Freesurfer October 2012

freesurfer@nmr.mgh.harvard.edu

119 participants
191 discussions

Dynamic PET _ Time frame averaging
by Christopher Coello 08 Oct '12

08 Oct '12

Dear Freesurfer community, Just a simple question : is there a command-line that allows averaging voxel values from different time frames, transforming dynamic 4D volume into a static 3D volume ? mri_convert allows to skip some early frames (--nskip) or drop some at the end (--ndrop), but I don't see any option for averaging. Thanks for your help, Best, -- Christopher Coello, Ph.D. Preclinical PET/CT unit http://www.med.uio.no/imb/english/research/about/infrastructure/pet/ Institute of Basic Medical Sciences Faculty of Medicine, University of Oslo tel. +4745154516

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Brain imaging PhD projects available
by Diederick Stoffers 07 Oct '12

07 Oct '12

Dear all, Please find below three PhD projects I am posting on behalf of my group leader. Cheers, Diederick ------------- Three brain imaging PhD projects are available at the Sleep & Cognition group of the Netherlands Institute for Neuroscience in Amsterdam, The Netherlands. Projects are in collaboration with one or more partners in Freiburg, Basel or Strasbourg. Project 8: Individual differences in the spatiotemporal profile of brain activity during wake and sleep The project aims to elucidate how spatiotemporal profiles of brain activity develop from wakefulness to deep sleep. Assessments in good and poor sleepers will be done using the EGI MR-compatible 256-channel high density EEG-system in the quietest 3T MRI system presently available, a Toshiba Vantage Titan 3T with the Pianissimo technology. Analyses include graph theoretical and network complexity measures. Assessments will be made in Amsterdam, analyses both in Amsterdam, Freiburg and Basel. Project 6: Spatiotemporal patterns of cortical oscillations that determine subjective wake time during sleep The project aims to elucidate the neural correlates of the loss of consciousness during sleep. Spatiotemporal profiles of brain activity in good and poor sleepers will be obtained using the EGI 256-channel high density EEG-system, both during unperturbed sleep and in response to sensory stimulation. Analyses include graph theoretical and network complexity measures. Assessments will be made in Amsterdam, analyses both in Amsterdam and Freiburg. Project 4: Reward effects of light: phototherapy as a treatment for pathologies with motivational deficits The project aims to elucidate the involvement of brain regions regulating reward and motivation in the mood-improving effects of bright light. 3T MRI assessments will be done in good and poor sleepers. Assessments of behavior, circadian genes, proteins, neurotransmitters and hormones will be done in transgenic animals. Human studies will be performed in Amsterdam, animal studies in Strasbourg. Projects are open to students with a (pending) master (or equivalent) degree in Physics, Mathematics, Biology, Psychology, Neuroscience or Engineering or comparable. Experience with brain imaging, EEG, or sleep is an advantage for all projects. Experience with animal studies is an advantage for project 4. Especially students with some affinity with and/or background in mathematics and/or scientific programming are also encouraged to apply. A proficient level of familiarity with large datasets and programming is commendable, e.g. using Matlab. Mastery of the English language is essential for writing papers and a thesis; mastery of the local languages will facilitate recordings. If you're interested, please read additional information on http://www.neurotime-erasmus.org/ and contact e.van.someren(a)nin.knaw.nl. Thank you for your interest! Prof. dr. Eus J.W. Van Someren http://www.nin.knaw.nl/research_groups/van_someren_group/

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bad tissue segmentation, WM/GM boundary
by EK Kim 06 Oct '12

06 Oct '12

Dear all expert, Hello, I have been trying to solve this WM/GM boundary error. The data I attached here have a lots of problems, especially WM/GM boundary was not detected in temporal areas. Using mri_cnr function, I calculated the gray/white CNR of the norm.mgz. --------------------------------- norm.mgz white = 97.3+-10.3, gray = 77.3+-14.8, csf = 55.6+-19.5 gray/white CNR = 1.222, gray/csf CNR = 0.790 lh CNR = 1.006 white = 97.0+-11.2, gray = 76.9+-15.1, csf = 55.9+-19.3 gray/white CNR = 1.139, gray/csf CNR = 0.737 rh CNR = 0.938 total CNR = 0.972 ---------------------------------- 1. Does the low CNR affect the bad tissue segmentation results? How can I solve the problem? Is there a way to improve the low CNR value? 2. How can I delete the continuous areas, indicated by red arrow (axial, 134)? I use freesurfer-Darwin-leopard-i686-stable-pub-v5.1.0. Thank you for any comments or replies in advance. Best, EK

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subdividing consistently within aparc.annot
by Satrajit Ghosh 06 Oct '12

06 Oct '12

hi bruce, is there a way to divide consistently (same number of regions and one to one correspondence - obviously not the exact same areas) across subjects within aparc regions? cheers, satra

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Normalization
by Ana Arruda 06 Oct '12

06 Oct '12

Hello, I'm working on hippocampus segmentations obtained by Freesurfer to compare with manual and FSL segmentations. Do I have to normalize to make these comparisons more accurate? If so, what volume do I have to use? I've read about eTIV but I would like to confirm if there is any value for normalization purpose in the aseg.stats file. What does ICV include? Does it include the CSF between the brain and the skull? Best regards, Ana Arruda

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cortical parcellation question
by Daniel Ferreira 06 Oct '12

06 Oct '12

Dear experts, I have a couple of questions regarding the cortical parcellation atlas that is used in Freesurfer: 1) I would like to know if it is possible to obtain the Desikan-Killiany atlas in 3D analyze/nifti format. With each region of the brain assigned a discrete integer number (for example the all of the voxels of the left inferior temporal lobe have an intensity = 1, or the whole of the left hippocampus = 2). 2) Are the Harvard-Oxford cortical and subcortical atlases that can be downloaded with FSL the same as the cortical parcellation atlas that is used in Freesurfer? (i.e. are the neuroanatomical boundaries the same; does the left inferior temporal cortex in the Freesurfer cortical parcellation = the left inferior temporal cortex in the Harvard-Oxford atlas downloaded with FSL) Many thanks Daniel Ferreira

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I want to know a simple thing in tksurfer
by Seulgi Eun 06 Oct '12

06 Oct '12

I'm using 'freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0' and I have a problem. I used a command 'tksurfer fsaverage lh inflated -ov surfdata' on teminal. Then, I used 'configure overlay display' in veiw>configure>overlay to set proper threshold. I could set approximate threshold values easily by mouse. But I wanted to set the values by keyboard inputs(exact numbers). I think there is a way to type numbers(in my case, it is unable to type any words on the edit boxes). How can I do?

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transfer label from high-resolution mesh to low resolution mesh
by Longchuan Li 05 Oct '12

05 Oct '12

Hi, all I am trying to transfer some labels on a high-resolution white surface mesh (~100K) to a corresponding low-resolution white mesh(~10K) that is generated using FS function "mris_decimate". Could someone tell me what is the most efficient way to realize that? Many thanks in advance! Longchuan

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Import/export out of curry
by Inati, Souheil (NIH/NIMH) [E] 05 Oct '12

05 Oct '12

Has anyone used freesurfer segmentations/labels in Curry? -- Souheil Inati, PhD Staff Scientist Functional MRI Facility NIMH/NIH/DHHS souheil.inati(a)nih.gov

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Re: [Freesurfer] tracula question
by Anastasia Yendiki 05 Oct '12

05 Oct '12

Hola Fernando - Please send questions about tracula to the freesurfer list and not me personally, so that all users may benefit. This issue will be resolved in the next version. For now, if you're on a unix system that doesn't have the jot command, you'll just have to specify the runlist in your configuration file, even if you want to process all subjects on your list. So if you have 5 subjects for example: set runlist = (1 2 3 4 5) Hope this helps, a.y On Fri, 5 Oct 2012, Fernando Ventrice wrote: > Dear Anastasia Yendiki, > I have been trying to use TRACULA and I think I'm doing something wrong. Because it keeps on giving me this error (I tried within tcsh and bash): > > fventrice@xubuntu1204x64fleni:~$ trac-all -prep -c ${TUTORIAL_DATA}/diffusion_tutorial/scripts/dmrirc_single_subject > jot: Command not found. > INFO: SUBJECTS_DIR is /media/LEVIATAN01/LaboINEBA/testing_TRACULA/diffusion_recons > INFO: Diffusion root is /media/LEVIATAN01/LaboINEBA/testing_TRACULA/diffusion_tutorial > Actual FREESURFER_HOME /home/fventrice/CONTAINER_FLENI/Programs/freesurfer > > I use freesurfer and fsl perfectly well. I have also tried with the new version of trac-all. But keeps on giving the same error. > Best regards and thanks! > Fernando Ventrice > > El contenido del presente mensaje y el de sus adjuntos, es confidencial, privado y de uso exclusivo de los destinatarios a los cuales está dirigido, pudiendo contener información legalmente protegida. Queda prohibida la revisión, divulgación, publicación, modificación, copia, distribución o acción en relación con esta información, por personas o entidades distintas al destinatario. Si usted, por alguna razón, lo ha recibido por error, por favor tenga la amabilidad de eliminarlo de su sistema. Las opiniones contenidas, son exclusivas de su autor, y no representa necesariamente, la opinión de FLENI. > http://www.fleni.org.ar > > >

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Freesurfer October 2012