Freesurfer February 2014

freesurfer@nmr.mgh.harvard.edu

128 participants
236 discussions

Fw: Re: extracting mean thickness from specific cluster
by charujing123 24 Feb '14

24 Feb '14

Hi doug, I tried to generate the mean thickness of the cluster in uncorrected p value<0.005 for each subject by this command "mri_glmfit-sim --glmdir lh.score.dir --cwp 1 --cache 2.3 neg". It generates some files named with suffix ".pdf.dat,cluster.mgh,cluster.summary,masked.mgh,ocn.annot,ocn.mgh,voxel.mgh". I cannot find a file that can tell me the mean thickness for each subject. Did I miss something? Thanks. All the best. Rujing Zha 2014-02-22 charujing123 发件人："charujing123"<charujing123(a)163.com> 发送时间：2014-02-22 10:08 主题：Re: [Freesurfer] extracting mean thickness from specific cluster 收件人："freesurfer(a)nmr.mgh.harvard.edu"<freesurfer(a)nmr.mgh.harvard.edu> 抄送： Hi doug and others, Thanks doug. For 1st question:I find that file. However not all has that file.May I generate it manually? Thanks doug. All the best. Rujing Zha 2014-02-22 charujing123 发件人：Douglas Greve <greve(a)nmr.mgh.harvard.edu> 发送时间：2014-02-21 23:46 主题：Re: [Freesurfer] extracting mean thickness from specific cluster 收件人："freesurfer"<freesurfer(a)nmr.mgh.harvard.edu> 抄送： On 2/21/14 10:04 AM, charujing123 wrote: Hi all, I finished the mri_glmfit-sim, and got some clusters in the cluster summary. 1,I want to know how to extract mean thickness for each subject in this cluster? There should already be a file there called something like something.y.ocn.dat. This will have a row for each subject and a column for each cluster. The value will be the mean for that subject inside that cluster. 2,If I want to extract mean thickness of each subject according to a uncorrected p value, i.e. 0.005, what should I do to perform it? What do you mean? Over all vertices that survive? Or for each all cluster with a cluster-forming threshold of .005? If the latter, you can run mri_glmfit-sim with --cwp 1 --cache 2.3 abs Thanks. All the best. Rujing Zha 2014-02-21 charujing123 _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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error in mri_glmfit-sim when using --bg and doss
by charujing123 24 Feb '14

24 Feb '14

Hi FS experts, I ran the mri_glmfit with DOSS, followed by the mri_glmfit-sim(running with --bg option). I have 4 contrasts, but only the first one has some files of corrected results(i.e. mc-z.neg.3.sig.cluster.summary). I donot know why. So I upload the log file in the attachment. However, previously I ran mri_glmfit by DODS, and mri_glmfit-sim with --bg option.All the contrasts have corrected results. Thanks. All the best. Rujing Zha 2014-02-21 charujing123

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testing a quadratic effect of age
by Yang, Daniel 24 Feb '14

24 Feb '14

Hi FreeSurfer Experts, With age as a continuous variable, qdec can test the linear effect of age. To test the quadratic effect of age, do I just create a curvilinear term like age*age and add into the existing equation? For example: original equation: Y = intercept + age + Factor + age*Factor new equation: Y = intercept + age + Factor + age*Factor + age*age + age*age*Factor Best, Daniel -- Daniel (Yung-Jui) Yang, Ph.D. Postdoctoral Researcher Yale Child Study Center New Haven, CT Tel: (203) 737-5454 E-mail: yung-jui.yang(a)yale.edu

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Sub cortical volumes and CVS
by Jennifer Eastman 24 Feb '14

24 Feb '14

Hello, I am interested in comparing sub-cortical volumes across subjects in my data set. I am wondering if using the CVS registration step is useful in improving the accuracy of the sub-cortical volume measurements independently. I will not be examining the cortical thickness just sub-cortical. I have combed the literature that is available and watched the training video, but I am not clear if there is benefit to using CVS registration if I am just looking at the sub cortical structures. Thank you. Jennifer

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Re: [Freesurfer] [All] Sad News (fwd)
by Bruce Fischl 23 Feb '14

23 Feb '14

Hi All, for those who had not heard. The only think I have to add to Bruce's email about Jack is that he was a kind soul and that I will miss him. Bruce ---------- Forwarded message ---------- Date: Fri, 21 Feb 2014 14:14:45 -0500 From: Bruce Rosen <bruce(a)nmr.mgh.harvard.edu> To: all(a)nmr.mgh.harvard.edu Subject: Re: [All] Sad News On a very sad note, I wanted to share with you the news of the passing of John (Jack) Belliveau late last week. Jack has been a visionary member of our Martinos community for close to 30 years. Tom Brady first introduced him to me as a new graduate student from the Biophysics program at Harvard, and he quickly became a key contributor to our early efforts to measure perfusion with MRI. More importantly, however, it was Jacks passion for understanding how the human brain worked (he was convinced that someday we would be able to capture human thought) that led him to explore the use of these newly developed perfusion imaging tools to study human brain function - that work led to his Ph.D. thesis, "Functional NMR Imaging of the Brain", starting the revolution in "Functional Imaging" that would be used by thousands of investigators over the next 30 years. His publication of the first fMRI pictures led to the iconic image on the cover of Science that I’ve included below, along with some quotes from his thesis that have proven so prescient for how we perform dynamic fMRI today. This work was undisputedly the very first use of MRI for human brain mapping. It set in motion the entire field of fMRI, including Ken Kwong’s remarkable fMRI images formed without the use of contrast agents the following year. While Ken’s contribution was of undeniable creativity and impact, there is no doubt that the MGH’s exploration of the potential of MRI to study human brain function was started, and largely driven, by Jack and his vision for how MRI could transform how we study the human brain. For those of you who didn't know Jack personally, he was a remarkable person, intellectually and personally. He was a larger than life figure in our community (literally and spiritually), with an infectious enthusiasm for science that all who knew him learned to love. He showed a remarkable creativity and generosity throughout his career and life from the time he joined us as a graduate student until his passing. We will miss him very much here - I thought that you all should know. For now, Brigitte has asked for privacy as she and their daughter Amilee begin to deal with his loss, but I will be planning a memorial celebration of his life and science sometime soon, and of course will keep you all posted. -- Bruce Rosen, Ph.D., M.D. Director, Athinoula A. Martinos Center for Biomedical Imaging Department of Radiology, Massachusetts General Hospital Professor of Radiology and Health Sciences and Technology Harvard Medical School and the Massachusetts Institute of Technology Laurence Lamson Robbins Professor of Radiology, Harvard Medical School Massachusetts General Hospital Athinoula A. Martinos Center, Room 2301 Bldg. 149 13th Street Charlestown, MA 02129 Tel: 617-726-3197 Fx: 617-726-7422 Assistant: Donna Crowe Email: donna(a)nmr.mgh.harvard.edu http://www.nmr.mgh.harvard.edu/martinos/aboutUs/index.php _______________________________________________ All mailing list All(a)nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/all

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tessellate error in tksurfer
by charujing123 23 Feb '14

23 Feb '14

hi all, I want to visually check the cortical reconstruction output with tksurfer, as being said in surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/FinalSurfEx. It represented nothing but black in the window when I type "tksurfer CON_EIU01 lh orig". The appearance can be got in the attachment. Thanks. All the best. RujingZha 2014-02-24 charujing123

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extracting mean thickness from specific cluster
by charujing123 21 Feb '14

21 Feb '14

Hi all, I finished the mri_glmfit-sim, and got some clusters in the cluster summary. 1,I want to know how to extract mean thickness for each subject in this cluster? 2,If I want to extract mean thickness of each subject according to a uncorrected p value, i.e. 0.005, what should I do to perform it? Thanks. All the best. Rujing Zha 2014-02-21 charujing123

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talairach.lta manual alignment
by Mark Plantz 21 Feb '14

21 Feb '14

Hello freesurfers, I recently attempted to fix the talairach.lta file from a bad recon-all run for one of my subjects. I originally thought that the second pass of recon-all would automatically load this talairach file. However, it looks like the talairach alignment keeps restarting each time recon-all is run. I couldn't seem to find a recon-all flag to manually send the program this new talairach.lta.reg.dat file. Has anyone else encountered this type of problem? My command line is as follows: tkregister2 --mov /Applications/freesurfer/subjects/CMH-9018/mri/brainmask.mgz --targ /Applications/freesurfer/subjects/fsaverage/mri/brainmask.mgz --lta /Applications/freesurfer/subjects/CMH-9018/mri/transforms/talairach.lta --reg /Applications/freesurfer/subjects/CMH-9018/mri/transforms/talairach.lta.reg.dat --s CMH-9018 Thanks in advance! - Mark

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bug in dwri-motion
by Gerit Pfuhl 21 Feb '14

21 Feb '14

Dear Tracula Experts, after careful checking we still cannot run trac-all -qa or dwri-motion as the command always returns: could not open bvals but the same file is flawlessy opened/retrieved in version 5.2. [cat bvals is fine, trac-all -prep in 5.2. runs fine, trac-all -prep in 5.3 returns could not open bvals] Kind regards Gerit Pfuhl

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Neuroimaging Postdoctoral Research Position in Mild Traumatic Brain Injury and Posttraumatic Stress Disorder
by Scott Hayes 21 Feb '14

21 Feb '14

*Neuroimaging Postdoctoral Research Position in Mild Traumatic Brain Injury and Posttraumatic Stress Disorder* Memory Disorders Research Center and Translational Research Center for TBI and Stress Disorders The Boston University Memory Disorders Research Center and the Translational Research Center for TBI and Stress Disorders are seeking an advanced postdoctoral fellow with expertise in Magnetic Resonance Imaging. The postdoctoral fellow will work closely with neuropsychologists and neuroscientists on a clinical research program aimed at elucidating the neural and cognitive sequelae of posttraumatic stress disorder and blast-induced traumatic brain injury in returning Veterans, as well as cognitive and neural change subsequent to exercise training. The candidate will receive advanced training in multi-modal imaging (fMRI, diffusion tensor imaging, volumetric and surface-based analyses, ASL) and the use of cognitive and MRI outcome measures subsequent to exercise intervention in Veterans with mTBI and PTSD. Dr. Scott Hayes will be the primary mentor, and the fellow will also collaborate with an interdisciplinary team including Drs. Mieke Verfaellie, David Salat, Daniel Forman, and Jasmeet Pannu Hayes. The successful candidate will have a doctoral degree in cognitive neuroscience, neuropsychology, biomedical engineering, or a closely related field, and substantial experience in MRI data acquisition and analysis. Candidate should have expertise working with MRI analysis software such as AFNI, FSL, SPM, or FreeSurfer, as well as familiarity with unix and Matlab. Experience interpreting neuropsychological and/or exercise physiology data and previous work with clinical populations are also desirable. The postdoctoral fellow will interact with several research groups at VA Boston studying TBI and PTSD in returning veterans. The candidate should have a keen interest in developing an independent research career. The starting date is flexible. A minimum two-year commitment is required. Salary for highly qualified candidates may be up to $52,000. U.S. citizenship is required for consideration. Potential applicants are encouraged to *immediately* email a letter describing research interests and experience and CV and should arrange to have three letters of recommendation emailed to Dr. Scott Hayes at smhayes(a)bu.edu Lab website: www.bu.edu/brainlab The Department of Veterans Affairs is an Equal Opportunity Employer. -- Scott M. Hayes, Ph.D. Memory Disorders Research Center Neuroimaging Research Center VA Boston Healthcare System Assistant Professor Department of Psychiatry Boston University School of Medicine

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Freesurfer February 2014