Freesurfer January 2007

freesurfer@nmr.mgh.harvard.edu

51 participants
74 discussions

imaging and neuropsych intervening time
by Kirk, Gregory 30 Jan '07

30 Jan '07

Hello all, We are doing studies correlating neuropsychological measures of executive function in normal and clinical populations, epilepsy and sickle cell disease. I am looking at the issue of the amount of time allowed between acquiring the volumetric MR and performing the battery of neuropsych tests. We are working with pediatrics, 10 to 18 years and the frontal areas that are thought to be most correlated with executive function are also developing during this age span. Also there is quite limited knowledge from previous imaging studies of the growth curves for these regions. Since we are dealing also with clinical populations for which even less information is available concerning their deviation from normal growth curves( intractable partial focal epilepsies thought to be of frontal lobe onset ) Therefore I was thinking the imaging and testing should be less than one month apart, and perhaps 2 months would be absolutely two long. Since we are working with clinical populations it is not possible to always control the schedules so closely, our normal control populations have their imaging and neuro psych battery never more than a week apart. I would be pleased if one of the freesurfer PI's would give me their impression as to what they would find acceptable if they were reviewing a paper so I could have a second( higher ) opinion to back up the rules I have made for our studies. thanks Greg

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Re: [Freesurfer] surf2vol
by yanxia 30 Jan '07

30 Jan '07

Thanks, Bruce. >2. No, it's all done in what we call "conformed" space, which is the >original volume interpolated to 256^3, 1mm iso and 8 bits/voxel If the original volume is 256^3, 1mm iso and 8 bits/voxel, whether all output results are same as the original space? Yan At 10:17 AM 1/30/2007, Bruce Fischl wrote: >1. Yes. >2. No, it's all done in what we call "conformed" space, which is the >original volume interpolated to 256^3, 1mm iso and 8 bits/voxel >On Tue, 30 Jan 2007, yanxia wrote: > >>Thanks, Bruce. >> >>I have another questions: >> >>1> If the input binary segmentation is topologically correct, >>whether the surface generated with the utility mri_tessellate is >>topologically correct. >> >>2> All output results with "recon-all -s bert -autorecon-all" are >>based on normalized space (template), is it right? >> >>Best Regards, >>Yan >> >>At 05:50 PM 1/29/2007, Bruce Fischl wrote: >>>Hi Yan, >>>1. We generate a file named ribbon.mgz, which is the filled >>>interior etween the ?h.white and ?h.pial surfaces. >>>2. This is a whole research topic, and most of the stuff that >>>happens after the segmentation is for doing this. The utility >>>mri_tessellate will generate a surface from a binary segmentation >>>but it won't be smooth or topologically correct. >>>cheers, >>>Bruce >>> On Mon, 29 Jan 2007, yanxia wrote: >>> >>>>Dear All, >>>>I am a new user of FreeSurfer. I have two questions: >>>>1> How can I use mri_surf2vol or others to convert .pial to .mgz? >>>>2> I have a binary .mgz file. How can I generate .pial file so >>>>that I can view it with tksurfer? >>>>Thanks. >>>>Yan >>>> >>>> >>>>_______________________________________________ >>>>Freesurfer mailing list >>>>Freesurfer(a)nmr.mgh.harvard.edu >>>>https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>>_______________________________________________ >>>Freesurfer mailing list >>>Freesurfer(a)nmr.mgh.harvard.edu >>>https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> >>

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Re: [Freesurfer] surf2vol
by yanxia 30 Jan '07

30 Jan '07

Thanks, Bruce. I have another questions: 1> If the input binary segmentation is topologically correct, whether the surface generated with the utility mri_tessellate is topologically correct. 2> All output results with "recon-all -s bert -autorecon-all" are based on normalized space (template), is it right? Best Regards, Yan At 05:50 PM 1/29/2007, Bruce Fischl wrote: >Hi Yan, > >1. We generate a file named ribbon.mgz, which is the filled interior >etween the ?h.white and ?h.pial surfaces. > >2. This is a whole research topic, and most of the stuff that >happens after the segmentation is for doing this. The utility >mri_tessellate will generate a surface from a binary segmentation >but it won't be smooth or topologically correct. > >cheers, >Bruce > > On Mon, 29 Jan 2007, yanxia wrote: > >>Dear All, >> >>I am a new user of FreeSurfer. I have two questions: >> >>1> How can I use mri_surf2vol or others to convert .pial to .mgz? >> >>2> I have a binary .mgz file. How can I generate .pial file so that >>I can view it with tksurfer? >> >>Thanks. >> >>Yan >> >> >> >> >>_______________________________________________ >>Freesurfer mailing list >>Freesurfer(a)nmr.mgh.harvard.edu >>https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> >_______________________________________________ >Freesurfer mailing list >Freesurfer(a)nmr.mgh.harvard.edu >https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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1) annot files on T1 and 2) seed points
by Joan Fisher 30 Jan '07

30 Jan '07

Hi all -- I'm still having difficulty with 2 problems that I think are solvable, but I can't figure them out. 1) When I call up aparc+aseg on the T1 image, I get the cortex that has been parcellated, but I do not get the parcellation -- that information is in the .annot files that seem to be viewable only using tksurfer and not tkmedit. Is there a way to see the full parcellation on T1.mgz? 2) Trying to run freesurfer on only the Right hemisphere on a child who has no left hemisphere, I've run into the problem where freesurfer wants to divide the intact hemisphere into half. When I try to use the seed points, it hasn't fixed the problem. Is this a problem of syntax or something else? These are the commands I used that I thought would work: mri_fill -C -93 -18 89 -P -35 -22 28 -rh -59 -23 105 subjects/005/mri.mgz subjects/005/mri/filled.mgz That part seemed to work, then: recon-all -hemi rh -s 005 -autorecon2-wm This part seemed to work until it got to CORRECTING DEFECT 1, where it said recon-all exited with ERRORS after it said "reading wm segmentation from wm.." Have I missed a step or misunderstood how to do the seed points? Thanks again, Joan

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Freesurfer and AFNI
by Anil Roy 29 Jan '07

29 Jan '07

Dear Freesurfers, I am checking out the functionality of using Freesurfer with AFNI and was wondering if someone could point me in the direction of any good documentation for this. So far, I can get Freesurfer to register the functional and hi-res structural but the functional overlay doesn't show up properly in tkmedit or tksurfer. Is there any recommended pipeline to be used for overlaying AFNI functionals on Freesurfer surfaces. Thanks, Anil.

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surf2vol
by yanxia 29 Jan '07

29 Jan '07

Dear All, I am a new user of FreeSurfer. I have two questions: 1> How can I use mri_surf2vol or others to convert .pial to .mgz? 2> I have a binary .mgz file. How can I generate .pial file so that I can view it with tksurfer? Thanks. Yan

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RE: [Freesurfer] -noaseg
by Nick Schmansky 27 Jan '07

27 Jan '07

Kazu, I should have mentioned this earlier, but when using the -noaseg flag, the talairach transform needs to be correct in order for mri_fill to properly cut the hemispheres vertically and the pons and cerebellum horizontally. It is obvious from your images that mri_fill is not cutting in this direction (and yes, the cerebellum should not appear in the filled.mgz, but it should appear in brainmask.mgz). I'm guessing that the transform, which is one of the early steps in recon-all, is off. Follow the instructions here: http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Talairach to align the monkey brain with the (human) talairach brain, as best as you can. Use this command: tkregister --mgz -s <subjid> --fstal which excludes the '--surf orig' option (since you don't yet have the orig surface). Once you feel you have a proper alignment (it can take awhile playing around with tkregister2 to get this, but it doesnt have to be perfect), then you can restart recon-all: recon-all -s <subjid> -autorecon2-wm -noaseg The cc and pons points were saved from the prior run, so they dont need to be specified. You will see them in the recon-all.log file. Actually, once the mri_fill step of recon-all creates the new filled.mgz, you may want to inspect it to make sure it cuts correctly, otherwise the topology fixing step will get stuck again on the huge defect. Nick On Fri, 2007-01-26 at 10:04 -0500, Tanji, Kazuyo (NIH/NIMH) [F] wrote: > Nick, > > Thanks for the suggestion. I saw 2 abnormal perpendicular lines inside white matter volume (as attached). Does it result from failure in defining cutting planes? Also I thought at this stage the cerebellum should not be displayed anymore. Is there ways to correct those manually? > > Best, > Kazu > > > -----Original Message----- > From: Nick Schmansky [mailto:nicks@nmr.mgh.harvard.edu] > Sent: Thu 1/25/2007 5:12 PM > To: Tanji, Kazuyo (NIH/NIMH) [F] > Subject: RE: [Freesurfer] -noaseg > > Kazu, > > In looking at the log, it appears to be stuck on correcting a defect > which has 27024 vertices, which is a huge number. This indicates > something is wrong with an earlier stage. > > Type: > > tkmedit <subj> orig.mgz -aux filled.mgz > > and make sure that the filled.mgz volume looks like it is properly > representing the white matter voxels (use Ctrl 1 and Ctrl 2 to flip > between volumes). > > Also: > > tksurfer <subj> lh orig > > will bring-up the tessellated 'filled' volume. Look for obvious > problems, like dimples or holes. > > You may need to edit the white matter to fix problems. See: > > http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/WhiteMatterEdits > > Also make sure your skull-strip worked properly: > > http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/SkullStripFix > > That is, make sure there are not bits of skull in brainmask.mgz > volume. > > Nick > > > > On Thu, 2007-01-25 at 14:45 -0500, Tanji, Kazuyo (NIH/NIMH) [F] wrote: > > Nick, > > > > Thanks for offering to take a look. I am attaching the log file. > > > > Best, > > Kazu > > > > > > -----Original Message----- > > From: Nick Schmansky [mailto:nicks@nmr.mgh.harvard.edu] > > Sent: Thu 1/25/2007 2:04 PM > > To: Tanji, Kazuyo (NIH/NIMH) [F] > > Subject: RE: [Freesurfer] -noaseg > > > > > > > > > > -----Original Message----- > > From: Nick Schmansky [mailto:nicks@nmr.mgh.harvard.edu] > > Sent: Thu 1/25/2007 2:04 PM > > To: Tanji, Kazuyo (NIH/NIMH) [F] > > Subject: RE: [Freesurfer] -noaseg > > > > Kazu, > > > > No it should not take so long...it usually takes no more than 10 hours. > > So this indicates something is unusual about the surface. Can you send me > > the recon-all.log file (in the subjects scripts dir)? I can check for > > problems in that. > > > > Nick > > > > > > > Hi Nick, > > > > > > Thanks so much for the suggestion. I specified the volume index and ran > > > recon-autorecon2-wm -noaseg. I started 5pm on Januray 22 (Monday) and it > > > has not finished processing. It is still at 'mris_fix_topology' (left > > > hemisphere). Could you suggest whether it is unusual for this step to take > > > this long or it is understandable given the non-standard method I am > > > trying? My CPU is quite new (Pentium D) and RAM is 2G. > > > > > > Thanks, > > > Kazu > > > > > > ________________________________ > > > > > > From: Nick Schmansky [mailto:nicks@nmr.mgh.harvard.edu] > > > Sent: Mon 1/22/2007 2:03 PM > > > To: Tanji, Kazuyo (NIH/NIMH) [F] > > > Cc: Freesurfer Mailing List > > > Subject: RE: [Freesurfer] -noaseg > > > > > > > > > > > > Kazu, > > > > > > This is for a non-human primate, right? If so, you will need to > > > manually define seed points for the corpus callosum and pons. To do so, > > > open the white matter volume in tkmedit: > > > > > > tkmedit <subjid> wm.mgz > > > > > > and using the cursor, identify the 'volume index' of the point where you > > > think the corpus callosum is located and make a note of it (for > > > instance, in an example subject 'bert', its around 128 117 123). Also > > > make a note of where the pons is located. > > > > > > Then, restart recon-all from mri_fill, passing those coordinates, for > > > example: > > > > > > recon-all -s bert -autorecon2-wm -noaseg \ > > > -cc-crs 128 117 123 \ > > > -pons-crs 128 154 108 > > > > > > Nick > > > > > > ps, i've posted this to the list as others may have a better suggestion. > > > > > > On Mon, 2007-01-22 at 12:55 -0500, Tanji, Kazuyo (NIH/NIMH) [F] wrote: > > >> Hi Nick, > > >> > > >> Thank you so much. It worked. > > >> Now I got an error message at 'mri_fill'. > > >> > > >> The message says: > > >> mri_fill: could not find corpus callosum > > >> INFO: Modifying dst c_(r,a,s), using the transform dst > > >> find_cutting_plane:seed point not in structure! Searching > > >> neighborhood... > > >> recon-all exited with ERRORS at Mon Jan 22 10:57:43 EST 2007 > > >> > > >> Is this error due to -noaseg flag? What should I do next? > > >> > > >> Kazu > > >> -----Original Message----- > > >> From: Nick Schmansky [mailto:nicks@nmr.mgh.harvard.edu] > > >> Sent: Sun 1/21/2007 6:38 PM > > >> To: Tanji, Kazuyo (NIH/NIMH) [F] > > >> Cc: Freesurfer Mailing List > > >> Subject: Re: [Freesurfer] -noaseg > > >> > > >> Kazu, > > >> > > >> It looks like the -noaseg option does make use of norm.mgz (a change > > >> that seems to have occurred since the option was created and tested). > > >> > > >> As a work-around, you should be able to do this: > > >> > > >> ln -s brainmask.mgz norm.mgz > > >> > > >> and then run the -autorecon2 -noaseg flags. brainmask.mgz is a close > > >> enough stand-in for norm.mgz. > > >> > > >> Nick > > >> > > >> > > >> On Sun, 2007-01-21 at 17:45 -0500, Tanji, Kazuyo (NIH/NIMH) [F] wrote: > > >> > Hi, > > >> > > > >> > I have a question on how to use -noaseg option. > > >> > > > >> > I tried a script: recon-all -autorecon2 -noaseg -subjid xxx. > > >> > > > >> > This seems to skip several steps of autorecon2 and start from > > >> 'mri_normalize' . This results in an error because norm.mgz is not > > >> existing. > > >> > > > >> > Could you suggest better ways to use -noaseg? > > >> > > > >> > Thanks, > > >> > Kazu > > >> > > > >> > > > >> > > > >> > > > >> > _______________________________________________ > > >> > Freesurfer mailing list > > >> > Freesurfer(a)nmr.mgh.harvard.edu > > >> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > >> > > > >> > > > >> > > >> > > >> > > > > > > > > > > > > > > > > > > > > >

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recon-all -long errors
by Chacko Cherian 26 Jan '07

26 Jan '07

Hello users, I was running longitudinal analysis for a couple of scans and recon-all exited with this error. CTABread(/usr/local/freesurfer/ASegStatsLUT.txt): could not open file No such file or directory atlas_icv = 1.74537e+06 Loading mri/aseg.mgz Loading mri/norm.mgz Loading mri/norm.mgz Loading mri/brainmask.mgz # nbrainmaskvoxels 1836053 # brainmaskvolume 1836053.0 # nbrainsegvoxels 1347237 # brainsegvolume 1347237.0 Voxel Volume is 1 mm^3 Generating list of segmentation ids ERROR: reading /usr/local/freesurfer/ASegStatsLUT.txt Linux snuffy 2.6.17-10-generic #2 SMP Tue Dec 5 22:28:26 UTC 2006 i686 GNU/Linux recon-all-long exited with ERRORS at Thu Jan 25 11:38:22 MST 2007 there were also a couple of lines like these where it couldn't find gc for labels. GCAmaxLikelihoodBorderLabel(138, 152, 124): couldn't find gc for label 28 GCAmaxLikelihoodBorderLabel(203, 103, 130): couldn't find gc for label 3 GCAmaxLikelihoodBorderLabel(154, 177, 130): couldn't find gc for label 3 GCAmaxLikelihoodBorderLabel(154, 178, 130): couldn't find gc for label 3 GCAmaxLikelihoodBorderLabel(203, 103, 131): couldn't find gc for label 3 GCAmaxLikelihoodBorderLabel(207, 126, 136): couldn't find gc for label 3 GCAmaxLikelihoodBorderLabel(207, 126, 137): couldn't find gc for label 3 GCAmaxLikelihoodBorderLabel(207, 127, 137): couldn't find gc for label 3 GCAmaxLikelihoodBorderLabel(150, 145, 150): couldn't find gc for label 3 GCAmaxLikelihoodBorderLabel(150, 146, 150): couldn't find gc for label 3 GCAmaxLikelihoodBorderLabel(150, 146, 151): couldn't find gc for label 3 GCAmaxLikelihoodBorderLabel(159, 157, 163): couldn't find gc for label 3 GCAmaxLikelihoodBorderLabel(135, 159, 163): couldn't find gc for label 42 GCAmaxLikelihoodBorderLabel(136, 159, 163): couldn't find gc for label 42 Thsnks in advance Chacko. ____________________________________________________________________________________ Expecting? Get great news right away with email Auto-Check. Try the Yahoo! Mail Beta. http://advision.webevents.yahoo.com/mailbeta/newmail_tools.html

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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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setting thresholds in tkmedit and tksurfer
by Doug Greve 26 Jan '07

26 Jan '07

I've just created two new env variables to help manage setting overlay thresholds in tkmedit and tksurfer. If you just: setenv FS_TKFTHRESH 3 setenv FS_TKFMAX 5 then the threshold will be set to 3 and the max/sat will be set to 5 in both tkmedit and tksurfer (so they will be consistent). You can still override them at the cmd line. I've just checked these changes in, so they will be live in dev on the next update. doug -- 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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Freesurfer January 2007