Freesurfer April 2011

freesurfer@nmr.mgh.harvard.edu

121 participants
166 discussions

Re: [Freesurfer] homologous left and right roi
by Prapti Gautam 15 Apr '11

15 Apr '11

Hi, I want to copy a label I've created on a region on the left hemisphere to the right (or vice versa) and was wondering if there has been any progress on the tools avaialable. Is there perhaps a beta version of the functionality that could be used? Thanks, Prapti ---------------------------------------------------------------------------- 5. Re: Homologous Right Left ROIs (Douglas N Greve) Message: 5 Date: Tue, 15 Mar 2011 11:22:13 -0400 From: Douglas N Greve <greve(a)nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] Homologous Right Left ROIs To: Lena Palaniyappan <Lena.Palaniyappan(a)nottingham.ac.uk> Cc: "freesurfer(a)nmr.mgh.harvard.edu" <freesurfer(a)nmr.mgh.harvard.edu> Message-ID: <4D7F8425.3030204(a)nmr.mgh.harvard.edu> Content-Type: text/plain; charset=windows-1252; format=flowed Hi Lena, we don't have tools released yet to do this. They should be available in the spring. dopug Lena Palaniyappan wrote: > Hi all > > I have a ROI label on left hemisphere ? I need to map this ROI onto > right hemisphere to get a homologous region (for testing hemispheric > differences). What is the best way for doing this? > > Cheers > Lena

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autostimdur vs noautostimdur
by Katie Bettencourt 15 Apr '11

15 Apr '11

I'm a bit confused about what the -autostimdur and -noautostimdur flags in mkanalysis-sess do. I've checked the help files, but the wording is a bit confusing, and when I run them on my event related design, I get different results depending on which flag I use, with the -noautostimdur being more of what I expect as far as results go. Also, they are only used in event related and AB designs, not blocked, correct? Katie

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sulcal depth
by Lugar, Heather 15 Apr '11

15 Apr '11

Is there a way to extract sulcal depth statistics for a group of subjects using a function like aparcstats2table for mean curve, thickness, volume, etc.? Thanks, Heather

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FreeSurfer ver 4.0 vs 5.0
by Keefe, Helen L 15 Apr '11

15 Apr '11

Hello Bruce and All, Here are some new questions to an ongoing issue. 1. What are advantages of version 5.0 over the former version? I have processed 82 scans so far in the former version and am debating whether to re-run them all in 5.0. We will eventually have a total of 560 scans, so we need to decide soon. 2. In version 5.0, when I run tksurfer $i lh pial -annotation aparc the corpus callossum is labeled as "none". Is there a way to have it be labeled correctly as itself in ver 5? Thanks, Helen ________________________________ Notice: This UI Health Care e-mail (including attachments) is covered by the Electronic Communications Privacy Act, 18 U.S.C. 2510-2521, is confidential and may be legally privileged. If you are not the intended recipient, you are hereby notified that any retention, dissemination, distribution, or copying of this communication is strictly prohibited. Please reply to the sender that you have received the message in error, then delete it. Thank you. ________________________________

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failing recon-all with freesurfer v5.0
by Saad Ramadan 14 Apr '11

14 Apr '11

Hi, I have upgraded to v5.0 assuming that I'll be in a better shape now. I issued this command: nohup recon-all -s ../NanditaGoodDataSetSubject5.0_run2 -i ./t1_svs.nii -autorecon-all & which failed after a while . I used nohup so that I can close shell with terminating the calculation. The tail of recon-all.log is show below (in red ). I do assume that I have no RAM problems as this computer is dedicated for such calculations. Any hint pls? Thanks #-------------------------------------------- #@# Smooth2 lh Wed Apr 13 17:48:03 EDT 2011 mris_smooth -n 3 -nw -seed 1234 ../surf/lh.white ../surf/lh.smoothwm /home/sramadan/freesurfer/subjects/NanditaGoodDataSetSubject5.0_run2/scripts smoothing for 3 iterations setting seed for random number generator to 1234 smoothing surface tessellation for 3 iterations... smoothing complete - recomputing first and second fundamental forms... #-------------------------------------------- #@# Inflation2 lh Wed Apr 13 17:48:12 EDT 2011 /home/sramadan/freesurfer/subjects/NanditaGoodDataSetSubject5.0_run2/scripts mris_inflate ../surf/lh.smoothwm ../surf/lh.inflated avg radius = 46.7 mm, total surface area = 85687 mm^2 writing inflated surface to ../surf/lh.inflated writing sulcal depths to ../surf/lh.sulc step 000: RMS=0.119 (target=0.015) step 005: RMS=0.082 (target=0.015) step 010: RMS=0.060 (target=0.015) step 015: RMS=0.050 (target=0.015) step 020: RMS=0.043 (target=0.015) step 025: RMS=0.035 (target=0.015) step 030: RMS=0.029 (target=0.015) step 035: RMS=0.025 (target=0.015) step 040: RMS=0.022 (target=0.015) step 045: RMS=0.019 (target=0.015) step 050: RMS=0.017 (target=0.015) step 055: RMS=0.016 (target=0.015) step 060: RMS=0.015 (target=0.015) inflation complete. inflation took 1.6 minutes mris_curvature -thresh .999 -n -a 5 -w -distances 10 10 ../surf/lh.inflated normalizing curvature values. averaging curvature patterns 5 times. sampling 10 neighbors out to a distance of 10 mm 321 vertices thresholded to be in k1 ~ [-0.25 0.24], k2 ~ [-0.11 0.05] total integrated curvature = 0.502*4pi (6.303) --> 0 handles ICI = 1.4, FI = 9.5, variation=161.148 170 vertices thresholded to be in [-0.01 0.02] writing Gaussian curvature to ../surf/lh.inflated.K...thresholding curvature at 99.90% level curvature mean = 0.000, std = 0.001 148 vertices thresholded to be in [-0.14 0.12] done. writing mean curvature to ../surf/lh.inflated.H...curvature mean = -0.017, std = 0.022 done. #----------------------------------------- #@# Curvature Stats lh Wed Apr 13 17:52:48 EDT 2011 /home/sramadan/freesurfer/subjects/NanditaGoodDataSetSubject5.0_run2/surf mris_curvature_stats -m --writeCurvatureFiles -G -o ../stats/lh.curv.stats -F smoothwm NanditaGoodDataSetSubject5.0_run2 lh curv sulc Toggling save flag on curvature files [ ok ] Outputting results using filestem [ ../stats/lh.curv.stats ] Toggling save flag on curvature files [ ok ] Setting surface [ NanditaGoodDataSetSubject5.0_run2/lh.smoothwm ] Reading surface... [ ok ] Setting texture [ curv ] Reading texture... [ ok ] Setting texture [ sulc ] Reading texture... [ ok ] Calculating Discrete Principal Curvatures... Determining geometric order for vertex faces... [####################] [ ok ] Determining KH curvatures... [####################] [ ok ] Determining k1k2 curvatures... [####################] [ ok ] deltaViolations [ 258 ] WARN: S lookup min: -0.547240 WARN: S explicit min: 0.000000 vertex = 126 #-------------------------------------------- #@# Sphere lh Wed Apr 13 17:53:01 EDT 2011 /home/sramadan/freesurfer/subjects/NanditaGoodDataSetSubject5.0_run2/scripts mris_sphere -seed 1234 ../surf/lh.inflated ../surf/lh.sphere setting seed for random number genererator to 1234 $Id: mris_sphere.c,v 1.54 2010/04/14 15:16:23 fischl Exp $ $Id: mrisurf.c,v 1.678 2010/05/28 21:22:21 rpwang Exp $ reading original vertex positions... unfolding cortex into spherical form... surface projected - minimizing metric distortion... writing spherical brain to ../surf/lh.sphere spherical transformation took 4.62 hours scaling brain by 0.274... pass 1: epoch 1 of 3 starting distance error %20.44 pass 1: epoch 2 of 3 starting distance error %20.39 unfolding complete - removing small folds... starting distance error %20.32 removing remaining folds... final distance error %20.32 284: 0 negative triangles Linux cluster.bwh.harvard.edu 2.6.9-34.ELsmp #1 SMP Fri Feb 24 16:56:28 EST 2006 x86_64 x86_64 x86_64 GNU/Linux recon-all -s NanditaGoodDataSetSubject5.0_run2 exited with ERRORS at Wed Apr 13 22:30:15 EDT 2011

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mkanalysis.sess versus mkanalysis.sess.new
by Maryam Vaziri Pashkam 14 Apr '11

14 Apr '11

Hi Everyone, Two beginner question again. 1. What is the difference between mkanalysis-sess and mkanalysis-sess.new? which one should be preferably used and why? 2. What is the best way to exclude trials from the analysis: a) in the paradigm file define them as a separate condition and this way include them in the GLM analysis and later on ignore them in the contrast analysis? b) exclude the time points of that trial in the tpexclude.dat using the tpexclude flag? c) another way that I have not thought of? Thanks, Maryam

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high resolution segmentation
by Jonathan A Winawer 14 Apr '11

14 Apr '11

I recently started using freesurfer for gray-white segmentation with great success. However, I have had one problem I cannot solve myself: I have been unable to create a ribbon file at the native resolution of my T1 scans (0.7 mm isotropic voxels), and I am puzzled by the result. My strategy was as follows: 1. standard recon all (this works nicely) 2. resample aseg.mgz to match the slicing of rawavg.mgz 3. create new ribbon file using mris_volmask The standard recon at 1x1x1 mm resolution produces a nice ribbon file: http://white.stanford.edu/~winawer/brain/2011/axial_ribbon_1mm.tiff The hires recon after steps 2 and 3 above fails: http://white.stanford.edu/~winawer/brain/2011/axial_ribbon_hires.tiff If anyone knows why this is, I would greatly appreciate the help. For details, see below. Many thanks, Jon The hires t1 I started with is here: http://white.stanford.edu/~winawer/brain/2011/t1.nii.gz and the code I used for the initial recon and the creation of the new ribbon is here: # give the subject a name subj=homer # recon all using hires t1 (0.7 mm isotropic voxels) recon-all -i ~/t1.nii.gz -all -subjid $subj -all # define the working directory d=$SUBJECTS_DIR/$subj/mri # back up original ribbon and aseg files mkdir $d/1mm; mv $d/*ribbon* $d/aseg.mgz -t $d/1mm ## Create Hi-Res Ribbon##################### # reslice the aseg file to the size and resolution of rawavg mri_convert $d/1mm/aseg.mgz -o $d/aseg.mgz --reslice_like $d/rawavg.mgz --resample_type nearest # re-create surface at resolution of rawavg mris_volmask --label_left_white 2 --label_left_ribbon 3 --label_right_white 41 --label_right_ribbon 42 --save_ribbon --save_distance $subj ##################################### # back up high-res files mkdir $d/hires; cp $d/*ribbon* $d/aseg.mgz $d/hires/ # Compare the two ribbon files. Original (1x1x1 mm) looks good: tkmedit $subj 1mm/aseg.mgz -segmentation 1mm/ribbon.mgz # HiRes looks bad: tkmedit $subj hires/aseg.mgz -segmentation hires/ribbon.mgz ******************************* Jonathan Winawer Stanford University Department of Psychology Jordan Hall, Building 01-420 450 Serra Mall Stanford, CA 94305 Phone: 650-725-1255 winawer(a)stanford.edu http://www-psych.stanford.edu/~winawer/

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Re: [Freesurfer] creating labels in tksurfer
by Ilana Hairston 14 Apr '11

14 Apr '11

Thanks Bruce, It seems there are some display bugs on the server running freesurfer. In addition to the vanishing label (the label option was on), the scatter plots were messed up. After transferring the data to a different server it seems to be ok. Not sure what the issue is. ilana ______________________ If you can't be kind, be vague •••••••••••••••••••••••••••••••••••• Sent from my iPhone On Apr 4, 2011, at 10:23, Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> wrote: > Hi Ilana, > > it looks fine to me. Is it a left hemisphere label? If so, it looks like superior temporal gyrus. Make sure that label display is turned on in the tksurfer interface (the default may be off). It's one of the buttons on the top right. > > cheers > Bruce > > > On Sat, 2 Apr 2011, Ilana Hairston wrote: > >> sorry for the delay (can't ftp from the server). the file is attached >> >> On 2 April 2011 12:33, Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> wrote: >> >>> can you email us the label? >>> >>> On Sat, 2 Apr 2011, Ilana Hairston wrote: >>> >>> sorry, i probably should have said that this was on the fsaverage, after >>>> glmfit. >>>> basically i wanted to create a VOI and extract a stats table for it. >>>> >>>> >>>> On 1 April 2011 22:33, Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> wrote: >>>> >>>> Hi Ilana, >>>>> >>>>> usually a bizarre labeling means the annot is out of date. Try running >>>>> recon-all with -make all on that subject and see if it needs to recreate >>>>> anything. >>>>> >>>>> Not sure what's up with your label, but things can act strangely when the >>>>> surfaces are out of date >>>>> >>>>> cheers >>>>> Bruce >>>>> >>>>> On Fri, 1 Apr 2011, Ilana Hairston wrote: >>>>> >>>>> Hi there, >>>>> >>>>>> I'm having difficulty creating labels in tksurfer (v4.5). I followed >>>>>> the >>>>>> "Creating Labels" instructions on the Wiki, however clicking Fill on the >>>>>> closed path didn't seem to do anything. I used save label anyway, and >>>>>> tried >>>>>> to load this new label again, and even though it says "7681 nonzero >>>>>> vertices >>>>>> found", again i see nothing. >>>>>> Not quite sure what i'm doing wrong. >>>>>> >>>>>> Also - which LUT file is the correct one to go with aparc.annot? i get >>>>>> the >>>>>> most bizarre labeling with FreeSurferColorLUT >>>>>> Thanks >>>>>> ilana >>>>>> >>>>>> >>>>>> >>>>>> >>>>> 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. >>>>> >>>>> >>>>> >>>> >>>> >>>> >> >> >>

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?h.aparc.stats file question
by Tetiana Dadakova 14 Apr '11

14 Apr '11

Dear list, I was trying to find the values of volumes for different cortical regions. What I found is the 4th column (called GrayVol) in ?h.aparc.stats file. Although, the values don't really seem to be what I look for, as values are too small (e.g. 0.5 mm^3 for cuneus). Could you please guide me where I should look for these values, or probably how should I interpret the values in ?h.aparc.stats file. Thank you, Tanja.

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create summary images
by McLean John (NHS Greater Glasgow & Clyde) 14 Apr '11

14 Apr '11

I'd like to create some summary images (.tiff, .png ) so that I can quickly inspect subcortical structure segmentation quality on a large number of subjects. I know I can open tkmedit and extract a series of tiff images, I've also been playing with Slicer3 but again I have to load the data for each subject. I'd also like to hone in on particular structures, for example, to extract images only showing the hippocampus (whole segmentation or outline) on the T1 3D backdrop, does anything exist in Freesurfer to do this from the command line? Essentially I'm looking for something similar to the first_roi_slicerdir command in FSL as I found this a really quick way of visually checking segmented data. Any advice around this would be a great help, Thanks John ******************************************************************************************************************** This message may contain confidential information. If you are not the intended recipient please inform the sender that you have received the message in error before deleting it. Please do not disclose, copy or distribute information in this e-mail or take any action in reliance on its contents: to do so is strictly prohibited and may be unlawful. Thank you for your co-operation. NHSmail is the secure email and directory service available for all NHS staff in England and Scotland NHSmail is approved for exchanging patient data and other sensitive information with NHSmail and GSi recipients NHSmail provides an email address for your career in the NHS and can be accessed anywhere For more information and to find out how you can switch, visit www.connectingforhealth.nhs.uk/nhsmail ********************************************************************************************************************

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Freesurfer April 2011