[Freesurfer] request for move through slices
Dear FS experts, I am trying out freeview and am extremely fond of it. I have one feature request. In tkmedit in navigate mode it was possible moving through slices just using the mouse (middle mouse button pressed). Is it possible to implement the same in freeview - it appears that in freeview there are two zoom mouse actions scroll wheel and pressing-middle-mouse-button while moving up and down. Having this feature would ease checking and correcting data a lot. Thanks, Michael ___ 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] transforms/talairach_with_skull.lta during autorecon1 and autorecon2 - is it a bug or a feature
Dear Freesurfer experts, we are testing a grid computer infrastructure for running freesurfer analysis and are evaluating consistency and reliability of freesurfer results across platforms. Before we start our tests across platforms we conducted some freesurfer analysis on the same computer and had some unexpected results. Subsequent executions of the freesurfer pipeline (New invocation of recon-all) on a certain subject - without any manual editing in between - give different results. We have invoked recon-all up to four times and all results are different. We tested in particular the aseg.stats results, where we found different volume estimations (up to 4%) depending on the number of processing loops. Intermediate results have also been found to be different The effect is reproducible, meaning the nth invocation of recon-all on the subject gives always the nth result. We suspect that the cause is (following the pipeline documentation: http://surfer.nmr.mgh.harvard.edu/fswiki/ReconAllDevTable) the twofold generation of talairach_with_skull.lta, once in the autorecon-1 and a second time in the autorecon-2 phase: autorecon1: mri_em_register -skull nu.mgz $FREESURFER_HOME/average/RB_all_withskull_2008-03-26.gca transforms/talairach_with_skull.lta autorecon2: mri_em_register -skull -t transforms/talairach.lta nu_noneck.mgz $FREESURFER_HOME/average/RB_all_withskull_2008-03-26.gca transforms/talairach_with_skull.lta and it seems that the step in autorecon1 is skipped if the file talairach_with_skull.lta is already present. We were wondering if this behaviour is intended, so are the FreeSurfer results expected to improve with multiple invocations, even without manual intervention? Shall they converge after sufficient re-runs? Any help or comments are highly appreciated. Best, Michael ___ 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] change overlay color
Hi FS experts, I want to change the visualization of some overlay data in tkmedit. Instead of the Heat (Red-Yellow) Color-Scale I'd like to use a Green-Red or Rainbow Color Scale. Is there a way to achieve this? Do I need to create a respective LUT and where do I have to put it. thanks, michael ___ 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] Overlay Thickness Files in tkmedit
Hi, is there a way to visualize the lh.thickness or rh.thickness files as an overlay in tkmedit. Thanks, Michael ___ 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] manual entry for mri_concat
Dear FS experts, I recognized that there is no manual entry for mri_concat and fslcalc.fsl. Although there is an extensive help text just typing the command I would find a manual entry (man mri_concat) including exmaples very helpful (or an entry on the freesurfer command site). Thanks, Michael ___ 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] Fwd: advise on generating individual standard deviation map
Hi Doug, I think I solved the registration issue. This is my command: mri_surf2surf --hemi lh --srcsubject bert --srcsurfval thickness --src_type curv --trgsubject fsaverage --trgsurfval bert/surf/lh_av.thickness --trg_type curv Any objections? Thanks, Michael Begin forwarded message: From: Michael Scheel scheelmich...@googlemail.com Date: 10. Juni 2010 22:45:10 MESZ To: Doug Greve gr...@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] advise on generating individual standard deviation map Hi Doug, thanks for you reply. That is exactly what I want to do so many thanks for explaining that. However I have problems with the usage of mri_surf2surf michael$ mri_surf2surf --srcsubject bert --srcsurfval bert/surf/lh.thickness --trgsubject fsaverage --trgsurfval bert/surf/lh.thickness_average --hemi lh ERROR: could not determine type of bert/surf/lh.thickness_average Also when I run the example from the FS wiki site i get the following error (see below). Any idea what I'm doing wrong here? Thanks, Michael michael$ mri_surf2surf --hemi lh --srcsubject bert --srcsurfval thickness --src_type curv --trgsubject ico --trgicoorder 7 --trgsurfval bert-thickness-lh.img --trg_type analyze4d srcsubject = bert srcval = thickness srctype= curv trgsubject = ico trgval = bert-thickness-lh.img trgtype= analyze4d srcsurfreg = sphere.reg trgsurfreg = sphere.reg srchemi= lh trghemi= lh frame = 0 fwhm-in= 0 fwhm-out = 0 label-src = (null) label-trg = (null) Reading source surface reg /Users/michael/Desktop/TEST_FREESURFER/bert/surf/lh.sphere.reg Loading source data Reading curvature file /Users/michael/Desktop/TEST_FREESURFER/bert/surf/lh.thickness Reading icosahedron /Applications/MriSoftware/freesurfer/lib/bem/ic7.tri Done Mapping Source Volume onto Source Subject Surface surf2surf_nnfr: building source hash (res=16). Surf2Surf: Forward Loop (163842) surf2surf_nnfr: building target hash (res=16). Surf2Surf: Reverse Loop (131122) Reverse Loop had 21908 hits Surf2Surf: Dividing by number of hits (163842) INFO: nSrcLost = 0 nTrg121 = 146869, nTrgMulti = 16973, MnTrgMultiHits = 2.29076 nSrc121 = 89131, nSrcLost = 0, nSrcMulti = 41991, MnSrcMultiHits = 2.30095 Saving target data ANALYZE FORMAT ERROR: ncols 163842 in volume exceeds 32768 On 10.06.2010, at 12:05, Doug Greve wrote: I don't have anything explicitly that will compute a map of z-scores, but you could do a two group analysis with your subject as the only one in one group and then do a group analysis. Alternatively, you can transform you individual to the fsaverage space (mri_surf2surf), then compute the z using fscalc.fsl. You'd have to compute the group mean and stddev using mri_concat (--mean and --std), then use fscalc.fsl, something like fscalc.fsl --surf fsaverage lh lh.thickness.fsaverage.mgh -sub groupmean.mgh -div groupstd.mgh zscore.mgh doug On Wed, 9 Jun 2010, Michael Scheel wrote: Dear FS experts, could someone advise on how to create from an individual thickness file (?h.thickness) a standard deviation or z-score map of the thickness with respect to a control group. Thanks, Michael ___ 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: www.nmr.mgh.harvard.edu/facility/filedrop/index.html 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 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] advise on generating individual standard deviation map
Dear FS experts, could someone advise on how to create from an individual thickness file (?h.thickness) a standard deviation or z-score map of the thickness with respect to a control group. Thanks, Michael ___ 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] standard deviation map
Dear FS experts, I have a anatomical scan of a subject with a rare neurogenetical disorder. I'd like to compare this with a age matched control group. How can I visualize a z-score transform map of the cortical thickness, i.e. how would I compute and vizualize the number/amount of standard deviations that my subjects differs from the mean of the control group at each vertex? Thanks, Michael ___ 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] rerun auto-recon on error output
Hi freesurfer-experts, I was running the recon-all script and did get some errors due to a missing vtk and x-windows libraries. The output that was created seems fine though, just some files are missing. I was wondering if there is way to rerun the analysis, but only the parts that exited with error? these programs exited with error mris_volmask mri_aparc2aseg (several times with different options) and a final mri_segstats Thanks, Michael ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] building from source
Hi everybody, I have the opportunity to run my analysis with freesurfer on a big computer-cluster that is running on AIX. However to install freesurfer there I need to build it from source. Is the source code available? I found some older entries in the archives and the issue seemed at that time rather complicated. Are there any news regarding building from source? Thanks, Michael ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
