Freesurfer December 2013

freesurfer@nmr.mgh.harvard.edu

107 participants
197 discussions

3 groups and one covariate
by yashin7020＠libero.it 20 Dec '13

20 Dec '13

Hi experts, I'd like to find group difference (thickness) among 3 groups taking in account one covariate. I'd like to use DOSS. Is correct? I have read the guide and I have carried out fsgd file as suggest for Three Groups (One Factor/Three Levels), No Covariates. Now, my problem is "which are the .mtx that I should add?" Thanks a lot. Stef

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trac-all -path Help needed
by Francesco Baldacchini 20 Dec '13

20 Dec '13

Hi everybody, I'm having problems running the trac-all -path command. It's giving me this error: *Segmentation fault (core dumped) Linux opbg 3.11.0-15-generic #23-Ubuntu SMP Mon Dec 9 18:17:04 UTC 2013 x86_64 x86_64 x86_64 GNU/Linux trac-paths exited with ERRORS at mar 17 dic 2013, 16.09.33, CET* I searched but it seems I'm the only one getting this error. To give you more information I can show you how the trac-all -bedp command ended, to me it seems without error: *59 slices processed61 slices processedQueuing post processing stage/usr/local/freesurfer/bin/bedpostx_mgh: line 439: 5294 Terminated ${subjdir}.bedpostX/monitor* In attachment I loaded my drirc.tutorial configuration file. Thanks, Francesco Baldacchini

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mri_glmfit error
by Rujing Zha 19 Dec '13

19 Dec '13

Hi all, I try to run mri_glmfit, but it export "ERROR: matrix is ill-conditioned or badly scaled, condno = 1e+08 -------------------------------- Possible problem with experimental design: Check for duplicate entries and/or lack of range of continuous variables within a class.". I upload the data in the attachment, and the glmfit_output is the standard output of the "mri_glmfit". Thanks. All the best. 2013-12-19 Rujing Zha

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Surface ROIs
by Danielle Sliva 19 Dec '13

19 Dec '13

Dear FreeSurfer Experts, I have defined an ROI as a FreeSurfer label on the pial surface of a single subject. Could someone recommend the best way to determine the corresponding ROIs for other subjects in my study? Thanks in advance, Danielle -- Danielle Sliva, MA Boston Children's Hospital Division of Developmental Medicine Laboratories of Cognitive Neuroscience, Gaab Lab Fetal-Neonatal Neuroimaging & Developmental Science Center

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volume to surface
by 赵越 19 Dec '13

19 Dec '13

Hi All, I would like to use "mri_vol2surf" to overlay a volume onto a surface. The synopsis is mri_vol2surf [<options>] --src inputfile --out outpufile --srcreg registrationfile --hemi hemisphere.But I don't know how to generate the registrationfile. Could someone help me with that? Thanks a lot! Yue

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POST-DOCTORAL POSITION IN NEUROIMAGING, NEUROPSYCHOLOGY AND ADDICTION; UNIVERSITY OF WISCONSIN-MILWAUKEE
by Jon Wieser 19 Dec '13

19 Dec '13

POST-DOCTORAL POSITION IN NEUROIMAGING, NEUROPSYCHOLOGY AND ADDICTION; UNIVERSITY OF WISCONSIN-MILWAUKEE. Sponsor: Krista Lisdahl, Ph.D. A Postdoctoral Fellow position at the University of Wisconsin-Milwaukee (UWM), Psychology Department (http://www4.uwm.edu/letsci/psychology/) will be available starting September 2014 (start date is negotiable). Neuroimaging (fMRI, DTI) will be conducted at the Medical College of Wisconsin’s (MCW) world-renowned Center for Imaging Research (http://www.mcw.edu/biophysics/mri/cir.htm) Dr. Krista Lisdahl, a licensed clinical neuropsychologist with specialization in addiction and neuroimaging, will supervise the fellowship. The objective of this NIH-funded research is characterize the effects of marijuana (MJ) use on frontolimbic brain structure, functioning and connectivity in youth by the creation of IDEAA (Imaging Data in Emerging Adults with Addiction), a multi-site consortium comprised of investigators (Drs. Krista Lisdahl, Staci Gruber, Susan Tapert, Francesca Filbey) using common, overlapping neuroimaging and behavioral measures in over 600 MJ-using and healthy control adolescents and emerging adults. Other areas of study within the laboratory include chronic effects of alcohol/binge drinking, MJ, nicotine and ecstasy use on neurocognition; healthy adolescent and emerging adult neurodevelopment; imaging genetics; multi-modal neuroimaging research methods; effects of exercise and body fat on neurocognition; and neuropsychological measurement. Collaborative opportunities and rich didactic experiences at UWM and MCW are available within a wide range of disciplines, especially affective neuroscience, cognitive rehabilitation, clinical neuropsychology, and exercise science. Clinical Experience. Opportunities for supervised clinical neuropsychology work may be arranged at UWM, MCW or the Milwaukee VA for students interested in ABPP-CN certification. However, this is not an official part of the postdoc. Funding: The position will be funded by Dr. Lisdahl’s NIDA grants. Duties will include: processing and analyzing MRI data; completing neuropsychological assessments; managing research assistants; manuscript and grant preparation. Travel funding to conferences will be available. Requirements include: Ph.D. in psychology, neuroscience or related discipline with strong interest in developing research career in addiction neuroscience or adolescent neurodevelopment. Experience with fMRI/DTI-related research methods (e-prime programming; AFNI, Freesurfer, FSL processing; fcMRI analysis methods) are preferred. Position is available for 1 year with the option of extending up to 3 years, depending upon performance and mutual interest. To apply please send cover letter, CV, statement of research interests and goals, and 3 letters of reference to Dr. Krista Lisdahl (krista.medina(a)gmail.com) Applications due July 2014, but will be reviewed on a rolling basis. UWM and Dr. Lisdahl strongly value diversity and are committed to equal opportunity in employment.

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Does this registration need to be fixed?
by sujith vijayan 19 Dec '13

19 Dec '13

Hi All, I am wondering whether the talairach registration for one of my subjects needs to be fixed. It looks a little off to me, but I am not sure from reading the instructions on https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Talairach_freeview whether the degree of difference I am seeing is to be expected or not. I've attached a screen shot. Thanks, Sujith [image: Inline image 1]

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2 post-docs in cognitive neuroscience of memory (fMRI and neuropsychology)
by Chris Bird 19 Dec '13

19 Dec '13

Two post-doc positions in cognitive neuroscience of episodic memory Sussex is sunny. Memory is interesting. 2014 is looming. Time for a new job? Two 3-year positions are available to work with Chris Bird on a European Research Council funded project (TRANSMEM) at the University of Sussex in Brighton, UK. One of the post-docs will carry out fMRI investigations of episodic memory using video clips and virtual reality as memoranda. The other will combine fMRI and neuropsychology to investigate memory loss in Alzheimer's disease. Closing date for applications is 16th of January, so get applying! For more details see: http://www.jobs.ac.uk/job/AHV248/post-doctoral-research-fellows-cognitive-n… http://www.sussex.ac.uk/psychology/memory/index

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visualizing lh.gender_age.thickness.10.mgh after mris_preproc
by Rujing Zha 19 Dec '13

19 Dec '13

Dear all, I read the tutorial http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis and I want to know how to visualize the lh.gender_age.thickness.10.mgh. Thanks. All the best. 2013-12-17 Rujing Zha

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Re: [Freesurfer] New features in TRACULA
by Anastasia Yendiki 19 Dec '13

19 Dec '13

Hi Ruth - It's possible that your scans don't have any slices with excessive intensity drop-out. You can gauge that visually, by checking if there are any slices that are much darker than their neighbors. Any operation that performs interpolation on the image intensity values, and thus smooths the images, will affect estimates of intensity drop-out. To what extent exactly, it's impossible to guess. You can just try running them before the bias field correction and see what happens. a.y PS: Please send all tracula-related emails to the freesurfer list and not to me only. The freesurfer list gets archived so that users can search for answers and we can avoid replication of questions. Thanks! On Wed, 18 Dec 2013, Ruth Carper wrote: > So the images should be prior to bias field correction as well? I ran it on > images post bias field correction (but pre eddy_correct) and your dropout > measures (3rd and 4th values) were 0 and 1 respectively for every brain. > > --Ruth > > ____________________________________________________________________________ > From: Anastasia Yendiki <ayendiki(a)nmr.mgh.harvard.edu> > To: Ruth Carper <rcarper_99(a)yahoo.com> > Cc: freesurfer(a)nmr.mgh.harvard.edu > Sent: Wednesday, December 18, 2013 8:06 AM > Subject: Re: [Freesurfer] New features in TRACULA > > > Hi Ruth - If you apply the same mask to all the volumes in the DWI series, > it's not a problem. The important thing is not to have applied any > operation that would change the intensities of the images inside the > brain. So these should NOT be the DWIs after the eddy_correct step, they > should be before it. > > a.y > > On Tue, 17 Dec 2013, Ruth Carper wrote: > > > Thanks! I was able to run that with no problem. But as I read the wiki > > closely I notice that with your TRACULA pipeline dmri_motion is processing > > images that are still skull-on. Any thoughts on whether your algorithms > > would work properly if the skull was removed prior to eddy correction? I > > would think the rotation and translation measures would still be fine, but > I > > don't know how you've automated the 2 measures of signal dropout. My dwi > > file is also skull removed. > > > > --Ruth > > > >___________________________________________________________________________ > _ > > From: Anastasia Yendiki <ayendiki(a)nmr.mgh.harvard.edu> > > To: Ruth Carper <rcarper_99(a)yahoo.com> > > Cc: freesurfer(a)nmr.mgh.harvard.edu > > Sent: Tuesday, December 17, 2013 1:28 PM > > Subject: Re: [Freesurfer] New features in TRACULA > > > > > > Hi Ruth - If you download the update and unzip it, you'll see an > > executable called dmri_motion. You can run it without any arguments to see > > the help text. > > > > Try something like this: > > dmri_motion --dwi yourDWIs.nii.gz --mat your.ecclog --bval your.bvals > --out > > output.txt > > > > a.y > > > > On Fri, 13 > > Dec 2013, Ruth Carper wrote: > > > > > > > > Thanks. We haven't yet implemented TRACULA but have run eddy_correct on > > all > > > the brains in our existing pipeline and still have the ecc.log files. > Is > > > there a command line that would let us generate your motion measures > > without > > > running TRACULA? > > > > > > --Ruth > > > > > > > > > > >>__________________________________________________________________________ > _ > > _ > > > From: Anastasia Yendiki <ayendiki(a)nmr.mgh.harvard.edu> > > > To: Ruth Carper <rcarper_99(a)yahoo.com> > > > Cc: "freesurfer(a)nmr.mgh.harvard.edu" <freesurfer(a)nmr.mgh.harvard.edu> > > > Sent: Tuesday, December 10, 2013 8:28 PM > > > Subject: Re: [Freesurfer] New features in TRACULA > > > > > > > > > Hi Ruth - Glad to hear this is useful to you. The rotation and > translation > > > parameters are extracted from the affine registration of each DWI volume > > > to the first volume, which in trac-all is performed by eddy_correct. > > > > > > a.y > > > > > > On Tue, 10 Dec 2013, Ruth Carper wrote: > > > > > > > Hi Anastasia, > > > > We discussed your paper at our lab meeting yesterday so this was > perfect > > > > timing on the release of motion measures in your updated TRACULA. > But > > I > > > > wasn't clear where the numbers are coming from in your new update. Is > > > this > > > > from EDDY? eddy_correct? Some other registration step? > > > > > > > > Thanks, > > > > Ruth > > > > > > > > > > > > > > > > > > > > > > > > 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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Freesurfer December 2013