Freesurfer

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30099 discussions

FreeSurfer Course in Copenhagen
by Allison Stevens 15 Apr '14

15 Apr '14

FreeSurfer Course Copenhagen 2014 We are pleased to announce a European FreeSurfer Course that will be held from August 11th to 13th 2014 in Copenhagen, Denmark. The course will be organized by the Neurobiology Research Unit, Copenhagen University Hospital and the Department for Computer Science of the University of Copenhagen in cooperation with the Laboratory for Computational Neuroimaging of the Athinoula A. Martinos Center for Biomedical Imaging. The course will be a three-day course for beginners and experienced users of FreeSurfer and the lectures will be held by FreeSurfer developers from the Laboratory for Computational Neuroimaging of the Athinoula A. Martinos Center for Biomedical Imaging. For further information and to register for this course, please visit: https://fscph2014.nru.dk Allison

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Thickness values to a common space
by Jonathan Holt 15 Apr '14

15 Apr '14

I’m trying to find a way to extract thickness values at each vertex for a given subject, and as a part of that process I need to ensure that each subject has been mapped to a common area, such that their vertices have a direct correspondence, but I’m not entirely sure how to go about it. I’ve started with mris_preproc but the output is an mgh, which I’m not sure is useful for my endeavor.

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Mask and Label
by Reza Rajimehr 15 Apr '14

15 Apr '14

Hi, I have two unrelated questions: 1) I have three mask files: mask1.nii.gz, mask2.nii.gz, mask3.nii.gz. The masks might be overlapping. I want to make a new mask file in which vertices that are 1 in mask1 or mask2 or mask3 get the value of 1, and vertices that are 0 in all three masks get the value of 0. How can I do that? 2) I have a text file containing a list of vertices in a column format. How can I convert it to a label file? Thanks, Reza

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mri_vol2surf --projopt
by Joerg Pfannmoeller 15 Apr '14

15 Apr '14

Hello, I found an option in mri_vol2surf for which I could not find a documentation. The option is called: --projopt It would be nice if somebody could give a description of this option. Respectfully yours pfannmoe

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1 PostDoc + 2 PhD positions in Computational Cognitive NeuroImaging; University of Birmingham, UK
by Remi Gau 15 Apr '14

15 Apr '14

*2 PhD and 1 PostDoc positions in Computational Cognitive Neuroimaging; University of Birmingham, UK* In our natural dynamic environment the senses are constantly bombarded with many different signals. How does the human brain integrate information from multiple senses during perception? To study the neural mechanisms of multisensory integration and learning, we combine psychophysics, functional imaging (fMRI, EEG/MEG & interleaved TMS-fMRI) and models of Bayesian Inference and learning. The Computational Cognitive Neuroimaging Group (Prof Uta Noppeney) is seeking 1 enthusiastic PostDoc and 2 PhD candidates. Applicants should have astrong quantitative background and a degree in neuroscience, psychology, computer science, physics, medicine or related areas. Prior experience in functional imaging, MatLab, data analysis and/or machine learning would be an advantage. The lab is part of the Computational Neuroscience and Cognitive Robotics Centre and the Department of Psychology of the University of Birmingham, UK. The centre provides an excellent multidisciplinary and collaborative research environment combining expertise in cognitive neuroimaging, psychophysics and computational neuroscience. The psychology department was rated 3rd in the UK research assessment exercise. Applications will be considered until the positions are filled. Starting dates are flexible. For further information, please contact u.noppeney(a)bham.ac.uk <mailto:u.noppeney@bham.ac.uk> and see http://www.birmingham.ac.uk/research/activity/cncr/index.aspx <http://www.birmingham.ac.uk/schools/psychology/index.aspx> http://www.birmingham.ac.uk/schools/psychology/index.aspx <http://www.birmingham.ac.uk/schools/psychology/people/profile.aspx?Referenc…> http://www.birmingham.ac.uk/schools/psychology/people/profile.aspx?Referenc… For application to the PostDoc positions, please send applications to http://www.jobs.ac.uk/job/AIM528/research-fellow/ For application to the PhD positions, please send application including CV, statement of research interests, and the names and full contact details of two referees to:u.noppeney@bham.ac.uk <mailto:u.noppeney@bham.ac.uk>

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FS volume discrepancies
by zach.petr＠post.cz 15 Apr '14

15 Apr '14

I have several issues concerning automated volumes calculation. When you look at the aseg.stat for hippocampal volume (in mm3) it gives different value compared to hippocampal subfields volume calculation (which comes in voxels but there is stated that 1 voxel is 0.5mm3). How is it possible? I presume that anatomical definition and subfield incorporation is the same. Next - if you look at the whole hippocampal formation volume in hippocampal subfield calculations it is way lower compared to the summation of the CA1- CA4 + dentate gyrus = hippocampal formation. What could be explanation of this? Petr

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control numbers of cluster based on vertex numbers in each cluster
by charujing123 14 Apr '14

14 Apr '14

Hi FS experts and users After completing the mri_glmfit-sim, I get some cluster in the *.cluster.summary. I want to threshold some clusters whose vertex number are smaller than specific number such as 150. How can I do that? Thanks All the best Rujing Zha 2014-04-14 charujing123

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mri_surf2vol
by Franklin Lovell Orndorff-Plunkett 14 Apr '14

14 Apr '14

Hello Freesurfer Experts, Having morphed the surface data to fsaverage for individuals in our group of subjects, we need to convert MEG dSPM paint files of surface data to volume .nii format. I have attempted this using the following syntax and keep coming up with the subsequent errors: mri_surf2vol --surfval .${STC_DIR}/${SUBJECT}${STC_MORPH_SUFFIX}-30_45_80 --hemi lh --volreg ${SUBJECTS_DIR}/fsaverage/mri.2mm/reg.2mm.dat --template ${SUBJECTS_DIR}/fsaverage/mri/orig.mgz --outvol ${NII_DIR}/${SUBJECT}${STC_MORPH_SUFFIX}-lh.mgz # Right Hemisphere mri_surf2vol --surfval .${STC_DIR}/${SUBJECT}${STC_MORPH_SUFFIX}-30_45_80 --hemi rh --volreg ${SUBJECTS_DIR}/fsaverage/mri.2mm/reg.2mm.dat --template ${SUBJECTS_DIR}/fsaverage/mri/orig.mgz --outvol ${NII_DIR}/${SUBJECT}${STC_MORPH_SUFFIX}-rh.mgz gdiagno = -1 ERROR: cannot recognize the type of ./export/........to lh dspm paint file gdiagno = -1 ERROR: cannot recognize the type of ./export/........to rh dspm paint file ninputs = 2 Is there a format flag that one can put after the --surfval option so that the type would be recognized? I entered " ./ " before the path as the documentation says but from here I can't find a solution. Thank you, Franklin

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error running -qcache
by Giorgio Fumagalli 14 Apr '14

14 Apr '14

FREESURFER_HOME: /var/drc/software/64bit/freesurfer-5.1.0 Build stamp: freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0 RedHat release: Red Hat Enterprise Linux Workstation release 6.3 (Santiago) Kernel info: Linux 2.6.32-279.el6.x86_64 x86_64 ---------------------------------------------------------------------Please include the following additional information in your report: 1) subject name: G10 2) the entire command-line executed :recon-all -s G10 -qcache 3) the error message generatedERROR: number of vertices in /home/icarus/fumagalli/NIFTI/G10/surf/rh.jacobian_white does not match surface (-1162781980,123838)ERROR: reading curvature file 4) optionally include the subject's /script/recon-all.log I run qcache for all my subjects but one (G10) keeps exiting with this error (the other subjects had no problems) ThanksGiorgio

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vertex wise surface area measure?
by sabin khadka 14 Apr '14

14 Apr '14

Hi all, I am trying to extract vertexwise surface area values in an ascii files. For that I am doing mri_surf2surf --hemi ?h --srcsubject <subject dir> area --src_type curv --trgsubject fsaverage --trgsurfval XYZ-area --trg_type curv mris_convert -c XYZ-area ?h.white XYZ-area.asc However I am getting surface area values for some vertices as negative. 1) Am I following correct steps while writing vertex-wise values in ascii files? 2) Aren't values of surface-area supposed to be non-negative? I am not sure what I am missing here. Thanks for the help. -Sabin

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