Re: [Freesurfer] beta v5.3 for fedora 18 and ubuntu 13
Tested recon-all tonight on lubuntu 13.04. I did not encounter any problems. Also freeview runs without an error for the subject bert. On Mon, 13 May 2013 14:40:10 +0200 Jörg Pfannmöller pfannmo...@uni-greifswald.de wrote: Just for completeness, I refer to my first contribution: http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg28267.html On Mon, 13 May 2013 13:58:30 +0200 Joerg Pfannmoeller pfannmo...@uni-greifswald.de wrote: Hello Nick, just installed and tested the BETA version. Up to now no problem encountered. Recon-all is just running as a test (using -use-gpu). OS is Lubuntu 13.04. I report on the segmentation as soon as it is finished. So long Joerg On Sun, 12 May 2013 22:41:25 -0400 (EDT) Nick Schmansky ni...@nmr.mgh.harvard.edu wrote: Fedora 18, Ubuntu 13 and Gentoo 64 users, another beta of the upcoming v5.3 is available here: ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/5.3.0-BETA/freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0-BETA.tar.gz this one is just intended for the Fedora 18, Ubuntu 13, Gentoo 64 users who wished to test that the segfault problem in v5.2 and the prior beta v5.3 is fixed. Your help in testing this release is appreciated. Thanks, Nick 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. -- Joerg Pfannmoeller pfannmo...@uni-greifswald.de ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- pfannmo...@uni-greifswald.de ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Joerg Pfannmoeller pfannmo...@uni-greifswald.de ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] hematoma problem
hi I am working on severe TBI and most of them suffer from large hematoma and according to litterarture, the apearance on T1 changes accordind to the stage of the trauma, from 3days (early suba acute) to 14 days (late subacute) the T1 signal from hematoma is Hyperintense and after that it becomes hypointense. I want to know how freesurfer, especially the skull stripping or brain extraction step, deals with these two cases (i have both in my database). I want later to extract the cortical ribbon for tractography use. Thanks___ 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] rs-fMRI data on pial surface
Hi Freesurfers, For this analysis I plan to do, I want to map resting-state data in native (T1) space to the pial surface. The command I use for this is: mri_vol2surf --src fMRI_nat.nii --regheader subjID --hemi lh --projfrac-avg 0 1 0.05 --surf pial --o fMRI_2surf.mgh So the intention is to average the resting state data over the cortex and to map this to the pial surface. However, if I'm not mistaken the --projfrac-avg option projects along the outward pointing surface normal. Therefore, when using the pial surface, I expected that the proper call would be --projfrac-avg 0 -1 -0.05. However, this command does not run, whereas the command given above does, and yields (sensible) output. So is the command given above correct after all? And does this imply that for the pial surface, the volumetric data is actually projected along the inward pointing normals? Best regards, René ___ 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.
Re: [Freesurfer] hematoma problem
sorry, I don't have any experience with hematomas. You'll just have to try it and see On Tue, 14 May 2013, LAOUCHEDI MAKHLOUF wrote: hi I am working on severe TBI and most of them suffer from large hematoma and according to litterarture, the apearance on T1 changes accordind to the stage of the trauma, from 3days (early suba acute) to 14 days (late subacute) the T1 signal from hematoma is Hyperintense and after that it becomes hypointense. I want to know how freesurfer, especially the skull stripping or brain extraction step, deals with these two cases (i have both in my database). I want later to extract the cortical ribbon for tractography use. Thanks ___ 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.
Re: [Freesurfer] beta v5.3 for fedora 18 and ubuntu 13
Unfortunately encountered a problem in fs-fast stream during execution of selxavg3-sess. Added a relevant part of the log file below: sxa3pwd = /home/...removed... sxa3cmd = /usr/local/freesurfer/fsfast/bin/selxavg3-sess -s ./session02 -analysis harm.sm0.mni305 /usr/local/freesurfer/fsfast/toolbox/fast_selxavg3.m #@# session02 ### /home/...removed.../freesurfer_fMRT/session02 - $Id: fast_selxavg3.m,v 1.100.2.2 2012/11/30 18:40:38 greve Exp $ /usr/local/freesurfer/fsfast/toolbox/fast_selxavg3.m /usr/local/freesurfer/fsfast/toolbox/fast_ldanaflac.m /usr/local/freesurfer/matlab/MRIread.m - outtop = /home/...removed.../freesurfer_fMRT Extension format = nii.gz 1 stim-v-base.mat nruns = 1 autostimdur = outanadir = /home/...removed.../freesurfer_fMRT/session02/bold/harm.sm0.mni305 Found 45239/537168 ( 8.4) voxels in mask Creating Design Matrix ... creation time = 0.009 sec DoMCFit = 1 ntptot = 100, nX = 8, DOF = 92 Saving X matrix to /home/...removed.../freesurfer_fMRT/session02/bold/harm.sm0.mni305/Xtmp.mat XCond = 444.207 (normalized) Computing compensation for resdual AR1 bias 1 -0.5 -0.493933(t=0.004964) 2 -0.25 -0.269463(t=0.00648) 3 0 -0.0514275(t=0.00734) 4 0.25 0.155364(t=0.008221) 5 0.5 0.337574(t=0.009058) AR1 Correction M: 0.0769642 1.19552 Computing contrast matrices OLS Beta Pass run 1t= 0.0 Global Mean 725.29 Global In-Mask Mean = 725.295 (694.97) Rescale Target = 100 RescaleFactor = 0.137875 OLS Residual Pass run 1t= 0.0 Saving rho1 Smoothing ACF /usr/local/freesurfer/bin/mri_fwhm --mask /home/...removed.../freesurfer_fMRT/session02/bold/harm.sm0.mni305/mask.nii.gz --i /home/...removed.../freesurfer_fMRT/session02/bold/harm.sm0.mni305/rho1mn.nii.gz --o /home/...removed.../freesurfer_fMRT/session02/bold/harm.sm0.mni305/rho1mn.sm.nii.gz --fwhm 20.00 --smooth-only /usr/local/freesurfer/bin/mri_fwhm: /usr/local/matlab/R2008a/sys/os/glnxa64/libstdc++.so.6: version `GLIBCXX_3.4.11' not found (required by /usr/local/freesurfer/bin/mri_fwhm) /usr/local/freesurfer/bin/mri_fwhm: /usr/local/matlab/R2008a/sys/os/glnxa64/libstdc++.so.6: version `GLIBCXX_3.4.9' not found (required by /usr/local/freesurfer/bin/mri_fwhm) ERROR: /usr/local/freesurfer/bin/mri_fwhm --mask /home/...removed.../freesurfer_fMRT/session02/bold/harm.sm0.mni305/mask.nii.gz --i /home/...removed.../freesurfer_fMRT/session02/bold/harm.sm0.mni305/rho1mn.nii.gz --o /home/...removed.../freesurfer_fMRT/session02/bold/harm.sm0.mni305/rho1mn.sm.nii.gz --fwhm 20.00 --smooth-only -- ERROR: fast_selxavg3() failed\n Seemingly a problem with GLIBCXX_3.4.11. My OS is Lubuntu 13.04. On Tue, 14 May 2013 08:28:05 +0200 Joerg Pfannmoeller pfannmo...@uni-greifswald.de wrote: Tested recon-all tonight on lubuntu 13.04. I did not encounter any problems. Also freeview runs without an error for the subject bert. On Mon, 13 May 2013 14:40:10 +0200 Jörg Pfannmöller pfannmo...@uni-greifswald.de wrote: Just for completeness, I refer to my first contribution: http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg28267.html On Mon, 13 May 2013 13:58:30 +0200 Joerg Pfannmoeller pfannmo...@uni-greifswald.de wrote: Hello Nick, just installed and tested the BETA version. Up to now no problem encountered. Recon-all is just running as a test (using -use-gpu). OS is Lubuntu 13.04. I report on the segmentation as soon as it is finished. So long Joerg On Sun, 12 May 2013 22:41:25 -0400 (EDT) Nick Schmansky ni...@nmr.mgh.harvard.edu wrote: Fedora 18, Ubuntu 13 and Gentoo 64 users, another beta of the upcoming v5.3 is available here: ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/5.3.0-BETA/freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0-BETA.tar.gz this one is just intended for the Fedora 18, Ubuntu 13, Gentoo 64 users who wished to test that the segfault problem in v5.2 and the prior beta v5.3 is fixed. Your help in testing this release is appreciated. Thanks, Nick 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. -- Joerg Pfannmoeller pfannmo...@uni-greifswald.de ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu
Re: [Freesurfer] Show curvature and show overlay
Dear freesurfer experts, I am new to freesurfer and I want to project my single-subject MVPA (obtained in Matlab) results on a single-subject brain surface with curvature. I followed the steps from the tutorial: - reconstructed individual subject's brain surface - wrote my MVPA results map as a nifti image - resampled the map onto the surface Now I want to visualize it. The tutorial (http://ftp.nmr.mgh.harvard.edu/fswiki/FsTutorial/NavigateResampledParametricMap) suggests to use qsurfer, however I don't seem to have this command. I tried to open the surface with tksurfer and then load the overlay, as described in the tutorial on visualization. However, when I open an inflated surface file, both buttons show overlay and show curvature are not active (though I have the .sulc file in the /surf). This is probably a very simple question, but I am stuck here. I would appreciate any advise on how to do the visualization: either from the command line or with tksurfer tools. thank you, kind regards, Irina Simanova ___ 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.
Re: [Freesurfer] Show curvature and show overlay
Hi Irina you need to load the overlay (file-load overlay or -overlay fname on the cmdline) and the curvature file (file-load curvature or just -sulc on the cmdline I think) cheers Bruce On Tue, 14 May 2013, Irina Simanova wrote: Dear freesurfer experts, I am new to freesurfer and I want to project my single-subject MVPA (obtained in Matlab) results on a single-subject brain surface with curvature. I followed the steps from the tutorial: - reconstructed individual subject's brain surface - wrote my MVPA results map as a nifti image - resampled the map onto the surface Now I want to visualize it. The tutorial (http://ftp.nmr.mgh.harvard.edu/fswiki/FsTutorial/NavigateResampledParametricMap) suggests to use qsurfer, however I don't seem to have this command. I tried to open the surface with tksurfer and then load the overlay, as described in the tutorial on visualization. However, when I open an inflated surface file, both buttons show overlay and show curvature are not active (though I have the .sulc file in the /surf). This is probably a very simple question, but I am stuck here. I would appreciate any advise on how to do the visualization: either from the command line or with tksurfer tools. thank you, kind regards, Irina Simanova ___ 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.
Re: [Freesurfer] Still confused by group analysis..
Not sure whether anyone'd seen my last email (below). Again apologies for the multitude of questions, I hope this is the last batch for this analysis.. On 12 May 2013 16:45, Tudor Popescu tud...@gmail.com wrote: Dear Freesurfer experts, I very much appreciate your help with an additional set of questions. I feel I'm really close to getting this finished :) 1) In a design with group and gender as discrete factors and age as a continuous factor, why is it that QDEC only displays the contrast Does the avg thickness, accounting for gender, differ between group1 and group2? and not also ..acounting for gender and age,..? 2) In QDEC, if I am left with a cluster after setting the FDR rate to 0.1, does that qualify as a trend towads significance in the same way as when obtaining a p value .1 for a behavioural effect? 3) From the group tutorial, I see that mris_preproc has to be called with flag --cache-in ess.fwhm10thickn.fsaverage. However, after running recon-all (including with the –qcache option) on all my subjects, none of their folders contains a file named ?h.thickness.fwhm10.fsaverage.mgh 4) When comparing two healthy groups, is there anything to gain from using a fsaverage built from the sample (with make_average_subject) as opposed to using the default fsaverage? 5) What is the difference between running make_average_subject and running mris_preproc with --target fsaverage? 6) For my ROI mri_glmfit analysis, I wanted to use the FSGD and contrast files that were automatically created when I did my QDEC whole-brain analysis, since the design will be the same. However, although I identified the FSGD file (qdec.fsgd), I cannot see any plaintext file in the QDEC folder that looks like it contains contrast definitions! Thanks! Tudor ___ 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] Rejoindre mon réseau sur LinkedIn
LinkedIn Soo-Eun Chang souhaite se connecter à vous sur LinkedIn : -- Je vous invite à faire partie de mon réseau professionnel en ligne sur le site LinkedIn. Accepter l'invitation de Soo-Eun Chang http://www.linkedin.com/e/-qq80um-hgp5ye8d-68/qaAr-Z_86TRZ5lXG-dA9kZQ49qSe59qYFaT9QmQ47Ub3yw/blk/I457516488_65/3wOtCVFbmdxnSVFbm8JrnpKqlZJrmZzbmNJpjRQnOpBtn9QfmhBt71BoSd1p65Lr6lOfPkSnPwUd3oNdjsRd4ALhCxRkRZHm5kLc30MdPgQdzkOcP4LrCBxbOYWrSlI/eml-comm_invm-b-in_ac-inv28/?hs=falsetok=2BhvyDnTSU2lM1 Voir le profil de Soo-Eun Chang http://www.linkedin.com/e/-qq80um-hgp5ye8d-68/rso/76206546/HgJj/name/66471168_I457516488_65/?hs=falsetok=1iY1cuy3qU2lM1 -- Vous recevez des invitations par e-mail. Cet e-mail est destiné à Freesurfer List. Découvrez pourquoi nous avons inclus ceci : http://www.linkedin.com/e/-qq80um-hgp5ye8d-68/plh/http%3A%2F%2Fhelp%2Elinkedin%2Ecom%2Fapp%2Fanswers%2Fdetail%2Fa_id%2F4788/-GXI/?hs=falsetok=1Vj5Kxgq2U2lM1 (c) 2012, LinkedIn Corporation. 2029 Stierlin Ct, Mountain View, CA 94043, USA. ___ 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.
Re: [Freesurfer] rs-fMRI data on pial surface
Hi Rene, do you want it on the pial surface or the average over the ribbon? If the pial surface, then use your cmd below but use --projfrac 0. If you want the average use your cmd below but change pial to white (or don't spec --surf) doug On 05/14/2013 08:00 AM, René Besseling wrote: Hi Freesurfers, For this analysis I plan to do, I want to map resting-state data in native (T1) space to the pial surface. The command I use for this is: mri_vol2surf --src fMRI_nat.nii --regheader subjID --hemi lh --projfrac-avg 0 1 0.05 --surf pial --o fMRI_2surf.mgh So the intention is to average the resting state data over the cortex and to map this to the pial surface. However, if I'm not mistaken the --projfrac-avg option projects along the outward pointing surface normal. Therefore, when using the pial surface, I expected that the proper call would be --projfrac-avg 0 -1 -0.05. However, this command does not run, whereas the command given above does, and yields (sensible) output. So is the command given above correct after all? And does this imply that for the pial surface, the volumetric data is actually projected along the inward pointing normals? Best regards, René ___ 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.
Re: [Freesurfer] Still confused by group analysis..
On 05/14/2013 10:05 AM, Tudor Popescu wrote: Not sure whether anyone'd seen my last email (below). Again apologies for the multitude of questions, I hope this is the last batch for this analysis.. On 12 May 2013 16:45, Tudor Popescu tud...@gmail.com mailto:tud...@gmail.com wrote: Dear Freesurfer experts, I very much appreciate your help with an additional set of questions. I feel I'm really close to getting this finished :) 1) In a design with group and gender as discrete factors and age as a continuous factor, why is it that QDEC only displays the contrast Does the avg thickness, accounting for gender, differ between group1 and group2? and not also ..acounting for gender and age,..? I thought that it would have. Are you coding age as a nuisance variable? Also, are you coding gender as a continuous variable? That is something you should not do. 2) In QDEC, if I am left with a cluster after setting the FDR rate to 0.1, does that qualify as a trend towads significance in the same way as when obtaining a p value .1 for a behavioural effect? It is hard to related FDR to traditional FPR. FDR does not give clusters and there is no FDR associated with the cluster you found. It just gives a list of vertices that meet the FDR criteria. You form the clusters with your eyes. The 0.1 means that 10% of the vertices are falsely activated. If those 10% are all in your cluster, then that is a problem. 3) From the group tutorial, I see that mris_preproc has to be called with flag --cache-in ess.fwhm10thickn.fsaverage. However, after running recon-all (including with the –qcache option) on all my subjects, none of their folders contains a file named ?h.thickness.fwhm10.fsaverage.mgh Where does it say to use ess.fwhm10thickn.fsaverage? 4) When comparing two healthy groups, is there anything to gain from using a fsaverage built from the sample (with make_average_subject) as opposed to using the default fsaverage? Probably not. make_average_subject really just gives you a folding pattern to display your results on. If you want to analyze your data on the actual new average subject, you will need to register to that average subject (takes about 2 hours per subject), then specify the new registration with --surfreg. 5) What is the difference between running make_average_subject and running mris_preproc with --target fsaverage? make average subject makes the average subject. mris_preproc samples the data into a common space defined by the registration surface and concatenates the input subjects into a single stack. 6) For my ROI mri_glmfit analysis, I wanted to use the FSGD and contrast files that were automatically created when I did my QDEC whole-brain analysis, since the design will be the same. However, although I identified the FSGD file (qdec.fsgd), I cannot see any plaintext file in the QDEC folder that looks like it contains contrast definitions! Look for C.dat in the contrast folders doug Thanks! Tudor ___ 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.
Re: [Freesurfer] Still confused by group analysis..
Dear Doug and others, I'm sorry to hijack this thread. I noticed in FSL list that it has been recommended to demean gender (and probably other categorical variables) in GLM. As far as I understand, this implies treating a categorical variable as a continuous one. However, I can also see that you recommend not treating gender (and other categorical variables) as a continuous variable in Freesurfer. I would much appreciate if someone can help me to address this problem. I'm CC'ing FSL list so others may also help. All the best, -Arman On Tue, 2013-05-14 at 12:04 -0400, Douglas N Greve wrote: On 05/14/2013 10:05 AM, Tudor Popescu wrote: I thought that it would have. Are you coding age as a nuisance variable? Also, are you coding gender as a continuous variable? That is something you should not do. -- 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
Re: [Freesurfer] Still confused by group analysis..
Hi Arman, I have not followed the FSL thread, but you would only do this if you have a column of ones in your design matrix. Itdoes not imply that gender is being treated as a continous variable. A continuous variable for gender means that male=1 and female=2. This implies that you expect female thickness or slope vs age, etc, to be twice that of males. Probably this does not make sense. doug On 05/14/2013 12:24 PM, Arman Eshaghi wrote: Dear Doug and others, I'm sorry to hijack this thread. I noticed in FSL list that it has been recommended to demean gender (and probably other categorical variables) in GLM. As far as I understand, this implies treating a categorical variable as a continuous one. However, I can also see that you recommend not treating gender (and other categorical variables) as a continuous variable in Freesurfer. I would much appreciate if someone can help me to address this problem. I'm CC'ing FSL list so others may also help. All the best, -Arman On Tue, 2013-05-14 at 12:04 -0400, Douglas N Greve wrote: On 05/14/2013 10:05 AM, Tudor Popescu wrote: I thought that it would have. Are you coding age as a nuisance variable? Also, are you coding gender as a continuous variable? That is something you should not do. -- 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. -- 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
Re: [Freesurfer] beta v5.3 for fedora 18 and ubuntu 13
Joerg, I'm guessing you have some matlab setup script that has run prior to the freesurfer setup. I see this output: /usr/local/matlab/R2008a/sys/os/glnxa64/libstdc++.so.6 which is not something freesurfer would link against or require. normally it should use /usr/lib64/libstdc++.so.6. try running this prior to sourcing the freesurfer setup: setenv LD_LIBRARY_PATH Glad to see 5.3 works otherwise. Thanks for testing it. Nick On Tue, 2013-05-14 at 15:17 +0200, Joerg Pfannmoeller wrote: Unfortunately encountered a problem in fs-fast stream during execution of selxavg3-sess. Added a relevant part of the log file below: sxa3pwd = /home/...removed... sxa3cmd = /usr/local/freesurfer/fsfast/bin/selxavg3-sess -s ./session02 -analysis harm.sm0.mni305 /usr/local/freesurfer/fsfast/toolbox/fast_selxavg3.m #@# session02 ### /home/...removed.../freesurfer_fMRT/session02 - $Id: fast_selxavg3.m,v 1.100.2.2 2012/11/30 18:40:38 greve Exp $ /usr/local/freesurfer/fsfast/toolbox/fast_selxavg3.m /usr/local/freesurfer/fsfast/toolbox/fast_ldanaflac.m /usr/local/freesurfer/matlab/MRIread.m - outtop = /home/...removed.../freesurfer_fMRT Extension format = nii.gz 1 stim-v-base.mat nruns = 1 autostimdur = outanadir = /home/...removed.../freesurfer_fMRT/session02/bold/harm.sm0.mni305 Found 45239/537168 ( 8.4) voxels in mask Creating Design Matrix ... creation time = 0.009 sec DoMCFit = 1 ntptot = 100, nX = 8, DOF = 92 Saving X matrix to /home/...removed.../freesurfer_fMRT/session02/bold/harm.sm0.mni305/Xtmp.mat XCond = 444.207 (normalized) Computing compensation for resdual AR1 bias 1 -0.5 -0.493933(t=0.004964) 2 -0.25 -0.269463(t=0.00648) 3 0 -0.0514275(t=0.00734) 4 0.25 0.155364(t=0.008221) 5 0.5 0.337574(t=0.009058) AR1 Correction M: 0.0769642 1.19552 Computing contrast matrices OLS Beta Pass run 1t= 0.0 Global Mean 725.29 Global In-Mask Mean = 725.295 (694.97) Rescale Target = 100 RescaleFactor = 0.137875 OLS Residual Pass run 1t= 0.0 Saving rho1 Smoothing ACF /usr/local/freesurfer/bin/mri_fwhm --mask /home/...removed.../freesurfer_fMRT/session02/bold/harm.sm0.mni305/mask.nii.gz --i /home/...removed.../freesurfer_fMRT/session02/bold/harm.sm0.mni305/rho1mn.nii.gz --o /home/...removed.../freesurfer_fMRT/session02/bold/harm.sm0.mni305/rho1mn.sm.nii.gz --fwhm 20.00 --smooth-only /usr/local/freesurfer/bin/mri_fwhm: /usr/local/matlab/R2008a/sys/os/glnxa64/libstdc++.so.6: version `GLIBCXX_3.4.11' not found (required by /usr/local/freesurfer/bin/mri_fwhm) /usr/local/freesurfer/bin/mri_fwhm: /usr/local/matlab/R2008a/sys/os/glnxa64/libstdc++.so.6: version `GLIBCXX_3.4.9' not found (required by /usr/local/freesurfer/bin/mri_fwhm) ERROR: /usr/local/freesurfer/bin/mri_fwhm --mask /home/...removed.../freesurfer_fMRT/session02/bold/harm.sm0.mni305/mask.nii.gz --i /home/...removed.../freesurfer_fMRT/session02/bold/harm.sm0.mni305/rho1mn.nii.gz --o /home/...removed.../freesurfer_fMRT/session02/bold/harm.sm0.mni305/rho1mn.sm.nii.gz --fwhm 20.00 --smooth-only -- ERROR: fast_selxavg3() failed\n Seemingly a problem with GLIBCXX_3.4.11. My OS is Lubuntu 13.04. On Tue, 14 May 2013 08:28:05 +0200 Joerg Pfannmoeller pfannmo...@uni-greifswald.de wrote: Tested recon-all tonight on lubuntu 13.04. I did not encounter any problems. Also freeview runs without an error for the subject bert. On Mon, 13 May 2013 14:40:10 +0200 Jörg Pfannmöller pfannmo...@uni-greifswald.de wrote: Just for completeness, I refer to my first contribution: http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg28267.html On Mon, 13 May 2013 13:58:30 +0200 Joerg Pfannmoeller pfannmo...@uni-greifswald.de wrote: Hello Nick, just installed and tested the BETA version. Up to now no problem encountered. Recon-all is just running as a test (using -use-gpu). OS is Lubuntu 13.04. I report on the segmentation as soon as it is finished. So long Joerg On Sun, 12 May 2013 22:41:25 -0400 (EDT) Nick Schmansky ni...@nmr.mgh.harvard.edu wrote: Fedora 18, Ubuntu 13 and Gentoo 64 users, another beta of the upcoming v5.3 is available here: ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/5.3.0-BETA/freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0-BETA.tar.gz this one is just intended for the Fedora 18, Ubuntu 13, Gentoo 64 users who wished to test that the segfault problem in v5.2 and the prior beta v5.3 is fixed. Your help in testing this release is appreciated. Thanks, Nick
Re: [Freesurfer] Still confused by group analysis..
1) In a design with group and gender as discrete factors and age as a continuous factor, why is it that QDEC only displays the contrast Does the avg thickness, accounting for gender, differ between group1 and group2? and not also ..acounting for gender and age,..? I thought that it would have. Are you coding age as a nuisance variable? Also, are you coding gender as a continuous variable? That is something you should not do. I was not coding age as a nuisance variable but as a continuous variable (co-variate). Gender was a discrete/fixed factor but I'm not sure whether this means 'continuous' in the sense discussed in your exchange with Arman. Anyway, in this configuration, it seems gender and age are not accounted (controlled) for at the same time. 3) From the group tutorial, I see that mris_preproc has to be called with flag --cache-in ess.fwhm10thickn.fsaverage. However, after running recon-all (including with the –qcache option) on all my subjects, none of their folders contains a file named ?h.thickness.fwhm10.fsaverage.mgh Where does it say to use ess.fwhm10thickn.fsaverage? Sorry, typo. The flag is actually --cache-in thickness.fwhm10.fsaverage, I file that I do not have after having run recon-all (including with the --qcache option) 5) What is the difference between running make_average_subject and running mris_preproc with --target fsaverage? make average subject makes the average subject. mris_preproc samples the data into a common space defined by the registration surface and concatenates the input subjects into a single stack. But should the registration surface used by mris_preproc (i.e. its --target flag) come from the 'average' subject or from 'fsaverage'? In other words, which one of these becomes the study-specific template? 6) For my ROI mri_glmfit analysis, I wanted to use the FSGD and contrast files that were automatically created when I did my QDEC whole-brain analysis, since the design will be the same. However, although I identified the FSGD file (qdec.fsgd), I cannot see any plaintext file in the QDEC folder that looks like it contains contrast definitions! Look for C.dat in the contrast folders I have no C.dat under /contrasts, only files such as lh-Avg-Intercept-thickness.mat. Don't the different clickable questions that appear in QDEC's Display screen each correspond to a contrast, with each contrast sitting in its own file? _ And a couple more.. A) Why does mris_preproc need to be pointed to a .FSGD, when its output should just be a concatenation of registered structurals, and thus independent from the design of any particular analysis? B) All concatenated volumes from mris_preproc's output files (?h.thickness.mgh) appear blank in freeview, even though the individual structurals all look fine. Also, lh.thickness.mgh and rh.thickness.mgh have, surprisingly, *exactly* the same file size, which is also a bit small (~25MB) to be able to contain 38 registered structurals, which suggests something went wrong... C) When running mri_surf2surf, I get an error saying that file /surf/lh.white cannot be opened. The 'average' folder produced after I ran make_average_subject does not contain a /surf/lh.white file, only a /surf/lh.white_avg file! I didn’t find a log file from make_average_subject so i don’t know if it gave any errors.. Thanks again Doug! ___ 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.
Re: [Freesurfer] beta v5.3 for fedora 18 and ubuntu 13
Hi, all I have just finnished my FS 5.3-Beta recon-all test in Fedora 18 and compared to FS 5.2 in CentOS6. Both OS are installed in the same machine but different HDs. I used recon-all -all -hippo-subfield in the same subject for both runs and it worked great. The time in both versions were similar: Fedora 18 (FS 5.3 Beta) CentOS6 (FS 5.2 release) Start Tue May 14 02:09:57 2013 Sun April 14 23:45:26 2013 End Tue May 14 14:23:31 2013 Mon April 15 12:50:12 2013 Processing time 12:13:34 13:04:46 As I said in previous post. tksurfer and tkmedit are all Ok. Freeview runs but volumes and surfaces are misaligned. Comparing the results from recon-all, some like volume of the hippocampi subfields and eTIV are identical but other numbers like Brain Segmentation Volume are quite different. I am attaching aseg.stats from both runs. Em Dom, 2013-05-12 às 22:41 -0400, Nick Schmansky escreveu: Fedora 18, Ubuntu 13 and Gentoo 64 users, another beta of the upcoming v5.3 is available here: ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/5.3.0-BETA/freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0-BETA.tar.gz this one is just intended for the Fedora 18, Ubuntu 13, Gentoo 64 users who wished to test that the segfault problem in v5.2 and the prior beta v5.3 is fixed. Your help in testing this release is appreciated. Thanks, Nick 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. # Title Segmentation Statistics # # generating_program mri_segstats # cvs_version $Id: mri_segstats.c,v 1.75.2.9 2013/02/16 00:09:33 greve Exp $ # cmdline mri_segstats --seg mri/aseg.mgz --sum stats/aseg.stats --pv mri/norm.mgz --empty --brainmask mri/brainmask.mgz --brain-vol-from-seg --excludeid 0 --excl-ctxgmwm --supratent --subcortgray --in mri/norm.mgz --in-intensity-name norm --in-intensity-units MR --etiv --surf-wm-vol --surf-ctx-vol --totalgray --euler --ctab /home/marcos/freesurfer/ASegStatsLUT.txt --subject gus # sysname Linux # hostname freesurfer # machine x86_64 # user marcos # anatomy_type volume # # SUBJECTS_DIR /home/marcos/freesurfer/subjects # subjectname gus # Measure BrainSeg, BrainSegVol, Brain Segmentation Volume, 1139453.00, mm^3 # Measure BrainSegNotVent, BrainSegVolNotVent, Brain Segmentation Volume Without Ventricles, 1122310.00, mm^3 # Measure BrainSegNotVentSurf, BrainSegVolNotVentSurf, Brain Segmentation Volume Without Ventricles from Surf, 1123071.316664, mm^3 # Measure lhCortex, lhCortexVol, Left hemisphere cortical gray matter volume, 262768.814347, mm^3 # Measure rhCortex, rhCortexVol, Right hemisphere cortical gray matter volume, 266640.410169, mm^3 # Measure Cortex, CortexVol, Total cortical gray matter volume, 529409.224516, mm^3 # Measure lhCorticalWhiteMatter, lhCorticalWhiteMatterVol, Left hemisphere cortical white matter volume, 211530.623754, mm^3 # Measure rhCorticalWhiteMatter, rhCorticalWhiteMatterVol, Right hemisphere cortical white matter volume, 214452.468393, mm^3 # Measure CorticalWhiteMatter, CorticalWhiteMatterVol, Total cortical white matter volume, 425983.092148, mm^3 # Measure SubCortGray, SubCortGrayVol, Subcortical gray matter volume, 63239.00, mm^3 # Measure TotalGray, TotalGrayVol, Total gray matter volume, 669867.224516, mm^3 # Measure SupraTentorial, SupraTentorialVol, Supratentorial volume, 1033963.316664, mm^3 # Measure SupraTentorialNotVent, SupraTentorialVolNotVent, Supratentorial volume, 1020057.316664, mm^3 # Measure SupraTentorialNotVentVox, SupraTentorialVolNotVentVox, Supratentorial volume voxel count, 1017844.00, mm^3 # Measure Mask, MaskVol, Mask Volume, 1501537.00, mm^3 # Measure BrainSegVol-to-eTIV, BrainSegVol-to-eTIV, Ratio of BrainSegVol to eTIV, 0.757655, unitless # Measure MaskVol-to-eTIV, MaskVol-to-eTIV, Ratio of MaskVol to eTIV, 0.998415, unitless # Measure lhSurfaceHoles, lhSurfaceHoles, Number of defect holes in lh surfaces prior to fixing, 17, unitless # Measure rhSurfaceHoles, rhSurfaceHoles, Number of defect holes in rh surfaces prior to fixing, 17, unitless # Measure SurfaceHoles, SurfaceHoles, Total number of defect holes in surfaces prior to fixing, 34, unitless # Measure EstimatedTotalIntraCranialVol, eTIV, Estimated Total Intracranial Volume, 1503920.190724, mm^3 # SegVolFile mri/aseg.mgz # SegVolFileTimeStamp 2013/04/15 05:59:23 # ColorTable /home/marcos/freesurfer/ASegStatsLUT.txt # ColorTableTimeStamp 2013/02/26 03:23:16 # InVolFile mri/norm.mgz # InVolFileTimeStamp 2013/04/15 00:44:47 # InVolFrame
[Freesurfer] Problems with hippocampus subfields segmentation
Hi FreeSurfer Experts! I try to run the hippocampus subfield reconstructions. Because I already run reconall -all on my subjects (without errors, all necessary manual edits were done) I try to reconstruct only the hippo-subfields: recon-all -s my_subjects -hippo-subfields The shell output is given below... Any ideas? Best wishes, Luke Subject Stamp: freesurfer-Darwin-lion-stable-pub-v5.2.0 Current Stamp: freesurfer-Darwin-lion-stable-pub-v5.2.0 INFO: SUBJECTS_DIR is /Users/lscheef/Desktop/subjects Actual FREESURFER_HOME /Applications/freesurfer -rw-rw-r-- 1 lscheef staff 490363 May 14 20:08 /Users/lscheef/Desktop/subjects/p119/scripts/recon-all.log Darwin luke 12.3.0 Darwin Kernel Version 12.3.0: Sun Jan 6 22:37:10 PST 2013; root:xnu-2050.22.13~1/RELEASE_X86_64 x86_64 # #@# Hippocampal Subfields processing Tue May 14 20:16:08 CEST 2013 \n mkdir -p /Users/lscheef/Desktop/subjects/p119/tmp/subfieldResults \n kvlSegmentHippocampalSubfields.sh p119 left /Users/lscheef/Desktop/subjects /Users/lscheef/Desktop/subjects/p119/tmp/subfieldResults \n Doing left side meshFileName: /Applications/freesurfer/data/GEMS/CurrentMeshCollection30.gz compressionLookupTableFileName: /Applications/freesurfer/data/GEMS/compressionLookupTable_left.txt boundingBoxFileName: /Applications/freesurfer/data/GEMS/imageDump.mgz subjectName: p119 side: left inputDirectory: /Users/lscheef/Desktop/subjects outputDirectory: /Users/lscheef/Desktop/subjects/p119/tmp/subfieldResults directory /Users/lscheef/Desktop/subjects/p119/tmp/subfieldResults/p119 already exists directory /Users/lscheef/Desktop/subjects/p119/tmp/subfieldResults/p119/left already exists cd /Users/lscheef/Desktop/subjects/p119/tmp/subfieldResults/p119/left cp -f /Users/lscheef/Desktop/subjects/p119/mri/nu.mgz . cp -f /Users/lscheef/Desktop/subjects/p119/mri/aseg.mgz . cp -f /Users/lscheef/Desktop/subjects/p119/mri/transforms/talairach.xfm . cp /Applications/freesurfer/data/GEMS/imageDump.mgz . kvlApplyTransform imageDump.mgz -0.9991 -0.0328 0.0258 144.0010 -0.0330 0.9994 -0.0086 2.6560 0.0255 0.0094 0.9996 -3.1939 dyld: Library not loaded: libITKCommon.3.16.dylib Referenced from: /Applications/freesurfer/bin/kvlApplyTransform Reason: image not found /Applications/freesurfer/bin/kvlSegmentHippocampalSubfields.sh: line 18: 89411 Trace/BPT trap: 5 kvlApplyTransform imageDump.mgz -0.9991 -0.0328 0.0258 144.0010 -0.0330 0.9994 -0.0086 2.6560 0.0255 0.0094 0.9996 -3.1939 failed to do kvlApplyTransform imageDump.mgz -0.9991 -0.03280.0258 144.0010 -0.0330 0.9994 -0.00862.65600.02550.0094 0.9996 -3.1939 Darwin luke 12.3.0 Darwin Kernel Version 12.3.0: Sun Jan 6 22:37:10 PST 2013; root:xnu-2050.22.13~1/RELEASE_X86_64 x86_64 recon-all -s p119 exited with ERRORS at Tue May 14 20:16:08 CEST 2013___ 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] averaging lh and rh thickness maps on fsaverage_sym surface
Hi, I want to create an average thickness map of lh and rh. I have run surfreg steps to map lh to lh sym and rh to rh sym. Can you advise what to do next to mke average thickness maps between two hemispheres ? Will either mris_calc or mri_average work to make the average map ? Thank you Subha ___ 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] Recon-all error
Hi freesurfers, I recently ran a reconstruction, but it's errored. I'm not sure why thought, but I've attached the recon log. Thanks, Mia -- SUBJECT MGH009_SurferOutput DATE Mon May 13 11:25:37 EDT 2013 USER miaborz HOST huygens PROCESSOR x86_64 OS Linux Linux huygens 2.6.32-358.2.1.el6.x86_64 #1 SMP Wed Mar 13 00:26:49 UTC 2013 x86_64 x86_64 x86_64 GNU/Linux $Id: recon-all,v 1.379.2.65 2013/02/19 22:34:56 nicks Exp $ /usr/local/freesurfer/stable5_2_0/bin/recon-all PWD /autofs/space/huygens_001/users/mia/subjects/MGH009_SurferOutput/mri CMD talairach_afd -T 0.005 -xfm transforms/talairach.xfm ___ 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.
Re: [Freesurfer] Problems with hippocampus subfields segmentation
Hello Luke, A patch was released to fix this problem. In order to fix this issue please follow these instruction: 1) Download the file kvl.zip from this link: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/fsdev/zkaufman/kvl.zip 2) Overwrite the existing kvl files in your /Application/freesurfer/bin with the files in kvl.zip I was able to replicate your issue and solve it using the steps above. If these steps do not solve the issue for you, please let me know. Hope this helps. -Zeke On 05/14/2013 02:41 PM, lukas.sch...@ukb.uni-bonn.de wrote: Hi FreeSurfer Experts! I try to run the hippocampus subfield reconstructions. Because I already run reconall -all on my subjects (without errors, all necessary manual edits were done) I try to reconstruct only the hippo-subfields: recon-all -s my_subjects -hippo-subfields The shell output is given below... Any ideas? Best wishes, Luke Subject Stamp: freesurfer-Darwin-lion-stable-pub-v5.2.0 Current Stamp: freesurfer-Darwin-lion-stable-pub-v5.2.0 INFO: SUBJECTS_DIR is /Users/lscheef/Desktop/subjects Actual FREESURFER_HOME /Applications/freesurfer -rw-rw-r-- 1 lscheef staff 490363 May 14 20:08 /Users/lscheef/Desktop/subjects/p119/scripts/recon-all.log Darwin luke 12.3.0 Darwin Kernel Version 12.3.0: Sun Jan 6 22:37:10 PST 2013; root:xnu-2050.22.13~1/RELEASE_X86_64 x86_64 # #@# Hippocampal Subfields processing Tue May 14 20:16:08 CEST 2013 \n mkdir -p /Users/lscheef/Desktop/subjects/p119/tmp/subfieldResults \n kvlSegmentHippocampalSubfields.sh p119 left /Users/lscheef/Desktop/subjects /Users/lscheef/Desktop/subjects/p119/tmp/subfieldResults \n Doing left side meshFileName: /Applications/freesurfer/data/GEMS/CurrentMeshCollection30.gz compressionLookupTableFileName: /Applications/freesurfer/data/GEMS/compressionLookupTable_left.txt boundingBoxFileName: /Applications/freesurfer/data/GEMS/imageDump.mgz subjectName: p119 side: left inputDirectory: /Users/lscheef/Desktop/subjects outputDirectory: /Users/lscheef/Desktop/subjects/p119/tmp/subfieldResults directory /Users/lscheef/Desktop/subjects/p119/tmp/subfieldResults/p119 already exists directory /Users/lscheef/Desktop/subjects/p119/tmp/subfieldResults/p119/left already exists cd /Users/lscheef/Desktop/subjects/p119/tmp/subfieldResults/p119/left cp -f /Users/lscheef/Desktop/subjects/p119/mri/nu.mgz . cp -f /Users/lscheef/Desktop/subjects/p119/mri/aseg.mgz . cp -f /Users/lscheef/Desktop/subjects/p119/mri/transforms/talairach.xfm . cp /Applications/freesurfer/data/GEMS/imageDump.mgz . kvlApplyTransform imageDump.mgz -0.9991 -0.0328 0.0258 144.0010 -0.0330 0.9994 -0.0086 2.6560 0.0255 0.0094 0.9996 -3.1939 dyld: Library not loaded: libITKCommon.3.16.dylib Referenced from: /Applications/freesurfer/bin/kvlApplyTransform Reason: image not found /Applications/freesurfer/bin/kvlSegmentHippocampalSubfields.sh: line 18: 89411 Trace/BPT trap: 5 kvlApplyTransform imageDump.mgz -0.9991 -0.0328 0.0258 144.0010 -0.0330 0.9994 -0.0086 2.6560 0.0255 0.0094 0.9996 -3.1939 failed to do kvlApplyTransform imageDump.mgz -0.9991 -0.03280.0258 144.0010 -0.03300.9994 -0.00862.6560 0.02550.00940.9996 -3.1939 Darwin luke 12.3.0 Darwin Kernel Version 12.3.0: Sun Jan 6 22:37:10 PST 2013; root:xnu-2050.22.13~1/RELEASE_X86_64 x86_64 recon-all -s p119 exited with ERRORS at Tue May 14 20:16:08 CEST 2013 ___ 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.
[Freesurfer] problem with func2roi-sess
Hello Freesurfers, I would appreciate any advice or help you can provide.
I am using the following command, run under Stable 3 (to keep the current
analysis comparable to prior papers):
func2roi-sess -roidef MedOrbitofrontal_LH_t6_0_sm5_0thresh -analysis
newROIs_tap_lh_long_CD_R01BTX_pat9_sess1_sm5 -maskcontrast
newROIs_tap_lh_long_CD_R01BTX_pat9_sess1_sm5_contrast -labelfile
/cluster/ablood/1/AdjustedParadigmFiles/Adjusted_recons/CD_R01BTX_pat9_sess1_recon/label/MedOrbitofrontal_LH_CD_R01BTX_pat9_sess1.label
-maskthresh 6.0 -masktail pos -maskmap t -s CD_R01BTX_pat9_sess1 -df
sessdirfile
The error message is as follows (it outputs exactly like this, apparently
intermingled with another output):
ras2vox src (tkreg) Qsrc -
-0.320 -0.000 -0.000 32.000;
-0.000 -0.00mri_vol2roi: could not scan # of lines from
/autofs/cluster/ablood/1/AdjustedParadigmFiles/Adjusted_recons/CD_R01BTX_pat9_sess1_recon/label/MedOrbitofrontal_LH_CD_R01BTX_pat9_sess1.label
No such file or directory
0 -0.320 32.000;
0.000 0.200 0.000 15.000;
0.000 0.000 0.000 1.000;
I have never seen this error before - any suggestions why I'm getting it?
This same command structure ran perfectly on separate ROIs over the last
few days. I confirmed that the corresponding .label files are structured
identically to those for other ROIs that worked.
Just in case it's helpful, this is the command that I used to generate the
.label files:
mri_cor2label --c
/cluster/ablood/1/${experimental_directory}/${recons_directory}/${identifier}_recon/mri/aparc+aseg.mgz
--id 1014 --l
/cluster/ablood/1/${experimental_directory}/${recons_directory}/${identifier}_recon/label/MedOrbitofrontal_LH_${identifier}.label.
Thank you!
Jeff
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Re: [Freesurfer] averaging lh and rh thickness maps on fsaverage_sym surface
Just run the next step, ie, mris_preproc but leave off the --paired-diff. Then run mri_concat preproc.out.mgh --mean preproc.out.mean.mgh doug On 05/14/2013 04:12 PM, Subhabrata Chaudhury wrote: Hi, I want to create an average thickness map of lh and rh. I have run surfreg steps to map lh to lh sym and rh to rh sym. Can you advise what to do next to mke average thickness maps between two hemispheres ? Will either mris_calc or mri_average work to make the average map ? Thank you Subha ___ 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.
Re: [Freesurfer] problem with func2roi-sess
it looks like ther is something wrong with that label
On 05/14/2013 04:34 PM, jwa...@nmr.mgh.harvard.edu wrote:
Hello Freesurfers, I would appreciate any advice or help you can provide.
I am using the following command, run under Stable 3 (to keep the current
analysis comparable to prior papers):
func2roi-sess -roidef MedOrbitofrontal_LH_t6_0_sm5_0thresh -analysis
newROIs_tap_lh_long_CD_R01BTX_pat9_sess1_sm5 -maskcontrast
newROIs_tap_lh_long_CD_R01BTX_pat9_sess1_sm5_contrast -labelfile
/cluster/ablood/1/AdjustedParadigmFiles/Adjusted_recons/CD_R01BTX_pat9_sess1_recon/label/MedOrbitofrontal_LH_CD_R01BTX_pat9_sess1.label
-maskthresh 6.0 -masktail pos -maskmap t -s CD_R01BTX_pat9_sess1 -df
sessdirfile
The error message is as follows (it outputs exactly like this, apparently
intermingled with another output):
ras2vox src (tkreg) Qsrc -
-0.320 -0.000 -0.000 32.000;
-0.000 -0.00mri_vol2roi: could not scan # of lines from
/autofs/cluster/ablood/1/AdjustedParadigmFiles/Adjusted_recons/CD_R01BTX_pat9_sess1_recon/label/MedOrbitofrontal_LH_CD_R01BTX_pat9_sess1.label
No such file or directory
0 -0.320 32.000;
0.000 0.200 0.000 15.000;
0.000 0.000 0.000 1.000;
I have never seen this error before - any suggestions why I'm getting it?
This same command structure ran perfectly on separate ROIs over the last
few days. I confirmed that the corresponding .label files are structured
identically to those for other ROIs that worked.
Just in case it's helpful, this is the command that I used to generate the
.label files:
mri_cor2label --c
/cluster/ablood/1/${experimental_directory}/${recons_directory}/${identifier}_recon/mri/aparc+aseg.mgz
--id 1014 --l
/cluster/ablood/1/${experimental_directory}/${recons_directory}/${identifier}_recon/label/MedOrbitofrontal_LH_${identifier}.label.
Thank you!
Jeff
___
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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/
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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.
Re: [Freesurfer] Recon-all error
Hi Mia, I think you meant to attach the recon-all.log instead of the recon-all.error, the former is more informative. Regardless it looks like the talairach registration step failed for this subject. See this wiki page for info on checking and fixing that if necessary. https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Talairach -Louis On Tue, 14 May 2013, Borzello, Mia wrote: Hi freesurfers, I recently ran a reconstruction, but it's errored. I'm not sure why thought, but I've attached the recon log. Thanks, Mia ___ 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.
Re: [Freesurfer] Recon-all error
sorry, recon-all.log attached! From: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Borzello, Mia Sent: Tuesday, May 14, 2013 4:23 PM To: freesurfer Subject: [Freesurfer] Recon-all error Hi freesurfers, I recently ran a reconstruction, but it's errored. I'm not sure why thought, but I've attached the recon log. Thanks, Mia recon-all.log Description: recon-all.log ___ 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.
Re: [Freesurfer] Recon-all error
Mia, Hi, in looking at the mri/orig/001.mgz, the image in the sagital and coronal planes look inverted. also, i noticed this mri_info: dimensions: 566 x 256 x 992 voxel sizes: 1., 1., 1. which seems like unusual input. how was this converted from the dicom? did it necessitate altering the header? Nick On Tue, 2013-05-14 at 20:23 +, Borzello, Mia wrote: Hi freesurfers, I recently ran a reconstruction, but it's errored. I'm not sure why thought, but I've attached the recon log. Thanks, Mia ___ 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.
Re: [Freesurfer] problem with func2roi-sess
I have checked the label file directly - it is of comparable size with
others, and has the same structure. I've rerun the mri_cor2label command
and regenerated the labels for all subjects. Most confusing, func2roi
works for some subjects in this cohort and not others. In contrast, the
whole cohort has been used with parallel labels with no problem.
If there is something wrong with [my] label, what things could it be?
Has anyone else seen this particular error message?
Thanks,
Jeff
it looks like ther is something wrong with that label
On 05/14/2013 04:34 PM, jwa...@nmr.mgh.harvard.edu wrote:
Hello Freesurfers, I would appreciate any advice or help you can
provide.
I am using the following command, run under Stable 3 (to keep the
current
analysis comparable to prior papers):
func2roi-sess -roidef MedOrbitofrontal_LH_t6_0_sm5_0thresh -analysis
newROIs_tap_lh_long_CD_R01BTX_pat9_sess1_sm5 -maskcontrast
newROIs_tap_lh_long_CD_R01BTX_pat9_sess1_sm5_contrast -labelfile
/cluster/ablood/1/AdjustedParadigmFiles/Adjusted_recons/CD_R01BTX_pat9_sess1_recon/label/MedOrbitofrontal_LH_CD_R01BTX_pat9_sess1.label
-maskthresh 6.0 -masktail pos -maskmap t -s CD_R01BTX_pat9_sess1 -df
sessdirfile
The error message is as follows (it outputs exactly like this,
apparently
intermingled with another output):
ras2vox src (tkreg) Qsrc -
-0.320 -0.000 -0.000 32.000;
-0.000 -0.00mri_vol2roi: could not scan # of lines from
/autofs/cluster/ablood/1/AdjustedParadigmFiles/Adjusted_recons/CD_R01BTX_pat9_sess1_recon/label/MedOrbitofrontal_LH_CD_R01BTX_pat9_sess1.label
No such file or directory
0 -0.320 32.000;
0.000 0.200 0.000 15.000;
0.000 0.000 0.000 1.000;
I have never seen this error before - any suggestions why I'm getting
it?
This same command structure ran perfectly on separate ROIs over the last
few days. I confirmed that the corresponding .label files are
structured
identically to those for other ROIs that worked.
Just in case it's helpful, this is the command that I used to generate
the
.label files:
mri_cor2label --c
/cluster/ablood/1/${experimental_directory}/${recons_directory}/${identifier}_recon/mri/aparc+aseg.mgz
--id 1014 --l
/cluster/ablood/1/${experimental_directory}/${recons_directory}/${identifier}_recon/label/MedOrbitofrontal_LH_${identifier}.label.
Thank you!
Jeff
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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/
___
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https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
___
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Freesurfer@nmr.mgh.harvard.edu
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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] 5.3 mri_convert bug?
Hi, Tried running recon-all on two different linux systems and same error occurs in the mri_nu_correct.mni.log when running mri_convert on the nu1.mnc ie.. . . . Processing:.Done Processing:.Done Processing:.Done Processing:.Done Processing:.Done Number of iterations: 64 CV of field change: 0.000946853 Outputting Volume: mri_convert ./tmp.mri_nu_correct.mni.24934/nu1.mnc orig_nu.mgz --like orig.mgz --conform mri_convert ./tmp.mri_nu_correct.mni.24934/nu1.mnc orig_nu.mgz --like orig.mgz --conform ncopen: filename ./tmp.mri_nu_correct.mni.24934/nu1.mnc: Not a netCDF file miopen: MINC package entry point Error opening ./tmp.mri_nu_correct.mni.24934/nu1.mnc mincRead(): error reading volume from file ./tmp.mri_nu_correct.mni.24934/nu1.mnc $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from ./tmp.mri_nu_correct.mni.24934/nu1.mnc... Any help appreciated. Thanks, Chris ___ 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.
