Freesurfer April 2014

freesurfer@nmr.mgh.harvard.edu

147 participants
229 discussions

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>

1 0

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

1 0

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

1 0

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

1 0

T2 flag
by Righart, Ruthger 14 Apr '14

14 Apr '14

Dear Freesurfers, I have run several subjects using the -T2pial flag, to correct for dura. For several subjects the pial surface was badly positioned after the -T2pial flag was used (these errors did not occur when the flag was not used, in the same subject, see PDF, left vs right panel). I was wondering if adding this flag might be problematic in some patient groups, like cerebrovascular disease or multiple sclerosis, with regard to T2 (hyperintense) lesions. Best, Ruthger

2 3

Convert surface to contour
by Ed Gronenschild 14 Apr '14

14 Apr '14

Hi, When using tkmedit or freeview, a surface is converted into a contour superimposed onto T1. I would like to do the same using the command: mri_surf2vol --surf pial --hemi lh --template subjID/mri/T1.mgz \ --identity --o lh.pial.mgz --mkmask I notice that the "contour" in lh.pial.mgz is not contiguous, a lot of gaps are present. How can I obtain a nice contiguous contour? Cheers, Ed

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Freesurfer April 2014