Freesurfer

freesurfer@nmr.mgh.harvard.edu

16 participants
30084 discussions

error in qdec
by chenhf_uestc 08 Oct '15

08 Oct '15

Dear Freesurfer experts, I used qdec for group comparison, but there is error (acctached error.png). I check all the files but do not find where is the erros. Could anyone give me some suggestions? Best, Feng

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mri_glmfit dev
by Dídac Vidal 07 Oct '15

07 Oct '15

Hi Freesurfers! I am using development version of mri_glmfit (as I want to take advantadge of --frame-mask option). As control analysis I performed an identical (simple) analysis both in mri_glmfit and its dev version. Suprisingly, while F.nii.gz were identical for the given contrast sig.nii.gz map differed betweem both versions. If possible (and If I am not doing anything wrong), I'd like to know the reason why they differ and also which one I should stick with. Thank you in advance -- Dídac Vidal Piñeiro

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extract time series from surface vertices
by Yun Wang 07 Oct '15

07 Oct '15

Hi All, If I use mri_vol2surf to sample the functional volume onto surface, how can I extract the time series from surface vertices corresponding to certain ROI or Label which were created by freesurfer. Thanks! Yun

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Query about the calculation of surface area
by chenhf_uestc 07 Oct '15

07 Oct '15

Dear Freesurfer experts, I have a question about the calculation of surface area. The cortical thickness is the distance between the pial and white matter. But, what about the surface area? Calculation based on pial or white matter? Or average the area of both of them. Is the area of each vertex obtained by the average the area of triangles surrounding the vertex? In addition, where can I find the definition of meancurv, gauscurv, foldind, curvind? I do not find it in the fswiki. Best, Feng

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Individual regions of CorticalParcellation_Yeo2011
by Yi-Chia Erica Kung 07 Oct '15

07 Oct '15

Dear Prof. Yeo, I would like to extract the brain regions of the functional canonical network, such as DMN, SAL, or CEN, withFreesurfer. And I found that you have provided the split regions of 7&17 Network in previous discussion string. (https://www.mail-archive.com/freesurfer %40nmr.mgh.harvard.edu/msg41288.html ) However, the dropbox download link you offered has expired. Would you mind uploading it again? Thank you very much. Erica

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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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