Freesurfer January 2007

freesurfer@nmr.mgh.harvard.edu

51 participants
74 discussions

old vs. new recons and functional overlays...
by Mark Fenske 26 Jan '07

26 Jan '07

Hi there, I'm trying to compare regions of activation in functional data collected in two different studies-- one study conducted a few years ago (i.e., before the advent of -autorecon and filled ventricles) and another that was conducted last summer (i.e., all new recons). The problem is that there are serious distortions in the group- averaged statistical activation maps whenever I use a common surface (e.g., fsaverage) to visualize the results of both studies (details and an example are below). I imagine that this discrepancy is due to the difference in surface geometry around the medial wall of the new vs. old recons. Is it possible to resample/transform the old surface-based activation maps in some way that accounts for or side-steps the difference in the old vs. new recons, and thereby save us from having to re-run all of the old recons and all of the old fs-fast analyses? Would using mri_surf2vol to go from the old surface to the volume and then mri_vol2surf to go from the volume to fsaverage retain better localization? Thanks, Mark Details and example: -------------------------------- Consider this .jpg: http://barlab.mgh.harvard.edu/web_pics/old_recon.jpg It shows a left medial view with clear regions of activation in medial prefrontal (in white circle) and parahippocampal (in white square) cortices. It was obtained after running the following commands, : source /usr/local/freesurfer/nmr-std-env setenv SUBJECTS_DIR /space/odin/12/users/subjects cd /space/frigg/4/users/mark/average tksurfer bar_nouchine lh inflated -overlay strvwk_lh_6/osgm/sig.mgh The next .jpg shows the same contrast resampled onto fsaverage. The distortion in relative localization of activation should be readily apparent (note the empty circle and square): http://barlab.mgh.harvard.edu/web_pics/fsaverage.jpg I obtained this view using mri_surf2surf to resample and then mri_glmfit to get the activation map: mri_surf2surf --hemi lh --srcsubject bar_nouchine --sval strvwk_lh_6.mgh --trgsubject fsaverage --tval ./ strvwk_lh_6_fsaverage.mgh mri_glmfit --y strvwk_lh_6_fsaverage.mgh --osgm --glmdir glm_strvwk_lh_6_fsaverage tksurfer fsaverage lh inflated -overlay glm_strvwk_lh_6_fsaverage/ osgm/sig.mgh ----- Mark J. Fenske, Ph.D. MGH Martinos Center for Biomedical Imaging - Harvard Medical School Tel: (617) 726-9034 | Fax: 726-7422 | http:// barlab.mgh.harvard.edu/fenske.htm

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mris_preproc --paired diff
by Reschke, Cole 26 Jan '07

26 Jan '07

When using the -paired-diff option for mris_preproc, does this signify (scan1 minus scan2) or (scan2 minus scan1)? Cole Reschke Data Manager, PET Center Banner Alzheimer Institute Banner Good Samaritan Medical Center Phone: (602) 239-4868

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group-analysis error
by Chacko Cherian 25 Jan '07

25 Jan '07

Hello all, Here's an error that i got while running group analysis on a couple of subjects...i checked the rh.orig file and the rh.sphere.reg and i could open both using tksurfer. Reading /ud/chacko/freesurfer/subjects/AD_norm_cor25all111/AD_norm_group_analysis/subj1/surf/rh.sphere.reg mrisReadTriangleFile(/ud/chacko/freesurfer/subjects/AD_norm_cor25all111/AD_norm_group_analysis/subj1/surf/rh.orig): surface doesn't match /ud/chacko/freesurfer/subjects/AD_norm_cor25all111/AD_norm_group_analysis/subj1/surf/rh.sphere.reg No such file or directory mrisReadTriangleFile failed. No such file or directory MRISreadOriginalProperties: could not read surface file orig No such file or directory mris_make_average_surface: could not read orig file for rh. No such file or directory Thanks in advance Chacko. ____________________________________________________________________________________ Finding fabulous fares is fun. Let Yahoo! FareChase search your favorite travel sites to find flight and hotel bargains. http://farechase.yahoo.com/promo-generic-14795097

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RE: [Freesurfer] re-running recon-all
by Don Hagler 25 Jan '07

25 Jan '07

Hi Catherine, You might find this modified version of recon-all useful (called fs_recon, which is attached). It checks for whether the touch files exist before doing a particular step. This behavior can be overridden with the force flag. I fear that my modified script will become out of date as the guys at mgh continue to make changes to recon-all, but I needed this functionality now. Don >From: Catherine Hartley <cate(a)nyu.edu> >To: <freesurfer(a)nmr.mgh.harvard.edu> >Subject: [Freesurfer] re-running recon-all >Date: Wed, 24 Jan 2007 13:52:41 -0500 > >Hi, > >If recon-all is interrupted after several hours of processing (someone >shutdown the machine), if I run recon-all again on the same set of data, >will it go through all of the processing steps again, or will it note the >progress made and essentially check through until it reaches the prior >point >of termination? > >Thanks, >Cate > >_______________________________________________ >Freesurfer mailing list >Freesurfer(a)nmr.mgh.harvard.edu >https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer _________________________________________________________________ Turn searches into helpful donations. Make your search count. http://click4thecause.live.com/search/charity/default.aspx?source=hmemtagli…

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Basal Ganglia Segmentation
by Paul Greenberg 24 Jan '07

24 Jan '07

Hello, I'm having trouble getting an accurate subcortical segmentation (aseg.mgz, and aparc+aseg.mgz) in the Left Hemisphere Nucleus Accumbens area of one subject. Specifically, regions that appear to be the Left Nucleus Accumbens are being labeled as Left Cerebral Cortex. The two images (attached) illustrate the problem. Image 1 shows only pial and white matter surfaces on the "brainmask.mgz" file while image 2 shows the pial and white matter surfaces on "brainmask.mgz" along with the aparc+aseg.mgz segmentation. For this subject I added control points to fix other inaccuracies in other regions, and edited the wm.mgz to cover all regions I considered basal ganglia (the white matter surface still appears to invade regions of the basal ganglia). I reprocessed this data with recon-all -autorecon2-cp -autorecon3, but am still not satisfied with the results. What would you suggest as the best way to more accurately identify the accumbens regions in this case? Thanks much!, Paul

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Registration problems when ovelaying maps on brain surface
by qz4＠ee.duke.edu 24 Jan '07

24 Jan '07

Hi all, I got some problems when I tried to overlay some maps one brain surface. The following steps is just for test. 1. recon-all -all -notalairach -i MP-rage/001.dcm s test 2. I use matlab to load the save dataset (MP-rage/001.dcm ~ 160.dcm) and then mark the back-head (>1000). The output is test_mark.img (analyze format) 3. thregister2 --targ ./test/mri/orig/001.mgz --mov test_mark.img regheader reg reg.dat So I got reg.dat in this step 4. thsurfer test lh inflated --overlay test_mark.img overlay-reg reg.dat fthresh 1000 The weird thing happened in the final surface image. The mark is not shown in back-head. It is located in the botton of the brain surface. If in the 4, I do the following instead (no registration) thsurfer test lh inflated --overlay test_mark.img --fthresh 1000 The mark is in the right location (back-head), but a little offset. Whats wrong in my procedure? Am I doing right in the registion part? Is it correct to register to /mri/orig/001.mgz? Thanks! Elva

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re-running recon-all
by Catherine Hartley 24 Jan '07

24 Jan '07

Hi, If recon-all is interrupted after several hours of processing (someone shutdown the machine), if I run recon-all again on the same set of data, will it go through all of the processing steps again, or will it note the progress made and essentially check through until it reaches the prior point of termination? Thanks, Cate

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RE: [Freesurfer] interpret analysis results
by Reschke, Cole 23 Jan '07

23 Jan '07

Thank you, I have three follow up questions: Threshold is -log10(p), why are negative values showing up on the display? I am using fsaverage to display my results, would it make any difference if I created my own average subject based on the analysis? Is it possible to export the voxel-by-voxel intensities (or the brain surface data) used in Freesurfer's analysis; and then re-import the some external analysis results back to Freesurfer format for display purposes? Cole ________________________________ From: freesurfer-bounces(a)nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] On Behalf Of Doug Greve Sent: Monday, January 22, 2007 11:56 AM To: Reschke, Cole Cc: freesurfer(a)nmr.mgh.harvard.edu Subject: Re: [Freesurfer] interpret analysis results The values are -log10(p), so p < .01 would require a threshold of 2, etc. I don't use t, z, or F because I have not memorized the various tables that convert them to p:). The sig will map to any surface, including pial. doug Reschke, Cole wrote: First, thanks to Doug for all his help up to this point. Next, I have three questions. In my analysis, I used the -paired-diff and -osgm options in mris_preproc and mri_glmfit, respectively. I have successfully loaded sig.mgh onto the inflated surface. Are the values from the color chart [-5,5] representative of a t-score or an F-score (t^2)? I adjust the threshold by changing the 'Min' value in the 'Configure Overlay Display'? Ex. If Min ==3, then p < 0.001 ? Is the sig.mgh created solely for the inflated surface, or is it able to be uploaded on others (pial, wm, etc.)? Thank you, Cole Cole Reschke Data Manager, PET Center Banner Alzheimer Institute Banner Good Samaritan Medical Center Phone: (602) 239-4868 ________________________________ _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center greve(a)nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 In order to help us help you, please follow the steps in: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting

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the dorsolateral prefrontal cortex
by wan＠vt.edu 23 Jan '07

23 Jan '07

Hello All, We want to get the information about the dorsolateral prefrontal cortex. However, two parcellation maps (?h.aparc.annot and ?h.aparc.a2005s.annot)didn't show this structure directly. Can you please tell me how to draw the ROI for the dorsolateral prefrontal cortex in the Final Surface of the brain? and how to get values for thickness and volume for this structure? Thanks, Li

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thickness reproducibility-longitudinal?
by Chacko Cherian 23 Jan '07

23 Jan '07

Hello all, http://surfer.nmr.mgh.harvard.edu/fswiki/ThicknessRepeatibility Is this page on thickness reproducibility intended for longitudinal analysis or is it just a general group analysis procedure? THanks in advance, Chacko. ____________________________________________________________________________________ Want to start your own business? Learn how on Yahoo! Small Business. http://smallbusiness.yahoo.com/r-index

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Freesurfer January 2007