Freesurfer July 2017

freesurfer@nmr.mgh.harvard.edu

118 participants
198 discussions

Switch FreeSurfer Desikan-Killiany atlas to Civet
by 沙志强 14 Jul '17

14 Jul '17

Hello FreeSurfer Developers, I am attempting to switch the Desikan-Killiany atlas of FreeSurfer to Civet. But I have no idea to solve the problem. Would you like to give me some suggestions or some detailed steps to help me accomplish the tasks ? Best wishes, Zhiqiang Sha

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problems with recon-all in 6.0
by Lars M. Rimol 14 Jul '17

14 Jul '17

Hi, I'm trying to run recon-all in FreeSurfer 6.0 but I keep getting error messages and some strange behavior: ls 01001/0/2/ 100.dcm 106.dcm 111.dcm 117.dcm 122.dcm 128.dcm 133.dcm 139.dcm 144.dcm 14.dcm 155.dcm 160.dcm 166.dcm 171.dcm 17.dcm 22.dcm 28.dcm 33.dcm 39.dcm 44.dcm 4.dcm 55.dcm 60.dcm 66.dcm 71.dcm 77.dcm 82.dcm 88.dcm 93.dcm 99.dcm 101.dcm 107.dcm 112.dcm 118.dcm 123.dcm 129.dcm 134.dcm 13.dcm 145.dcm 150.dcm 156.dcm 161.dcm 167.dcm 172.dcm 18.dcm 23.dcm 29.dcm 34.dcm 3.dcm 45.dcm 50.dcm 56.dcm 61.dcm 67.dcm 72.dcm 78.dcm 83.dcm 89.dcm 94.dcm 9.dcm 102.dcm 108.dcm 113.dcm 119.dcm 124.dcm 12.dcm 135.dcm 140.dcm 146.dcm 151.dcm 157.dcm 162.dcm 168.dcm 173.dcm 19.dcm 24.dcm 2.dcm 35.dcm 40.dcm 46.dcm 51.dcm 57.dcm 62.dcm 68.dcm 73.dcm 79.dcm 84.dcm 8.dcm 95.dcm 103.dcm 109.dcm 114.dcm 11.dcm 125.dcm 130.dcm 136.dcm 141.dcm 147.dcm 152.dcm 158.dcm 163.dcm 169.dcm 174.dcm 1.dcm 25.dcm 30.dcm 36.dcm 41.dcm 47.dcm 52.dcm 58.dcm 63.dcm 69.dcm 74.dcm 7.dcm 85.dcm 90.dcm 96.dcm 104.dcm 10.dcm 115.dcm 120.dcm 126.dcm 131.dcm 137.dcm 142.dcm 148.dcm 153.dcm 159.dcm 164.dcm 16.dcm 175.dcm 20.dcm 26.dcm 31.dcm 37.dcm 42.dcm 48.dcm 53.dcm 59.dcm 64.dcm 6.dcm 75.dcm 80.dcm 86.dcm 91.dcm 97.dcm 105.dcm 110.dcm 116.dcm 121.dcm 127.dcm 132.dcm 138.dcm 143.dcm 149.dcm 154.dcm 15.dcm 165.dcm 170.dcm 176.dcm 21.dcm 27.dcm 32.dcm 38.dcm 43.dcm 49.dcm 54.dcm 5.dcm 65.dcm 70.dcm 76.dcm 81.dcm 87.dcm 92.dcm 98.dcm recon-all -subject 1001_c1 -i 01001/0/2/1.dcm -all ................................ writing to /work/projects/nn9208k/tbi/morfometri_test/�1001_c1/mri/orig/001.mgz... #-------------------------------------------- #@# MotionCor fr. 14. juli 10:04:21 +0200 2017 ERROR: no run data found in /work/projects/nn9208k/tbi/morfometri_test/�1001_c1/mri. Make sure to have a volume called 001.mgz in /work/projects/nn9208k/tbi/morfometri_test/�1001_c1/mri/orig. If you have a second run of data call it 002.mgz, etc. See also: http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Conversion Linux compute-16-36.local 2.6.32-696.3.2.el6.x86_64 #1 SMP Tue Jun 20 01:26:55 UTC 2017 x86_64 x86_64 x86_64 GNU/Linux recon-all -s �1001_c1 exited with ERRORS at fr. 14. juli 10:04:21 +0200 2017 Not sure why it crashes, and why does it add "?" to the subject name? Thank you! sincerely yours, Lars M. Rimol, PhD Senior researcher, Norwegian Advisory Unit for functional MRI Department of Radiology, St. Olav's University hospital, 7006 Trondheim, Norway

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Mid point on Freeview
by Trisanna Sprung-Much 14 Jul '17

14 Jul '17

Hi there I have a question concerning viewing a surface in Freeview (FS 6.0): *What does the "mid point" variable refer to?* I can change it and it seems to change the shading within the sulci when I am looking at a white matter surface. Many thanks Trisanna -- Ph.D. Candidate McGill University Integrated Program in Neuroscience Psychology

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Re: [Freesurfer] Switch FreeSurfer Desikan-Killiany atlas to Civet
by Antonin Skoch 14 Jul '17

14 Jul '17

Dear Zhiquiang, as a regular user of FreeSurfer I am wondering, what is the advantage of using Civet instead of FreeSurfer? Are there some functionalities in Civet which are not available in FreeSurfer? Or does Civet offer better performance/accuracy/precision in estimation of surface models for some situations/datasets? Antonin Skoch Hello FreeSurfer Developers, I am attempting to switch the Desikan-Killiany atlas of FreeSurfer to Civet. But I have no idea to solve the problem. Would you like to give me some suggestions or some detailed steps to help me accomplish the tasks ? Best wishes, Zhiqiang Sha

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HELP! FDR vs clusterwise correction for multiple comparisons
by marco mcsweeney 14 Jul '17

14 Jul '17

Dear Doug and Bruce I have a couple of questions regarding multiple comparison correction. Any help with this would be really appreciated! I am conducting a cortical thickness analysis between 2 groups (patients vs controls). My understanding is that first I should check for an age-cortical thickness interaction using DODS. If no interaction is found I can use DOSS. My problem is that when I run the analysis for age-cortical thickness interaction and correct for multiple comparisons using FDR there is no significant age-cortical thickness interaction for left or right hem. So DOSS can be used to check for group differences in cortical thickness. When I run the same analysis, this time using clusterwise correction, I find an age-cortical thickness interaction resulting in 1 cluster in the right hem. However, this cortical region is not present in the DOSS age independent cortical thickness difference between the patients and controls. I am aware that FDR and clusterwise correction are doing 2 very different things but if FDR finds no difference between groups for age-cortical thickness interaction, would it be justified to stick with FDR if a difference was present using clusterwise correction? Having looked into this, it appears to me that both FDR and clusterwise correction are equally valid, just different approaches. I am really stuck on this point, as my understanding of this area is somewhat limited. Thank you so much in advance Best wishes Marco

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R: Re: R: Re: 3G1V.fsgd
by stdp82＠virgilio.it 14 Jul '17

14 Jul '17

Hi list, by applying the model reported above I obtained opposite maps for slope and intercept. E.g. In HC-MCI folder, the sig.nii.gz for slope and intercept show the same maps which inverse color (pos/neg). I guess that there is an error in my model for 3GV1. Please could you check in. Thanks Stefano >----Messaggio originale---- >Da: "Douglas N Greve" <greve(a)nmr.mgh.harvard.edu> >Data: 14-lug-2017 0.45 >A: <freesurfer(a)nmr.mgh.harvard.edu> >Ogg: Re: [Freesurfer] R: Re: 3G1V.fsgd > >those are correct > > >On 07/13/2017 05:44 PM, stdp82(a)virgilio.it wrote: >> Many thanks! >> >> In conclusion, you can confirm that the complete list of contrast reported >> below is corrected for 3g1v, please? >> >> Contrast 1) HC-MCI_intercept.mtx >> 1 -1 0 0 0 0 >> >> Contrast 2) HC-MCI_slope.mtx >> 0 0 0 1 -1 0 >> >> Contrast 3) HC-AD_intercept.mtx >> 1 0 -1 0 0 0 >> >> Contrast 4) HC-AD_slope.mtx >> 0 0 0 1 0 -1 >> >> Contrast 5) MCI-AD_intercept.mtx >> 0 1 -1 0 0 0 >> >> Contrast 6) MCI-AD_slope.mtx >> 0 0 0 0 1 -1 >> >> Contrast 7) effect.intercept.mtx >> 1 -1 0 0 0 0 >> 1 0 -1 0 0 0 >> >> Contrast 8) effect.slope.mtx >> 0 0 0 1 -1 0 >> 0 0 0 1 0 -1 >> >> Contrast 9) HC+MCI-vs-AD.intercept.mtx >> 0.5 0.5 -1 0 0 0 >> >> Contrast 10) HC+MCI-vs-AD.slope.mtx >> 0 0 0 0.5 0.5 -1 >> >> Kind regards, >> >> >> Stefano >> >> >>> ----Messaggio originale---- >>> Da: "Douglas N Greve" <greve(a)nmr.mgh.harvard.edu> >>> Data: 13-lug-2017 22.30 >>> A: <freesurfer(a)nmr.mgh.harvard.edu> >>> Ogg: Re: [Freesurfer] 3G1V.fsgd >>> >>> >>> >>> On 07/13/2017 10:37 AM, stdp82(a)virgilio.it wrote: >>>> Dear FS group, >>>> >>>> I don't understand how I should build the contrast for 3 groups 1 >>>> covariate. >>>> No specific example is provided within fsgd example and also other >>>> colleagues report the same problem in the mail list. >>>> Please could you provide us details on this topic? >>>> Especially, how should be the g3v1.intercept and g31v.slope? >>>> >>>> 1 -1 0 0 0 0 >>>> 1 0 -1 0 0 0 >>>> for g3v1.intercept.mtx >>> This is the main effect of group on the intercept regressing out the >>> effect of covariate. >>>> and >>>> 0 0 0 1 -1 0 >>>> 0 0 0 1 0 -1 >>>> for g3v1.slope.mtx >>> This is the main effect of group on the slope regressing out the effect >>> of group intercept. >>>> >>>> are corrected? >>>> >>>> Waiting for you very wellcome suggestions >>>> >>>> Thanks and kind regards >>>> >>>> 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. >>> >>> >> _______________________________________________ >> 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 >

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R: Re: 3G1V.fsgd
by stdp82＠virgilio.it 13 Jul '17

13 Jul '17

Many thanks! In conclusion, you can confirm that the complete list of contrast reported below is corrected for 3g1v, please? Contrast 1) HC-MCI_intercept.mtx 1 -1 0 0 0 0 Contrast 2) HC-MCI_slope.mtx 0 0 0 1 -1 0 Contrast 3) HC-AD_intercept.mtx 1 0 -1 0 0 0 Contrast 4) HC-AD_slope.mtx 0 0 0 1 0 -1 Contrast 5) MCI-AD_intercept.mtx 0 1 -1 0 0 0 Contrast 6) MCI-AD_slope.mtx 0 0 0 0 1 -1 Contrast 7) effect.intercept.mtx 1 -1 0 0 0 0 1 0 -1 0 0 0 Contrast 8) effect.slope.mtx 0 0 0 1 -1 0 0 0 0 1 0 -1 Contrast 9) HC+MCI-vs-AD.intercept.mtx 0.5 0.5 -1 0 0 0 Contrast 10) HC+MCI-vs-AD.slope.mtx 0 0 0 0.5 0.5 -1 Kind regards, Stefano >----Messaggio originale---- >Da: "Douglas N Greve" <greve(a)nmr.mgh.harvard.edu> >Data: 13-lug-2017 22.30 >A: <freesurfer(a)nmr.mgh.harvard.edu> >Ogg: Re: [Freesurfer] 3G1V.fsgd > > > >On 07/13/2017 10:37 AM, stdp82(a)virgilio.it wrote: >> Dear FS group, >> >> I don't understand how I should build the contrast for 3 groups 1 >> covariate. >> No specific example is provided within fsgd example and also other >> colleagues report the same problem in the mail list. >> Please could you provide us details on this topic? >> Especially, how should be the g3v1.intercept and g31v.slope? >> >> 1 -1 0 0 0 0 >> 1 0 -1 0 0 0 >> for g3v1.intercept.mtx >This is the main effect of group on the intercept regressing out the >effect of covariate. >> >> and >> 0 0 0 1 -1 0 >> 0 0 0 1 0 -1 >> for g3v1.slope.mtx >This is the main effect of group on the slope regressing out the effect >of group intercept. >> >> >> are corrected? >> >> Waiting for you very wellcome suggestions >> >> Thanks and kind regards >> >> 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. > >

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R: R: Re: 3G1V.fsgd
by stdp82＠virgilio.it 13 Jul '17

13 Jul '17

I obtain this error ERROR: dimension mismatch between X and contrast group.effect.intercept. mtx X has 6 cols, C has 3 cols Stefano >----Messaggio originale---- >Da: stdp82(a)virgilio.it >Data: 13-lug-2017 23.44 >A: "Freesurfer support list"<freesurfer(a)nmr.mgh.harvard.edu> >Ogg: [Freesurfer] R: Re: 3G1V.fsgd > >Many thanks! > >In conclusion, you can confirm that the complete list of contrast reported >below is corrected for 3g1v, please? > >Contrast 1) HC-MCI_intercept.mtx >1 -1 0 0 0 0 > >Contrast 2) HC-MCI_slope.mtx >0 0 0 1 -1 0 > >Contrast 3) HC-AD_intercept.mtx >1 0 -1 0 0 0 > >Contrast 4) HC-AD_slope.mtx >0 0 0 1 0 -1 > >Contrast 5) MCI-AD_intercept.mtx >0 1 -1 0 0 0 > >Contrast 6) MCI-AD_slope.mtx >0 0 0 0 1 -1 > >Contrast 7) effect.intercept.mtx >1 -1 0 0 0 0 >1 0 -1 0 0 0 > >Contrast 8) effect.slope.mtx >0 0 0 1 -1 0 >0 0 0 1 0 -1 > >Contrast 9) HC+MCI-vs-AD.intercept.mtx >0.5 0.5 -1 0 0 0 > >Contrast 10) HC+MCI-vs-AD.slope.mtx >0 0 0 0.5 0.5 -1 > >Kind regards, > > >Stefano > > >>----Messaggio originale---- >>Da: "Douglas N Greve" <greve(a)nmr.mgh.harvard.edu> >>Data: 13-lug-2017 22.30 >>A: <freesurfer(a)nmr.mgh.harvard.edu> >>Ogg: Re: [Freesurfer] 3G1V.fsgd >> >> >> >>On 07/13/2017 10:37 AM, stdp82(a)virgilio.it wrote: >>> Dear FS group, >>> >>> I don't understand how I should build the contrast for 3 groups 1 >>> covariate. >>> No specific example is provided within fsgd example and also other >>> colleagues report the same problem in the mail list. >>> Please could you provide us details on this topic? >>> Especially, how should be the g3v1.intercept and g31v.slope? >>> >>> 1 -1 0 0 0 0 >>> 1 0 -1 0 0 0 >>> for g3v1.intercept.mtx >>This is the main effect of group on the intercept regressing out the >>effect of covariate. >>> >>> and >>> 0 0 0 1 -1 0 >>> 0 0 0 1 0 -1 >>> for g3v1.slope.mtx >>This is the main effect of group on the slope regressing out the effect >>of group intercept. >>> >>> >>> are corrected? >>> >>> Waiting for you very wellcome suggestions >>> >>> Thanks and kind regards >>> >>> 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. >> >> > >_______________________________________________ >Freesurfer mailing list >Freesurfer(a)nmr.mgh.harvard.edu >https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >

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Regression diagnostic in context of surface-based analysis
by Antonin Skoch 13 Jul '17

13 Jul '17

Dear experts, I am looking for a way how to effectively run a regression model diagnostic in context of surface-based analysis. My example case is the regression model where response variable is cortical thickness and explanatory variable is continuous (disease duration). The statistical linear modelling uses several principial approaches to find model which best describes the studied relation in the data, namely: 1. model simplification by elimination of insignificant effects 2. transformation of dependent variable to improve normality of residuals 3. transformation of explanatory variable to improve model fit or use of linear combination of various terms in explanatory variable (for example apart from linear term to include also quadratic and higher-order polynomial terms) My question is, how to effectively exploit methods 2 and 3 in context of vertex-wise surface-based analysis? Could you please comment on what tools inside FreeSurfer framework can be used for this purpose? What is your common aproach to find regression model which best approximates the relation present in the data? Thank you in advance for pointing me to right direction. Regards, Antonin Skoch

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GLM Analysis Number of vertices and Area
by Aman Montazeri 13 Jul '17

13 Jul '17

Hello Friends, Sorry for the simple question. I am doing GLM analysis using QDEC between two groups (one discrete variable), then I run the Monte-Carlo clustering and got the stats of my cluster. My supervisor asked me to get the Stats of blobs/clusters (area and number of vertices in each area) before applying the Monte-Carlo (only after GLM analysis/comparison) I would really appreciate if you could help me with getting those stats, as I can't figure out how to do it. Thank you, Aman

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Freesurfer July 2017