Freesurfer October 2017

freesurfer@nmr.mgh.harvard.edu

119 participants
179 discussions

Fwd: running cross sectional analysis on .long outputs only
by Garret O'Connell 18 Oct '17

18 Oct '17

Hello FreeSurfer experts, I am trying to do a cross-sectional baseline analysis from the outputs of the longitudinal processing stream, following the advice on a previous question's thread: https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2016- March/044681.html >From my reading of the issue, I need to run the following command, entering the cross-sectional title folder as the first input. recon-all -long "subj_crossfolder" "subj_base" -qcache For this step, i know it is necessary that recon-all knows where the cross folders are located, although from my understanding, it does not actually use data from these folders., instead using the data in the .long folders. My issue is that I do not have access to the cross folders anymore, and was wondering if there was a work around to do the cross sectional analysis without them? Thanks for any help! Garret

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ERROR: no voxels found in mask selxavg3-sess
by 王剑葆 18 Oct '17

18 Oct '17

Dear FreeSurfers, I'm trying to perform First level analysis using "selxavg3-sess -sf sessid -analysis color.sm0.mni305". However, the analysis was interrupted by the following error. ... ... Smoothing ACF /usr/local/freesurfer/bin/mri_fwhm --mask /media/bob/DATA/FreeSUBcolorv2v4/functional01/Sess01/bold/color.sm0.mni305/mask.nii.gz --i /media/bob/DATA/FreeSUBcolorv2v4/functional01/Sess01/bold/color.sm0.mni305/rho1mn.nii.gz --o /media/bob/DATA/FreeSUBcolorv2v4/functional01/Sess01/bold/color.sm0.mni305/rho1mn.sm.nii.gz --fwhm 20.000000 --smooth-only voxelvolume 1 mm3 Loading mask /media/bob/DATA/FreeSUBcolorv2v4/functional01/Sess01/bold/color.sm0.mni305/mask.nii.gz ERROR: no voxels found in mask ERROR: /usr/local/freesurfer/bin/mri_fwhm --mask /media/bob/DATA/FreeSUBcolorv2v4/functional01/Sess01/bold/color.sm0.mni305/mask.nii.gz --i /media/bob/DATA/FreeSUBcolorv2v4/functional01/Sess01/bold/color.sm0.mni305/rho1mn.nii.gz --o /media/bob/DATA/FreeSUBcolorv2v4/functional01/Sess01/bold/color.sm0.mni305/rho1mn.sm.nii.gz --fwhm 20.000000 --smooth-only ans = 1 I also loaded the mask and found that all the values are 0. I finished mkanalysis-sess and mkcontrast-sess without error. Is there anything possible wrong in the previous steps when generating the mask? Best, Bob

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Creation of V1 mask in volume
by Florence Campana 17 Oct '17

17 Oct '17

Dear freesurfer experts, I am trying to create a V1 mask in volume, based on the V1 label, in fsaverage space. I use the following command: mri_label2vol --label /Applications/freesurfer/subjects/fsaverage/label/rh.V1.label --temp /Applications/freesurfer/subjects/fsaverage/mri/orig.mgz --hemi rh --identity --o v1volume.nii When I check out the output (in freeview, I load orig,mgz and v1volume.nii as a mask), V1 as defined in v1volume.nii seems to be mislocated. I am surprised since I would think that I use the proper inputs ; or is my command line somehow wrong? Thank you very much, Florence

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Advice on covariates in qdec or mri_glmfit
by Jeff Crawford 17 Oct '17

17 Oct '17

Hello everyone. I am having trouble understanding the statistical effects of a covariate versus a nuisance factor in freesurfer and I would appreciate some advice. I want to run a correlation between cortical volume and the measurement of an enzyme while covarying for ETICV. In qdec, I select volume as the measure, set the enzyme as a covariate, and select ETICV as a nuisance factor. This works fine, however, I want to also control for the difference in using two separate scanners. This would be a categorical variable and I understand that Freesurfer does not allow categorical variables to be nuisance variables. The solution I found to this problem from two separate emails is that you either use the Manuel stream of mri_glmfit or use set scanner as a fixed factor, which produces a description of: "Does the correlation between volume and enzyme, accounting for scanner, differ from zero? Nuisance factors: ETicV" This sounds right to me, but I am confused as to the difference between "accounting for scanner" and "Nuisance factors: ETicV", when I thought they were the same thing. Am I approaching this right? Do I need to use mri_glmfit to properly control for scanner? If so, then how would I specify a nuisance variable in a contrast?

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Skull-stripped data submitted on FreeSurfer version 6.0.0
by Duran, Tugce 17 Oct '17

17 Oct '17

Dear FreeSurfer Team, I have recently submitted my skull-stripped data into FreeSurfer v6. Since this is a separate process than the default recon-all –all, I followed the recommended steps that are posted on the FSwiki website, here is the link for it: https://surfer.nmr.mgh.harvard.edu/fswiki/UserContributions/FAQ#Q.Ihavealre… By doing so, I accidentally submitted my data both with recon-all -autorecon1 -noskullstrip -s <subjid> and –all flag at the beginning. Using PBS script, here is an example of this: list="E001_V1 E002_V1 E003_V1 E004_V1 E005_V1 E006_V1 E008_V1 E010_V1 E011_V1 E013_V1 E014_V1 E015_V1" echo $list OUTDIR="/pathtodirectory/logs_KT" PREFIX="recon-all" for index in $list; do recon-all –autorecon1 –noskullstrip -i /pathtodirectory/$index/"$index".nii -subject $index -sd /pathtodirectory -all 1>$OUTDIR/$PREFIX.$index.out 2>$OUTDIR/$PREFIX.$index.err & done wait I forgot to remove the flag –all at the end of this command. Therefore, freesurfer v6 processed my data all the way till the end and Viola it worked! And I am wondering If I could trust this data since it looks OKAY when I look at the segmentation, parcellation. Can I trust this skull-stripped processes data with –autorecon1 –noskullstrip and –all options? I hope my explanation and question makes sense. Thanks, Tugce Duran durant(a)iupui.edu

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recon-all error message
by lanbo Wang 17 Oct '17

17 Oct '17

recon-all.log <https://drive.google.com/file/d/0B8gDmAZ-2iJ6VzRyZ01UbXRMdFlId2pZR2cyZHJLNH…> Dear All, When I run recon-all -long, the error happend. This is the error message that I get at the end of the recon-all log file: /HD4/Subjects/subj_23_1.long.s23_base/surf mris_calc -o rh.area.mid rh.area add rh.area.pial Saving result to 'rh.area.mid' (type = MRI_CURV_FILE) [ ok ] mris_calc -o rh.area.mid rh.area.mid div 2 Saving result to 'rh.area.mid' (type = MRI_CURV_FILE) [ ok ] mris_calc -o rh.volume rh.area.mid mul rh.thickness WARNING: # of slices=-59 in header - assuming 124... read_signa(/HD4/Subjects/subj_23_1.long.s23_base/surf/I.001): could not open file No such file or directory mris_calc: Sorry, but I seem to have encountered an error. While checking on input filetype sizes, I found a size mismatch, i.e. len(input1)!=len(input2) Any help is greatly appreciated. All best, Lanbo Wang

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R: Re: R: Re: R: Re: R: Re: R: Re: R: Re: R: Re: R: Re: Map of covariance
by stdp82＠virgilio.it 16 Oct '17

16 Oct '17

Thanks. The maps produced in slope and intercept folders are very similar and opposite in colors. I have already applied this contrast but I think that they did not fit with my goals. Why the intercept did not produce the same results of G4VO? The slope effect is very similar to the inverse of intercept... >----Messaggio originale---- >Da: "Douglas Greve" <greve(a)nmr.mgh.harvard.edu> >Data: 16-ott-2017 17.41 >A: <freesurfer(a)nmr.mgh.harvard.edu> >Ogg: Re: [Freesurfer] R: Re: R: Re: R: Re: R: Re: R: Re: R: Re: R: Re: Map of covariance > >they all look ok except that these should be >C13) gr1+gr2-vs-gr3+gr4.intercept 0.5 0.5 -0.5 -0.5 0 0 0 0 >C14) gr1+gr2-vs-gr3+gr4.slope 0 0 0 0 0.5 0.5 -0.5 -0.5 > > >On 10/13/17 11:30 AM, stdp82(a)virgilio.it wrote: >> I have applied the contrasts that we discussed in the previous mails but they >> produce doubt results. >> >> In summary, I aim to look at: >> A- Difference between groups without considerer the covariate effect (I >> suppose that the maps will be in the intercept folder) ---> ANOVA between 4 >> groups >> B- Clusters in which the fMRI (dependent variable) is associated to the >> structural data (covariate), taking in account the groups (I suppose that the >> maps will be in the slope folder) ---> MANOVA between 4 groups >> >> Please could you check the contrast reported below? I suspect that there are >> some errors because, looking at results: >> The slope map is the inverse in color of the intercept map and the intercept >> did not correspond to the results which I obtain by using G4V0 >> >> C1) gr1-gr2_intercept 1 -1 0 0 0 0 0 0 >> C2 )gr1-gr2_slope 0 0 0 0 1 -1 0 0 >> C3) gr1-gr3_intercept 1 0 -1 0 0 0 0 0 >> C4) gr1-gr3_slope 0 0 0 0 1 0 -1 0 >> C5) gr1-gr4_intercept 1 0 0 -1 0 0 0 0 >> C6) gr1-gr4_slope 0 0 0 0 1 0 0 -1 >> C7) gr2-gr3_intercept 0 1 -1 0 0 0 0 0 >> C8) gr2-gr3_slope 0 0 0 0 0 1 -1 0 >> C9) gr2-gr4_intercept 0 1 0 -1 0 0 0 0 >> C10) gr2-gr4_slope 0 0 0 0 0 1 0 -1 >> C11) gr3-gr4_intercept 0 0 1 -1 0 0 0 0 >> C12) gr3-gr4_slope 0 0 0 0 0 0 1 -1 >> C13) gr1+gr2-vs-gr3+gr4.intercept 0.25 0.25 0.25 0.25 0 0 0 0 >> C14) gr1+gr2-vs-gr3+gr4.slope 0 0 0 0 0.25 0.25 0.25 0.25 >> C15) group.effect.intercept >> 1 -1 0 0 0 0 0 0 >> 1 0 -1 0 0 0 0 0 >> 1 0 0 -1 0 0 0 0 >> C16) group.effect.slope >> 0 0 0 0 1 -1 0 0 >> 0 0 0 0 1 0 -1 0 >> 0 0 0 0 1 0 0 -1 >> >> Best regards >> >> >> Stefano >> >> >>> ----Messaggio originale---- >>> Da: "Douglas N Greve" <greve(a)nmr.mgh.harvard.edu> >>> Data: 11-ott-2017 17.28 >>> A: <stdp82(a)virgilio.it>, <freesurfer(a)nmr.mgh.harvard.edu> >>> Ogg: Re: [Freesurfer] R: Re: R: Re: R: Re: R: Re: R: Re: R: Re: Map of >> covariance >>> the rational is to make them sum to 1.0 so that the gamma.mgh file has >>> units of mm (or whatever the input units are). It is unimportant for >>> p-values. >>> >>> >>> On 10/10/2017 01:54 PM, stdp82(a)virgilio.it wrote: >>>> Thanks >>>> >>>> In which contrast I must change "1" with "0.25"? >>>> What is the rationale to use 0.25? >>>> >>>> >>>> Sent from Virgilio Mobile >>>> ________________________________ >>>> >>>> Il 10/10/2017, Douglas N Greve <greve(a)nmr.mgh.harvard.edu> ha scritto: >>>> >>>> I don't understand what you mean by "where I should use" >>>> >>>> I thought I looked through all those contrasts a few weeks ago, no? >>>> >>>> >>>> On 10/10/2017 04:22 AM, stdp82(a)virgilio.it wrote: >>>>> You have suggested to use >>>>> 0 0 0 0 .25 .25 .25 .25 >>>>> to look the map where, considering the group differences, the covariate >>>>> predicts the dependent variable (functional connectivity) in 4GV1. >>>>> >>>>> Below I'm reporting the contrast that I have used. >>>>> Please could you check it and suggest correction? >>>>> Could you explain where I should use 0 0 0 0 .25 .25 .25 .25, please? >>>>> >>>>> Thanks >>>>> >>>>> C1) gr1-gr2_intercept 1 -1 0 0 0 0 0 0 >>>>> C2 )gr1-gr2_slope 0 0 0 0 1 -1 0 0 >>>>> C3) gr1-gr3_intercept 1 0 -1 0 0 0 0 0 >>>>> C4) gr1-gr3_slope 0 0 0 0 1 0 -1 0 >>>>> C5) gr1-gr4_intercept 1 0 0 -1 0 0 0 0 >>>>> C6) gr1-gr4_slope 0 0 0 0 1 0 0 -1 >>>>> C7) gr2-gr3_intercept 0 1 -1 0 0 0 0 0 >>>>> C8) gr2-gr3_slope 0 0 0 0 0 1 -1 0 >>>>> C9) gr2-gr4_intercept 0 1 0 -1 0 0 0 0 >>>>> C10) gr2-gr4_slope 0 0 0 0 0 1 0 -1 >>>>> C11) gr3-gr4_intercept 0 0 1 -1 0 0 0 0 >>>>> C12) gr3-gr4_slope 0 0 0 0 0 0 1 -1 >>>>> C13) gr1+gr2-vs-gr3+gr4.intercept 0.5 0.5 -0.5 -0.5 0 0 0 0 >>>>> C14) gr1+gr2-vs-gr3+gr4.slope 0 0 0 0 0.5 0.5 -0.5 -0.5 >>>>> C15) group.effect.intercept >>>>> 1 -1 0 0 0 0 0 0 >>>>> 1 0 -1 0 0 0 0 0 >>>>> 1 0 0 -1 0 0 0 0 >>>>> C16) group.effect.slope >>>>>> 0 0 0 0 1 -1 0 0 >>>>>> 0 0 0 0 1 0 -1 0 >>>>>> 0 0 0 0 1 0 0 -1 >>>>> >>>>> >>>>> >>>>> >>>>> >>>>> On 10/6/17 9:24 AM, stdp82(a)virgilio.it wrote: >>>>>> Thank you very much. >>>>>> Where I should put 0 0 0 0 .25 .25 .25 .25? >>>>>> Which are the contrast reported below that I should modify? >>>>>> >>>>>> C1) gr1-gr2_intercept 1 -1 0 0 0 0 0 0 >>>>>> C2 )gr1-gr2_slope 0 0 0 0 1 -1 0 0 >>>>>> C3) gr1-gr3_intercept 1 0 -1 0 0 0 0 0 >>>>>> C4) gr1-gr3_slope 0 0 0 0 1 0 -1 0 >>>>>> C5) gr1-gr4_intercept 1 0 0 -1 0 0 0 0 >>>>>> C6) gr1-gr4_slope 0 0 0 0 1 0 0 -1 >>>>>> C7) gr2-gr3_intercept 0 1 -1 0 0 0 0 0 >>>>>> C8) gr2-gr3_slope 0 0 0 0 0 1 -1 0 >>>>>> C9) gr2-gr4_intercept 0 1 0 -1 0 0 0 0 >>>>>> C10) gr2-gr4_slope 0 0 0 0 0 1 0 -1 >>>>>> C11) gr3-gr4_intercept 0 0 1 -1 0 0 0 0 >>>>>> C12) gr3-gr4_slope 0 0 0 0 0 0 1 -1 >>>>>> C13) gr1+gr2-vs-gr3+gr4.intercept 0.5 0.5 -0.5 -0.5 0 0 0 0 >>>>>> C14) gr1+gr2-vs-gr3+gr4.slope 0 0 0 0 0.5 0.5 -0.5 -0.5 >>>>>> C15) group.effect.intercept >>>>>> 1 -1 0 0 0 0 0 0 >>>>>> 1 0 -1 0 0 0 0 0 >>>>>> 1 0 0 -1 0 0 0 0 >>>>>> C16) group.effect.slope >>>>>> 0 0 0 0 1 -1 0 0 >>>>>> 0 0 0 0 1 0 -1 0 >>>>>> 0 0 0 0 1 0 0 -1 >>>>>> ----Messaggio originale---- >>>>>> Da: "Douglas Greve" <greve(a)nmr.mgh.harvard.edu> >>>>>> Data: 9-ott-2017 22.56 >>>>>> A: <freesurfer(a)nmr.mgh.harvard.edu> >>>>>> Ogg: Re: [Freesurfer] R: Re: R: Re: R: Re: R: Re: Map of covariance >>>>>> >>>>>> I don't know what you are asking >>>>>> >>>>>> >>>>>> On 10/6/17 9:24 AM, stdp82(a)virgilio.it wrote: >>>>>>> Thank you very much. >>>>>>> Where I should put 0 0 0 0 .25 .25 .25 .25? >>>>>>> Which are the contrast reported below that I should modify? >>>>>>> >>>>>>> C1) gr1-gr2_intercept 1 -1 0 0 0 0 0 0 >>>>>>> C2 )gr1-gr2_slope 0 0 0 0 1 -1 0 0 >>>>>>> C3) gr1-gr3_intercept 1 0 -1 0 0 0 0 0 >>>>>>> C4) gr1-gr3_slope 0 0 0 0 1 0 -1 0 >>>>>>> C5) gr1-gr4_intercept 1 0 0 -1 0 0 0 0 >>>>>>> C6) gr1-gr4_slope 0 0 0 0 1 0 0 -1 >>>>>>> C7) gr2-gr3_intercept 0 1 -1 0 0 0 0 0 >>>>>>> C8) gr2-gr3_slope 0 0 0 0 0 1 -1 0 >>>>>>> C9) gr2-gr4_intercept 0 1 0 -1 0 0 0 0 >>>>>>> C10) gr2-gr4_slope 0 0 0 0 0 1 0 -1 >>>>>>> C11) gr3-gr4_intercept 0 0 1 -1 0 0 0 0 >>>>>>> C12) gr3-gr4_slope 0 0 0 0 0 0 1 -1 >>>>>>> C13) gr1+gr2-vs-gr3+gr4.intercept 0.5 0.5 -0.5 -0.5 0 0 0 0 >>>>>>> C14) gr1+gr2-vs-gr3+gr4.slope 0 0 0 0 0.5 0.5 -0.5 -0.5 >>>>>>> C15) group.effect.intercept >>>>>>> 1 -1 0 0 0 0 0 0 >>>>>>> 1 0 -1 0 0 0 0 0 >>>>>>> 1 0 0 -1 0 0 0 0 >>>>>>> C16) group.effect.slope >>>>>>> 0 0 0 0 1 -1 0 0 >>>>>>> 0 0 0 0 1 0 -1 0 >>>>>>> 0 0 0 0 1 0 0 -1 >>>>>>> >>>>>>> >>>>>>>> ----Messaggio originale---- >>>>>>>> Da: "Douglas Greve" <greve(a)nmr.mgh.harvard.edu> >>>>>>>> Data: 3-ott-2017 16.19 >>>>>>>> A: <freesurfer(a)nmr.mgh.harvard.edu> >>>>>>>> Ogg: Re: [Freesurfer] R: Re: R: Re: R: Re: Map of covariance >>>>>>>> >>>>>>>> probably you want 0 0 0 0 .25 .25 .25 .25 >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>> On 10/3/17 10:10 AM, stdp82(a)virgilio.it wrote: >>>>>>>>> Many thank for your response. >>>>>>>>> Claryfing my question on point 3, >>>>>>>>> When I look in group.effect.slope, the map show the group difference >>>>>>> removing >>>>>>>>> the effect of the covariate. >>>>>>>>> Conversely, I would to obtain the map reporting only the effect of >>>>>>> covariate >>>>>>>>> on dependent variable (functional connectivity). >>>>>>>>> Is possible to look on it? >>>>>>>>> Regards >>>>>>>>> Stefano >>>>>>>>> >>>>>>>>> >>>>>>>>>> ----Messaggio originale---- >>>>>>>>>> Da: "Douglas N Greve" <greve(a)nmr.mgh.harvard.edu> >>>>>>>>>> Data: 2-ott-2017 16.58 >>>>>>>>>> A: <freesurfer(a)nmr.mgh.harvard.edu> >>>>>>>>>> Ogg: Re: [Freesurfer] R: Re: R: Re: Map of covariance >>>>>>>>>> >>>>>>>>>> >>>>>>>>>> >>>>>>>>>> On 10/01/2017 05:08 PM, stdp82(a)virgilio.it wrote: >>>>>>>>>>> Hi, >>>>>>>>>>> on 4 groups, 1 covariate (4GV1) >>>>>>>>>>> >>>>>>>>>>> I run mri_glmfit using the following .mtx >>>>>>>>>>> >>>>>>>>>>> C1) gr1-gr2_intercept 1 -1 0 0 0 0 0 0 >>>>>>>>>>> C2 )gr1-gr2_slope 0 0 0 0 1 -1 0 0 >>>>>>>>>>> C3) gr1-gr3_intercept 1 0 -1 0 0 0 0 0 >>>>>>>>>>> C4) gr1-gr3_slope 0 0 0 0 1 0 -1 0 >>>>>>>>>>> C5) gr1-gr4_intercept 1 0 0 -1 0 0 0 0 >>>>>>>>>>> C6) gr1-gr4_slope 0 0 0 0 1 0 -1 0 >>>>>>>>>> should be >>>>>>>>>> >>>>>>>>>> 0 0 0 0 1 0 0 -1 >>>>>>>>>> >>>>>>>>>>> C7) gr2-gr3_intercept 0 1 -1 0 0 0 0 0 >>>>>>>>>>> C8) gr2-gr3_slope 0 0 0 0 0 1 -1 0 >>>>>>>>>>> C9) gr2-gr4_intercept 0 1 0 -1 0 0 0 0 >>>>>>>>>>> C10) gr2-gr4_slope 0 0 0 0 0 1 0 -1 >>>>>>>>>>> C11) gr3-gr4_intercept 0 0 1 -1 0 0 0 0 >>>>>>>>>>> C12) gr3-gr4_slope 0 0 0 0 0 0 1 -1 >>>>>>>>>>> C13) gr1+gr2-vs-gr3+gr4.intercept 0.5 0.5 -0.5 -0.5 0 0 0 0 >>>>>>>>>>> C14) gr1+gr2-vs-gr3+gr4.slope 0 0 0 0 0.5 0.5 -0.5 -0.5 >>>>>>>>>>> C15) group.effect.intercept >>>>>>>>>>> 1 -1 0 0 0 0 0 0 >>>>>>>>>>> 1 0 -1 0 0 0 0 0 >>>>>>>>>>> 1 0 0 -1 0 0 0 0 >>>>>>>>>>> C16) group.effect.slope >>>>>>>>>>> 0 0 0 0 1 -1 0 0 >>>>>>>>>>> 0 0 0 0 1 0 -1 0 >>>>>>>>>>> 0 0 0 0 1 0 0 -1 >>>>>>>>>>> >>>>>>>>>>> Please: >>>>>>>>>>> 1) Could you check whether the all .mtx are complete and corrected, >> in >>>>>>>>>>> particular the gr1+gr2-vs-gr3+gr4.intercept and the gr1+gr2-vs- >> gr3+gr4. >>>>>>>>> slope? >>>>>>>>>> they look correct, except for the one i noted >>>>>>>>>>> 2) Could you explain the meaning of: >>>>>>>>>>> gr1+gr2-vs-gr3+gr4.slope - does the average slope of grp1 and grp2 >>>>> differ >>>>>>>>> from that of grp3 and 4 >>>>>>>>>>> gr1+gr2-vs-gr3+gr4.intercept - same >>>>>>>>>>> group.effect.slope - interaction between group and covariate >>>>>>>>>>> group.effect.intercept - is there an effect of group on the inercept >>>>>>>>>>> 3) Which is the contrast identifying the effect of covariate on >> group >>>>>>>>>>> differences? >>>>>>>>>> not sure what you mean >>>>>>>>>>> Thanks >>>>>>>>>>> >>>>>>>>>>> Best regards >>>>>>>>>>> >>>>>>>>>>> >>>>>>>>>>> Stefano >>>>>>>>>>> >>>>>>>>>>> >>>>>>>>>>> >>>>>>>>>>>> ----Messaggio originale---- >>>>>>>>>>>> Da: "Douglas N Greve" <greve(a)nmr.mgh.harvard.edu> >>>>>>>>>>>> Data: 5-set-2017 22.59 >>>>>>>>>>>> A: <freesurfer(a)nmr.mgh.harvard.edu> >>>>>>>>>>>> Ogg: Re: [Freesurfer] R: Re: Map of covariance >>>>>>>>>>>> >>>>>>>>>>>> you would need to create a contrast to look for the interaction. If >>>>> you >>>>>>>>>>>> have four gruops and 1 covariate, then it would be >>>>>>>>>>>> >>>>>>>>>>>> 0 0 0 0 1 -1 0 0 >>>>>>>>>>>> >>>>>>>>>>>> 0 0 0 0 1 0 -1 0 >>>>>>>>>>>> >>>>>>>>>>>> 0 0 0 0 1 0 0 -1 >>>>>>>>>>>> >>>>>>>>>>>> >>>>>>>>>>>> >>>>>>>>>>>> On 09/05/2017 04:32 PM, stdp82(a)virgilio.it wrote: >>>>>>>>>>>>> Hi, >>>>>>>>>>>>> e.g., by considering two or more groups, I would like to map the >>>>>>> clusters >>>>>>>>>>>>> reporting the covariance between the functional connectivity or >>>>>>> cortical >>>>>>>>>>>>> thickness (dependent variable) and age, tacking in account the >> group >>>>>>>>>>>>> differences. >>>>>>>>>>>>> Instead, I'm not interested to map the group differences, taking >> in >>>>>>>>> account >>>>>>>>>>>>> the nuisance factors. >>>>>>>>>>>>> Thanks, >>>>>>>>>>>>> Stefano >>>>>>>>>>>>> >>>>>>>>>>>>>> ----Messaggio originale---- >>>>>>>>>>>>>> Da: "Douglas N Greve" <greve(a)nmr.mgh.harvard.edu> >>>>>>>>>>>>>> Data: 5-set-2017 18.12 >>>>>>>>>>>>>> A: <freesurfer(a)nmr.mgh.harvard.edu> >>>>>>>>>>>>>> Ogg: Re: [Freesurfer] Map of covariance >>>>>>>>>>>>>> >>>>>>>>>>>>>> I don't understand what you are asking. can you elaborate? >>>>>>>>>>>>>> >>>>>>>>>>>>>> >>>>>>>>>>>>>> On 08/30/2017 12:50 PM, stdp82(a)virgilio.it wrote: >>>>>>>>>>>>>>> Hi list, >>>>>>>>>>>>>>> by applying a design e.g. 4GV1 in fsgd I could assess the >>>>> dependence >>>>>>>>>>>>>>> of group differences taking in account the effect of covariate. >>>>>>>>>>>>>>> Anyway, where I should look if I want assess the the map showing >>>>> the >>>>>>>>>>>>>>> clusters in which the dependent variable is associated to >>>>> covariate, >>>>>>>>>>>>>>> tacking in account the group difference? Please could you >> suggest >>>>> my >>>>>>>>>>>>>>> the path? >>>>>>>>>>>>>>> Thanks >>>>>>>>>>>>>>> >>>>>>>>>>>>>>> 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 >>>>>>>>>>>> >>>>>>>>>>> _______________________________________________ >>>>>>>>>>> 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 >>>>>>>>>> >>>>>>>>> _______________________________________________ >>>>>>>>> Freesurfer mailing list >>>>>>>>> Freesurfer(a)nmr.mgh.harvard.edu >>>>>>>>> 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 >>>>>>>> >>>>>>> _______________________________________________ >>>>>>> Freesurfer mailing list >>>>>>> Freesurfer(a)nmr.mgh.harvard.edu >>>>>>> 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/ >>> >>> _______________________________________________ >>> Freesurfer mailing list >>> Freesurfer(a)nmr.mgh.harvard.edu >>> 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 >> >> > >_______________________________________________ >Freesurfer mailing list >Freesurfer(a)nmr.mgh.harvard.edu >https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >

1 0

LGI calculation
by Serian doma 16 Oct '17

16 Oct '17

Dear All, I designed an adaptive filter according to local gyrification index values and then want to see the lgi histogram of new smoothed brain volume. However freesurfer gave an error as: ERROR: mritotal failed, see transforms/talairach.log It seems that the input volume orientation has changed. But the input volume is the smoothed version of norm.mgz which is also an output of freesurfer. Could anyone come up with a solution for this issue? -- Serian DOMA

1 0

TRACULA bedpostx step with gpu
by Mehta, Chintan 16 Oct '17

16 Oct '17

Dear FreeSurfer users, I am using Freesurfer 6.0 and Tracula 6.0 for processing MRI and DTI scans. The second step of the trac-all pipeline performs the ball-and-stick fit with the bedpost function from FSL. Documentation for FSL suggests that the use of GPUs can considerably speed this process (from ~15 hours on a single-threaded machine to 30 minutes on GPU; see bulletpoint 7 under processing pipeline at https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/FDT/UserGuide#Processing_pipeline) Using GPU requires calling "bedpostx_gpu" (instead of "bedpostx") on a machine with a NVIDIA GPU and CUDA toolkit, both of which I have access to. The "bedpostx_gpu" function has, otherwise, the same flags as "bedpostx". While there is another post on the FreeSurfer forum on this topic (https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg54498.html) the answer there does not refer to how "bedpostx_gpu" can be used. Is there a way to call on "bedpostx_gpu" instead of "bedpostx" in the second step of the trac-all pipeline? More precisely, is there a way to adjust the command: > trac-all -bedp -c dmrirc to take advantage of GPU capabilities? Alternatively, is the source code for the "trac-all" binary available? For example, if is there a bash script that performs the same steps as the "trac-all -bedp -c dmrirc" available, then GPU capabilities can be exploited by running that script except replacing "bedpostx" with "bedpostx_gpu". Thank you. Best, Chintan

2 1

Longitudinal analysis using data with only two timepoints and LME
by Christoph Abé 16 Oct '17

16 Oct '17

Dear FreeSurfer community, I have a few questions regarding the usage of the LME matlab tools for longitudinal data analyses, and how to set up the model. We have patients and control data that we want to compare with respect to cortical changes over time (two time points: baseline and follow-up). We are also dealing with several cases (100 out of 300) with only one time point. The model is set up with “time” between scans, group, group*time, sex, and age as regressors. But, dealing with only two time points raised some questions: 1) I have read mixed opinions about fitting random slopes when dealing with two time points. Even though it seems to make sense to model individual random slopes, a fit through two time points may actually cause a problem. It also seems redundant to include 2 random factors (intercept and slope) in that case, as fitting random intercepts seems to be sufficient for the covariance estimation. So my question: Is it recommended to model only one random factor (intercept), or even wrong to model two (intercept and slope), when dealing with 2 TPs (especially when dealing with drop outs)? 2) This question is regarding how to set up the time variable. We have a large variance in that measure, meaning the follow-up scans were done between 5-7 years after baseline. As this contributes to the variance of the dependent variable, I would like to include the exact time interval as continuous number in the model (thus a slightly different number for each participant), rather than using time as a two-level factor (e.g. “0” for baseline and “6” for all follow-up cases). I am wondering which approach is recommended and whether there are any significant benefits of using one method (time as two-level factor) over the other (time as continuous) in a LME model with two time points. 3) We have several cases with data at one single time point (ca 100 out of 300). In the design matrix, I include single rows for drop out cases, with time=0. I assume that their number of repeated measures (1) will be handled by the ni-vector generated by the sorting procedure (sortData in matlab). However, we also have cases who were scanned only during clinical follow-up intervention (6 years after the baseline data was collected). Ideally, I would like to avoid assigning those to the baseline time point, for several reasons (e.g. treatment effects, potential scanner drifts over 6 years, etc). Instead, I want to assign them to the follow-up time point. If the better choice in point 2) is to use the actual (continuous) numbers for “time”, I am thinking about assigning the population median of the time difference between scans to those cases. Is this a reasonable approach? Does not seem to be the cleanest way of doing it, as we introduce some error, but may be a reasonable trade off to avoid dropping data of ca. 50 individuals. What is your opinion on that matter? Thanks for any help and opinions. Best, Christoph

2 1

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Freesurfer October 2017