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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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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

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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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Re: [Freesurfer] Intermediate stages of cortical inflation
by Xuelong Zhao 14 Apr '14

14 Apr '14

Addendum to the previous post: Can I use lh.orig as the input surface instead of lh.inflated? Also, I ran the command you suggested (I changed -w flag to 10 and used lh.orig as the input surface): mris_sphere -w 10 lh.orig lh.sphere_test However, when I viewed the output of the intermediate forms, all of them were nearly spherical, only lh.sphere_test0010 deviated slightly from the sphere. Even so, it seems its very hard to capture the unfolding process from the cortex to the sphere. Should I be using some other flags? For instance, if I used -w 1 instead, would this help? Thanks. From: andrewzhao(a)live.com.au To: fischl(a)nmr.mgh.harvard.edu Subject: RE: [Freesurfer] Intermediate stages of cortical inflation Date: Fri, 11 Apr 2014 16:20:33 +1000 Great, will give this a try. Thanks for clarifying the command flags. Is it also possible to specify the scale using the flag - scale 1? > Date: Fri, 11 Apr 2014 01:38:01 -0400 > From: fischl(a)nmr.mgh.harvard.edu > To: andrewzhao(a)live.com.au > CC: freesurfer(a)nmr.mgh.harvard.edu > Subject: RE: [Freesurfer] Intermediate stages of cortical inflation > > sorry, it shouldn't say "patch", but "file". We will fix that. I wouldn't > run it with -n. Without it, it will run until it asymptotes. I would try: > > mris_sphere -w 20 lh.inflated lh.sphere > > cheers > Bruce > > > cheers > Bruce > > > On Fri, 11 > Apr 2014, Xuelong Zhao wrote: > > > Thanks for pointing this binary out- I didn't realize the user could access it outside > > of recon-all. > > I've had a look at the fswiki for mris_sphere and it doesn't seem to be complete. I > > used it in the following format but not sure if this is correct: > > > > mris_sphere -n 160 -w 20 -scale 1 lh.orig lh.sphere_test > > > > I want to check that the above command converts lh.org to a sphere in 160 iterations, > > writes out every 20th iteration and ensures the area is preserved? > > > > Also, on the fswiki site: > > > > * > > > > mris_sphere [options] <surface file> <patch file name> <output patch> > > > > > > I'm not certain if <output patch> is synonymous with output surface? Also, what is the > > purpose of a <patch file name>? Thanks. > > > > > > > Date: Thu, 10 Apr 2014 11:30:15 -0400 > > > From: fischl(a)nmr.mgh.harvard.edu > > > To: xuelongzhao(a)hotmail.com > > > CC: freesurfer(a)nmr.mgh.harvard.edu; greve(a)nmr.mgh.harvard.edu > > > Subject: Re: [Freesurfer] Intermediate stages of cortical inflation > > > > > > yes, many of our binaries take the -w <n> flag to write out a snapshot of > > > the minimization every nth step, including mris_sphere > > > > > > cheers > > > Bruce > > > > > > > > > On Thu, 10 Apr 2014, Xuelong Zhao wrote: > > > > > > > Is it also possible to track the inflation all the way to the sphere? I was hoping > > that > > > > I could take snapshots of equi-area intermediate forms as the cortex is unfolded > > onto > > > > the sphere instead of stopping at the inflated cortex. Thanks. > > > > > > > > > > > > > > > > > Date: Wed, 9 Apr 2014 08:31:46 -0400 > > > > > From: fischl(a)nmr.mgh.harvard.edu > > > > > To: freesurfer(a)nmr.mgh.harvard.edu > > > > > CC: greve(a)nmr.mgh.harvard.edu > > > > > Subject: Re: [Freesurfer] Intermediate stages of cortical inflation > > > > > > > > > > you can use -w 1 to write out every step in the inflation process and > > > > > choose what you want. If you want it to preserve surface area during > > > > > inflation (as opposed to just at the end), also include -scale 1 > > > > > > > > > > cheers > > > > > Bruce > > > > > > > > > > > > > > > On Wed, 9 Apr 2014, Xuelong Zhao wrote: > > > > > > > > > > > Hi, > > > > > > > > > > > > I would like to ask whether it is possible to display different levels of > > > > > > cortical inflation? > > > > > > > > > > > > I have been using the command: mris_inflate > > > > > > > > > > > > but the -dist and -n flags do not seem to make that much difference. Also, > > > > > > if I use fsaverage lh.orig as the input file and using the default options > > > > > > for mris_Inflate I don't seem to be able to recover the lh.inflated surface. > > > > > > > > > > > > Are there any alternative commands to control the level of inflation? > > > > > > Thanks. > > > > > > > > > > > > > > > > > > > > > > > > > > > > > _______________________________________________ > > > > > 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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Calculation to create pc1fit metrics
by Rees, Elin 12 Apr '14

12 Apr '14

Dear FreeSurfer Experts, I am wanting to create my own pc1fit metrics of change for each atlas region for each subject in order to calculate regional effect sizes. All documents describe this as the percent change with respect to the value at tp1, evaluated from the linear fit?. What does the linear fit refer to exactly and how can I compute this on my raw thickness data extracted with aparcstats2table? Many thanks, Elin

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