] Linear regression > > > On 12/02/2013 02:22 PM, stdp82(a)virgilio.it wrote: > > Hi list, > > > > I have some questions, please. > > > > I performed linear regression by qdec to find the regions where the > > cortical thinning correlates with neuropsychological test (NPS), > > taking in account 3 nuisance factors. > > > > A- I individuated some posterior regions and now I'd like to build a > > table with partials correlations of individuals ROIs with NPS. How can > > I obtain the values for each region? > Do you mean the partial correlation coeff (PCC) at each voxel averaged > over region? You can get PCC maps using the mri_glmfit_pcc matlab > command. You can then do the averaging over region using mri_segstats. > > > > B- I'd like to obtain the covariance matrix of the regression made > > between cortical thickness,group and covariates. How can I do it? > I'm not sure what you mean. Would this be a different matrix for each > vertex? > > > > C- Is there a specific reference for qdec? > No, it is just a GLM so any GLM reference will do. > > > > Thank you very much, > > > > > > Stefano > > > > > > > > > > > > _______________________________________________ > > 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 > greve(a)nmr.mgh.harvard.edu > Phone Number: 617-724-2358 > Fax: 617-726-7422 > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 > www.nmr.mgh.harvard.edu/facility/filedrop/index.html > Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ > > _______________________________________________ > 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. > > > -- 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: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/

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how do display a particular region for visucalization
by tulu＠ms36.hinet.net 04 Dec '13

04 Dec '13

Dear freesurfer experts I try to display some of particular regions in freeview. The below figure is an example. Is there any script or manual descript how to do that ? Sincerely yours JLH <?xml:namespace prefix = v ns = "urn:schemas-microsoft-com:vml" /> <?xml:namespace prefix = o ns = "urn:schemas-microsoft-com:office:office" />

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mri_ca_normalize error
by Mark Plantz 04 Dec '13

04 Dec '13

Hello all, I am experiencing an error during the mri_ca_normalize step of auto-recon-1 using a non-default atlas (for infant brains). Essentially, "norm.mgz" and "ctrl_pts.mgz" are both outputting as blank files (completely black). However, brainmask.mgz looks completely fine, which leads me to believe that skull-stripping and alignment should be OK. Subsequently, zero control points were found during the "mri_ca_normalize" step. While mri_ca_normalize does not fail, I believe the lack of control points causes the following error in the "mri_ca_label" step: *searching scale 1 Z rot 2.3 * *searching scale 1 Z rot 2.5 * *searching scale 1 Z rot 2.8 * *searching scale 1 Z rot 3.0 * *searching scale 1 Z rot 3.3 * *searching scale 1 Z rot 3.5 * *searching scale 1 Z rot 3.8 * *searching scale 1 Z rot 4.0 * *searching scale 1 Z rot 4.3 * *searching scale 1 Z rot 4.5 * *searching scale 1 Z rot 4.8 * *searching scale 1 Z rot 5.0 * *searching scale 1 Z rot 5.3 * *searching scale 1 Z rot 5.5 * *searching scale 1 Z rot 5.8 * *searching scale 1 Z rot 6.0 * *searching scale 1 Z rot 6.3 * *searching scale 1 Z rot 6.5 * *searching scale 1 Z rot 6.8 global minimum found at slice 0.0, rotations (90.00, -0.00)* *final transformation (x=0.0, yr=90.000, zr=-0.000):* *-0.000 0.000 1.000 128.000;* *-0.000 1.000 -0.000 128.000;* *-1.000 0.000 0.000 128.000;* * 0.000 0.000 0.000 1.000;* *Segmentation fault* I am wondering if anyone knows why the control points would not be found and if there is anyway to solve the problem? I can also attach the .gca atlas that I am using if that would help. I also noticed that the "aseg.auto_noCCseg.mgz" file seems to have shifted significantly from the position of the GCA atlas. In fact, it shifted so far that some of the occipital lobe appears to have been cut out [I attached an image for details]. I am not sure if this is a related problem, but I figured I should mention it. I appreciate the help! Best, Mark

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how to extract DTI data with bvals/bvects
by ryu＠nmr.mgh.harvard.edu 04 Dec '13

04 Dec '13

Dear All, I used unpacksdcmdir to unpack DTI data from Bay 3. The log file shows "DTI is in non-moasic form, so cannot extract bvals/bvects" My question is how to get bvals/bvects files from unpack? The files look like: 42 DIFFUSION_HighRes ok 128 128 62 1 MR.1.3.12.2.1107.5.2.32.35162.2013031117224812856938134 43 DIFFUSION_HighRes ok 128 128 62 1 MR.1.3.12.2.1107.5.2.32.35162.2013031117224812950738135 44 DIFFUSION_HighRes ok 128 128 62 1 MR.1.3.12.2.1107.5.2.32.35162.2013031117224813055538136 45 DIFFUSION_HighRes ok 128 128 62 1 MR.1.3.12.2.1107.5.2.32.35162.2013031117224813122838137 46 DIFFUSION_HighRes ok 128 128 62 1 MR.1.3.12.2.1107.5.2.32.35162.2013031117224813209438138 47 DIFFUSION_HighRes ok 128 128 1 62 MR.1.3.12.2.1107.5.2.32.35162.2013031117224813279838139 Cheers, Jacky

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Problems with longitudinal analysis
by Knut J Bjuland 04 Dec '13

04 Dec '13

Hi, I have used a linear mixed model for longitudinal data analysis on a FreeSurfer 5.3, Matlab 2013b on a system with Ubuntu 12.04. I used mris_preproc --qdec-long qdec.table.dat --target fsaverage --hemi lh --meas thickness --out lh.thickness.mgh to concatenate thickness surf files, and smoothed with mri_surf2surf --hemi lh --s fsaverage --sval lh.thickness.mgh --tval lh.thickness_sm30.mgh --fwhm-trg 30 --cortex –noreshape. I then used the same command and options in a Matlab script, as shown at http://freesurfer.net/fswiki/LinearMixedEffectsModel found in the example for mass-univariate data analyses. . I used this design matrix: interception, time, group, group*time, gender, gender*time, and I used two random effect on interception and time. I did not compare the two random effect models with one random effect model. I used this contrast vector C=[0 0 1 0 0] for these images which are included in the email. The script ran fine but when I looked at sig.mgh, it contained many visible quadrate shapes boxes even after FDR correction, and the image looks quite different than the image in the paper in Neuroimage (Spatiotemporal Linear Mixed Effects Modeling for the Mass-univariate Analysis of Longitudinal ). Any idea what went wrong here? Thank you! Best regards, Knut Jørgen

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5.1 to 5.3
by Jonathan Holt 04 Dec '13

04 Dec '13

Hey guys, Moving a ton of data from v 5.1 to v 5.3, is there anything special that needs to be done with our 5.1 processed data to ensure consistency with data to be processed in 5.3? best, jon

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To believe non-convergence?
by Seán Froudist Walsh 04 Dec '13

04 Dec '13

Dear Jorge and FreeSurfers, I have just been running lme_mass_fit_vw for 6 hours, and I have seen many thousands of messages like the following: "Location 337813: Convergence at iteration 4. Initial and final likelihoods: 607.8828, 611.1052. Location 337812: Convergence at iteration 4. Initial and final likelihoods: 603.0934, 604.4513." etc.... There was the very occasional message saying the algorithm did not converge at some location, a message I saw only 2 or three times (although I wasn't looking at the matlab window for 6 hours straight, thankfully). I thought, so far, so good. I came in to work this morning however, and found that it had finished, with the following ugly message waiting for me: "Algorithm did not converge at 99.9997 percent of the total number of locations. Total elapsed time is 357.4368 minutes." I have two questions please. 1) Should I believe this message, even though it seems to contradict what has been printed to the screen while lme_mass_fit_vw was running? 2) If it really is a problem, what would you recommend I do to remedy it? Set the convergence epsilon to 10^5? Any help is much appreciated. Best wishes, Seán

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Re: [Freesurfer] [martinos-tech] FSFAST between-conditions contrasts
by Douglas N Greve 04 Dec '13

04 Dec '13

Hi Sue, that looks correct. I think it is an open question as to whether you should use the corrected maps or use the uncorrected and then correct the final map. Maybe someone else can chime in. doug On 10/23/2013 09:49 AM, Susan Ruiz wrote: > Hi Doug, > > This is /very/ helpful. > > Procedurally, would this be the correct approach? > > For positive % signal change from baseline clusters, use these files > resulting from mri_glmfit-sim: > condAvFix.th3.pos.sig.cluster.nii > condBvFix.th3.pos.sig.cluster.nii > condAvscondB.th3.pos.sig.cluster.nii > > then run: > % mri_concat --i condAvFix.th3.pos.sig.cluster.nii --i > condBvFix.th3.pos.sig.cluster.nii --i > condAvscondB.th3.pos.sig.cluster.nii --conjunct --o positive.AvsB.nii > > For negative % signal change from baseline clusters, use these files > resulting from mri_glmfit-sim: > condAvFix.th3.neg.sig.cluster.nii > condBvFix.th3.neg.sig.cluster.nii > condAvscondB.th3.pos.sig.cluster.niigrf.th3.pos.sig.cluster.nii > > then run: > % mri_concat --i condAvFix.th3.neg.sig.cluster.nii --i > condBvFix.th3.neg.sig.cluster.nii --i > condAvscondB.th3.pos.sig.cluster.nii --conjunct --o negative.AvsB.nii > > Note that for positive activation differences I would use sign=pos for > each condition vs fixation during mri_glmfit-sim, and for > "deactivation" clusters I use sign=neg for each condition vs fixation > during mri_glmfit-sim. BUT for both cases I use sign=pos for condition > A vs. condition B. > > Thanks so much! > > Best, > ~Sue > > > > On Tue, Oct 22, 2013 at 10:50 AM, Douglas N Greve > <greve(a)nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> wrote: > > > Hi Sue, I agree that they are not the same thing. There is not a > single > flag that will do what you want. What you are describing is a post-hoc > test. So you look for places where A != B, then within those > voxels you > do posthoc tests. You can implement this with a conjunction analysis > where you set up threeway conjunction A>B and A>0 and B>0. You can do > this with the --conjunt option to mri_concat > doug > > > On 10/21/2013 02:13 PM, Susan Ruiz wrote: > > Hi all, > > > > When running a functional analysis and comparing two experimental > > conditions, we observed that there are some voxels/vertices > where both > > condition A and condition B have a positive % signal change from > > baseline, and condition A has greater activity than condition B. > > > > In other regions, both condition A and condition B have negative % > > signal change from baseline, but condition B has a greater absolute > > value % signal change (thus relative to baseline condition B has > more > > "deactivation"--a term I am using since you all know what I mean > even > > if the term itself is imperfect). > > > > Since, in both cases, the % signal change is technically > condition A > > > condition B, the between-conditions maps do not distinguish > these two > > scenarios. FS-FAST sees these as being the same. Is there a way to > > tell FS-FAST to cluster these scenarios separately? Is there a > > compelling reason why I should not consider these different > > situations? It seems to me that the interpretation of what's taking > > place in these two scenarios is not identical. Agree or > disagree? Can > > FS-FAST distinguish these with a flag I don't know about? > > > > Thank you, > > ~Sue > > > > -- > > * * ** *** ***** ******** ************* > > Susan Mosher Ruiz, Ph.D. > > Research Scientist > > Boston University School of Medicine > > Laboratory of Neuropsychology > > VA Boston Healthcare System > > smosher(a)bu.edu <mailto:smosher@bu.edu> <mailto:smosher@bu.edu > <mailto:smosher@bu.edu>> > > * * ** *** ***** ******** ************* > > > > -- > 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: https://gate.nmr.mgh.harvard.edu/filedrop2 > 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. > > > > ------------------------------------ > > Yahoo! Groups Links > > <*> To visit your group on the web, go to: > http://groups.yahoo.com/group/martinos-tech/ > > <*> Your email settings: > Individual Email | Traditional > > <*> To change settings online go to: > http://groups.yahoo.com/group/martinos-tech/join > (Yahoo! ID required) > > <*> To change settings via email: > martinos-tech-digest(a)yahoogroups.com > <mailto:martinos-tech-digest@yahoogroups.com> > martinos-tech-fullfeatured(a)yahoogroups.com > <mailto:martinos-tech-fullfeatured@yahoogroups.com> > > <*> To unsubscribe from this group, send an email to: > martinos-tech-unsubscribe(a)yahoogroups.com > <mailto:martinos-tech-unsubscribe@yahoogroups.com> > > <*> Your use of Yahoo! Groups is subject to: > http://info.yahoo.com/legal/us/yahoo/utos/terms/ > > > > > -- > * * ** *** ***** ******** ************* > Susan Mosher Ruiz, Ph.D. > Research Scientist > Boston University School of Medicine > Laboratory of Neuropsychology > VA Boston Healthcare System > smosher(a)bu.edu <mailto:smosher@bu.edu> > * * ** *** ***** ******** ************* > __._,_.___ > Reply via web post > <http://groups.yahoo.com/group/martinos-tech/post;_ylc=X3oDMTJwa21mMTlwBF9TA…> > Reply to sender > <mailto:smosher@bu.edu?subject=Re%3A%20%5Bmartinos-tech%5D%20FSFAST%20between-conditions%20contrasts> > Reply to group > <mailto:martinos-tech@yahoogroups.com?subject=Re%3A%20%5Bmartinos-tech%5D%20FSFAST%20between-conditions%20contrasts> > Start a New Topic > <http://groups.yahoo.com/group/martinos-tech/post;_ylc=X3oDMTJlZjd2ZDVnBF9TA…> > Messages in this topic > <http://groups.yahoo.com/group/martinos-tech/message/5844;_ylc=X3oDMTM0a2Nkb…> > (3) > > Recent Activity: > > Visit Your Group > <http://groups.yahoo.com/group/martinos-tech;_ylc=X3oDMTJlcXY1cjhnBF9TAzk3Mz…> > > Yahoo! Groups > <http://groups.yahoo.com/;_ylc=X3oDMTJkdW8xcWpkBF9TAzk3NDc2NTkwBGdycElkAzQ5O…> > > Switch to: Text-Only > <mailto:martinos-tech-traditional@yahoogroups.com?subject=Change%20Delivery%20Format:%20Traditional>, > Daily Digest > <mailto:martinos-tech-digest@yahoogroups.com?subject=Email%20Delivery:%20Digest> > • Unsubscribe > <mailto:martinos-tech-unsubscribe@yahoogroups.com?subject=Unsubscribe> > • Terms of Use <http://info.yahoo.com/legal/us/yahoo/utos/terms/> • > Send us Feedback > <mailto:ygroupsnotifications@yahoogroups.com?subject=Feedback%20on%20the%20redesigned%20individual%20mail%20v1> > . > > __,_._,___ -- 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: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/

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can FSL read FS thickness files?
by Kaiming Yin 04 Dec '13

04 Dec '13

Dear FS guys, I have run the FS 5.3 and get thickness files e.g. lh.thickness and rh.thickness, could FSL read these? should we use files like nii instead of mgz, or is there some options for FSL to read mgz too? Thanks, Kaiming

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manual edits boundary 2 screenshots example for 3T adult
by Kaiming Yin 04 Dec '13

04 Dec '13

Dear guys, I have a simple question in the manual edits parts. I am using freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 with Ubuntu 13.10, for a trial on a 3T adult data, and I attached the data 2 screenshot common examples here, personally I am not sure if the wm boundary seems good or not. So I hope if you can help have a look and see if this data has any place need edits. And also usually, for a 3T data like this, how many edits will be approximately needed? I mean will it usually cost several corrections enough? Or 10s? 30s? or even more? (sorry for the oversize of last email attachment) Great thanks, Kaiming

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Freesurfer December 2013