Freesurfer

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30135 discussions

FS V6.0 gtmseg unsegmented WM
by Pradeep 15 Sep '16

15 Sep '16

Dear Freesurfers, I am interested us using centrum semiovale as reference region while calculation SUVR values. Is there a way to save the unsegmented white matter [5001& 5002] during the gtmseg step ? in other words looking for an option like this --keep-unsegmented-WM :do not relabel unsegmented_WM as WM Thanks, Pradeep

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group by age-squared interaction on thickness
by Eryilmaz, H. Hamdi 15 Sep '16

15 Sep '16

Dear Doug/FreeSurfers, We are looking at effects of age-squared on cortical thickness in two different groups. We are interested in age-squared by group interactions on cortical thickness across the surface. Nuisance covariates include age, sex, scanner, and total brain volume. The sig map for the interaction shows numerous highly significant regions. When we extract cortical thickness from individual subjects for these regions, and then plot the relationship between age-squared and cortical thickness (after adjusting for the covariates) in group 1 versus group 2, the interaction is very clear. However, using linear regression in SPSS, we are not able to reproduce these results. I suspect we are not using the same model in SPSS that FreeSurfer is using to do the interaction analysis. This is how our fsgd file looks like: GroupDescriptorFile 1 Title GroupAgesqInteraction Class Group1 Class Group2 Variables Agesq Age Gender Scanner TBV Input 3662291 Group1 0.607 0.654 -1.061 1.041 0.706 Input 3665043 Group1 1.294 1.237 -1.061 1.041 -0.747 . . This is the contrast we used: [0 0 1 -1 0 0 0 0 0 0 0 0] What would be the translation of this contrast to a linear model, where we are interested in the age -squared by group interaction on cortical thickness after controlling for the four nuisance covariates? Thanks very much! Hamdi and Josh

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(no subject)
by Rodriguez-Thompson, Anais 14 Sep '16

14 Sep '16

Hi FreeSurfer experts, I'm running a task-based analysis on mni305 space, running a regression of load-dependent activation on RBC folate values, regressing out the effects of age and gender. The analysis runs fine, but when I visualize the sig.mgh map in tkmedit there is a border of functional values that are ridiculously high (10000000000 and -10000000000). I've attached an image of one of the slices to this email as well as the mri_glmfit log, the fsgd file, and the contrast matrix. My glmfit command is mri_glmfit --y cluster/roffman/users/Stable5_PerRun/Analyses_GDD/GDD_Adults/136_GDD_2vFix_RBC_Folate/SIRP_LoadRegression_Stable5.3_012616_sm5_mni305/Cond2vFix/ces.nii.gz --fsgd /cluster/roffman/users/fsgd/GDD/136_GDD_2vFix_Covary_RBC_Folate_linear.fsgd --no-prune --fwhm 6 --C /cluster/roffman/users/fsgd/OneGroupOneCovariateRegressOut2Covariates.mtx --glmdir /cluster/roffman/users/Stable5_PerRun/Analyses_GDD/GDD_Adults/136_GDD_2vFix_RBC_Folate/SIRP_LoadRegression_Stable5.3_012616_sm5_mni305/Cond2vFix/Tal2vFix_Covary_RBCFolate_Nuis_Gender_Age_noprune Do you know why my command is creating these artificially high values and how to fix it? Any guidance would be greatly appreciated. Thanks, Anais Rodriguez-Thompson Clinical Research Coordinator Brain Genomics Laboratory Martinos Center for Biomedical Imaging Massachusetts General Hospital Phone: (617) 643-3215

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"Talairach Transform: transforms/talairach.xfm ***FAILED***"
by Uquillas, Federico D'Oleire 14 Sep '16

14 Sep '16

Dear fellow FreeSurfer users, I can't get a subject to recon-all all the way through without crashing, regardless of the FS version used (deleted and started from scratch several times). It always fails with a Talairach transform fail error. Wondering if anybody else has experienced this issue before and if there's a way to solve it. Thank you very much. All the best, Fred

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Convert 4D volume time-series into surface time-series
by Prokopis Prokopiou 14 Sep '16

14 Sep '16

Hello freesurfer experts, I am trying to register a functional volumetric image (.nii) into a surface (.gii) to produce a functional surface image (.gii), where each node of the image will contain a time-series. My purpose for doing this is to use freeview to visualize the time-series of each node. I've tried to do this using bbregister to obtain a registration matrix of the functional image into a structural image, mri_vol2surf to resample the functional volume, and finally mris_convert to convert the resampled functional volume into a (4d) functional surface. The details of how I used these commands are as follow: bbregister --s AL_subject/AL \ --mov /home/osboxes/Desktop/Windows-Share/EEG_fMRI_Data_CUBRIC/AL/eyesshut_mc_bet. feat/filtered_func_data.nii \ --reg /home/osboxes/Desktop/AL_registrations/AL.mat \ --init-fsl --t2 mri_vol2surf --mov /home/osboxes/Desktop/Windows-Share/EEG_fMRI_Data_CUBRIC/AL/eyesshut_mc_bet. feat/filtered_func_data.nii --reg /home/osboxes/Desktop/AL_registrations/AL.mat --projfrac 0.5 --hemi lh --o /home/osboxes/Desktop/AL_registrations/AL_surface_time_series_lh.mgh --projfrac 0.5 --interp nearest mris_convert -f /home/osboxes/Desktop/AL_registrations/AL_surface_time_series_lh.mgh \ /home/osboxes/Desktop/Windows-Share/EEG_fMRI_Data_CUBRIC/EEG_fMRI_FreeSurfer _anatomies/AL_subject/AL/surf/lh.white \ /home/osboxes/Desktop/AL_registrations/AL_surface_time_series_lh.gii Although these commands run without any error, the result (AL_surface_time_series_lh.gii) cannot be opened in freeview, presumably because the produced 4d functional surface does not have the necessary surface information (vertices, faces) needed by freeview in order to open it. More specifically, when I try to open it I get MRISread failed mriseadGIFTIfile: mris is NULL! found when parsing file /home/osboxes/Desktop/AL_registrations/AL_surface_time_series_lh.gii in the terminal. I am new user of freesurfer and I would appreciate if someone could help me with this. Thanks, Prokopis

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Cortical thickness to volume
by neuroimage analyst 14 Sep '16

14 Sep '16

Hi, Freesurfer Users. I tried searching for this question on the mailing list but couldn't get an answer. Hence, I am posting this here again. I ran the freesurfer analysis and got cortical thickness map for my group. I want to build an adjacency matrix by finding the correlation between the cortical thickness of various ROIs on an atlas (Either the default freesurfer atlas or AAL atlas). 1) How can I map the cortical thickness map to freesurfer template volume so that I can average the cortical thickness in the ROI to build the connectivity matrix? 2) Instead of mapping to freesurfer template, if I have to use AAL atlas can I simply map the cortical thickness map to MNI template and use AAL atlas in MNI template to carry out step (1). If yes, how should I go about doing that? I would appreciate any response. Thanks Regards!

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QA tools
by John Anderson 14 Sep '16

14 Sep '16

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convert FSFAST files to gifti format
by Sabin Khadka 14 Sep '16

14 Sep '16

Hi all, Is there a way to convert FSFAST files (fmcpr.odd.sm5.fsaverage.?h.nii.gz) files to convert into gifti format? I've tried mris_convert but it does not work. Thanks for help. Cheers, Sabin Khadka

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two postdoctoral positions at Florida International University, Miami, open immediately
by Anthony Dick 14 Sep '16

14 Sep '16

Dear colleagues--Please share widely, we are looking to hire immediately. Thanks! The S.E.L.F Regulation Laboratory (http://self-regulationlab.fiu.edu/; PI Dr. Paulo Graziano, PhD) in collaboration with the Developmental Cognitive Neuroscience Laboratory (http://dcn.fiu.edu; PI Dr. Anthony Dick, PhD) at Florida International University (Miami, FL) is seeking two postdoctoral fellows to participate in an NIMH funded study to examine the neurobiology of attention deficit hyperactivity disorder in young children with a particular focus on their executive function and emotion regulation functioning. Candidates should have a PhD in psychology, developmental science, neuroscience, clinical science, or related discipline. The project will use neuropsychological tests, psychophysiology, diffusion-weighted imaging, and functional magnetic resonance imaging on children 5-7-years-old (with and without ADHD), and thus experience in neuroimaging data collection and analysis, and excellent computational and statistical know-how, is highly desired. Experience working with young children with developmental disabilities is a plus, as is a clinical science background. The positions are for one year with the possibility of renewal for multiple years. Salary is $50,000 plus benefits. The positions are open immediately and we hope to fill them by November 1, 2016. FIU is a multi-campus public research university located in Miami, a vibrant, international city. It has a recently established medical school that emphasizes medical research and community based medicine, and a new imaging facility with a 3 Tesla Siemens Prisma scanner. FIU offers more than 180 baccalaureate, masters, professional and doctoral degree programs to over 50,000 students. Interested candidates should send application materials (curriculum vitae, sample publications, three references, and a letter describing research interests) directly to Dr. Paulo Graziano (pgrazian(a)fiu.edu) or Dr. Anthony Dick (adick(a)fiu.edu) Reviews of applications will begin immediately. -- Anthony Steven Dick, Ph.D. Associate Professor Director, Cognitive Neuroscience Program and Graduate Certificate in Cognitive Neuroscience Department of Psychology Florida International University Modesto A. Maidique Campus AHC4 454 11200 S.W. 8th Street Miami, FL 33199 Ph: 305-348-4202; Lab Ph: 305-348-9055; Fx: 305-348-3879 Email: adick(a)fiu.edu Webpage: http://myweb.fiu.edu/adick Join the Society for the Study of Human Development: http://www.sshdonline.org

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colour scale
by Trisanna Sprung-Much 13 Sep '16

13 Sep '16

Hi there is there a way to view a colour scale bar in Freeview rather than Tksurfer, for instance, for a probability map? I can alter the Min and Max by "Configure Overlay" but cannot seem to display the bar next to my surface. Many thanks Trisanna -- Ph.D. Candidate McGill University Integrated Program in Neuroscience Psychology

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