Hi Yuwen - This file is generated by the command dmri_paths, which is run before the dmri_pathstats command. You can see the exact command lines in scripts/trac-all.cmd (and the full output in scripts/trac-all.log).
Best, a.y ________________________________________ From: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Yuwen Hung [yuw...@mit.edu] Sent: Friday, July 14, 2017 8:17 AM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] what program generates "path.map.txt" for dmri_pathstats to run? Dear DTI experts: I am wondering if anybody could provide any information to help me out with this constant error that I am desperate to resolve? I just need to know what program generates this "path.map.txt" for the tracula script dmri_pathstats to run through? dmri_pathstats --intrc START_610/dpath/lh.cst_AS_avg33_mni_bbr --dtbase START_610/dmri/dtifit --path lh.cst --subj START_610 --out START_610/dpath/lh.cst_AS_avg33_mni_bbr/pathstats.overall.txt --outvox START_610/dpath/lh.cst_AS_avg33_mni_bbr/pathstats.byvoxel.txt --debug cwd /gablab/p/START/NEW_DTI_ANALYSIS_2017/START_610 cmdline dmri_pathstats --intrc START_610/dpath/lh.cst_AS_avg33_mni_bbr --dtbase START_610/dmri/dtifit --path lh.cst --subj START_610 --out START_610/dpath/lh.cst_AS_avg33_mni_bbr/pathstats.overall.txt --outvox START_610/dpath/lh.cst_AS_avg33_mni_bbr/pathstats.byvoxel.txt --debug sysname Linux hostname node031 machine x86_64 user yuwenh Input tracula directory: /gablab/p/START/NEW_DTI_ANALYSIS_2017/START_610/START_610/dpath/lh.cst_AS_avg33_mni_bbr Input DTI fit base: /gablab/p/START/NEW_DTI_ANALYSIS_2017/START_610/START_610/dmri/dtifit Pathway name: lh.cst Subject name: START_610 Output file for overall measures: /gablab/p/START/NEW_DTI_ANALYSIS_2017/START_610/START_610/dpath/lh.cst_AS_avg33_mni_bbr/pathstats.overall.txt Output file for voxel-by-voxel measures: /gablab/p/START/NEW_DTI_ANALYSIS_2017/START_610/START_610/dpath/lh.cst_AS_avg33_mni_bbr/pathstats.byvoxel.txt Lower threshold for probability: 0.200000 Computing statistics on /gablab/p/START/NEW_DTI_ANALYSIS_2017/START_610/START_610/dpath/lh.cst_AS_avg33_mni_bbr... ERROR: Could not open /gablab/p/START/NEW_DTI_ANALYSIS_2017/START_610/START_610/dpath/lh.cst_AS_avg33_mni_bbr/path.map.txt for reading Your help is being greatly appreciated, Yuwen -----Original Message----- From: freesurfer-boun...@nmr.mgh.harvard.edu [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of freesurfer-requ...@nmr.mgh.harvard.edu Sent: Friday, July 14, 2017 4:14 AM To: freesurfer@nmr.mgh.harvard.edu Subject: Freesurfer Digest, Vol 161, Issue 25 Send Freesurfer mailing list submissions to freesurfer@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-requ...@nmr.mgh.harvard.edu You can reach the person managing the list at freesurfer-ow...@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: PETsurfer AC/TOF (Douglas N Greve) 2. Re: 3G1V.fsgd (Douglas N Greve) 3. Re: GLM Analysis Number of vertices and Area (Douglas N Greve) 4. Regression diagnostic in context of surface-based analysis (Antonin Skoch) 5. bbregister + mri_vol2vol different results (Paul Glad Mihai) 6. R: Re: 3G1V.fsgd (std...@virgilio.it) 7. R: R: Re: 3G1V.fsgd (std...@virgilio.it) 8. Re: R: Re: 3G1V.fsgd (Douglas N Greve) 9. Mid point on Freeview (Trisanna Sprung-Much) 10. vertex-wise contra-lateral mapping on an ico surface (Burke Rosen) 11. Re: Mid point on Freeview (Bruce Fischl) 12. Re: ERROR: dimension mismatch between input volume and seg - VolumeROICorticalThickness (M Janani) 13. R: Re: R: Re: 3G1V.fsgd (std...@virgilio.it) 14. problems with recon-all in 6.0 (Lars M. Rimol) ---------------------------------------------------------------------- Message: 1 Date: Thu, 13 Jul 2017 16:28:24 -0400 From: Douglas N Greve <gr...@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] PETsurfer AC/TOF To: freesurfer@nmr.mgh.harvard.edu Message-ID: <d5234734-a0cc-e310-cd02-d73229c94...@nmr.mgh.harvard.edu> Content-Type: text/plain; charset=utf-8; format=flowed Sorry, I don't know what the difference is. I always use the mean update volume as the template for registration. On 07/13/2017 01:57 PM, Fu, Jason (NIH/NINDS) [F] wrote: > ac/tof is attenuation corrected/time of flight. Ac/hd is attenuation > corrected/head. > > -----Original Message----- > From: Douglas N Greve [mailto:gr...@nmr.mgh.harvard.edu] > Sent: Thursday, July 13, 2017 12:52 PM > To: freesurfer@nmr.mgh.harvard.edu > Subject: Re: [Freesurfer] PETsurfer AC/TOF > > sorry, what is an ac/tof file? > > > On 07/13/2017 12:12 PM, Fu, Jason (NIH/NINDS) [F] wrote: >> 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 >> >> >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > gr...@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@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@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@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: 2 Date: Thu, 13 Jul 2017 16:30:54 -0400 From: Douglas N Greve <gr...@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] 3G1V.fsgd To: freesurfer@nmr.mgh.harvard.edu Message-ID: <1139ca82-1846-fbb5-9650-f10a5ad86...@nmr.mgh.harvard.edu> Content-Type: text/plain; charset=utf-8; format=flowed On 07/13/2017 10:37 AM, std...@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@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@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: Thu, 13 Jul 2017 16:38:21 -0400 From: Douglas N Greve <gr...@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] GLM Analysis Number of vertices and Area To: freesurfer@nmr.mgh.harvard.edu Message-ID: <7ef1f42e-31d6-fe1e-7e89-9e04338a8...@nmr.mgh.harvard.edu> Content-Type: text/plain; charset=utf-8; format=flowed I'm not sure what you mean. Do you want stats for every cluster regardless of significance? If so, you can run the monte carlo correction with a clusterwise p-value (--cwp in mri_glmfit-sim) of 1.0 On 07/13/2017 11:52 AM, Aman Montazeri wrote: > 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 > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@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: Thu, 13 Jul 2017 22:48:03 +0200 From: Antonin Skoch <a...@ikem.cz> Subject: [Freesurfer] Regression diagnostic in context of surface-based analysis To: freesurfer@nmr.mgh.harvard.edu Message-ID: <1034294575-17...@posta.medicon.cz> Content-Type: text/plain; charset="utf-8" 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 -------------- next part -------------- An HTML attachment was scrubbed... URL: http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20170713/11005295/attachment-0001.html ------------------------------ Message: 5 Date: Thu, 13 Jul 2017 23:02:49 +0200 (CEST) From: Paul Glad Mihai <mi...@cbs.mpg.de> Subject: [Freesurfer] bbregister + mri_vol2vol different results To: freesurfer@nmr.mgh.harvard.edu Message-ID: <928982793.64522.1499979769498.javamail.zim...@cbs.mpg.de> Content-Type: text/plain; charset="utf-8" Hello, I'm getting two different results from the coregistration step. When I run bbregister on the mean epi it coregisters properly and writes out _bbreg.nii. The next step involves registering the realigned epi time series to the T1 image using the same transform matrix calculated from the mean image. But the results fail miserably. I've attached some sample images. I came across the same result after transforming the matrix it to ITK space and applying the transform using ANTs' applyTransform, which tells me that the ITK conversion works, but this registration goes wrong. Or I may not really understand what I'm doing, lol. Here are the commands: bbregister --t2 --epi-mask --init-header --fslmat /data/pt_nmc002/TDMGB_FMRI_coreg/tmp/preproc/_subject_id_sub-01/bbreg/mapflow/_bbreg0/meanusub-01_task-spespk_run-01_bold_bbreg_sub-01.mat --reg /data/pt_nmc002/TDMGB_FMRI_coreg/tmp/preproc/_subject_id_sub-01/bbreg/mapflow/_bbreg0/meanusub-01_task-spespk_run-01_bold_bbreg_sub-01.dat --o /data/pt_nmc002/TDMGB_FMRI_coreg/tmp/preproc/_subject_id_sub-01/bbreg/mapflow/_bbreg0/meanusub-01_task-spespk_run-01_bold_bbreg.nii --mov /data/pt_nmc002/TDMGB_FMRI_coreg/tmp/preproc/_subject_id_sub-01/bbreg/mapflow/_bbreg0/meanusub-01_task-spespk_run-01_bold.nii --s sub-01 mri_vol2vol --fsl /data/pt_nmc002/TDMGB_FMRI_coreg/tmp/preproc/_subject_id_sub-01/bbreg/mapflow/_bbreg0/meanusub-01_task-spespk_run-01_bold_bbreg_sub-01.mat --mov /data/pt_nmc002/TDMGB_FMRI_coreg/tmp/preproc/_subject_id_sub-01/coreg_func/mapflow/_coreg_func0/usub-01_task-spespk_run-01_bold.nii --targ /data/pt_nmc002/TDMGB_FMRI_coreg/tmp/preproc/_subject_id_sub-01/brainextract/sub-01_acq-T1w_brain.nii.gz --o /data/pt_nmc002/TDMGB_FMRI_coreg/tmp/preproc/_subject_id_sub-01/coreg_func/mapflow/_coreg_func0/usub-01_task-spespk_run-01_bold_warped.nii Regards, Glad -- Paul Glad Mihai, PhD Independent Research Group "Neural Mechanisms of Human Communication" Max Planck Institute for Human Cognitive and Brain Sciences Stephanstra?e 1A, 04103 Leipzig, Germany Phone: +49 (0) 341-9940-2478 E-mail: mi...@cbs.mpg.de -------------- next part -------------- A non-text attachment was scrubbed... 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Name: sub-01_acq-T1w_brain_bbreg_mean_epi.png Type: image/png Size: 99341 bytes Desc: not available Url : http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20170713/9ac9c23e/attachment-0005.png ------------------------------ Message: 6 Date: Thu, 13 Jul 2017 23:44:48 +0200 (CEST) From: <std...@virgilio.it> Subject: [Freesurfer] R: Re: 3G1V.fsgd To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu> Message-ID: <1509518625.6040911499982288185.javamail.ht...@fep-webmail-06.iol.local> Content-Type: text/plain;charset="UTF-8" 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" <gr...@nmr.mgh.harvard.edu> >Data: 13-lug-2017 22.30 >A: <freesurfer@nmr.mgh.harvard.edu> >Ogg: Re: [Freesurfer] 3G1V.fsgd > > > >On 07/13/2017 10:37 AM, std...@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@nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > >-- >Douglas N. Greve, Ph.D. >MGH-NMR Center >gr...@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@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. > > ------------------------------ Message: 7 Date: Fri, 14 Jul 2017 00:41:31 +0200 (CEST) From: <std...@virgilio.it> Subject: [Freesurfer] R: R: Re: 3G1V.fsgd To: freesurfer@nmr.mgh.harvard.edu Message-ID: <1639912009.6043261499985691175.javamail.ht...@fep-webmail-06.iol.local> Content-Type: text/plain;charset="UTF-8" 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: std...@virgilio.it >Data: 13-lug-2017 23.44 >A: "Freesurfer support list"<freesurfer@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" <gr...@nmr.mgh.harvard.edu> >>Data: 13-lug-2017 22.30 >>A: <freesurfer@nmr.mgh.harvard.edu> >>Ogg: Re: [Freesurfer] 3G1V.fsgd >> >> >> >>On 07/13/2017 10:37 AM, std...@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@nmr.mgh.harvard.edu >>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >>-- >>Douglas N. Greve, Ph.D. >>MGH-NMR Center >>gr...@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@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@nmr.mgh.harvard.edu >https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > ------------------------------ Message: 8 Date: Thu, 13 Jul 2017 18:45:43 -0400 From: Douglas N Greve <gr...@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] R: Re: 3G1V.fsgd To: freesurfer@nmr.mgh.harvard.edu Message-ID: <a851f3c8-8a16-6e47-8ab3-ebaae99fa...@nmr.mgh.harvard.edu> Content-Type: text/plain; charset=utf-8; format=flowed those are correct On 07/13/2017 05:44 PM, std...@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" <gr...@nmr.mgh.harvard.edu> >> Data: 13-lug-2017 22.30 >> A: <freesurfer@nmr.mgh.harvard.edu> >> Ogg: Re: [Freesurfer] 3G1V.fsgd >> >> >> >> On 07/13/2017 10:37 AM, std...@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@nmr.mgh.harvard.edu >>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> -- >> Douglas N. Greve, Ph.D. >> MGH-NMR Center >> gr...@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@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@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@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: 9 Date: Thu, 13 Jul 2017 19:55:16 -0400 From: Trisanna Sprung-Much <trisanna.sprung-m...@mail.mcgill.ca> Subject: [Freesurfer] Mid point on Freeview To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu> Message-ID: <cag+torvxamwxgerdkyugqfbthr2o0j5t37kaod7-3cuvgxg...@mail.gmail.com> Content-Type: text/plain; charset="utf-8" Hi there I have a question concerning viewing a surface in Freeview (FS 6.0): *What does the "mid point" variable refer to?* I can change it and it seems to change the shading within the sulci when I am looking at a white matter surface. Many thanks Trisanna -- Ph.D. Candidate McGill University Integrated Program in Neuroscience Psychology -------------- next part -------------- An HTML attachment was scrubbed... URL: http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20170713/9f5d4ec4/attachment-0001.html ------------------------------ Message: 10 Date: Thu, 13 Jul 2017 17:38:52 -0700 From: Burke Rosen <bqro...@gmail.com> Subject: [Freesurfer] vertex-wise contra-lateral mapping on an ico surface To: freesurfer@nmr.mgh.harvard.edu Message-ID: <CAOBOJhrfbxDL=mrewac-jlkwx0ol_0sxd2fek6umgtanout...@mail.gmail.com> Content-Type: text/plain; charset="utf-8" Hello, I've created single subject surfaces sampled in ico7 space with make_average_subject --ico with a single input subject. Because of the ico7 sampling, both hemispheres have the same number of vertices. I am interested in the index-to-index mapping between equivalent contra-lateral vertices. How do I compute this mapping? Thank you, -Burke Rosen -------------- next part -------------- An HTML attachment was scrubbed... URL: http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20170713/f2359328/attachment-0001.html ------------------------------ Message: 11 Date: Thu, 13 Jul 2017 22:01:23 -0400 (EDT) From: Bruce Fischl <fis...@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] Mid point on Freeview To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu> Message-ID: <alpine.lrh.2.20.1707132200370.5...@door.nmr.mgh.harvard.edu> Content-Type: text/plain; charset=US-ASCII; format=flowed Hi do you mean in the curvature display? If so, it is the "0" point at which red transitions to green (for positive and negative curvature) cheers Bruce On Thu, 13 Jul 2017, Trisanna Sprung-Much wrote: > Hi there > I have a question concerning viewing a surface in Freeview (FS 6.0): What > does the "mid point" variable refer to? I can change it and it seems to > change the shading within the sulci when I am looking at a white matter > surface. > > Many thanks > > Trisanna > -- > Ph.D. CandidateMcGill University > Integrated Program in Neuroscience > Psychology > > > > ------------------------------ Message: 12 Date: Fri, 14 Jul 2017 06:05:56 +0000 From: M Janani <janan...@hcl.com> Subject: Re: [Freesurfer] ERROR: dimension mismatch between input volume and seg - VolumeROICorticalThickness To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu> Message-ID: <ps1pr0401mb140212fc3921c85c6551df23d6...@ps1pr0401mb1402.apcprd04.prod.outlook.com> Content-Type: text/plain; charset="us-ascii" Hi Douglas Greve<https://www.mail-archive.com/search?l=freesurfer@nmr.mgh.harvard.edu&q=from:%22Douglas+Greve%22>, Thanks for your support. I tried with the --reshape-factor 6. But it didn't work for me. The segmentation was created using the below mentioned data 1. SPM standard ROI 2. .dat file generated using the T1.nii(available in SPM8 template) and fsaverage. Please help us to proceed further. Regards, Janani ----------------------------------------------------------------------------------------------------------------------------------------------------------------------- How did you create the segmentation? You can change the shape of the seg with mri_surf2surf --reshape 6 --s fsaverage --hemi lh --sval seg.mgh --tval seg.reshape.mgh On 7/7/17 10:15 AM, M Janani wrote: Hi Team, I'm attempting to extract cortical thickness values for a region-of-interest (ROI) defined in volume spacesubject for PiB MRI. I got the below mentioned error while computing the stats value cwd cmdline mri_segstats --seg freesurfer/subjects/fsaverage/surf/lh.fsaverage.CBLROI.mgh --in lh.thickness.fsaverage.mgh --sum segstats-CBLROI.txt sysname Linux hostname teslak80 machine x86_64 user lakshman UseRobust 0 Loading /freesurfer/subjects/fsaverage/surf/lh.fsaverage.CBLROI.mgh Loading lh.thickness.fsaverage.mgh ERROR: dimension mismatch between input volume and seg input 27307 1 6 seg 23406 1 7 I tried with the solution provided in the below mail, but it didn't work for me https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2013-January/027405.html<https://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/2013-January/027405.html> <https://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/2013-January/027405.html> Any help would be really helpful. Regards, Janani ::DISCLAIMER:: ---------------------------------------------------------------------------------------------------------------------------------------------------- The contents of this e-mail and any attachment(s) are confidential and intended for the named recipient(s) only. E-mail transmission is not guaranteed to be secure or error-free as information could be intercepted, corrupted, lost, destroyed, arrive late or incomplete, or may contain viruses in transmission. The e mail and its contents (with or without referred errors) shall therefore not attach any liability on the originator or HCL or its affiliates. Views or opinions, if any, presented in this email are solely those of the author and may not necessarily reflect the views or opinions of HCL or its affiliates. Any form of reproduction, dissemination, copying, disclosure, modification, distribution and / or publication of this message without the prior written consent of authorized representative of HCL is strictly prohibited. If you have received this email in error please delete it and notify the sender immediately. Before opening any email and/or attachments, please check! them for viruses and other defects. ---------------------------------------------------------------------------------------------------------------------------------------------------- _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer _______________________________________________ Freesurfer mailing list Freesurfer@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. -------------- next part -------------- An HTML attachment was scrubbed... URL: http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20170714/39ae16a9/attachment-0001.html ------------------------------ Message: 13 Date: Fri, 14 Jul 2017 10:01:37 +0200 (CEST) From: <std...@virgilio.it> Subject: [Freesurfer] R: Re: R: Re: 3G1V.fsgd To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu> Message-ID: <607673702.20602801500019297209.javamail.ht...@fep-webmail-08.iol.local> Content-Type: text/plain;charset="UTF-8" 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" <gr...@nmr.mgh.harvard.edu> >Data: 14-lug-2017 0.45 >A: <freesurfer@nmr.mgh.harvard.edu> >Ogg: Re: [Freesurfer] R: Re: 3G1V.fsgd > >those are correct > > >On 07/13/2017 05:44 PM, std...@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" <gr...@nmr.mgh.harvard.edu> >>> Data: 13-lug-2017 22.30 >>> A: <freesurfer@nmr.mgh.harvard.edu> >>> Ogg: Re: [Freesurfer] 3G1V.fsgd >>> >>> >>> >>> On 07/13/2017 10:37 AM, std...@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@nmr.mgh.harvard.edu >>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>> -- >>> Douglas N. Greve, Ph.D. >>> MGH-NMR Center >>> gr...@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@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@nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> > >-- >Douglas N. Greve, Ph.D. >MGH-NMR Center >gr...@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@nmr.mgh.harvard.edu >https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > ------------------------------ Message: 14 Date: Fri, 14 Jul 2017 10:13:20 +0200 From: "Lars M. Rimol" <lari...@gmail.com> Subject: [Freesurfer] problems with recon-all in 6.0 To: FS maling list <freesurfer@nmr.mgh.harvard.edu> Message-ID: <ca+nyyyr9dqiq48ffvwmqfpkv7ornydy87qrqssjdr73r357...@mail.gmail.com> Content-Type: text/plain; charset="utf-8" Hi, I'm trying to run recon-all in FreeSurfer 6.0 but I keep getting error messages and some strange behavior: ls 01001/0/2/ 100.dcm 106.dcm 111.dcm 117.dcm 122.dcm 128.dcm 133.dcm 139.dcm 144.dcm 14.dcm 155.dcm 160.dcm 166.dcm 171.dcm 17.dcm 22.dcm 28.dcm 33.dcm 39.dcm 44.dcm 4.dcm 55.dcm 60.dcm 66.dcm 71.dcm 77.dcm 82.dcm 88.dcm 93.dcm 99.dcm 101.dcm 107.dcm 112.dcm 118.dcm 123.dcm 129.dcm 134.dcm 13.dcm 145.dcm 150.dcm 156.dcm 161.dcm 167.dcm 172.dcm 18.dcm 23.dcm 29.dcm 34.dcm 3.dcm 45.dcm 50.dcm 56.dcm 61.dcm 67.dcm 72.dcm 78.dcm 83.dcm 89.dcm 94.dcm 9.dcm 102.dcm 108.dcm 113.dcm 119.dcm 124.dcm 12.dcm 135.dcm 140.dcm 146.dcm 151.dcm 157.dcm 162.dcm 168.dcm 173.dcm 19.dcm 24.dcm 2.dcm 35.dcm 40.dcm 46.dcm 51.dcm 57.dcm 62.dcm 68.dcm 73.dcm 79.dcm 84.dcm 8.dcm 95.dcm 103.dcm 109.dcm 114.dcm 11.dcm 125.dcm 130.dcm 136.dcm 141.dcm 147.dcm 152.dcm 158.dcm 163.dcm 169.dcm 174.dcm 1.dcm 25.dcm 30.dcm 36.dcm 41.dcm 47.dcm 52.dcm 58.dcm 63.dcm 69.dcm 74.dcm 7.dcm 85.dcm 90.dcm 96.dcm 104.dcm 10.dcm 115.dcm 120.dcm 126.dcm 131.dcm 137.dcm 142.dcm 148.dcm 153.dcm 159.dcm 164.dcm 16.dcm 175.dcm 20.dcm 26.dcm 31.dcm 37.dcm 42.dcm 48.dcm 53.dcm 59.dcm 64.dcm 6.dcm 75.dcm 80.dcm 86.dcm 91.dcm 97.dcm 105.dcm 110.dcm 116.dcm 121.dcm 127.dcm 132.dcm 138.dcm 143.dcm 149.dcm 154.dcm 15.dcm 165.dcm 170.dcm 176.dcm 21.dcm 27.dcm 32.dcm 38.dcm 43.dcm 49.dcm 54.dcm 5.dcm 65.dcm 70.dcm 76.dcm 81.dcm 87.dcm 92.dcm 98.dcm recon-all -subject 1001_c1 -i 01001/0/2/1.dcm -all ................................ writing to /work/projects/nn9208k/tbi/morfometri_test/?1001_c1/mri/orig/001.mgz... #-------------------------------------------- #@# MotionCor fr. 14. juli 10:04:21 +0200 2017 ERROR: no run data found in /work/projects/nn9208k/tbi/morfometri_test/?1001_c1/mri. Make sure to have a volume called 001.mgz in /work/projects/nn9208k/tbi/morfometri_test/?1001_c1/mri/orig. If you have a second run of data call it 002.mgz, etc. See also: http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Conversion Linux compute-16-36.local 2.6.32-696.3.2.el6.x86_64 #1 SMP Tue Jun 20 01:26:55 UTC 2017 x86_64 x86_64 x86_64 GNU/Linux recon-all -s ?1001_c1 exited with ERRORS at fr. 14. juli 10:04:21 +0200 2017 Not sure why it crashes, and why does it add "?" to the subject name? Thank you! sincerely yours, Lars M. Rimol, PhD Senior researcher, Norwegian Advisory Unit for functional MRI Department of Radiology, St. Olav's University hospital, 7006 Trondheim, Norway -------------- next part -------------- An HTML attachment was scrubbed... URL: http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20170714/e0413278/attachment.html ------------------------------ _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer End of Freesurfer Digest, Vol 161, Issue 25 ******************************************* _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
