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30090 discussions

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

13 Jul '17

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 01 0 -1 0 0 0for g3v1.intercept.mtx and 0 0 0 1 -1 00 0 0 1 0 -1for g3v1.slope.mtx are corrected? Waiting for you very wellcome suggestions Thanks and kind regards Stefano

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PETsurfer AC/TOF
by Fu, Jason (NIH/NINDS) [F] 13 Jul '17

13 Jul '17

Hi, I am currently using PETsurfer PVC to determine glucose metabolism differences in certain structures between the brain hemispheres. I am currently using ac/tof files to coregister to the anatomy. One of the patients did not have the ac/tof files, would ac/hd files work instead? Thanks, Jason Fu

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Re: [Freesurfer] Simple math with freesurfer surfaces
by Van Der Deijl, Rosanne 13 Jul '17

13 Jul '17

Dear Doug, Thanks for replying about fscalc. I read in the documentation that the two input files should typically be generated on the same subject. What I want to do is to add all the thickness .mgh files from my subjects together into one file. Is this possible with fscalc or another way? Right now I get an error about a size mismatch. Thank you again! Kind regards, Rose ________________________________________ From: freesurfer-bounces(a)nmr.mgh.harvard.edu [freesurfer-bounces(a)nmr.mgh.harvard.edu] on behalf of freesurfer-request(a)nmr.mgh.harvard.edu [freesurfer-request(a)nmr.mgh.harvard.edu] Sent: Thursday, July 13, 2017 12:00 PM To: freesurfer(a)nmr.mgh.harvard.edu Subject: Freesurfer Digest, Vol 161, Issue 23 Send Freesurfer mailing list submissions to freesurfer(a)nmr.mgh.harvard.edu To subscribe or unsubscribe via the World Wide Web, visit https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer or, via email, send a message with subject or body 'help' to freesurfer-request(a)nmr.mgh.harvard.edu You can reach the person managing the list at freesurfer-owner(a)nmr.mgh.harvard.edu When replying, please edit your Subject line so it is more specific than "Re: Contents of Freesurfer digest..." Today's Topics: 1. Re: UPDATE: Matlab Problem LME (Diers, Kersten /DZNE) 2. Re: mri_glmfit-sim ERROR cannot find mc-z.csd file (Douglas N Greve) 3. Re: Subject with missing fMRI data {Disarmed} (Douglas N Greve) 4. Re: Running segmentation on spatially normalized data (Douglas N Greve) 5. Re: asegstats2table error (Douglas N Greve) 6. Re: Strange Discrepancy Between Activation Location on Surface vs. Volume (Douglas N Greve) 7. Re: Qdec error in analysis (Douglas N Greve) 8. Re: petsurfer stats for multiple segmentations (Douglas N Greve) 9. Re: Problem with drawing gifti contour on nifty volume in Freeview 2.0 but not in 1.0 (Douglas N Greve) 10. Re: Subject with missing fMRI data {Disarmed} (Sadie Marvel) 11. Re: Pial surface editing (Michelle VanTieghem) 12. Differences in volume between mri_segstats and mris_anatomical_stats (Bruss, Joel E) 13. Re: dmri_pathstats error (Yuwen Hung) 14. Re: dmri_pathstats error (Yuwen Hung) 15. Re: Pial surface editing (Bruce Fischl) 16. Re: petsurfer stats for multiple segmentations (Lu Zhao) 17. Re: Subject with missing fMRI data {Disarmed} (Douglas N Greve) 18. Re: petsurfer stats for multiple segmentations (Douglas N Greve) 19. Re: Differences in volume between mri_segstats and mris_anatomical_stats (Douglas N Greve) 20. Re: mkbrainmask-sess: couldn't find register.dof6.lta (Douglas N Greve) 21. Re: Subject with missing fMRI data {Disarmed} (Sadie Marvel) 22. Re: How to edit Fsgdf4G2V about the group.effect.mtx (Douglas N Greve) 23. TAR fs files (Schumman Resonance) 24. Re: BBRegister + partial FoV fail (Douglas N Greve) 25. Re: GLM question (Douglas N Greve) 26. Re: Simple math with freesurfer surfaces (Douglas N Greve) 27. Re: TAR fs files (Douglas N Greve) 28. Re: smoothing data (Douglas N Greve) 29. Re: smoothing data (Matt Glasser) 30. Re: TAR fs files (Bruce Fischl) 31. Re: TAR fs files (Schumman Resonance) 32. Re: How to edit Fsgdf4G2V about the group.effect.mtx (haidong wang) 33. Re: How to edit Fsgdf4G2V about the group.effect.mtx (Douglas Greve) 34. Re: BBRegister + partial FoV fail (Paul Glad Mihai) 35. 3G1V.fsgd (stdp82(a)virgilio.it) 36. FS 6.0 (Del Re, Elisabetta) 37. Re: FS 6.0 (Bruce Fischl) 38. Re: [External] Re: Differences in volume between mri_segstats and mris_anatomical_stats (Bruss, Joel E) 39. Pediatric Atlas/Template (Jessica Reynolds) 40. Pediatric Atlas/Template (Jessica Reynolds) 41. Pediatric Atlas/Template (Jessica Reynolds) 42. GLM Analysis Number of vertices and Area (Aman Montazeri) ---------------------------------------------------------------------- Message: 1 Date: Wed, 12 Jul 2017 18:14:58 +0200 From: "Diers, Kersten /DZNE" <Kersten.Diers(a)dzne.de> Subject: Re: [Freesurfer] UPDATE: Matlab Problem LME To: "freesurfer(a)nmr.mgh.harvard.edu" <freesurfer(a)nmr.mgh.harvard.edu> Message-ID: <1327935B-0065-4A56-98A8-8AF8F4DED407(a)dzne.de> Content-Type: text/plain; charset="us-ascii" Hi Clara, thanks for the additional information, this is helpful! If you are calling the scripts with [lhRgs,lhRgMeans] = lme_mass_RgGrow(lhsphere, lhRe, lhTh0, lhcortex, 2, 95); then 'lhcortex' will contain the analysis mask, i.e. indices for those vertices for which the analysis will be performed. 'lhcortex' should already be a subset of the vertices specified by 'lhsphere', i.e. excluding some portions of the medial wall. If you have zero-valued columns in your data matrix, one thing worth trying is to remove the corresponding indices from 'lhcortex', i.e. further restrict the analysis mask. This should be done before the initial covariance estimation, i.e. prior to calling lme_mass_fit_init or lme_mass_fit_EMinit. In addition, it is of course worthwhile to investigate the cause of the zero-columns. Best, Kersten ------------------------------ Message: 2 Date: Wed, 12 Jul 2017 12:17:45 -0400 From: Douglas N Greve <greve(a)nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] mri_glmfit-sim ERROR cannot find mc-z.csd file To: freesurfer(a)nmr.mgh.harvard.edu Message-ID: <a1d5416e-5e09-d7ab-e2c1-10c802dbe8be(a)nmr.mgh.harvard.edu> Content-Type: text/plain; charset=utf-8; format=flowed Is this for a volume analysis? If so, then you'll need to use the --grf option instead of using the mcz simulations (those are just for surface) On 07/08/2017 01:03 PM, Aly Negreira wrote: > Hi Doug! > > Thank you for the reply! Re-ran w/ --debug as first option. Below is > the output. Not sure if this is helpful, but when I cd to > /Applications/freesurfer/average/mult-comp-cor/fsaverage > there are only directories for lh and rh, nothing for mni. > > Thanks for the help! > > Aly > > Alysons-iMac:~/analyses/EMOT_REG_FX_DISS] aneg% mri_glmfit-sim \ > --debug \ > > --glmdir > GROUP_SESSID_HC_DISS_setwdelay/emotreg_mni305_4cond_fir_TR2_pf2_tpexclude_HC_DISS_setwdelay/bu_negVbu_neut/my-glm.wls/ > \ > > --cache 1.3 abs \ > > --cwp 0.05\ > > --3spaces \? --debug \ > > ? --glmdir > GROUP_SESSID_HC_DISS_setwdelay/emotreg_mni305_4cond_fir_TR2_pf2_tpexclude_HC_DISS_setwdelay/bu_negVbu_neut/my-glm.wls/ > \ > > ? --cache 1.3 abs \ > > ? --cwp 0.05\ > > ? --3spaces \ > > ? > > set echo = 1 ; > > breaksw > > breaksw > > > end > > end > > while ( $#argv != 0 ) > > while ( 8 != 0 ) > > > set flag = $argv[1] ; shift ; > > set flag = --glmdir > > shift > > > switch ( $flag ) > > switch ( --glmdir ) > > if ( $#argv < 0 ) goto arg1err ; > > if ( 7 < 0 ) goto arg1err > > set glmdir = $argv[1] ; shift ; > > set glmdir = > GROUP_SESSID_HC_DISS_setwdelay/emotreg_mni305_4cond_fir_TR2_pf2_tpexclude_HC_DISS_setwdelay/bu_negVbu_neut/my-glm.wls/ > > shift > > breaksw > > breaksw > > > end > > end > > while ( $#argv != 0 ) > > while ( 6 != 0 ) > > > set flag = $argv[1] ; shift ; > > set flag = --cache > > shift > > > switch ( $flag ) > > switch ( --cache ) > > if ( $#argv < 2 ) goto arg2err ; > > if ( 5 < 2 ) goto arg2err > > set thresh = $argv[1] ; shift ; > > set thresh = 1.3 > > shift > > set simsign = $argv[1] ; shift ; > > set simsign = abs > > shift > > set UseCache = 1 ; > > set UseCache = 1 > > set DoSim = 0 ; > > set DoSim = 0 > > set thresh = `printf %2.1f $thresh` > > set thresh = `printf %2.1f $thresh` > > printf %2.1f 1.3 > > if ( $thresh != 1.3 && $thresh != 2.0 && $thresh != 2.3 && $thresh != > 3.0 && $thresh != 3.3 && $thresh != 4.0 ) then > > if ( 1.3 != 1.3 && 1.3 != 2.0 && 1.3 != 2.3 && 1.3 != 3.0 && 1.3 != > 3.3 && 1.3 != 4.0 ) then > > breaksw > > breaksw > > > end > > end > > while ( $#argv != 0 ) > > while ( 3 != 0 ) > > > set flag = $argv[1] ; shift ; > > set flag = --cwp > > shift > > > switch ( $flag ) > > switch ( --cwp ) > > case "--cwpvalthresh": > > case --cwpvalthresh: > > if ( $#argv < 1 ) goto arg1err ; > > if ( 2 < 1 ) goto arg1err > > set cwpvalthresh = $argv[1] ; shift ; > > set cwpvalthresh = 0.05 > > shift > > breaksw > > breaksw > > > end > > end > > while ( $#argv != 0 ) > > while ( 1 != 0 ) > > > set flag = $argv[1] ; shift ; > > set flag = --3spaces > > shift > > > switch ( $flag ) > > switch ( --3spaces ) > > set Bonferroni = 3 ; > > set Bonferroni = 3 > > breaksw > > breaksw > > > end > > end > > while ( $#argv != 0 ) > > while ( 0 != 0 ) > > > goto parse_args_return ; > > goto parse_args_return > > > goto check_params ; > > goto check_params > > if ( $#glmdir == 0 ) then > > if ( 1 == 0 ) then > > if ( $DoSim ) then > > if ( 0 ) then > > > if ( $DiagCluster && $DoBackground ) then > > if ( 0 && 0 ) then > > if ( $DiagCluster && $DoPBSubmit ) then > > if ( 0 && 0 ) then > > if ( $DiagCluster && $DoSim == 0 ) then > > if ( 0 && 0 == 0 ) then > > > goto check_params_return ; > > goto check_params_return > > > if ( ! -e $glmdir ) then > > if ( ! -e > GROUP_SESSID_HC_DISS_setwdelay/emotreg_mni305_4cond_fir_TR2_pf2_tpexclude_HC_DISS_setwdelay/bu_negVbu_neut/my-glm.wls/ > ) then > > > set glmfitlog = $glmdir/mri_glmfit.log > > set glmfitlog = > GROUP_SESSID_HC_DISS_setwdelay/emotreg_mni305_4cond_fir_TR2_pf2_tpexclude_HC_DISS_setwdelay/bu_negVbu_neut/my-glm.wls//mri_glmfit.log > > if ( ! -e $glmfitlog ) then > > if ( ! -e > GROUP_SESSID_HC_DISS_setwdelay/emotreg_mni305_4cond_fir_TR2_pf2_tpexclude_HC_DISS_setwdelay/bu_negVbu_neut/my-glm.wls//mri_glmfit.log > ) then > > > set mask = `stem2fname $glmdir/mask` > > set mask = `stem2fname $glmdir/mask` > > stem2fname > GROUP_SESSID_HC_DISS_setwdelay/emotreg_mni305_4cond_fir_TR2_pf2_tpexclude_HC_DISS_setwdelay/bu_negVbu_neut/my-glm.wls//mask > > if ( $status ) then > > if ( 0 ) then > > > if ( $nulltype != perm ) then > > if ( != perm ) then > > set fwhmfile = $glmdir/fwhm.dat > > set fwhmfile = > GROUP_SESSID_HC_DISS_setwdelay/emotreg_mni305_4cond_fir_TR2_pf2_tpexclude_HC_DISS_setwdelay/bu_negVbu_neut/my-glm.wls//fwhm.dat > > if ( ! -e $fwhmfile ) then > > if ( ! -e > GROUP_SESSID_HC_DISS_setwdelay/emotreg_mni305_4cond_fir_TR2_pf2_tpexclude_HC_DISS_setwdelay/bu_negVbu_neut/my-glm.wls//fwhm.dat > ) then > > > set fwhm = `cat $fwhmfile` ; > > set fwhm = `cat $fwhmfile` > > cat > GROUP_SESSID_HC_DISS_setwdelay/emotreg_mni305_4cond_fir_TR2_pf2_tpexclude_HC_DISS_setwdelay/bu_negVbu_neut/my-glm.wls//fwhm.dat > > else > > else > > > set glmfitcwd = `cat $glmfitlog | awk '{if($1 == "cwd") print $2}'` > > set glmfitcwd = `cat $glmfitlog | awk '{if($1 == "cwd") print $2}'` > > cat > GROUP_SESSID_HC_DISS_setwdelay/emotreg_mni305_4cond_fir_TR2_pf2_tpexclude_HC_DISS_setwdelay/bu_negVbu_neut/my-glm.wls//mri_glmfit.log > > awk {if($1 == "cwd") print $2} > > if ( ! -e $glmfitcwd ) then > > if ( ! -e /Users/aneg/analyses/EMOT_REG_FX_DISS ) then > > > set anattype = volume ; > > set anattype = volume > > set subject = ( ) ; > > set subject = ( ) > > set hemi = ( ) ; > > set hemi = ( ) > > set surf = "white" ; > > set surf = white > > set y = ( ) ; > > set y = ( ) > > set wls = ( ) ; > > set wls = ( ) > > > set glmfitcwd = `cat $glmfitlog | awk '{if($1 == "cwd") print $2}'` > > set glmfitcwd = `cat $glmfitlog | awk '{if($1 == "cwd") print $2}'` > > cat > GROUP_SESSID_HC_DISS_setwdelay/emotreg_mni305_4cond_fir_TR2_pf2_tpexclude_HC_DISS_setwdelay/bu_negVbu_neut/my-glm.wls//mri_glmfit.log > > awk {if($1 == "cwd") print $2} > > > > set glmfitcmd0 = `cat $glmfitlog | awk '{if($1 == "cmdline") print $0}'` > > set glmfitcmd0 = `cat $glmfitlog | awk '{if($1 == "cmdline") print $0}'` > > cat > GROUP_SESSID_HC_DISS_setwdelay/emotreg_mni305_4cond_fir_TR2_pf2_tpexclude_HC_DISS_setwdelay/bu_negVbu_neut/my-glm.wls//mri_glmfit.log > > awk {if($1 == "cmdline") print $0} > > set glmfitcmd = ( $glmfitcmd0 ) ; > > set glmfitcmd = ( cmdline mri_glmfit --y > GROUP_SESSID_HC_DISS_setwdelay/emotreg_mni305_4cond_fir_TR2_pf2_tpexclude_HC_DISS_setwdelay/bu_negVbu_neut/ces.nii.gz > --wls > GROUP_SESSID_HC_DISS_setwdelay/emotreg_mni305_4cond_fir_TR2_pf2_tpexclude_HC_DISS_setwdelay/bu_negVbu_neut/cesvar.nii.gz > --osgm --glmdir > GROUP_SESSID_HC_DISS_setwdelay/emotreg_mni305_4cond_fir_TR2_pf2_tpexclude_HC_DISS_setwdelay/bu_negVbu_neut/my-glm.wls/ > --nii.gz ) > > echo $glmfitcmd > > echo cmdline mri_glmfit --y > GROUP_SESSID_HC_DISS_setwdelay/emotreg_mni305_4cond_fir_TR2_pf2_tpexclude_HC_DISS_setwdelay/bu_negVbu_neut/ces.nii.gz > --wls > GROUP_SESSID_HC_DISS_setwdelay/emotreg_mni305_4cond_fir_TR2_pf2_tpexclude_HC_DISS_setwdelay/bu_negVbu_neut/cesvar.nii.gz > --osgm --glmdir > GROUP_SESSID_HC_DISS_setwdelay/emotreg_mni305_4cond_fir_TR2_pf2_tpexclude_HC_DISS_setwdelay/bu_negVbu_neut/my-glm.wls/ > --nii.gz > > cmdline mri_glmfit --y > GROUP_SESSID_HC_DISS_setwdelay/emotreg_mni305_4cond_fir_TR2_pf2_tpexclude_HC_DISS_setwdelay/bu_negVbu_neut/ces.nii.gz > --wls > GROUP_SESSID_HC_DISS_setwdelay/emotreg_mni305_4cond_fir_TR2_pf2_tpexclude_HC_DISS_setwdelay/bu_negVbu_neut/cesvar.nii.gz > --osgm --glmdir > GROUP_SESSID_HC_DISS_setwdelay/emotreg_mni305_4cond_fir_TR2_pf2_tpexclude_HC_DISS_setwdelay/bu_negVbu_neut/my-glm.wls/ > --nii.gz > > set gd2mtx = dods > > set gd2mtx = dods > > set label = ( ) ; > > set label = ( ) > > while ( $#glmfitcmd ) > > while ( 10 ) > > set flag = $glmfitcmd[1] ; shift glmfitcmd ; > > set flag = cmdline > > shift glmfitcmd > > > switch ( $flag ) > > switch ( cmdline ) > > case "mri_glmfit" > > case mri_glmfit > > case "--osgm" > > case --osgm > > case "--prune" > > case --prune > > case "--no-prune" > > case --no-prune > > case "--pca" > > case --pca > > case "--synth" > > case --synth > > case "--allowsubjrep" > > case --allowsubjrep > > case "--illcond" > > case --illcond > > case "--debug" > > case --debug > > case "--synth" > > case --synth > > case "--cortex" > > case --cortex > > case "--kurtosis" > > case --kurtosis > > case "--nii" > > case --nii > > case "--nii.gz" > > case --nii.gz > > case "--rescale-x" > > case --rescale-x > > case "--no-rescale-x" > > case --no-rescale-x > > case "dods" > > case dods > > breaksw > > breaksw > > end > > end > > while ( $#glmfitcmd ) > > while ( 9 ) > > set flag = $glmfitcmd[1] ; shift glmfitcmd ; > > set flag = mri_glmfit > > shift glmfitcmd > > > switch ( $flag ) > > switch ( mri_glmfit ) > > case "--osgm" > > case --osgm > > case "--prune" > > case --prune > > case "--no-prune" > > case --no-prune > > case "--pca" > > case --pca > > case "--synth" > > case --synth > > case "--allowsubjrep" > > case --allowsubjrep > > case "--illcond" > > case --illcond > > case "--debug" > > case --debug > > case "--synth" > > case --synth > > case "--cortex" > > case --cortex > > case "--kurtosis" > > case --kurtosis > > case "--nii" > > case --nii > > case "--nii.gz" > > case --nii.gz > > case "--rescale-x" > > case --rescale-x > > case "--no-rescale-x" > > case --no-rescale-x > > case "dods" > > case dods > > breaksw > > breaksw > > end > > end > > while ( $#glmfitcmd ) > > while ( 8 ) > > set flag = $glmfitcmd[1] ; shift glmfitcmd ; > > set flag = --y > > shift glmfitcmd > > > switch ( $flag ) > > switch ( --y ) > > set y = $glmfitcwd/$glmfitcmd[1] ; shift glmfitcmd ; > > set y = > /Users/aneg/analyses/EMOT_REG_FX_DISS/GROUP_SESSID_HC_DISS_setwdelay/emotreg_mni305_4cond_fir_TR2_pf2_tpexclude_HC_DISS_setwdelay/bu_negVbu_neut/ces.nii.gz > > shift glmfitcmd > > if ( ! -e $y ) then > > if ( ! -e > /Users/aneg/analyses/EMOT_REG_FX_DISS/GROUP_SESSID_HC_DISS_setwdelay/emotreg_mni305_4cond_fir_TR2_pf2_tpexclude_HC_DISS_setwdelay/bu_negVbu_neut/ces.nii.gz > ) then > > breaksw > > breaksw > > end > > end > > while ( $#glmfitcmd ) > > while ( 6 ) > > set flag = $glmfitcmd[1] ; shift glmfitcmd ; > > set flag = --wls > > shift glmfitcmd > > > switch ( $flag ) > > switch ( --wls ) > > set wls = $glmfitcwd/$glmfitcmd[1] ; shift glmfitcmd ; > > set wls = > /Users/aneg/analyses/EMOT_REG_FX_DISS/GROUP_SESSID_HC_DISS_setwdelay/emotreg_mni305_4cond_fir_TR2_pf2_tpexclude_HC_DISS_setwdelay/bu_negVbu_neut/cesvar.nii.gz > > shift glmfitcmd > > if ( ! -e $wls ) then > > if ( ! -e > /Users/aneg/analyses/EMOT_REG_FX_DISS/GROUP_SESSID_HC_DISS_setwdelay/emotreg_mni305_4cond_fir_TR2_pf2_tpexclude_HC_DISS_setwdelay/bu_negVbu_neut/cesvar.nii.gz > ) then > > breaksw > > breaksw > > end > > end > > while ( $#glmfitcmd ) > > while ( 4 ) > > set flag = $glmfitcmd[1] ; shift glmfitcmd ; > > set flag = --osgm > > shift glmfitcmd > > > switch ( $flag ) > > switch ( --osgm ) > > case "--prune" > > case --prune > > case "--no-prune" > > case --no-prune > > case "--pca" > > case --pca > > case "--synth" > > case --synth > > case "--allowsubjrep" > > case --allowsubjrep > > case "--illcond" > > case --illcond > > case "--debug" > > case --debug > > case "--synth" > > case --synth > > case "--cortex" > > case --cortex > > case "--kurtosis" > > case --kurtosis > > case "--nii" > > case --nii > > case "--nii.gz" > > case --nii.gz > > case "--rescale-x" > > case --rescale-x > > case "--no-rescale-x" > > case --no-rescale-x > > case "dods" > > case dods > > breaksw > > breaksw > > end > > end > > while ( $#glmfitcmd ) > > while ( 3 ) > > set flag = $glmfitcmd[1] ; shift glmfitcmd ; > > set flag = --glmdir > > shift glmfitcmd > > > switch ( $flag ) > > switch ( --glmdir ) > > case "--o" > > case --o > > case "--C" > > case --C > > case "--X" > > case --X > > case "--w" > > case --w > > case "--fwhm" > > case --fwhm > > case "--mask" > > case --mask > > case "--seed" > > case --seed > > case "--var-fwhm" > > case --var-fwhm > > case "--yffxvar" > > case --yffxvar > > case "--ffxdof" > > case --ffxdof > > case "--ffxdofdat" > > case --ffxdofdat > > shift glmfitcmd ; > > shift glmfitcmd > > breaksw > > breaksw > > end > > end > > while ( $#glmfitcmd ) > > while ( 1 ) > > set flag = $glmfitcmd[1] ; shift glmfitcmd ; > > set flag = --nii.gz > > shift glmfitcmd > > > switch ( $flag ) > > switch ( --nii.gz ) > > case "--rescale-x" > > case --rescale-x > > case "--no-rescale-x" > > case --no-rescale-x > > case "dods" > > case dods > > breaksw > > breaksw > > end > > end > > while ( $#glmfitcmd ) > > while ( 0 ) > > > if ( $UseGRF && $anattype != volume ) then > > if ( 0 && volume != volume ) then > > if ( $UseGRF ) then > > if ( 0 ) then > > > if ( $#subjectOverride ) set subject = $subjectOverride > > if ( 0 ) set subject = > > > > if ( $#subject != 0 ) then > > if ( 0 != 0 ) then > > > > if ( $#tmpdir == 0 ) set tmpdir = $glmdir/tmp.mri_glmfit-sim-$$ > > if ( 0 == 0 ) set tmpdir = > GROUP_SESSID_HC_DISS_setwdelay/emotreg_mni305_4cond_fir_TR2_pf2_tpexclude_HC_DISS_setwdelay/bu_negVbu_neut/my-glm.wls//tmp.mri_glmfit-sim-21128 > > set tmpdir = > GROUP_SESSID_HC_DISS_setwdelay/emotreg_mni305_4cond_fir_TR2_pf2_tpexclude_HC_DISS_setwdelay/bu_negVbu_neut/my-glm.wls//tmp.mri_glmfit-sim-21128 > > mkdir -p $tmpdir > > mkdir -p > GROUP_SESSID_HC_DISS_setwdelay/emotreg_mni305_4cond_fir_TR2_pf2_tpexclude_HC_DISS_setwdelay/bu_negVbu_neut/my-glm.wls//tmp.mri_glmfit-sim-21128 > > set clist = ( $glmdir/*/C.dat ) > > set clist = ( > GROUP_SESSID_HC_DISS_setwdelay/emotreg_mni305_4cond_fir_TR2_pf2_tpexclude_HC_DISS_setwdelay/bu_negVbu_neut/my-glm.wls//*/C.dat > ) > > if ( $status ) then > > if ( 0 ) then > > set clist2 = ( ) ; > > set clist2 = ( ) > > set conlist = ( ) ; > > set conlist = ( ) > > foreach c ( $clist ) > > foreach c ( > GROUP_SESSID_HC_DISS_setwdelay/emotreg_mni305_4cond_fir_TR2_pf2_tpexclude_HC_DISS_setwdelay/bu_negVbu_neut/my-glm.wls//osgm/C.dat > ) > > set tmp = `dirname $c` > > set tmp = `dirname $c` > > dirname > GROUP_SESSID_HC_DISS_setwdelay/emotreg_mni305_4cond_fir_TR2_pf2_tpexclude_HC_DISS_setwdelay/bu_negVbu_neut/my-glm.wls//osgm/C.dat > > set conname = `basename $tmp` > > set conname = `basename $tmp` > > basename > GROUP_SESSID_HC_DISS_setwdelay/emotreg_mni305_4cond_fir_TR2_pf2_tpexclude_HC_DISS_setwdelay/bu_negVbu_neut/my-glm.wls//osgm > > set conlist = ( $conlist $conname ) ; > > set conlist = ( osgm ) > > set confile = $tmpdir/$conname.mtx > > set confile = > GROUP_SESSID_HC_DISS_setwdelay/emotreg_mni305_4cond_fir_TR2_pf2_tpexclude_HC_DISS_setwdelay/bu_negVbu_neut/my-glm.wls//tmp.mri_glmfit-sim-21128/osgm.mtx > > cp $c $confile > > cp > GROUP_SESSID_HC_DISS_setwdelay/emotreg_mni305_4cond_fir_TR2_pf2_tpexclude_HC_DISS_setwdelay/bu_negVbu_neut/my-glm.wls//osgm/C.dat > GROUP_SESSID_HC_DISS_setwdelay/emotreg_mni305_4cond_fir_TR2_pf2_tpexclude_HC_DISS_setwdelay/bu_negVbu_neut/my-glm.wls//tmp.mri_glmfit-sim-21128/osgm.mtx > > set clist2 = ( $clist2 --C $confile ) ; > > set clist2 = ( --C > GROUP_SESSID_HC_DISS_setwdelay/emotreg_mni305_4cond_fir_TR2_pf2_tpexclude_HC_DISS_setwdelay/bu_negVbu_neut/my-glm.wls//tmp.mri_glmfit-sim-21128/osgm.mtx > ) > > > > set sig = `stem2fname $glmdir/$conname/sig` > > set sig = `stem2fname $glmdir/$conname/sig` > > stem2fname > GROUP_SESSID_HC_DISS_setwdelay/emotreg_mni305_4cond_fir_TR2_pf2_tpexclude_HC_DISS_setwdelay/bu_negVbu_neut/my-glm.wls//osgm/sig > > if ( $status ) then > > if ( 0 ) then > > > > if ( $DoSim ) then > > if ( 0 ) then > > end > > end > > > set StartDate = `date` > > set StartDate = `date` > > date > > > > if ( $#LF == 0 ) then > > if ( 0 == 0 ) then > > if ( $UseCache == 0 ) then > > if ( 1 == 0 ) then > > > set LF = $glmdir/cache.mri_glmfit-sim.log > > set LF = > GROUP_SESSID_HC_DISS_setwdelay/emotreg_mni305_4cond_fir_TR2_pf2_tpexclude_HC_DISS_setwdelay/bu_negVbu_neut/my-glm.wls//cache.mri_glmfit-sim.log > > endif > > endif > > rm -f $LF > > rm -f > GROUP_SESSID_HC_DISS_setwdelay/emotreg_mni305_4cond_fir_TR2_pf2_tpexclude_HC_DISS_setwdelay/bu_negVbu_neut/my-glm.wls//cache.mri_glmfit-sim.log > > endif > > endif > > echo "log file is $LF" > > echo log file is > GROUP_SESSID_HC_DISS_setwdelay/emotreg_mni305_4cond_fir_TR2_pf2_tpexclude_HC_DISS_setwdelay/bu_negVbu_neut/my-glm.wls//cache.mri_glmfit-sim.log > > log file is > GROUP_SESSID_HC_DISS_setwdelay/emotreg_mni305_4cond_fir_TR2_pf2_tpexclude_HC_DISS_setwdelay/bu_negVbu_neut/my-glm.wls//cache.mri_glmfit-sim.log > > > echo "" | tee -a $LF > > tee -a > GROUP_SESSID_HC_DISS_setwdelay/emotreg_mni305_4cond_fir_TR2_pf2_tpexclude_HC_DISS_setwdelay/bu_negVbu_neut/my-glm.wls//cache.mri_glmfit-sim.log > > echo > > > echo "cd `pwd`" | tee -a $LF > > tee -a > GROUP_SESSID_HC_DISS_setwdelay/emotreg_mni305_4cond_fir_TR2_pf2_tpexclude_HC_DISS_setwdelay/bu_negVbu_neut/my-glm.wls//cache.mri_glmfit-sim.log > > echo cd `pwd` > > pwd > > cd /Users/aneg/analyses/EMOT_REG_FX_DISS > > echo $0 | tee -a $LF > > tee -a > GROUP_SESSID_HC_DISS_setwdelay/emotreg_mni305_4cond_fir_TR2_pf2_tpexclude_HC_DISS_setwdelay/bu_negVbu_neut/my-glm.wls//cache.mri_glmfit-sim.log > > echo /Applications/freesurfer/bin/mri_glmfit-sim > > /Applications/freesurfer/bin/mri_glmfit-sim > > echo $inputargs | tee -a $LF > > tee -a > GROUP_SESSID_HC_DISS_setwdelay/emotreg_mni305_4cond_fir_TR2_pf2_tpexclude_HC_DISS_setwdelay/bu_negVbu_neut/my-glm.wls//cache.mri_glmfit-sim.log > > echo --debug --glmdir > GROUP_SESSID_HC_DISS_setwdelay/emotreg_mni305_4cond_fir_TR2_pf2_tpexclude_HC_DISS_setwdelay/bu_negVbu_neut/my-glm.wls/ > --cache 1.3 abs --cwp 0.05 --3spaces > > --debug --glmdir > GROUP_SESSID_HC_DISS_setwdelay/emotreg_mni305_4cond_fir_TR2_pf2_tpexclude_HC_DISS_setwdelay/bu_negVbu_neut/my-glm.wls/ > --cache 1.3 abs --cwp 0.05 --3spaces > > echo "" | tee -a $LF > > tee -a > GROUP_SESSID_HC_DISS_setwdelay/emotreg_mni305_4cond_fir_TR2_pf2_tpexclude_HC_DISS_setwdelay/bu_negVbu_neut/my-glm.wls//cache.mri_glmfit-sim.log > > echo > > > echo $VERSION | tee -a $LF > > tee -a > GROUP_SESSID_HC_DISS_setwdelay/emotreg_mni305_4cond_fir_TR2_pf2_tpexclude_HC_DISS_setwdelay/bu_negVbu_neut/my-glm.wls//cache.mri_glmfit-sim.log > > echo $Id: mri_glmfit-sim,v 1.36.2.5 2012/10/01 22:31:37 greve Exp $ > > $Id: mri_glmfit-sim,v 1.36.2.5 2012/10/01 22:31:37 greve Exp $ > > date | tee -a $LF > > date > > tee -a > GROUP_SESSID_HC_DISS_setwdelay/emotreg_mni305_4cond_fir_TR2_pf2_tpexclude_HC_DISS_setwdelay/bu_negVbu_neut/my-glm.wls//cache.mri_glmfit-sim.log > > Sat Jul 8 12:57:27 EDT 2017 > > uname -a | tee -a $LF > > uname -a > > tee -a > GROUP_SESSID_HC_DISS_setwdelay/emotreg_mni305_4cond_fir_TR2_pf2_tpexclude_HC_DISS_setwdelay/bu_negVbu_neut/my-glm.wls//cache.mri_glmfit-sim.log > > Darwin Alysons-iMac.local 15.6.0 Darwin Kernel Version 15.6.0: Tue Apr > 11 16:00:51 PDT 2017; root:xnu-3248.60.11.5.3~1/RELEASE_X86_64 x86_64 > > echo $user | tee -a $LF > > tee -a > GROUP_SESSID_HC_DISS_setwdelay/emotreg_mni305_4cond_fir_TR2_pf2_tpexclude_HC_DISS_setwdelay/bu_negVbu_neut/my-glm.wls//cache.mri_glmfit-sim.log > > echo aneg > > aneg > > echo "setenv SUBJECTS_DIR $SUBJECTS_DIR" | tee -a $LF > > tee -a > GROUP_SESSID_HC_DISS_setwdelay/emotreg_mni305_4cond_fir_TR2_pf2_tpexclude_HC_DISS_setwdelay/bu_negVbu_neut/my-glm.wls//cache.mri_glmfit-sim.log > > echo setenv SUBJECTS_DIR /Users/aneg/analyses/EMOT_REG_RECON_DISS > > setenv SUBJECTS_DIR /Users/aneg/analyses/EMOT_REG_RECON_DISS > > echo "FREESURFER_HOME $FREESURFER_HOME" | tee -a $LF > > tee -a > GROUP_SESSID_HC_DISS_setwdelay/emotreg_mni305_4cond_fir_TR2_pf2_tpexclude_HC_DISS_setwdelay/bu_negVbu_neut/my-glm.wls//cache.mri_glmfit-sim.log > > echo FREESURFER_HOME /Applications/freesurfer > > FREESURFER_HOME /Applications/freesurfer > > echo "" | tee -a $LF > > tee -a > GROUP_SESSID_HC_DISS_setwdelay/emotreg_mni305_4cond_fir_TR2_pf2_tpexclude_HC_DISS_setwdelay/bu_negVbu_neut/my-glm.wls//cache.mri_glmfit-sim.log > > echo > > > echo "Original mri_glmfit command line:" | tee -a $LF > > tee -a > GROUP_SESSID_HC_DISS_setwdelay/emotreg_mni305_4cond_fir_TR2_pf2_tpexclude_HC_DISS_setwdelay/bu_negVbu_neut/my-glm.wls//cache.mri_glmfit-sim.log > > echo Original mri_glmfit command line: > > Original mri_glmfit command line: > > echo $glmfitcmd0 | tee -a $LF > > tee -a > GROUP_SESSID_HC_DISS_setwdelay/emotreg_mni305_4cond_fir_TR2_pf2_tpexclude_HC_DISS_setwdelay/bu_negVbu_neut/my-glm.wls//cache.mri_glmfit-sim.log > > echo cmdline mri_glmfit --y > GROUP_SESSID_HC_DISS_setwdelay/emotreg_mni305_4cond_fir_TR2_pf2_tpexclude_HC_DISS_setwdelay/bu_negVbu_neut/ces.nii.gz > --wls > GROUP_SESSID_HC_DISS_setwdelay/emotreg_mni305_4cond_fir_TR2_pf2_tpexclude_HC_DISS_setwdelay/bu_negVbu_neut/cesvar.nii.gz > --osgm --glmdir > GROUP_SESSID_HC_DISS_setwdelay/emotreg_mni305_4cond_fir_TR2_pf2_tpexclude_HC_DISS_setwdelay/bu_negVbu_neut/my-glm.wls/ > --nii.gz > > cmdline mri_glmfit --y > GROUP_SESSID_HC_DISS_setwdelay/emotreg_mni305_4cond_fir_TR2_pf2_tpexclude_HC_DISS_setwdelay/bu_negVbu_neut/ces.nii.gz > --wls > GROUP_SESSID_HC_DISS_setwdelay/emotreg_mni305_4cond_fir_TR2_pf2_tpexclude_HC_DISS_setwdelay/bu_negVbu_neut/cesvar.nii.gz > --osgm --glmdir > GROUP_SESSID_HC_DISS_setwdelay/emotreg_mni305_4cond_fir_TR2_pf2_tpexclude_HC_DISS_setwdelay/bu_negVbu_neut/my-glm.wls/ > --nii.gz > > echo "" | tee -a $LF > > tee -a > GROUP_SESSID_HC_DISS_setwdelay/emotreg_mni305_4cond_fir_TR2_pf2_tpexclude_HC_DISS_setwdelay/bu_negVbu_neut/my-glm.wls//cache.mri_glmfit-sim.log > > echo > > > echo "DoSim = $DoSim" | tee -a $LF > > tee -a > GROUP_SESSID_HC_DISS_setwdelay/emotreg_mni305_4cond_fir_TR2_pf2_tpexclude_HC_DISS_setwdelay/bu_negVbu_neut/my-glm.wls//cache.mri_glmfit-sim.log > > echo DoSim = 0 > > DoSim = 0 > > echo "UseCache = $UseCache" | tee -a $LF > > tee -a > GROUP_SESSID_HC_DISS_setwdelay/emotreg_mni305_4cond_fir_TR2_pf2_tpexclude_HC_DISS_setwdelay/bu_negVbu_neut/my-glm.wls//cache.mri_glmfit-sim.log > > echo UseCache = 1 > > UseCache = 1 > > echo "DoPoll = $DoPoll" | tee -a $LF > > tee -a > GROUP_SESSID_HC_DISS_setwdelay/emotreg_mni305_4cond_fir_TR2_pf2_tpexclude_HC_DISS_setwdelay/bu_negVbu_neut/my-glm.wls//cache.mri_glmfit-sim.log > > echo DoPoll = 0 > > DoPoll = 0 > > echo "DoPBSubmit = $DoPBSubmit" | tee -a $LF > > tee -a > GROUP_SESSID_HC_DISS_setwdelay/emotreg_mni305_4cond_fir_TR2_pf2_tpexclude_HC_DISS_setwdelay/bu_negVbu_neut/my-glm.wls//cache.mri_glmfit-sim.log > > echo DoPBSubmit = 0 > > DoPBSubmit = 0 > > echo "DoBackground = $DoBackground" | tee -a $LF > > tee -a > GROUP_SESSID_HC_DISS_setwdelay/emotreg_mni305_4cond_fir_TR2_pf2_tpexclude_HC_DISS_setwdelay/bu_negVbu_neut/my-glm.wls//cache.mri_glmfit-sim.log > > echo DoBackground = 0 > > DoBackground = 0 > > echo "DiagCluster = $DiagCluster" | tee -a $LF > > tee -a > GROUP_SESSID_HC_DISS_setwdelay/emotreg_mni305_4cond_fir_TR2_pf2_tpexclude_HC_DISS_setwdelay/bu_negVbu_neut/my-glm.wls//cache.mri_glmfit-sim.log > > echo DiagCluster = 0 > > DiagCluster = 0 > > echo "gd2mtx = $gd2mtx" | tee -a $LF > > tee -a > GROUP_SESSID_HC_DISS_setwdelay/emotreg_mni305_4cond_fir_TR2_pf2_tpexclude_HC_DISS_setwdelay/bu_negVbu_neut/my-glm.wls//cache.mri_glmfit-sim.log > > echo gd2mtx = dods > > gd2mtx = dods > > if ( $#Seed ) echo "Seed = $Seed" | tee -a $LF > > tee -a > GROUP_SESSID_HC_DISS_setwdelay/emotreg_mni305_4cond_fir_TR2_pf2_tpexclude_HC_DISS_setwdelay/bu_negVbu_neut/my-glm.wls//cache.mri_glmfit-sim.log > > if ( 0 ) echo Seed = > > echo "fwhm = $fwhm" | tee -a $LF > > tee -a > GROUP_SESSID_HC_DISS_setwdelay/emotreg_mni305_4cond_fir_TR2_pf2_tpexclude_HC_DISS_setwdelay/bu_negVbu_neut/my-glm.wls//cache.mri_glmfit-sim.log > > echo fwhm = 9.625207 > > fwhm = 9.625207 > > if ( $#fwhmOverride ) then > > if ( 0 ) then > > > if ( $UseCache ) then > > if ( 1 ) then > > set fwhm = `cat $glmdir/fwhm.dat` ; > > set fwhm = `cat $glmdir/fwhm.dat` > > cat > GROUP_SESSID_HC_DISS_setwdelay/emotreg_mni305_4cond_fir_TR2_pf2_tpexclude_HC_DISS_setwdelay/bu_negVbu_neut/my-glm.wls//fwhm.dat > > set fwhmStr = `perl -e "printf('"'%02d'"',int ( $fwhm+.5 ) ) "` > > set fwhmStr = `perl -e "printf('"'%02d'"',int ( $fwhm+.5 ) ) "` > > perl -e printf('%02d',int ( 9.625207+.5 ) ) > > set threshStr = `perl -e "print 10*$thresh"` ; > > set threshStr = `perl -e "print 10*$thresh"` > > perl -e print 10*1.3 > > set csdCache = > $CacheDir/$subject/$hemi/$CacheLabel/fwhm$fwhmStr/$simsign/th$threshStr/mc-z.csd > > set csdCache = > /Applications/freesurfer/average/mult-comp-cor///cortex/fwhm10/abs/th13/mc-z.csd > > if ( ! -e $csdCache ) then > > if ( ! -e > /Applications/freesurfer/average/mult-comp-cor///cortex/fwhm10/abs/th13/mc-z.csd > ) then > > echo "ERROR: cannot find $csdCache" | tee -a $LF > > tee -a > GROUP_SESSID_HC_DISS_setwdelay/emotreg_mni305_4cond_fir_TR2_pf2_tpexclude_HC_DISS_setwdelay/bu_negVbu_neut/my-glm.wls//cache.mri_glmfit-sim.log > > echo ERROR: cannot find > /Applications/freesurfer/average/mult-comp-cor///cortex/fwhm10/abs/th13/mc-z.csd > > ERROR: cannot find > /Applications/freesurfer/average/mult-comp-cor///cortex/fwhm10/abs/th13/mc-z.csd > > exit 1 ; > > exit 1 > > > > > _______________________________________________ > 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/ ------------------------------ Message: 3 Date: Wed, 12 Jul 2017 12:19:17 -0400 From: Douglas N Greve <greve(a)nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] Subject with missing fMRI data {Disarmed} To: freesurfer(a)nmr.mgh.harvard.edu Message-ID: <5f1ae473-c099-44f9-396d-cff4730d1883(a)nmr.mgh.harvard.edu> Content-Type: text/plain; charset=UTF-8; format=flowed it might not be possible to use the frame mask with wls. Does it work without it? On 07/09/2017 04:46 PM, Sadie Marvel wrote: > So now that I am using --no-prune, I'm getting this error: > group wrfx error: MRInormWeights: value less than or eq to 0. > ?I found another thread in the mailing list about this error saying > that there may be values in cesvar.nii that are =0, and that pruning > normally masks out these values. But here, I am trying to use my own > masks to do so. Is it possible now that my masks and my --y input have > different sizes? If so, how can I solve this? > ------------------------------------------------------------------------ > *From:* freesurfer-bounces(a)nmr.mgh.harvard.edu > <freesurfer-bounces(a)nmr.mgh.harvard.edu> on behalf of Douglas Greve > <greve(a)nmr.mgh.harvard.edu> > *Sent:* Friday, July 7, 2017 11:57 AM > *To:* freesurfer(a)nmr.mgh.harvard.edu > *Subject:* Re: [Freesurfer] Subject with missing fMRI data {Disarmed} > > Add --no-prune > > > On 7/7/17 11:38 AM, Sadie Marvel wrote: >> >> ?When I use a script like this, >> >> mri_glmfit --y ces.nii --wls cesvar.nii --osgm --frame-mask masks.nii >> --surface fsaverage rh --glmdir my-glm2.wls --nii.gz? >> >> using the individual binary masks for all the subjects, the command >> seems to revert to using mask.nii, the single mask that was averaged >> over subjects. The output then just looks like it was using the >> single mask instead of being subject specific. Any idea why? >> >> >> >> ------------------------------------------------------------------------ >> *From:* freesurfer-bounces(a)nmr.mgh.harvard.edu >> <freesurfer-bounces(a)nmr.mgh.harvard.edu> on behalf of Douglas Greve >> <greve(a)nmr.mgh.harvard.edu> >> *Sent:* Thursday, July 6, 2017 12:58 PM >> *To:* freesurfer(a)nmr.mgh.harvard.edu >> *Subject:* Re: [Freesurfer] Subject with missing fMRI data {Disarmed} >> >> yes >> >> >> On 7/6/17 12:50 PM, Sadie Marvel wrote: >>> >>> From using isxconcat-sess to concatenate all of my subjects >>> together, the command creates binary masks called masks.nii and >>> mask.nii, masks.nii being all of the binary masks for each subject. >>> Is this what I would use with --frame-mask? >>> >>> >>> Thanks, >>> >>> Sadie >>> >>> ------------------------------------------------------------------------ >>> *From:* freesurfer-bounces(a)nmr.mgh.harvard.edu >>> <freesurfer-bounces(a)nmr.mgh.harvard.edu> on behalf of Douglas Greve >>> <greve(a)nmr.mgh.harvard.edu> >>> *Sent:* Wednesday, July 5, 2017 7:28 PM >>> *To:* freesurfer(a)nmr.mgh.harvard.edu >>> *Subject:* Re: [Freesurfer] Subject with missing fMRI data >>> >>> We don't have any tools to do imputation. It is possible to have a >>> subject specific mask with the --frame-mask option to mri_glmfit. >>> The frame mask must be the same size as the input (--y) with 1s and >>> 0s to indicate whether a given voxel for a given subject should be >>> included in the model. I've not been happy with this method as it >>> can create some strange results as different voxels will now have >>> different DOFs. >>> >>> >>> On 6/29/17 8:49 AM, Sadie Marvel wrote: >>>> >>>> Hi List, >>>> >>>> >>>> I am currently doing a group analysis of 26 subjects, one of which >>>> has missing fMRI data where the signal cuts off through parts of >>>> the occipital and temporal lobes. I was wondering if freesurfer has >>>> any way of dealing with this, such as multiple imputation, or other >>>> methods of filling the missing data. Alternatively, is there a way >>>> to only use the portions of the brain that have data when doing >>>> mri_glmfit? Does freesurfer do this automatically? >>>> >>>> >>>> Thanks. >>>> >>>> >>>> >>>> _______________________________________________ >>>> Freesurfer mailing list >>>> Freesurfer(a)nmr.mgh.harvard.edu >>>> *MailScanner has detected a possible fraud attempt from >>>> "urldefense.proofpoint.com" claiming to be* >>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>> >>> >>> >>> _______________________________________________ >>> Freesurfer mailing list >>> Freesurfer(a)nmr.mgh.harvard.edu >>> *MailScanner has detected a possible fraud attempt from >>> "urldefense.proofpoint.com" claiming to be* >>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer(a)nmr.mgh.harvard.edu >> *MailScanner has detected a possible fraud attempt from >> "urldefense.proofpoint.com" claiming to be* >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > _______________________________________________ > 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/ ------------------------------ Message: 4 Date: Wed, 12 Jul 2017 12:23:53 -0400 From: Douglas N Greve <greve(a)nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] Running segmentation on spatially normalized data To: freesurfer(a)nmr.mgh.harvard.edu Message-ID: <9c6996a8-dbd2-8c58-4f06-ae7cc2c6ae8f(a)nmr.mgh.harvard.edu> Content-Type: text/plain; charset=windows-1252; format=flowed sorry, I don't know anything about .tlrc files (or much about AFNI). If the transform is linear, then you should be able to map between the spaces with mri_vol2vol or mri_label2vol, but you will need to get the transform into a FS-compatible format. On 07/06/2017 01:50 PM, Lauren Stephanie Hopkins wrote: > > Hi all: > > > We ran FreeSurfer's recon sequence of anatomy files that had already > been aligned to the MNI template - so spatially normalized. We're > doing all of our processing in AFNI and the resulting segmentation > output files open in AFNI's orig space, not in tlrc space. So > basically we can't overlay the segmentation files on our anat+tlrc > files where they should already be aligned to each other. When we > converted the file to a .tlrc file with the AFNI command 3dcopy we > could then overlay the mask on the normalized anatomy but it was no > longer aligned. > > > So I suppose my question is - is there any way to have the > segmentation files maintain their positioning or output in .tlrc space > so they are still aligned to our anatomy files? > > Thanks for any insight. > > Lauren > > > > _______________________________________________ > 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/ ------------------------------ Message: 5 Date: Wed, 12 Jul 2017 12:27:20 -0400 From: Douglas N Greve <greve(a)nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] asegstats2table error To: freesurfer(a)nmr.mgh.harvard.edu Message-ID: <614c9872-917a-9eb3-748e-12c1247ec242(a)nmr.mgh.harvard.edu> Content-Type: text/plain; charset=utf-8; format=flowed Not sure what the problem is, but it might be something specific to your site (looks like it cannot find the proper libraries to import). Can you run it at all. Eg, if just run the script without any arguments, do you get the same thing? What about if you run it with -h ? On 07/06/2017 03:33 AM, Elizabeth Dao wrote: > Dear experts, > > I have completed recon-all with no errors. Now I would like to use the > 'asegstats2table' command but I've received the error below. I would > appreciate any help in solving this problem. I am using FreeSurfer > v6.0.0 on a Linux CentOS machine. > > [TLA@CogmobCentOS MCI]$ asegstats2table --subjects 201.MR1 202.MR1 > 203.MR1 --meas volume --tablefile aseg_stats_all.txt > 'import site' failed; use -v for traceback > Traceback (most recent call last): > File "/home/TLA/Desktop/Liz/freesurfer6/bin/asegstats2table", line > 4, in <module> > import os > File "/usr/local/lib/python2.7/os.py", line 398, in <module> > import UserDict > File "/usr/local/lib/python2.7/UserDict.py", line 84, in <module> > _abcoll.MutableMapping.register(IterableUserDict) > File "/usr/local/lib/python2.7/abc.py", line 109, in register > if issubclass(subclass, cls): > File "/usr/local/lib/python2.7/abc.py", line 184, in __subclasscheck__ > cls._abc_negative_cache.add(subclass) > File "/usr/local/lib/python2.7/_weakrefset.py", line 84, in add > self.data.add(ref(item, self._remove)) > TypeError: cannot create weak reference to 'classobj' object > > Thank you in advance for your help! > > Liz > > > _______________________________________________ > 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/ ------------------------------ Message: 6 Date: Wed, 12 Jul 2017 12:32:02 -0400 From: Douglas N Greve <greve(a)nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] Strange Discrepancy Between Activation Location on Surface vs. Volume To: freesurfer(a)nmr.mgh.harvard.edu Message-ID: <7e0e01ff-08b1-636d-bdf7-aec2586ea290(a)nmr.mgh.harvard.edu> Content-Type: text/plain; charset=utf-8; format=flowed Hi Johnmark, sorry, I can't reconstruct the thread from the earlier emails. Can you resubmit with just the thread from your email and not all 29 threads from July 5? thanks doug On 07/06/2017 02:00 PM, Taylor, Johnmark wrote: > The subject name when I call tksurfer, the subject name when I call > tkmedit, and the subject name in the registration file are all exactly > the same: red_badger. One thing I noticed is that in the left > hemisphere everything seems normal (the activation is in the expected > location); things only look weird in the right hemisphere. There's no > possibility that the surface reconstruction could have been off the > mark? Though it seems implausible that it would take the IPS and > somehow warp it all the way onto the medial surface of the brain... > > Here are pictures of both the volume and surface views of the > activation in question (it's the medial patch on the surface view, the > patch with the red cursor in the volume view), in case they didn't > load before for some reason. > > ????https://ibb.co/b8HFCv > https://ibb.co/cWYcQF > > On Thu, Jul 6, 2017 at 12:00 PM, > <freesurfer-request(a)nmr.mgh.harvard.edu > <mailto:freesurfer-request@nmr.mgh.harvard.edu>> wrote: > > Send Freesurfer mailing list submissions to > freesurfer(a)nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu> > > To subscribe or unsubscribe via the World Wide Web, visit > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> > or, via email, send a message with subject or body 'help' to > freesurfer-request(a)nmr.mgh.harvard.edu > <mailto:freesurfer-request@nmr.mgh.harvard.edu> > > You can reach the person managing the list at > freesurfer-owner(a)nmr.mgh.harvard.edu > <mailto:freesurfer-owner@nmr.mgh.harvard.edu> > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of Freesurfer digest..." > > > Today's Topics: > > 1. Re: error message while using autorecon1 (Hoopes, Andrew) > 2. Re: error message while using autorecon1 (Buckless, Colleen) > 3. Re: Additional surface area (Bruce Fischl) > 4. Fwd: remove skull from gtmseg.mgz (miracle ozzoude) > 5. Re: error message while using autorecon1 (Hoopes, Andrew) > 6. Re: error message while using autorecon1 (Buckless, Colleen) > 7. Re: error message while using autorecon1 (Hoopes, Andrew) > 8. Re: recon-all on newborn (Lilla Zollei) > 9. Re: recon-all on newborn (Das S.) > 10. Re: Still confused by group analysis.. (Douglas Greve) > 11. Re: Raw Cortical thickness values (Douglas Greve) > 12. Re: Average myelination within ROI (Douglas Greve) > 13. Re: bbregister vs spmregister vs mri_coreg (Douglas Greve) > 14. Re: Recon-all: too many ('s (Douglas Greve) > 15. Re: Using multimodal slab input for hippocampus subfield > segmentation in FS6 (Douglas Greve) > 16. Re: Strange Discrepancy Between Activation Location on > Surface vs. Volume (Douglas Greve) > 17. Re: negative header after preproc-sess (Douglas Greve) > 18. Re: freesurfer(a)nmr.mgh.harvard.edu > <mailto:freesurfer@nmr.mgh.harvard.edu> (Douglas Greve) > 19. Re: Building your own fsaverage (Douglas Greve) > 20. Re: Qdec error in analysis (Douglas Greve) > 21. Re: mri_glmfit error (mri_reshape number of elements) > (Douglas Greve) > 22. Re: Fwd: remove skull from gtmseg.mgz (Douglas Greve) > 23. Re: GLM fitting for the cortical volume (Douglas Greve) > 24. Re: Subject with missing fMRI data (Douglas Greve) > 25. Re: Question mri_glmfit fwhm smoothing (Douglas Greve) > 26. Re: viewing mri_glmfit FDR corrected results (Douglas Greve) > 27. Re: content of "subjects_dir" (Douglas Greve) > 28. Re: Qdec error in analysis (AYUSHI SHUKLA) > 29. asegstats2table error (Elizabeth Dao) > 30. Re: Fwd: remove skull from gtmseg.mgz (miracooloz(a)gmail.com > <mailto:miracooloz@gmail.com>) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Wed, 5 Jul 2017 17:29:23 +0000 > From: "Hoopes, Andrew" <AHOOPES(a)mgh.harvard.edu > <mailto:AHOOPES@mgh.harvard.edu>> > Subject: Re: [Freesurfer] error message while using autorecon1 > To: "'freesurfer(a)nmr.mgh.harvard.edu > <mailto:freesurfer@nmr.mgh.harvard.edu>'" > <freesurfer(a)nmr.mgh.harvard.edu > <mailto:freesurfer@nmr.mgh.harvard.edu>> > Message-ID: > > <BLUPR04MB4662F945780124666F30CD2F9D40(a)BLUPR04MB466.namprd04.prod.outlook.com > <mailto:BLUPR04MB4662F945780124666F30CD2F9D40@BLUPR04MB466.namprd04.prod.outlook.com>> > > Content-Type: text/plain; charset="Windows-1252" > > Hi Colleen, > If you source freesurfer, and run: > ls $FREESURFER_HOME/mni/bin > It should output a list of mni tools, including nu_correct. Is > this what you see? There's a possibility that your mni > sub-directory isn't sourced. > Andrew > ________________________________________ > From: freesurfer-bounces(a)nmr.mgh.harvard.edu > <mailto:freesurfer-bounces@nmr.mgh.harvard.edu> > <freesurfer-bounces(a)nmr.mgh.harvard.edu > <mailto:freesurfer-bounces@nmr.mgh.harvard.edu>> on behalf of > Buckless, Colleen <Buckless(a)kennedykrieger.org > <mailto:Buckless@kennedykrieger.org>> > Sent: Wednesday, July 05, 2017 12:18 PM > To: 'freesurfer(a)nmr.mgh.harvard.edu > <mailto:freesurfer@nmr.mgh.harvard.edu>' > Subject: [Freesurfer] error message while using autorecon1 > > Hi All, > I am using the newest version of freesurfer, and I keep getting > errors when I run recon-all ?autorecon1. It appears that the error > might have to do with nu_correct, and I have attached the > recon-all.log. > Any suggestions on how to fix this? > Thanks, > > Colleen Buckless > Research Assistant > Center for Neurodevelopmental and Imaging Research > Kennedy Krieger Institute > 443-923-2747 <tel:443-923-2747> > Buckless(a)kennedykrieger.org <mailto:Buckless@kennedykrieger.org> > > ________________________________ > Disclaimer: > > > The materials in this e-mail are private and may contain Protected > Information. Please note that e-mail communication is not > encrypted by default. You have the right to request further emails > be encrypted by notifying the sender. Your continued use of e-mail > constitutes your acknowledgment of these confidentiality and > security limitations. If you are not the intended recipient, be > advised that any unauthorized use, disclosure, copying, > distribution, or the taking of any action in reliance on the > contents of this information is strictly prohibited. If you have > received this e-mail in error, please immediately notify the > sender via telephone or return e-mail. > > > > ------------------------------ > > Message: 2 > Date: Wed, 5 Jul 2017 17:36:47 +0000 > From: "Buckless, Colleen" <Buckless(a)kennedykrieger.org > <mailto:Buckless@kennedykrieger.org>> > Subject: Re: [Freesurfer] error message while using autorecon1 > To: "'freesurfer(a)nmr.mgh.harvard.edu > <mailto:freesurfer@nmr.mgh.harvard.edu>'" > <freesurfer(a)nmr.mgh.harvard.edu > <mailto:freesurfer@nmr.mgh.harvard.edu>> > Message-ID: > <6F20C54B58C269489AA5CC858A1F58AF95125F(a)GSP-MAIL1.kki.org > <mailto:6F20C54B58C269489AA5CC858A1F58AF95125F@GSP-MAIL1.kki.org>> > Content-Type: text/plain; charset="us-ascii" > > Hi Andrew, > The output list includes nu_correct. > Thanks, > Colleen > > -----Original Message----- > From: freesurfer-bounces(a)nmr.mgh.harvard.edu > <mailto:freesurfer-bounces@nmr.mgh.harvard.edu> > [mailto:freesurfer-bounces@nmr.mgh.harvard.edu > <mailto:freesurfer-bounces@nmr.mgh.harvard.edu>] On Behalf Of > Hoopes, Andrew > Sent: Wednesday, July 05, 2017 1:29 PM > To: 'freesurfer(a)nmr.mgh.harvard.edu > <mailto:freesurfer@nmr.mgh.harvard.edu>' > Subject: Re: [Freesurfer] error message while using autorecon1 > > Hi Colleen, > If you source freesurfer, and run: > ls $FREESURFER_HOME/mni/bin > It should output a list of mni tools, including nu_correct. Is > this what you see? There's a possibility that your mni > sub-directory isn't sourced. > Andrew > ________________________________________ > From: freesurfer-bounces(a)nmr.mgh.harvard.edu > <mailto:freesurfer-bounces@nmr.mgh.harvard.edu> > <freesurfer-bounces(a)nmr.mgh.harvard.edu > <mailto:freesurfer-bounces@nmr.mgh.harvard.edu>> on behalf of > Buckless, Colleen <Buckless(a)kennedykrieger.org > <mailto:Buckless@kennedykrieger.org>> > Sent: Wednesday, July 05, 2017 12:18 PM > To: 'freesurfer(a)nmr.mgh.harvard.edu > <mailto:freesurfer@nmr.mgh.harvard.edu>' > Subject: [Freesurfer] error message while using autorecon1 > > Hi All, > I am using the newest version of freesurfer, and I keep getting > errors when I run recon-all -autorecon1. It appears that the error > might have to do with nu_correct, and I have attached the > recon-all.log. > Any suggestions on how to fix this? > Thanks, > > Colleen Buckless > Research Assistant > Center for Neurodevelopmental and Imaging Research Kennedy Krieger > Institute > 443-923-2747 <tel:443-923-2747> > Buckless(a)kennedykrieger.org <mailto:Buckless@kennedykrieger.org> > > ________________________________ > Disclaimer: > > > The materials in this e-mail are private and may contain Protected > Information. Please note that e-mail communication is not > encrypted by default. You have the right to request further emails > be encrypted by notifying the sender. Your continued use of e-mail > constitutes your acknowledgment of these confidentiality and > security limitations. If you are not the intended recipient, be > advised that any unauthorized use, disclosure, copying, > distribution, or the taking of any action in reliance on the > contents of this information is strictly prohibited. If you have > received this e-mail in error, please immediately notify the > sender via telephone or return e-mail. > > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > https://urldefense.proofpoint.com/v2/url?u=https-3A__mail.nmr.mgh.harvard.e… > <https://urldefense.proofpoint.com/v2/url?u=https-3A__mail.nmr.mgh.harvard.e…> > > > 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 > https://urldefense.proofpoint.com/v2/url?u=http-3A__www.partners.org_compli… > <https://urldefense.proofpoint.com/v2/url?u=http-3A__www.partners.org_compli…> > . 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. > > > > > ------------------------------ > > Message: 3 > Date: Wed, 5 Jul 2017 13:51:41 -0400 (EDT) > From: Bruce Fischl <fischl(a)nmr.mgh.harvard.edu > <mailto:fischl@nmr.mgh.harvard.edu>> > Subject: Re: [Freesurfer] Additional surface area > To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu > <mailto:freesurfer@nmr.mgh.harvard.edu>> > Message-ID: > > <alpine.LRH.2.20.1707051351070.31440(a)gate.nmr.mgh.harvard.edu > <mailto:alpine.LRH.2.20.1707051351070.31440@gate.nmr.mgh.harvard.edu>> > Content-Type: text/plain; charset=US-ASCII; format=flowed > > Hi Michael > > you need to look in the volume to see what is causing it. I would > guess > some dura that is being incorrectly included, but you will be able > to tell > in the slice view > > cheers > Bruce > > > On Mon, 3 Jul > 2017, Michael Davies wrote: > > > > > Hello, when inspecting a subject i discovered an anomaly on top > of the 3D > > surface i have not previously encountered on other subjects i have > > inspected. Could you please let me know if this would be > problematic when at > > the analysing group data please? > > > > > > Kind regards, Michael > > > > > > > > > ------------------------------ > > Message: 4 > Date: Wed, 5 Jul 2017 13:53:57 -0400 > From: miracle ozzoude <miracooloz(a)gmail.com > <mailto:miracooloz@gmail.com>> > Subject: [Freesurfer] Fwd: remove skull from gtmseg.mgz > To: Douglas N Greve <freesurfer(a)nmr.mgh.harvard.edu > <mailto:freesurfer@nmr.mgh.harvard.edu>> > Message-ID: > > <CANfOk0h=UyBU_4ZV0E9mEaoE0NMvvx1_A-x63JxaLxj=54nuLg(a)mail.gmail.com > <mailto:54nuLg@mail.gmail.com>> > Content-Type: text/plain; charset="utf-8" > > ---------- Forwarded message ---------- > From: miracle ozzoude <miracooloz(a)gmail.com > <mailto:miracooloz@gmail.com>> > Date: Tue, Jul 4, 2017 at 10:23 AM > Subject: remove skull from gtmseg.mgz > To: Douglas N Greve <freesurfer(a)nmr.mgh.harvard.edu > <mailto:freesurfer@nmr.mgh.harvard.edu>> > > > Hello Freesurfer, > > After running the first step of PETsurfer (https://surfer.nmr.mgh. > harvard.edu/fswiki/PetSurfer > <http://harvard.edu/fswiki/PetSurfer>). I viewed the image it > created using > freeview. When I change, the color map to Lookup Table, the image also > included the skull. How can I remove the skull from > gtmseg.mgz/prevent it > from showing? Any help will be appreciated. Thanks. Please, see > attached > image > > Best, > Paul >

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