Freesurfer

freesurfer@nmr.mgh.harvard.edu

17 participants
30086 discussions

freesurfer surfaces in different orientation
by Tina Jeon 17 Apr '14

17 Apr '14

Hello creators of freesurfer, I am trying to align my surfaces with DTI data and ultimately display them in Amira. I noticed that during the step mris_make_surfaces there is an orientation change from lh.orig to lh.white. I attached a snapshot of the two surfaces overlayed with my b0 data. You can see that the lh.orig (which is perfectly registered with b0) and lh.white files are not perfectly aligned but differ by some orientation change. Is there a way to undo this orientation change? Or perhaps output a text of shift so that I can change the coordinates in the surfaces? The command is mris_make_surfaces -whiteonly -noaparc -mgz -T1 brain.finalsurfs subj_id lh Thank you in advance for any guidance. Sincerely, Tina Jeon, M.S. Biomedical Engineering Graduate Student Dr. Hao Huang's Lab Advanced Imaging Research Center UT Southwestern Medical Center (310) 592-1853 ________________________________ UT Southwestern Medical Center The future of medicine, today.

1 0

Group Average Thickness
by Jonathan Holt 17 Apr '14

17 Apr '14

Hi all, I’m currently trying to generate an average subject for two groups so that I might be able to display average thickness for both groups. I’m confused as to whether I should be following the GroupAnalysis workflow in the wiki, or if I should use make_average_subject and mris_preproc in tandem, but for the latter option (if it is the appropriate one) how should I use the two together, if that’s the right approach? jon

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Question about how to get Talairach step to work on brains with bright scalp areas
by David M. Perlman 17 Apr '14

17 Apr '14

Hello, I have a question about how to get freesurfer to work correctly with images that have problematic contrast. We have a bunch of images that were taken with a new 32-channel head coil. For some of these images, the contrast value for the scalp cutaneous fat is dramatically higher than the contrast value for the brain tissue itself. http://brainimaging.waisman.wisc.edu/~perlman/images/1280_2_MPRAGE_sag.png Many of the images that look like this are processed just fine, but some of them fail. When they fail, it looks like this in the log (see pasted log text below). I looked at the link that it told me to check but it was an invalid page in the wiki: http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Talairach I tracked down this page instead: http://surfer.nmr.mgh.harvard.edu/fswiki/FreeSurferTalairach On that page it suggests: When you see a big bright neck region, an option is to edit the volume to erase the bright neck region and run mritotal on the edited volume. It usually works by a simple editing, setting all the region to zero where y > certain value (around 170). This worked better than using "brain" volume. I thresholded one of my trouble images with this command: poblano:/study/gates/data/mri/preprocessed/VIPR_IR/MPRAGE$ 3dcalc -a 1221_2_MPRAGE_reorient.nii.gz -expr 'step(a-1000)*1000 + step(1000-a)*a' -prefix 1221_2_MPRAGE_reorient_clip1000.nii.gz ++ 3dcalc: AFNI version=AFNI_2011_12_21_1014 (Mar 31 2014) [64-bit] ++ Authored by: A cast of thousands ++ Output dataset ./1221_2_MPRAGE_reorient_clip1000.nii.gz The image certainly looked better after that. http://brainimaging.waisman.wisc.edu/~perlman/images/1280_2_MPRAGE_sag_trim… I tried it again with the command: poblano:/study/gates/data/mri/preprocessed/VIPR_IR/MPRAGE/freesurfer_nu_test$ recon-all -i /study/gates/data/mri/preprocessed/VIPR_IR/MPRAGE/1221_2_MPRAGE_reorient_clip1000.nii.gz -subject 1221_2_clip1000 -all but the result was the same. The talairach.xfm matrix is this: Transform_Type = Linear; Linear_Transform = 0.755387127399445 -0.110331535339355 -0.538617014884949 -24.9059925079346 0.544680178165436 0.0255524087697268 0.75865626335144 15.3778610229492 -0.0748601630330086 -0.927396953105927 0.0849819406867027 -111.666954040527; which definitely doesn't look right. We tried turning up the --nuiterations option to a much higher value, but this step doesn't run until after the Talairach transform so it is unable to help that process. (Wouldn't it make more sense to swap that order?) I was wondering if you could give me any advice on other steps I could try, to get this brain to process with recon_all? Thanks! INFO: Attempting MINC mritotal to perform Talairach align #-------------------------------------------- #@# Talairach Mon Apr 14 10:54:57 CDT 2014 /study1/gates/data/mri/analysis/SA/freesurfer/test_mprage_fail/1221_2/mri mri_nu_correct.mni --n 1 --proto-iters 1000 --distance 50 --no-rescale --i orig.mgz --o orig_nu.mgz talairach --i orig_nu.mgz --xfm transforms/talairach.auto.xfm /study1/gates/data/mri/analysis/SA/freesurfer/test_mprage_fail/1221_2/mri /apps/x86_64_sci6/freesurfer-latest/bin/talairach --i orig_nu.mgz --xfm transforms/talairach.auto.xfm $Id: talairach,v 1.7 2011/03/02 20:16:40 nicks Exp $ Linux c114.keck.waisman.wisc.edu 2.6.32-431.5.1.el6.x86_64 #1 SMP Tue Feb 11 13:30:01 CST 2014 x86_64 x86_64 x86_64 GNU/Linux Mon Apr 14 10:55:50 CDT 2014 tmpdir is transforms/tmp.talairach.30831 /study1/gates/data/mri/analysis/SA/freesurfer/test_mprage_fail/1221_2/mri mri_convert orig_nu.mgz transforms/tmp.talairach.30831/src.mnc mri_convert orig_nu.mgz transforms/tmp.talairach.30831/src.mnc $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from orig_nu.mgz... TR=4.55, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, 0) j_ras = (0, 0, -1) k_ras = (0, 1, 0) writing to transforms/tmp.talairach.30831/src.mnc... -------------------------------------------- mritotal -verbose -debug -clobber -modeldir /apps/x86_64_sci6/freesurfer-latest/mni/bin/../share/mni_autoreg -protocol icbm transforms/tmp.talairach.30831/src.mnc transforms/talairach.auto.xfm Mon Apr 14 10:56:11 CDT 2014 talairach done cp transforms/talairach.auto.xfm transforms/talairach.xfm #-------------------------------------------- #@# Talairach Failure Detection Mon Apr 14 10:56:12 CDT 2014 /study1/gates/data/mri/analysis/SA/freesurfer/test_mprage_fail/1221_2/mri talairach_afd -T 0.005 -xfm transforms/talairach.xfm ERROR: talairach_afd: Talairach Transform: transforms/talairach.xfm ***FAILED*** (p=0.0000, pval=0.0000 < threshold=0.0050) Manual Talairach alignment may be necessary, or include the -notal-check flag to skip this test, making sure the -notal-check flag follows -all or -autorecon1 in the command string. See http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Talairach -- -dave------------------------------------------------------------------------ "Let us work without theorizing... 'tis the only way to make life endurable." - Voltaire, Candide, Chapter 30

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recon-all error
by Boric, Katica A. 17 Apr '14

17 Apr '14

Hello Freesurfers! This case of recon-all -s MGHXXX_SurferOutput exited with ERRORS. Attach is the recon-all log file. Any advice on how to solve this issue, please ? Thank you very much!!! Katica

2 2

Extract vertex-wise cortical thickness, surface area and lgi values in ascii files?
by sabin khadka 17 Apr '14

17 Apr '14

Hi all, I want to extract to extract thickness, area and lgi values vertex wise in ascii files for group of subjects. Could anyone suggest me on how to do it. Thank you for your help. -Sabin

2 3

Research Assistant Position Available in Human Brain Mapping at New York's Feinstein Institute for Medical Research
by David Groppe 16 Apr '14

16 Apr '14

The Laboratory for Multimodal Human Brain Mapping at the Feinstein Institute for Medical Research is looking for a research assistant to help with their research into (1) improving the identification of functional and pathological brain regions in individuals suffering from epilepsy, (2) the neural mechanisms of cognition, and (3) characterizing macroscale human brain networks. The lab works exclusively with patients being evaluated for epilepsy surgery using methods such as electrocorticography, MRI, fMRI, and direct electrical brain stimulation. The responsibilities of the research assistant include assisting with the collection and analysis of the aforementioned data, managing data archives and lab equipment, working with a research coordinator on IRB matters, and helping to present lab findings at conferences and in journals. This unique position will expose the successful applicant to basic and clinical neuroscience as well as neurosurgery, neurology, and neuropsychology. It is a great opportunity for recent post-bacs interested in medical school or graduate school in neuroscience/biomedical engineering. Past research assistants in the lab have been co-authors on lab publications and have gone on to MD or PhD programs after spending 1-2 years in the lab. ------------- Qualifications ------------- Minimum: -B.A./B.S./B.E. in an appropriate discipline (e.g., neuroscience, psychology, biomedical engineering, computer science, physics) -1 year commitment Highly Desirable: -Experience with at least one programming language (preferably MATLAB) and statistical analyses -Prior experience working with neuroimaging, EEG/MEG, or brain stimulation data -Previous experience working with patients -Previous work in a research laboratory that shows evidence of independent scholarship, problem solving, and motivation -2 year commitment preferred For more information about the lab see: http://www.feinsteininstitute.org/faculty/ashesh-mehta-md-phd/ For more information about the position please send curriculum vitae and cover letter to Dr. David Groppe (david.m.groppe(a)gmail.com) -- David Groppe, Ph.D. Postdoctoral Researcher Laboratory for Multimodal Human Brain Mapping Feinstein Institute for Medical Research Manhasset, New York http://www.cogsci.ucsd.edu/~dgroppe/

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minimal data needed for maintaining edits
by Satrajit Ghosh 16 Apr '14

16 Apr '14

hi, some of our freesurfer directories have become bloated with all kinds of non-freesurfer data. if i want to rerun a subject in a new location while maintaining the edits, is there a minimal list of files i should copy over? cheers, satra

1 1

Question about how to get Talairach step to work on brains with bright scalp areas
by David M. Perlman 16 Apr '14

16 Apr '14

Hello, I have a question about how to get freesurfer to work correctly with images that have problematic contrast. We have a bunch of images that were taken with a new 32-channel head coil. For some of these images, the contrast value for the scalp cutaneous fat is dramatically higher than the contrast value for the brain tissue itself. (See one attached image) Many of the images that look like this are processed just fine, but some of them fail. When they fail, it looks like this in the log (see pasted log text below). I looked at the link that it told me to check but it was an invalid page in the wiki: http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Talairach I tracked down this page instead: http://surfer.nmr.mgh.harvard.edu/fswiki/FreeSurferTalairach On that page it suggests: When you see a big bright neck region, an option is to edit the volume to erase the bright neck region and run mritotal on the edited volume. It usually works by a simple editing, setting all the region to zero where y > certain value (around 170). This worked better than using "brain" volume. I thresholded one of my trouble images with this command: poblano:/study/gates/data/mri/preprocessed/VIPR_IR/MPRAGE$ 3dcalc -a 1221_2_MPRAGE_reorient.nii.gz -expr 'step(a-1000)*1000 + step(1000-a)*a' -prefix 1221_2_MPRAGE_reorient_clip1000.nii.gz ++ 3dcalc: AFNI version=AFNI_2011_12_21_1014 (Mar 31 2014) [64-bit] ++ Authored by: A cast of thousands ++ Output dataset ./1221_2_MPRAGE_reorient_clip1000.nii.gz The image certainly looked better after that. (See other attached image) I tried it again with the command: poblano:/study/gates/data/mri/preprocessed/VIPR_IR/MPRAGE/freesurfer_nu_test$ recon-all -i /study/gates/data/mri/preprocessed/VIPR_IR/MPRAGE/1221_2_MPRAGE_reorient_clip1000.nii.gz -subject 1221_2_clip1000 -all but the result was the same. The talairach.xfm matrix is this: Transform_Type = Linear; Linear_Transform = 0.755387127399445 -0.110331535339355 -0.538617014884949 -24.9059925079346 0.544680178165436 0.0255524087697268 0.75865626335144 15.3778610229492 -0.0748601630330086 -0.927396953105927 0.0849819406867027 -111.666954040527; which definitely doesn't look right. We tried turning up the --nuiterations option to a much higher value, but this step doesn't run until after the Talairach transform so it is unable to help that process. (Wouldn't it make more sense to swap that order?) I was wondering if you could give me any advice on other steps I could try, to get this brain to process with recon_all? Thanks! INFO: Attempting MINC mritotal to perform Talairach align #-------------------------------------------- #@# Talairach Mon Apr 14 10:54:57 CDT 2014 /study1/gates/data/mri/analysis/SA/freesurfer/test_mprage_fail/1221_2/mri mri_nu_correct.mni --n 1 --proto-iters 1000 --distance 50 --no-rescale --i orig.mgz --o orig_nu.mgz talairach --i orig_nu.mgz --xfm transforms/talairach.auto.xfm /study1/gates/data/mri/analysis/SA/freesurfer/test_mprage_fail/1221_2/mri /apps/x86_64_sci6/freesurfer-latest/bin/talairach --i orig_nu.mgz --xfm transforms/talairach.auto.xfm $Id: talairach,v 1.7 2011/03/02 20:16:40 nicks Exp $ Linux c114.keck.waisman.wisc.edu 2.6.32-431.5.1.el6.x86_64 #1 SMP Tue Feb 11 13:30:01 CST 2014 x86_64 x86_64 x86_64 GNU/Linux Mon Apr 14 10:55:50 CDT 2014 tmpdir is transforms/tmp.talairach.30831 /study1/gates/data/mri/analysis/SA/freesurfer/test_mprage_fail/1221_2/mri mri_convert orig_nu.mgz transforms/tmp.talairach.30831/src.mnc mri_convert orig_nu.mgz transforms/tmp.talairach.30831/src.mnc $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from orig_nu.mgz... TR=4.55, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, 0) j_ras = (0, 0, -1) k_ras = (0, 1, 0) writing to transforms/tmp.talairach.30831/src.mnc... -------------------------------------------- mritotal -verbose -debug -clobber -modeldir /apps/x86_64_sci6/freesurfer-latest/mni/bin/../share/mni_autoreg -protocol icbm transforms/tmp.talairach.30831/src.mnc transforms/talairach.auto.xfm Mon Apr 14 10:56:11 CDT 2014 talairach done cp transforms/talairach.auto.xfm transforms/talairach.xfm #-------------------------------------------- #@# Talairach Failure Detection Mon Apr 14 10:56:12 CDT 2014 /study1/gates/data/mri/analysis/SA/freesurfer/test_mprage_fail/1221_2/mri talairach_afd -T 0.005 -xfm transforms/talairach.xfm ERROR: talairach_afd: Talairach Transform: transforms/talairach.xfm ***FAILED*** (p=0.0000, pval=0.0000 < threshold=0.0050) Manual Talairach alignment may be necessary, or include the -notal-check flag to skip this test, making sure the -notal-check flag follows -all or -autorecon1 in the command string. See http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Talairach -- -dave------------------------------------------------------------------------ "Let us work without theorizing... 'tis the only way to make life endurable." - Voltaire, Candide, Chapter 30

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Units of Flat-Patch Coordinates
by Sam Norman-Haignere 16 Apr '14

16 Apr '14

I assume that the units of the surface vertex coordinates in the flattened patches (e.g. in "rh.cortex.patch.flat.asc") correspond approximately to millimeters on the cortical surface. I was hoping someone could confirm this, because I couldn't find a definite answer searching online. Thanks, Sam Norman-Haignere BCS, MIT

2 1

TRACULA lesions
by Florian Borsodi 16 Apr '14

16 Apr '14

Dear Freesurfer TRACULA Experts, We are trying to run TRACULA on patients with lesions and found out, that TRACULA had problems tracking streamlines trough the lesions, which is understandable. The problem is, if TRACULA gets lost in the lesions, the whole streamline is not considered, even if the streamline until the lesion might be correct! Is there any possibility to hand TRACULA lesionmasks, so that the regions with lesions are ignored? If not, is there a possibility to maintain the lost streamlines, or at least parts of it? Thank you in advance for your help. With kind regards, Florian Borsodi, Lukas Pirpamer Department of Neurology Medical Universtiy of Graz

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