Freesurfer September 2019

freesurfer@nmr.mgh.harvard.edu

93 participants
143 discussions

Researcher Position in Artificial Intelligence on Magnetic Resonance Imaging for Alzheimer's Prevention
by Juan Domingo Gispert López 20 Sep '19

20 Sep '19

External Email - Use Caution The Barcelonabta Brain Research Center (BBRC <https://barcelonabeta.org/>) is looking for a researcher to develop deep learning methods to predict preclinical Alzheimer’s disease based on Magnetic Resonance and wet biomarkers, as part of its Alzheimer’s Prevention Program. This is a full-time position and the person selected will report to the Neuroimaging´s group leader. Main Responsibilities: - To develop and apply Machine/Deep learning (ML/DL) techniques to MRI data to predict preclinical AD stages on the ALFA/ALFA+ datasets from the BBRC - To develop the ML/DL algorithms so that they are compatible with use in real-world scenarios - To liaise with third parties to validate the performance of the developed algorithms - To write technical reports, journal articles and present results in scientific conferences We offer: - The research position is scheduled initially for two years (open to renewal). - Salary will be in accordance with qualifications and experience Further information and application instructions: https://fpmaragall.org/wp-content/uploads/2014/07/Researcher-Position-in-De… -- *Juan Domingo Gispert*Group Leader - Neuroimaging *BarcelonaBeta* * Brain Research Center (BBRC) *jdgispert(a)barcelonabeta.org T. (+34) 93 326 31 67 C/ Wellington, 30 <https://maps.google.com/?q=C/+Wellington,+30+08005+Barcelona&entry=gmail&so…> 08005 Barcelona <https://maps.google.com/?q=C/+Wellington,+30+08005+Barcelona&entry=gmail&so…> www.barcelonabeta.org www.fpmaragall.org ------------------------------ Confidencialitat correu electrònic BBRC <https://www.barcelonabeta.org/ca/politica-privacitat-web>. Confidencialidad correo electrónico BBRC <https://www.barcelonabeta.org/es/politica-privacidad-web>. E-mail confidentiality BBRC <https://www.barcelonabeta.org/en/privacy-policy-web>. Gràcies per estalviar paper. *Gracias por ahorrar papel. *Thanks for saving paper.

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PALM Analysis
by Harikumar, Amritha 19 Sep '19

19 Sep '19

Hi there, I am trying to run a Permutation Analysis of Linear Models (PALM) for analyzing subcortical areas in the nucleus accumbens, caudate, and putamen. Upon trying to run the script after reading the Freesurfer wiki, I am not sure what it is referring to regarding applying fsPalm in MATLAB. My questions are - do we a.) copy paste the existing fspalm command in Matlab and run it after setting the two Freesurfer paths listed in the wiki, or what is the correct procedure to run it? I tried running it in terminal as well, but didn’t have any luck. My existing Matlab script has set up the two Freesurfer paths, and is trying to run the fsPalm command for each subcortical area of the three ROIs mentioned above, but that isn’t working either. Any help in running fsPalm would be greatly appreciated! Thanks, Amritha Amritha Harikumar Clinical Research Coordinator Holt Emotion and Social Neuroscience Lab Department of Psychiatric Neuroimaging Martinos Center for Biomedical Imaging Massachusetts General Hospital ___________________________ 149 13th Street, Rm 2620A Charlestown, MA 02129 Phone: 617-724-3283

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Obtaining MNI Coordinates for HCP annotations
by Dev vasu 19 Sep '19

19 Sep '19

External Email - Use Caution Dear all, I would like to obtain MNI coordinates for HCP annotations , i have annotation files for both lh and rh ( which are attached ) , i would like to obtain MNI coordinates for them . I was going through the post https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2015-November/042446… , but i could not get a better understanding on how to generate MNI values for each label in annot files , that i would like to use for graphical analysis. Thanks Vasudev

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Recon-all on a cluster error
by Lauricella, Michael 19 Sep '19

19 Sep '19

External Email - Use Caution Dear Freesurfer Experts, I have a an error when running recon-all on a computing cluster. I've checked the environment and so have some of my more knowledgeable colleagues but we can't see anything wrong with the environment. I was wondering if anyone else has experienced difficulties like the one below when trying to run recon-all on a computing cluster and might have some advice. Error of my run is below and the full log file is attached. Thank you in advance for your help! "Iteration 1 Wed Aug 7 13:53:08 PDT 2019 nu_correct -clobber ./tmp.mri_nu_correct.mni.18980/nu0.mnc ./tmp.mri_nu_correct.mni.18980/nu1.mnc -tmpdir ./tmp.mri_nu_correct.mni.18980/0/ -iterations 1000 -distance 50 [mlauricella@qb3-id115:/mnt/freesurfer_subjs/SUBJECT_ID/mri/] [2019-08-07 13:53:08] running: /mnt/neuroimaging/FreeSurfer/V6.0.0/mni/bin/nu_estimate_np_and_em -parzen -log -sharpen 0.15 0.01 -iterations 1000 -stop 0.001 -shrink 4 -auto_mask -nonotify -b_spline 1.0e-7 -distance 50 -quiet -execute -clobber -nokeeptmp -tmpdir ./tmp.mri_nu_correct.mni.18980/0/ ./tmp.mri_nu_correct.mni.18980/nu0.mnc ./tmp.mri_nu_correct.mni.18980/nu1.imp Assertion failed at line 742 in file templates/CachedArray.cc nu_estimate_np_and_em: crashed while running volume_stats (termination status=256) nu_correct: crashed while running nu_estimate_np_and_em (termination status=256) ERROR: nu_correct Linux qb3-id115 3.10.0-957.21.3.el7.x86_64 #1 SMP Tue Jun 18 16:35:19 UTC 2019 x86_64 x86_64 x86_64 GNU/Linux recon-all -s SUBJECT_ID exited with ERRORS at Wed Aug 7 13:53:09 PDT 2019 To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting" Best, Michael

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fsPALM - Path Issue?
by Harikumar, Amritha 19 Sep '19

19 Sep '19

Hello, I had emailed the Freesurfer Forum a few weeks back about trying the PALM analysis for permutation testing. I recently tried fsPalm again on running some of our subcortical analyses for the caudate, putamen, and nucleus accumbens, and we performed the following steps: * Set our respective ROIs (e.g. caudate, putamen, nucleus accumbens) * Set the paths for fsPalm to run for each of the ROIs * Ran mri_glmfit as noted in the Freesurfer Help documentation for fsPalm for the three ROIs We ran into several issues. When we looked in the ‘run_palm.m’ output file under the subfolder for our first ROI that we tried to run PALM analysis for, it mentions ‘error in run_palm: zthresh = fast_p2z(pthresh)'. We are not sure where this function fast_p2z is supposed to be called from, as it is not located in any of the Matlab scripts when downloading the package for fsPalm (e.g. the palm-alpha115 file from Freesurfer). My question is - are we missing a path, or several paths that we have to put into the Matlab script, or does fsPalm no longer work for running such analyses? fsPalm has worked in the past for one of my colleagues using the palm-alpha112 file, but we are now having trouble running this using the palm-alpha115 file version. Any help would be greatly appreciated. Thanks, Amritha Amritha Harikumar Clinical Research Coordinator Holt Emotion and Social Neuroscience Lab Department of Psychiatric Neuroimaging Martinos Center for Biomedical Imaging Massachusetts General Hospital ___________________________ 149 13th Street, Rm 2620A Charlestown, MA 02129 Phone: 617-724-3283

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Cortical thickness (spc) extraction
by AKUDJEDU, THEOPHILUS 19 Sep '19

19 Sep '19

External Email - Use Caution Dear FreeSurfer, I used QDEC for the longitudinal two‐stage model analyses, where temporal data within each subject was reduced to a symmetrised percent rate of change (spc) maps using the long_mris_slopes function for data acquired at two time-point. I observed an abnormal region with different spc in patients relative to controls over time. How do I extract the spc for this region in each individual? What scripts do I use? Thanks Theo

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qdec contrast and data extraction
by Maximo, Jose Omar 19 Sep '19

19 Sep '19

External Email - Use Caution Hi, I plotted the data from the *.y.ocn.dat file and the graph still shows no apparent significant difference between the groups (see attached pic). Then I found a post with the following: the ocn.dat files have data that is uncorrected in that sense and might need to nuisance factors removed before plotting. There is a design matrix in there (Xg.dat). You can load that into matlab along with the ocn.dat, compute beta = inv(X'*X)*(X'*ocn) to get the betas. You can then compute yhat = X2*beta2 where X2 has nuisance columns removed and beta2 has the same nuisance coefficients removed, then treat yhat as your data to be plotted. I tried that since I have 2 nuisance factors (age and TICV) and want to plot my significant cluster w/o any nuisance effects. This is what I get 1.8973 1.8973 1.8973 … 3.4728 3.4728 3.4728 … Are these the mean averages for each group (cortical thickness). If so, is there a way to get a score for each subject? Best, Omar [cid:image001.png@01D568A6.6E149480] >Look in the *.y.ocn.dat file. > > From mri_glmfit-sim --help > >csdbase.y.ocn.dat - this is a summary of the input (y) over each >cluster. It has a column for each cluster. Each row is a subject. The >value is the average of the input (y) in each cluster. This is a >simple text file. > > > >On 9/3/2019 5:16 PM, Maximo, Jose Omar wrote: > External Email - Use Caution > > Hi, > > Which specific file should I load? I see cluster.mgh, cluster.summary, sign.ocn.annot, sig.ocn.mgh, sig.vertex.mgh, and pdf.dat. > > How can I extract the values from fsaverage space? > > Basically, what is the correct way to extract values from these significant clusters? > > Many thanks, > Omar > > Date: Tue, 3 Sep 2019 15:15:02 +0000 > From: "Greve, Douglas N.,Ph.D." <DGREVE at mgh.harvard.edu<https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>> > Subject: Re: [Freesurfer] qdec contrast and data extraction > To: "freesurfer at nmr.mgh.harvard.edu<https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>" <freesurfer at nmr.mgh.harvard.edu<https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>> > Message-ID: <2286f9bf-37a4-1be9-2252-0bccc833a218 at mgh.harvard.edu<https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>> > Content-Type: text/plain; charset="utf-8" > > You might have done something wrong along the way. When you run the montecarlo correction, it will create a file with the thickness values in it for each cluster. the first thing to do is to load that and see if you see the expected differences. The other thing is to not go back into native space to extract the numbers. There are several operations that happen as it moves into fsaverage space and in preparation for group analysis (interpolation, and smoothing); sometimes these make a big difference. if the ROI is small, it may not map accurately back into the native space (and you should not need to draw it in the first place) > > On 8/30/2019 11:36 AM, Maximo, Jose Omar wrote: > > External Email - Use Caution > Hi, > > I have a question: > > My design is 2 groups (HC and Patients in that respective order) and 2 nuisance factors (age and eTIV). When I look at the average volume difference between the 2 groups, I get blue and red clusters. I presume the color coding is where each group is greater than the other (Blue = Patients > HC and Red = HC > Patients). > > Then, I processed to extract individual values from each cluster in order to plot them. When I extract data from the blue clusters and plot them, the two groups show no difference in thickness at all, whereas when I look at volume, HC show more than patients in blue clusters (see attached figure). I would assume that both figures would show patients > HC based on the negative statistic. > > Am I interpreting the colors wrong? Or am I doing something wrong? > > These are my steps 1) After applying montecarlo correction, I drew my ROIs to extract the data from; 2) map it onto every single subject; and then 3) used mris_anatomical_stats to extract the data from each subject. > > Any suggestions are welcome. > > Best, > Omar > > Jose O. Maximo, Ph.D. | Postdoctoral Fellow > Department of Psychiatry & Behavioral Neurobiology > UAB School of Medicine > University of Alabama at Birmingham > Cell Phone: (619) 252-3492 > Email: jomaximo at uabmc.edu<https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer><mailto:jomaximo at uabmc.edu<https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>>

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FS6.0 on 2yo subjects
by Alexopoulos, Dimitrios 18 Sep '19

18 Sep '19

External Email - Use Caution We have acquired 0.8mm isotropic T1-mprage sequences on 2 year old subjects. Although the output looks good (see below), is it recommended to use FS6.0 on a young cohort? [cid:image005.jpg@01D56E40.7241E0E0][cid:image006.jpg@01D56E40.7241E0E0] [cid:image007.jpg@01D56E40.7241E0E0] ________________________________ The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail.

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Research Assistant Position (infant/pediatric MR imaging) Boston Children's Hospital/Harvard Medical School
by Gaab, Nadine 18 Sep '19

18 Sep '19

The Gaab Lab (www.gaablab.com) is looking for a Clinical Research Assistant II to assist with all study phases of functional and structural MRI for our longitudinal infant MRI study. This position is ideal for anyone considering future graduate study in cognitive (developmental) neuroscience, computer science, cognitive science or neuroscience. This Clinical Research Assistant II will be responsible for: Subject recruitment for pediatric research studies which will include close interaction with schools and daycare centers in the Boston area. Scheduling of pediatric (infant) research subjects. Maintaining of database, implementing and maintaining of analysis software; pediatric testing (including MRI/fMRI scanning of young children, infants, and their parents) and data analyses (psychometrics, psychophysics and functional magnetic imaging), stimuli design and administrative work (e.g., preparation of internal review board proposals). Under general supervision coordinating activities of daily operations of clinical research studies. Screening, consenting, recruiting, and selecting patients for studies. Preparing IRB and/or CCI documentation and submissions in conjunction with the Principal Investigator and/or other members of the research team. Conducting data collection activities and preparing analytical reports regarding results of studies. Assisting in writing articles and summary papers for various publications. To qualify, you must have: A Bachelor's Degree in computer science, psychology, cognitive science, neuroscience, math, or related field required and one year of relevant work experience. Comfort with a heterogeneous computing environment (Linux/Unix, Mac, and Windows) as well as some programming experience preferred; knowledge of psychological experiment software (E Prime, Presentation, etc.) and/or fMRI analyses software helpful. Demonstrable pre-existing interest in cognitive neuroscience desired; knowledge of neuroanatomy or statistics helpful. Prior experience working with infants and small children (e.g. in a preschool or daycare setting or within a research project) will be a plus. Must be self-motivated and able to work in a fast-paced, changing environment and must like working with children. Boston Children’s Hospital offers competitive compensation and unmatched benefits, including a rotating days/evenings and week-end schedule, affordable health, vision and dental insurance, generous levels of time off, 403(b) Retirement Savings plan, Pension, Tuition Reimbursement, cell phone plan discounts and discounted rates on T-passes (50% off). Boston Children’s Hospital is an Equal Opportunity / Affirmative Action Employer. Qualified applicants will receive consideration for employment without regard to their race, color, religion, national origin, sex, sexual orientation, gender identity, protected veteran status or disability. Please apply through the Boston Children’s Hospital job portal. The ReqID is 52838BR: http://www.childrenshospital.org/career-opportunities "Nothing in science has any value to society if it is not communicated." Anne Roe (1904-1991) Nadine Gaab, PhD Associate Professor of Pediatrics Boston Children's Hospital/Harvard Medical School Department of Medicine/Division of Developmental Medicine Laboratories of Cognitive Neuroscience Mail stop code: BCH3178 1 Autumn Street (Office 643); Boston, MA 02115 nadine.gaab(a)childrens.harvard.edu<mailto:nadine.gaab@childrens.harvard.edu> phone: 857-218-3021 www.gaablab.com<http://www.gaablab.com/> www.bostonearlyliteracyscreener.com<http://www.bostonearlyliteracyscreener.com/> Twitter: Nadine Gaab (@GaabLab)

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mkcontrast-sess question
by Nasiriavanaki, Zahra 18 Sep '19

18 Sep '19

Dear Freesurfer experts Hi I have a question about weighting different contrasts using mkcontrast-sess commmand. I have single subject functional data with 18 different contrasts, and I am willing to weight the different contrasts as (for example) ascending linear. Something like: mkcontrast-sess -an $analysis -a 1 -a 2 -a 3 -a 4 -a 10 -a 11 -a 12 -a 13 -a 6 -a 7 -a 8 -a 9 -a 15 -a 16 -a 17 -a 18 In which contrast number two weights twice as contrast number one and contrast number 3 weights twice as contrast number 2 and so on. Is there any way I can do such a thing with mkcontrast-sess? or do you have any suggestion for such an analysis? Thanks Mona Zahra (Mona) Nasiriavanaki Postdoctoral Research Fellow Martinos Center for Biomedical Imaging Massachusetts General Hospital 149 13th Street, 149-2615 Charlestown, MA, USA, 02129

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Freesurfer September 2019