Freesurfer February 2011

freesurfer@nmr.mgh.harvard.edu

103 participants
152 discussions

residuals exactly zero
by Lars M. Rimol 28 Feb '11

28 Feb '11

Hi, We have experimented a little with different ways of computing the p-values in a GLM analysis based on FreeSurfer data. The way the Matlab reference implementation (fast_fratio.m) handles a situtation where the residuals are exactly zero, seems to be to set those vertices to F = 0 and p = 1. Is this correctly understood? Is this also the case in the underlying C-code? Thank you! LMR -- yours, Dr. Lars M. Rimol

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Qdec - ROI - different thickness results
by Alex Hanganu 28 Feb '11

28 Feb '11

Dear Freesurfer Experts, In qdec for question: "Does the average thickness differ between X and Y" we received blue colored regions, meaning that thickness for group Y is lower then X ? We created ROIs for each region, and extracted cortical thickness for each ROI for each subject using mris_anatomical_stats. in results: for each ROI, mean cortical thickness of Y group are higher then X. is it a mistake, or the question was misunderstood ? Sincerely, Alex.

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Postdoctoral Fellowship in multimodal developmental neuroimaging
by Michels Lars 28 Feb '11

28 Feb '11

Applications are invited for an 18 month postdoctoral fellowship in the human multimodal neuroimaging project "Linking the major system markers for typical and atypical brain development: a multimodal imaging and spectroscopy study" (http://www.zihp.uzh.ch/1610.php#45) funded by the Zürich Institute of Human Physiology. This study will investigate the major physiological markers of brain development, using a combination of multimodal brain imaging (e.g., simultaneous EEG-fMRI, see Lüchinger et al., 2011, NeuroImage, in press) and MR-spectroscopy methods (i.e., GABA, see O'Gorman et al., 2011, J. of Mag. Reson. Img., in press). The initial phase of the study will establish baseline neurotransmitter levels, cerebral blood flow (e.g., perfusion MRI) and EEG frequency and power at rest in children, adolescents, and adults. Examining the interactions between these markers and the changes they demonstrate with age and hormone levels will allow to better understanding the global and regional processes underlying brain maturation. In addition, we will investigate changes in these physiological markers with (a) memory tasks (see Michels et al., 2010, PLoS ONE) and (b) attention deficit hyperactivity disorder (ADHD, see Doehnert et al., Biol Psychiatry, 2010). The starting date of the position is May 2011. Our department is equipped with 64-channel fMRI-compatible EEG equipment and a 3 Tesla GE scanner, which is mainly dedicated for research questions. The successful applicant will have a PhD research background in Cognitive Neuroscience, Neurophysiology, Psychology, Neuropsychology, or related fields. Fluency in English and the ability to work within a multidisciplinary team are essential. Applicants must be experienced at conducting fMRI and/or EEG studies -demonstrated by at least 2 first author publications in international peer-reviewed journals- and be familiar with analysis software such as SPM/Matlab, BrainVoyager and/or FSL. Experience with stimulus presentation software (such as Presentation), UNIX, and programming languages a plus. Salaries are in accordance with the Swiss National Research Foundation. APPLICATION INSTRUCTIONS: To apply, please send a curriculum vitae, a personal statement describing research interests, 3 letters of recommendations, and up to 3 article reprints/preprints (max. 2 MB!!!) to: Dr Lars Michels lars.michels(a)kispi.uzh.ch MR-Zentrum University Children's Hospital Steinwiesstrasse 75 Zürich 8032 Switzerland Reviews of applications will begin on the 1st of March and will continue until the position is filled.

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parellizing Freesurfer
by Pablo Polosecki 27 Feb '11

27 Feb '11

Hi all, I was wondering if someone out there has any experience trying to parallelize their analysis streams in clusters or multiprocessor machines. I was thinking also about the cloud computing services offered by Google, Amazon or other. Has anyone tried or has any plans of implementing something along those lines? Best wishes, Pablo

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Re: [Freesurfer] fixing hippocampus segmentation
by Bruce Fischl 27 Feb '11

27 Feb '11

Hi Tetiana, I think what you're seeing are just the consequences of a voxel-based segmentation. The borders have to be voxelated. Note that much of this will be corrected in the volume calculation that performs a partial-volume correction. cheers Bruce On Wed, 23 Feb 2011, Tetiana Dadakova wrote: > Dear Bruce, dear all, > > I attach several images to show where I would like to manually > interfere into segmentation process. > > img1: Hippocampus' volume covers part of amygdala and parahippocampal > area. The intensity in these non-hippocampal regions are between > 75-95. > > img2: Segmentation of brain stem (problem point are shown by arrows). > This problem repeats more or less for every subject. > > img3: Edges of thalamus are too "pixelated". I mean, shouldn't the > line be smoother? Can this cause overestimation of thalamus' volume? > > Manual correction (drawing) of all the mis-segmented parts would take > a lot of time, so I would like to find out other way of controlling > the segmentation process. (Something like "putting control points" > would be perfect). > > Thank you, > Tanja. > > > On Mon, Feb 21, 2011 at 2:56 PM, Bruce Fischl > <fischl(a)nmr.mgh.harvard.edu> wrote: >> Hi Tanja, >> Can you send us an image? Is parahippocampal white matter significantly darker than 110? >> Bruce >> >> >> >> On Feb 21, 2011, at 6:41 AM, Tetiana Dadakova <tetiana.d(a)gmail.com> wrote: >> >>> Dear Freesurfer users, >>> >>> For some of my subjects Freesurfer strongly overestimates hippocampus' >>> volume. Is there any way to fix the segmentation of hippocampus by >>> e.g. adding some control points (like for white matter here >>> http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/ControlPoints)? >>> >>> Thank you, >>> Tanja. >>> _______________________________________________ >>> Freesurfer mailing list >>> Freesurfer(a)nmr.mgh.harvard.edu >>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>> >>> >> >

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installation problem
by Liukarl 26 Feb '11

26 Feb '11

Hello, Freesurfer experts: I emailed some installation problems a couple days ago, but haven’t answered yet. I am new to freesurfer and try to install the newest version of freesurfer in Ubuntu system. I closely followed the instructions, and the only difference is that I installed it in my Documents, instead of local folder. Below is the output after “source $FREESURFER_HOME/SetUpFreeSurfer.sh” -------- freesurfer-Linux-centos4-stable-pub-v5.0.0 -------- Setting up environment for FreeSurfer/FS-FAST (and FSL) FREESURFER_HOME /home/jie/Documents/freesurfer/ FSFAST_HOME /home/jie/Documents/freesurfer//fsfast FSF_OUTPUT_FORMAT nii SUBJECTS_DIR /home/jie/Documents/freesurfer//subjects MNI_DIR /home/jie/Documents/freesurfer//mni Everything seems fine and I also added the .license file to the freesurfer folder. But when I test it by “tkmedit bert orig.mgz”, it reponds “Illegal instruction” If I type in “recon-all”, it will show “ Required Arguments: -subjid <subjid> -<process directive>…... ” and the other arguments. How to fix the problem and make Fressurfer run? Any help is appreciated. Thanks a lot! PS: my Ubuntu is 32-bit and choose the 32-bit version Freesurfer. Jie

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qdec problems
by 汪贵宏 26 Feb '11

26 Feb '11

Hi all, I want to analyse the thickness difference between patients and normals,but I can not understand the results that I got from qdec-analysis .I hope someone can help me. Firstly,as the papers says, the Cortical (surface-based) Analysis measures the Distance between white and pial surfaces , get One value per vertex in result.And also,there are 33 areas when we choose to analyses,and we can only get the thickness of these 33 areas per hemisphere,so,my question is why it has just one thickness value in such a large area on the hemisphere? Secondly,in my opinion,there will be red or green in a large scale if it does exist thickness differences between the patients and normals in one areas,such as "lh_bankssts_thickness",but,the results seems not in that way,why? Do I explain my questions clearly? Thanks, wang

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tutorial course
by Pom Sailasuta 25 Feb '11

25 Feb '11

Hello, Is it too late to register for the April tutorial course at MGH? thanks -- Pom

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mni is already installed
by Pom Sailasuta 25 Feb '11

25 Feb '11

Hi Dr. Greve, mni is already installed, (came with freesurfer software) in /usr/local/freesurfer/mni. thank you -- Pom

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more errors
by Pom Sailasuta 25 Feb '11

25 Feb '11

Hi Bruce, Thank you so much. I got new error as follow ////////////////////////////// Pom@pom-PC subjects]$ recon-all -s 211-1029-MKA_elan -all Subject Stamp: freesurfer-Linux-centos4-stable-pub-v5.0.0 Current Stamp: freesurfer-Linux-centos4-stable-pub-v5.0.0 INFO: SUBJECTS_DIR is /usr/local/freesurfer/subjects Actual FREESURFER_HOME /usr/local/freesurfer Linux pom-PC.SME 2.6.35.6-45.fc14.i686 #1 SMP Mon Oct 18 23:56:17 UTC 2010 i686 i686 i386 GNU/Linux nu_correct: Command not found. #-------------------------------------------- #@# MotionCor Fri Feb 25 09:46:49 PST 2011 Found 1 runs /usr/local/freesurfer/subjects/211-1029-MKA_elan/mri//001.mgz WARNING: only one run found. This is OK, but motion correction cannot be performed on one run, so I'll copy the run to rawavg and continue. cp /usr/local/freesurfer/subjects/211-1029-MKA_elan/mri//001.mgz /usr/local/freesurfer/subjects/211-1029-MKA_elan/mri/rawavg.mgz /usr/local/freesurfer/subjects/211-1029-MKA_elan mri_convert /usr/local/freesurfer/subjects/211-1029-MKA_elan/mri/rawavg.mgz /usr/local/freesurfer/subjects/211-1029-MKA_elan/mri/orig.mgz --conform mri_convert /usr/local/freesurfer/subjects/211-1029-MKA_elan/mri/rawavg.mgz /usr/local/freesurfer/subjects/211-1029-MKA_elan/mri/orig.mgz --conform $Id: mri_convert.c,v 1.166.2.2 2010/08/10 19:11:50 greve Exp $ reading from /usr/local/freesurfer/subjects/211-1029-MKA_elan/mri/rawavg.mgz... TR=4083.33, TE=14.00, TI=0.00, flip angle=90.00 i_ras = (-1, -0, 0) j_ras = (-0, -1, 0) k_ras = (-0, -0, 1) Original Data has (1.0156, 1.0156, 3) mm size and (256, 256, 60) voxels. Data is conformed to 1 mm size and 256 voxels for all directions changing data type from short to uchar (noscale = 0)... MRIchangeType: Building histogram Reslicing using trilinear interpolation writing to /usr/local/freesurfer/subjects/211-1029-MKA_elan/mri/orig.mgz... mri_add_xform_to_header -c /usr/local/freesurfer/subjects/211-1029-MKA_elan/mri/transforms/talairach.xfm /usr/local/freesurfer/subjects/211-1029-MKA_elan/mri/orig.mgz /usr/local/freesurfer/subjects/211-1029-MKA_elan/mri/orig.mgz INFO: extension is mgz #-------------------------------------------- #@# Nu Intensity Correction Fri Feb 25 09:47:00 PST 2011 mri_nu_correct.mni --i orig.mgz --o nu.mgz --n 2 /usr/local/freesurfer/subjects/211-1029-MKA_elan/mri /usr/local/freesurfer/bin/mri_nu_correct.mni --i orig.mgz --o nu.mgz --n 2 nIters 2 $Id: mri_nu_correct.mni,v 1.12 2009/12/16 20:15:41 greve Exp $ Linux pom-PC.SME 2.6.35.6-45.fc14.i686 #1 SMP Mon Oct 18 23:56:17 UTC 2010 i686 i686 i386 GNU/Linux Fri Feb 25 09:47:00 PST 2011 nu_correct: Command not found. tmpdir is ./tmp.mri_nu_correct.mni.17383 /usr/local/freesurfer/subjects/211-1029-MKA_elan/mri mri_convert orig.mgz ./tmp.mri_nu_correct.mni.17383/nu0.mnc -odt float mri_convert orig.mgz ./tmp.mri_nu_correct.mni.17383/nu0.mnc -odt float $Id: mri_convert.c,v 1.166.2.2 2010/08/10 19:11:50 greve Exp $ reading from orig.mgz... TR=4083.33, TE=14.00, TI=0.00, flip angle=90.00 i_ras = (-1, 0, 0) j_ras = (0, 0, -1) k_ras = (0, 1, 0) changing data type from uchar to float (noscale = 0)... writing to ./tmp.mri_nu_correct.mni.17383/nu0.mnc... -------------------------------------------------------- Iteration 1 Fri Feb 25 09:47:03 PST 2011 nu_correct -clobber ./tmp.mri_nu_correct.mni.17383/nu0.mnc ./tmp.mri_nu_correct.mni.17383/nu1.mnc -tmpdir ./tmp.mri_nu_correct.mni.17383/0/ nu_correct: Command not found. ERROR: nu_correct Linux pom-PC.SME 2.6.35.6-45.fc14.i686 #1 SMP Mon Oct 18 23:56:17 UTC 2010 i686 i686 i386 GNU/Linux recon-all -s 211-1029-MKA_elan exited with ERRORS at Fri Feb 25 09:47:03 PST 2011 //////////////////////////////////////////// There is nu_correct in /usr/local/freesurfer/mni/bin as follows: [Pom@pom-PC subjects]$ which nu_correct /usr/local/freesurfer/mni/bin/nu_correct thanks again. -- Pom

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Freesurfer February 2011