Freesurfer

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30099 discussions

Re: [Freesurfer] Questions about the correction methods in Surfstat
by MCLAREN, Donald 06 Oct '15

06 Oct '15

>The output figure is attached. In the colorbar of the figure, left represents cluster corrected p value and right one represents the vertex >corrected p value, right? Right. >So, the warm color region in the figure can be survived by the RFT vertex correction, and the cool color region in the figure can be >survived by the RFT cluster correction, right? Right. RFT vertex correction is not a correct definition, it is a RFT correction based on the maximum peak in contrast with the larger cluster extent approach. >If so, the regions with either warm or cool color region that can be survived after correction. When I report the results, I can report the >regions with warm color (vertex level correction) or report the regions with cool color (cluster level correction), right? Both thresholdings can be reported but I prefer peak thresholds (warm colors) due to the lack of spatial specificity with clustering thresholds. >In addtion, how can I understand the region overlapped by the warm and cool color (like he postier cingulate cortex), can >simultaneously pass double correction of vertex level and cluster level? It is not a double corrections. The figure simply shows two different RFT thresholding approaches. The final question is about the RFT cluster correction method, in the SPM or other software (like REST). Generally, on the cluster level correction, you should be based on a voxel (vertex) uncorrected height threshold of e.g. p<0.001 combined with a RFT-correlated cluster threshould of e.g., p<0.05, right? What is the detailed correction procedure in the Surfstat software? Exactly the same, p=0.001 for defining supra-threshold clusters and p=0.05 for RFT correction. Regards, Felix. Best Regards, Donald McLaren, PhD On Sun, Sep 13, 2015 at 9:36 AM, chenhf_uestc <chenhf_uestc(a)163.com> wrote: > Dear Surfstat Users, > > I have a question about the RFT correction method in the Surfstat( > http://www.math.mcgill.ca/keith/surfstat/) > In the online manual, the command to perform RFT correction is as follows: > [ pval, peak, clus ] = SurfStatP( slm, mask ); > > pval.P contains P-values for peaks, and pval.C contains P-values for > clusters. This special structure is recognised by SurfStatView which draws > the figure in a special way: > > SurfStatView( pval, avsurf, 'Males-females removing age' ); > > The output figure is attached. In the colorbar of the figure, left > represents cluster corrected p value and right one represents the vertex > corrected p value, right? So, the warm color region in the figure can be > survived by the RFT vertex correction, and the cool color region in the > figure can be survived by the RFT cluster correction, right? If so, the > regions with either warm or cool color region that can be survived after > correction. When I report the results, I can report the regions with warm > color (vertex level correction) or report the regions with cool color > (cluster level correction), right? > > In addtion, how can I understand the region overlapped by the warm and > cool color (like he postier cingulate cortex), can simultaneously pass > double correction of vertex level and cluster level? > > The final question is about the RFT cluster correction method, in the SPM > or other software (like REST). Generally, on the cluster level correction, > you should be based on a voxel (vertex) uncorrected height threshold of > e.g. p<0.001 combined with a RFT-correlated cluster threshould of e.g., > p<0.05, right? What is the detailed correction procedure in the Surfstat > software? > > Any help would be greatly appreciate. > > Best, > Feng > > > > > > > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)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. > >

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freeview and ?h.cortex.patch.flat
by Xiaomin Yue 06 Oct '15

06 Oct '15

Hi, Can the developmental freeview display ?h.cortex.patch.flat? I can't find answers in the mail list. If not, is there any way to convert the patch.flat to a format freeview can display? Thanks,Xiaomin

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Postdoctoral Positions - Headache & Orofacial Pain Effort Lab, University of Michigan: Migraine and TMD Neuroimaging and Neuromodulation Research
by adasilva 06 Oct '15

06 Oct '15

The Headache and Orofacial Pain Effort (H.O.P.E.) Lab at the University of Michigan requests applications for two postdoctoral positions to work on migraine and TMD research programs funded by the National Institute of Health. The programs use novel methodologies in neuroimaging and neuromodulation to investigate and target central mechanisms of chronic pain in vivo. Extensive knowledge of neuromoimaging analysis software systems as well as programming experience is required, as is some level of comfort with novel neuromodulatory protocols. Previous research experience and publications with positron emission tomography (PET) and/or MRI-based neuroimaging methods and analyses are also needed. We are seeking applicants with advanced degrees and strong self-motivation to work in a highly creative, altruistic, and mentoring environment with students and residents from different departments across campus. The applicant will be exposed to several tech-innovations, many developed in house, for clinical translational pain research (e.g., migraine, TMD, dental and cancer pain), such as mobile technology, multimodal neuroimaging (PET, MRI, fNIRS, EEG) and neuromodulation montages (TMS and [HD]-tDCS). Initially, a curriculum vitae, letter of intent, and contact information for three professional references should be emailed to: adasilva(a)umich.edu <file:///x-msg/::71:adasilva@umich.edu> Alexandre F. DaSilva, DDS, DMedSc Director, Headache and Orofacial Pain Effort (H.O.P.E.) Lab Techno-Innovations in Pain Research, Therapeutics and Education http://media.dent.umich.edu/labs/hope/ <http://media.dent.umich.edu/labs/hope/> Biologic & Material Sciences, School of Dentistry The Molecular & Behavioral Neuroscience Institute (MBNI) University of Michigan The University of Michigan is an equal opportunity affirmative action employer.

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7T thalamic segmentation inconsistencies.
by Benjamin Peterson 06 Oct '15

06 Oct '15

We have three 7T scans of the same person done on separate days. After running all three T1 images using the "recon-all" function, we obtain thalamic volumes. The volumes varied by up to 25% which seems quite drastic for the same person. Is there a way to decrease this variability? Are there some parameters to change for 7T? Would the subcortical segmentation work better with a T2 or DTI image? Thanks in advance, Ben

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Postdoc position at Martinos Center for Biomedical Imaging
by Allison Stevens 06 Oct '15

06 Oct '15

Postdoc position at Martinos Center for Biomedical Imaging - Massachusetts General Hospital / Harvard Medical School The Laboratory for Computational Neuroimaging at the Martinos Center for Biomedical Imaging has a job opening for a post-doctoral fellow to work on modeling cortical layers and boundaries using Magnetic Resonance Imaging (MRI) and Optical Coherence Tomography (OCT). The project will take place at the Martinos Center (http://www.nmr.mgh.harvard.edu/) and will involve developing computational methods with the goal of extracting quantitative information from OCT images and leveraging the information for MRI analysis. Cutting-edge imaging infrastructure for both these modalities is available at the center and will be used for the project. The methods developed will have be to distributed to the research community through widely used Freesurfer software suite. Applicants are expected to have finished their PhD in medical image analysis, computer vision or a related field with a track record of relevant publications. The project requires experience with mathematical modeling and good programming skills in C/C++ and Matlab/Python. Experience with image registration, deformable surfaces/contours, machine vision techniques and neuroimaging are welcome. The postdoctoral fellow will work closely with Bruce Fischl and Ender Konukoglu. Applications must be sent by email to Ender Konukoglu (enderk(a)nmr.mgh.harvard.edu) and contain a CV, list of publications and names of three references. The intended start date for the position is December 2015 however, the exact date is negotiable.

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problem fast_selxavg3b
by Desiree Thielemann 06 Oct '15

06 Oct '15

Dear freesurfer experts, I included the new function fast_selxavg3b but I got another problem: First error: /opt/freesurfer/bin/mris_fwhm --mask /mnt/bp13dat/Studie43_Phantom_Arm/Statistik/4_MRT/fsfast/Thielemann/PT_2prae_VP01_2_f/bold/firstlevel.sm06.stc.lh/mask.nii.gz --i /mnt/bp13dat/Studie43_Phantom_Arm/Statistik/4_MRT/fsfast/Thielemann/PT_2prae_VP01_2_f/bold/firstlevel.sm06.stc.lh/rho1mn.nii.gz --o /mnt/bp13dat/Studie43_Phantom_Arm/Statistik/4_MRT/fsfast/Thielemann/PT_2prae_VP01_2_f/bold/firstlevel.sm06.stc.lh/rho1mn.sm.nii.gz --fwhm 20.000000 --smooth-only --s fsaverage --hemi lh --sd /mnt/bp13dat/Studie43_Phantom_Arm/Statistik/4_MRT/fsfast/Thielemann /opt/freesurfer/bin/mris_fwhm: symbol lookup error: /opt/freesurfer/bin/mris_fwhm: undefined symbol: ncerr ERROR: /opt/freesurfer/bin/mris_fwhm --mask /mnt/bp13dat/Studie43_Phantom_Arm/Statistik/4_MRT/fsfast/Thielemann/PT_2prae_VP01_2_f/bold/firstlevel.sm06.stc.lh/mask.nii.gz --i /mnt/bp13dat/Studie43_Phantom_Arm/Statistik/4_MRT/fsfast/Thielemann/PT_2prae_VP01_2_f/bold/firstlevel.sm06.stc.lh/rho1mn.nii.gz --o /mnt/bp13dat/Studie43_Phantom_Arm/Statistik/4_MRT/fsfast/Thielemann/PT_2prae_VP01_2_f/bold/firstlevel.sm06.stc.lh/rho1mn.sm.nii.gz --fwhm 20.000000 --smooth-only --s fsaverage --hemi lh --sd /mnt/bp13dat/Studie43_Phantom_Arm/Statistik/4_MRT/fsfast/Thielemann ans = 127 Second error with another server running the analyses: /opt/freesurfer/bin/mris_fwhm: /opt/matlab/R2010b/sys/os/glnxa64/libstdc++.so.6: version `GLIBCXX_3.4.11' not found (required by /opt/freesurfer/bin/mris_fwhm) /opt/freesurfer/bin/mris_fwhm: /opt/matlab/R2010b/sys/os/glnxa64/libstdc++.so.6: version `GLIBCXX_3.4.15' not found (required by /opt/freesurfer/bin/mris_fwhm) The problem seems to be the version of matlab. Which version would you suggest to use while using the function fast_selxavg3b? And why is there an undefined symbol? Do you have any suggestions how to solve the problem? Best regard, Desiree >> ------------------------------------------ ERROR: fast_selxavg3() failed\n Zitat von Douglas Greve <greve(a)nmr.mgh.harvard.edu>: > oops, sorry, that did not make it into the distribution. You can get it here > > ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/fast_selxavg3… > > thanks > doug > > > On 9/29/15 9:15 AM, Silvia Désirée Thielemann wrote: >> Dear members of the freesurfer mailing list, >> >> I'm using freesurfer-Linux-centos7_x86_64-dev-20150728. I started to >> analyse mri data with fs-fast. I did the preprocessing and used the >> function mkanalysis-sess and mkcontrast-sess without any problems. I >> tried to run the function selxavg3-sess next and it stopped with the >> error message: >> >>>>>>>>>> /opt/freesurfer/fsfast/toolbox/fast_selxavg3.m >>>> /opt/freesurfer/fsfast/toolbox/fast_ldanaflac.m >>>> /opt/freesurfer/matlab/MRIread.m >>>>>>>> ??? Undefined function or method 'fast_selxavg3b' for input >>>> arguments of type >> 'char'. >> >>>> ------------------------------------------ >> ERROR: fast_selxavg3() failed\n >> >> I looked for the function fast_selxavg3b in matlab. Unfortunatly only >> the function fast_selxavg3 is included in the fsfast/toolbox. By >> trying to use the function fast_selxavg3, it recommand me to use >> fast_selxavg3b. I could not find the function in the internet. >> >> Do you have any suggestions what to do? >> >> Best regards, >> Desiree >> >> _______________________________________________ >> 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 > > > 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(a)nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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Re: [Freesurfer] Lost toolbar in freeview
by Antonin Skoch 06 Oct '15

06 Oct '15

Dear Ruopeng, thank you, it worked! Only, just to let you know, this tiny popup menu item was completely blank in my case, without any inscription. When I left-clicked at it, the menu bar appeared, and on this popup menu item only checkmark newly appeared. Regards, Antonin

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Re: [Freesurfer] high area.pial values
by Andrews, Derek 06 Oct '15

06 Oct '15

Dear Bruce, Thank you for your response regarding high area values. I have indeed observed high values (I.e. >20) in both the white and pial surfaces of my subjects, albeit only at a few vertices. The vertices indices that contain the highest values in these surface appear around ~258,000-324,000. Would you consider this the end of the array? And if not, what could cause a value of ~80 in the ~258,000 vertex of a pial surface reconstruction? As a background to what I¹m hoping to accomplish: I am using Freesurfer features (arrays) as inputs for pattern classification, therefore I am interested in potential impact on my models due to these outliers. Smoothing reduces the effect of these outliers, however also raises the values of surrounding vertices. I am thinking of replacing these high values with an average area measure taken across all participants prior to smoothing. Again, thank you for your insights in this topic. Best, Derek ________________________________________ Derek Sayre Andrews, MSc PhD Candidate & IoPPN Student Forum Chair Department of Forensic and Neurodevelopmental Sciences & The Sackler Institute for Translational Neurodevelopment Institute of Psychiatry, Psychology & Neuroscience, King's College London Telephone: +44 (0)20 7848 5701 Email: Derek.Andrews(a)kcl.ac.uk On 25/09/2015 17:00, "Bruce Fischl" <fischl(a)nmr.mgh.harvard.edu> wrote: >are they only high on the pial and not on the white? I would have guessed >that they would be high on both, and further that it is due to the >topology >correction and the quirks of the way we retesselate. One easy way to find >out if this is true is if the vertex index is near the end of the list >(i.e. close to the total number of vertices, since the vertices added >during the correction are at the end of the array) > >cheers >Bruce > >On Fri, 25 Sep 2015, Andrews, Derek wrote: > >> Dear FreeSurfer Support Team >> >> First of all, I must thank you for your excellent software! >> >> I have been looking at distributions of various free surfer features >> (histograms of the vertex wise measures). I have noticed some high >>values >> among the pial and white matter surfaces, these values range from 20-85. >> Again, this in only in a handful of vertices (out of millions of >>measures). >> I am wondering what could account for such a high value? >> >> Thank you for your help in clarifying this. >> >> Best, Derek >> >> >> >>_________________________________________________________________________ >>___ >> >> Derek Sayre Andrews, MSc >> PhD Candidate >> >> Department of Forensic and Neurodevelopmental Sciences & >> >> The Sackler Institute for Translational Neurodevelopment >> Institute of Psychiatry, Psychology & Neuroscience, King's College >>London >> >> Telephone: +44 (0)20 7848 5701 >> Email: Derek.Andrews(a)kcl.ac.uk >> >> >> >>_______________________________________________ >Freesurfer mailing list >Freesurfer(a)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.

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Re: [Freesurfer] Calculate the cortical thickness in patients with brain tumor
by Bruce Fischl 06 Oct '15

06 Oct '15

Hi Feng it depends on where the tumor is cheers Bruce On Wed, 30 Sep 2015, chenhf_uestc wrote: > Hi, freesurfer experts, > > If my data came from the patients with brain tumors, could I perform > recon-all analyses to calculate cortical thickness, surface area and so on. > If not, could I mask the brain region with tumor and then conduct such > analyses? I think the tumor might lead to the inaccuracy of cortical > reconstruction > > Best, > Feng > >

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Re: [Freesurfer] Lost toolbar in freeview
by Antonin Skoch 06 Oct '15

06 Oct '15

Dear Ruopeng, I am using Ubuntu 12.04. LTS 32bits. There is no directory ~/Library/Preferences in my home directory. There is only "GNUstep" directory containing subdirectories "Defaults" and "Library". "Library" dir is empty and "Defaults" contains .GNUstepDefaults file, which is very short file containing only NSGlobalDomain entry. Regards, Antonin

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