Freesurfer

freesurfer@nmr.mgh.harvard.edu

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Re: [Freesurfer] FS install ubuntu 11.1
by Knut J Bjuland 09 Oct '12

09 Oct '12

This errer message mean that you are missing /usr/share/fsl/5.0/etc/fslconf/fslmachtype.sh in your /usr/share/fsl/5.0/etc/fslconf. You should get a copy of this file and place in /usr/share/fsl/5.0/etc/fslconf/f knut J On 10/09/2012 02:00 PM, David Soto wrote: > hi - so the output to source $FREESURFER_HOME/SetUpFreeSurfer.csh > > was: >> >>> -------- freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0 -------- >>> Setting up environment for FreeSurfer/FS-FAST (and FSL) >>> FREESURFER_HOME /usr/local/freesurfer >>> FSFAST_HOME /usr/local/freesurfer/fsfast >>> FSF_OUTPUT_FORMAT nii.gz >>> SUBJECTS_DIR /usr/local/freesurfer/subjects >>> MNI_DIR /usr/local/freesurfer/mni >>> /usr/share/fsl/5.0/etc/fslconf/fslmachtype.sh: Command not found. >>> FSL_DIR /usr/share/fsl/5.0 >> > > On Tue, Oct 9, 2012 at 11:54 AM, Knut J Bjuland <knutjbj(a)hotmail.com > <mailto:knutjbj@hotmail.com>> wrote: > > Can you please send me the output again? The files should not > prevent you from starting since fsl and freesurfer need that file > to be able to set the environment right. > > > On 10/09/2012 10:41 AM, David Soto wrote: >> thanks, I'll try though I have already reinstalled >> FSL now I have FSL 5.0.1- should that fine prevent >> FS from starting up anyway? >> Cheers >> >> On Tue, Oct 9, 2012 at 9:06 AM, Knut J Bjuland >> <knutjbj(a)hotmail.com <mailto:knutjbj@hotmail.com>> wrote: >> >> Hi >> >> You should reinstall FSL 5.0 since it is missing a file. >> >> Knut J >> >> >> >> On 10/08/2012 08:05 PM, David Soto wrote: >>> Hi, just trying to install Fresufer in Ubuntu OneiricOcelot >>> 11.10, >>> >>> I followed the installation steps in your web and seemed fine >>> >>> in one of the last steps I did >>> >>> wmen-dsoto3:/> source $FREESURFER_HOME/SetUpFreeSurfer.csh >>> -------- freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0 >>> -------- >>> Setting up environment for FreeSurfer/FS-FAST (and FSL) >>> FREESURFER_HOME /usr/local/freesurfer >>> FSFAST_HOME /usr/local/freesurfer/fsfast >>> FSF_OUTPUT_FORMAT nii.gz >>> SUBJECTS_DIR /usr/local/freesurfer/subjects >>> MNI_DIR /usr/local/freesurfer/mni >>> /usr/share/fsl/5.0/etc/fslconf/fslmachtype.sh: Command not >>> found. >>> FSL_DIR /usr/share/fsl/5.0 >>> >>> >>> the thing is that when I test the install by typing >>> >>> tkmedit >>> >>> it says command not found & cannot get Freesurfer to start >>> >>> can you help please? >>> >>> Thanks! >>> >>> David >>> http://www1.imperial.ac.uk/medicine/people/d.soto/ >>> >>> >>> _______________________________________________ >>> Freesurfer mailing list >>> Freesurfer(a)nmr.mgh.harvard.edu <mailto:Freesurfer@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. >> >> > >

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import dicom files with # in name and when to run talairach_avi --i nu.mgz --xfm transforms/talairach.xfm
by Knut J Bjuland 09 Oct '12

09 Oct '12

Hi, I have two questions about Freesurfer. How can I import dicom files, which include "#" as part of the files names into freesurfer witouth renaming the files? Recon-all -i seem to cut the files name after "#" so that image#1.dcm becomes image. Would you recommend me to run this command for all my processed subjects? As stated in the relase notes? Can I use QA_tools to measure the quality of the recons? cd subjid/mri talairach_avi --i nu.mgz --xfm transforms/talairach.xfm recon-all -s subjid -segstats

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FS install ubuntu 11.1
by David Soto 09 Oct '12

09 Oct '12

Hi, just trying to install Fresufer in Ubuntu OneiricOcelot 11.10, I followed the installation steps in your web and seemed fine in one of the last steps I did wmen-dsoto3:/> source $FREESURFER_HOME/SetUpFreeSurfer.csh -------- freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0 -------- Setting up environment for FreeSurfer/FS-FAST (and FSL) FREESURFER_HOME /usr/local/freesurfer FSFAST_HOME /usr/local/freesurfer/fsfast FSF_OUTPUT_FORMAT nii.gz SUBJECTS_DIR /usr/local/freesurfer/subjects MNI_DIR /usr/local/freesurfer/mni /usr/share/fsl/5.0/etc/fslconf/fslmachtype.sh: Command not found. FSL_DIR /usr/share/fsl/5.0 the thing is that when I test the install by typing tkmedit it says command not found & cannot get Freesurfer to start can you help please? Thanks! David http://www1.imperial.ac.uk/medicine/people/d.soto/

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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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