[Freesurfer] Postdoctoral Research Associate Position Available
External Email - Use Caution *Please direct all submission materials and inquiries to Dr. Michal Assaf @ michal.as...@hhchealth.org * *Postdoctoral Research Associate Position * The Olin Neuropsychiatry Research Center is seeking to fill a postdoctoral researcher/fellow position in the area of autism/cognitive neuroscience focusing on imaging data analysis. The fellow will join a lab conducting research using advanced neuroimaging methods (MRI, DTI, fMRI) in both healthy and psychiatric populations. The major focus will be developing and applying statistical analysis methods such as ICA and dynamic Functional Connectivity to neuroimaging data collected in an NIMH funded study, which examines brain function related to social cognition and emotion regulation in individuals with autism spectrum disorder. Applicants should have a Ph.D. in Psychology, Neuroscience, or related field. They should have an understanding of fMRI statistical methods and experimental design, and promising research experience. The ideal candidate will come from a doctoral program that has provided fMRI data analysis skills, solid theoretical understanding of cognitive neuroscience and psychology/psychiatry, and working knowledge of Linux, Matlab (programming experience preferred), and similar systems to conduct fMRI analyses, or to have an existing track record with fMRI analysis. In addition to opportunities to develop their own program of research compatible with the lab mission, the postdoctoral fellow will have access to several large archival neuroimaging datasets, training in sophisticated data analysis techniques (i.e., independent component analysis, multi-modal analysis, etc.), and access to the center’s data collection and analysis resources (e.g., fMRI, sMRI, DTI, EEG, genotyping, neuropsychological assessment). The fellowship is open for an initial two years, with an option to renew. The Olin Center is an established clinical neuroscience center at the Institute of Living/Hartford Hospital and is affiliated with Yale University with over 40 faculty, postdocs and research assistants. Our mission is to conduct cutting-edge clinical and cognitive neuroscience research that can ultimately translate to psychiatric care. The Olin Center is located on the grounds of the Institute of Living, providing access to thousands of psychiatric patients each year treated in numerous clinical programs. This is an exciting opportunity for a clinical or cognitive neuroscience postdoc looking to establish him/herself in the field through productivity, training in advanced analysis techniques, and access to ample scientific resources. If interested, please send a statement of scientific interests, accomplishments and relevant skills, a CV, and contact information for at least 3 academic references to Dr. Michal Assaf, Autism & Functional Mapping lab director, at michal.as...@hhchealth.org ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Fwd: TRACULA stat extraction issue
Hi Anastasia - Yes thats what i figured, however the way our pipeline system is setup this was the most straightfoward way of doing it. Anyways i did figure out how to extract the average values in a more convoluted fashion so we are all set with that. However, im trying to do the same with the trac-all -stat command now to extract pathbyvoxel stats and am having issues. I see that while assimilating group level info, the program automatically rejects or doesnt ouput a column for the subject that has failed, is there a quick and dirty fix to the code that will enable me to output all subjects data even if its failed (maybe replace the values with NaN or somethign similar for failed subjects?). Please let me know. Thanks Shashwath On Mon, Jul 4, 2016 at 3:25 AM, Anastasia Yendiki < ayend...@nmr.mgh.harvard.edu> wrote: > > Hi Shashwath - It looks like you have modified the directory structure of > the output files. Normally the dpath/ directory is right under the > directory with subject's name. From your file of inputs, it looks like > you've created some other subdirectories and now dpath/ is a few levels > down the hierarchy. I'd recommend reverting to the original structure that > the commands expect. > > Best, > a.y > > > On Fri, 10 Jun 2016, Shashwath Meda wrote: > > Dear Group - I seem to have run into an issue when attempting to >> assimilate the averaged pathway information from TRACULA into a group >> table. I have >> attached my input list of paths and my output table for one of the tracts. >> The below is the command that i have used but as you can see the values >> in my final table are all from one subject (just replicated) despite my >> input list >> having paths from different subjects, Has anyone encountered a similar >> situation? >> >> tractstats2table --load-pathstats-from-file fmajor_PP_avg33_mni_bbr.txt >> --overall --tablefile fmajor_PP_avg33_mni_bbr.table >> >> >> -- >> Best, >> Shashwath >> >> >> > ___ > Freesurfer mailing list > 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. > > -- Best, Shashwath ___ Freesurfer mailing list 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.
[Freesurfer] Calculating Skew for VOIs
Dear All - I am trying to estimate the skew and kurtosis of a VOI. Does anyone know of quick way to do this (maybe using a utility similar to FSUtils)? Any input would be greatly appreciated. Best Shashwath ___ Freesurfer mailing list 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.
[Freesurfer] Hippocampal Subfield Masks
Hi all - What would be the best way to create ROI masks of the individual hippo subfields that are generated in Freesurfer? Thanks! Shashwath Meda ___ Freesurfer mailing list 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.
Re: [Freesurfer] Hippocampal subfilelds label
Thanks, Koen. The issue is in my preliminary study this is the only subfield that shows a significant difference. So do you think it would still be worth reporting? On Wed, Aug 31, 2011 at 1:41 AM, Koen Van Leemput k...@nmr.mgh.harvard.eduwrote: Hi Shashwath, The label hippocampus was used in the tail of the hippocampus, where the manual labelers (who labeled the data our automated method is trained on) stopped trying to distinguish between the different subfields. If you want to compute the volume of the whole hippocampus, then you should take this in account - otherwise you can probably ignore it. Hope this helps, Koen On Tue, Aug 30, 2011 at 2:58 PM, Shashwath Meda shashwath...@gmail.com wrote: Hi Koen - I am looking at some hippocampal subfield measures on 3T and 7T and noticed that there is a label called hippocampus from your recent publications it was unclear what this label exactly meant? Is this a useful subfield measure to be considered for further analysis? What does this particular segment represent? Thanks, Shashwath Meda 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. -- with regards, Shashwath Meda *** Imaging Genetics Analyst III 515-F Light Hall Vanderbilt University Medical Center Cell: (313) 505-6847 Off: (615) 875-3086 *** ___ Freesurfer mailing list 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.
[Freesurfer] Hippocampal subfilelds label
Hi Koen - I am looking at some hippocampal subfield measures on 3T and 7T and noticed that there is a label called hippocampus from your recent publications it was unclear what this label exactly meant? Is this a useful subfield measure to be considered for further analysis? What does this particular segment represent? Thanks, Shashwath Meda ___ Freesurfer mailing list 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.
Re: [Freesurfer] Custom color table overlay for ROI analysis
Hi Alan - I dont see the instructions on how QDEC handles this? Could you point me out to the wiki page that has this info. Again I dont want to draw manual ROIs instead i want to assign my own value to the color tables corresponding to the aparc labels in FS. On Wed, Jun 15, 2011 at 4:28 PM, Alan Francis alandarkene...@gmail.comwrote: Hi Shashwath: The QDEC model in FS will allow you to do this. The website has all the details. best, Alan On Wed, Jun 15, 2011 at 5:02 PM, Shashwath Meda shashwath...@gmail.comwrote: Hello Freesurfers - I just finished up with some group ROI analyses on thickness and surface area measures derived from Freesurfer. Basically ran the recon-all command, extracted individual ROI measures from the aparc and aseg files and did my between-group analyses in SPSS. Now, i'd like to display the significant ROIs on the brain with its corresponding p/F value. What would be the easiest and most straightforward way to do this? Thanks, Shashwath ___ Freesurfer mailing list 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. -- with regards, Shashwath Meda *** Imaging Genetics Analyst III 515-F Light Hall Vanderbilt University Medical Center Cell: (313) 505-6847 Off: (615) 875-3086 *** ___ Freesurfer mailing list 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.
[Freesurfer] Custom color table overlay for ROI analysis
Hello Freesurfers - I just finished up with some group ROI analyses on thickness and surface area measures derived from Freesurfer. Basically ran the recon-all command, extracted individual ROI measures from the aparc and aseg files and did my between-group analyses in SPSS. Now, i'd like to display the significant ROIs on the brain with its corresponding p/F value. What would be the easiest and most straightforward way to do this? Thanks, Shashwath ___ Freesurfer mailing list 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.
[Freesurfer] Reconchecker error
Hi all - I am trying to run the reconchecker program to get some QA done on my data and I get the below error. Any help on this would be greatly appreciated! Also are there any other QA programs that would enable me to easily visualize the outputs at various stages of Freesurfer recon-all? ** Running recon_checker on: Thu Mar 10 17:17:23 EST 2011 Checking Last Version Used: /usr/analysis/bin/freesurfer/bin/recon-all Checking ALL Versions Used: /home/virtualuser/apps/freesurfer/bin/recon-all, /usr/analysis/bin/freesurfer/bin/recon-all, --- checking output files ... Running command: /autofs/space/tensor_017/users/jpacheco/QAtools/data_checker/recon_all_output_file_checker -subjid Dykens_2250_3_1_freesurfer --- /autofs/space/tensor_017/users/jpacheco/QAtools/data_checker/recon_all_output_file_checker: Command not found. /autofs/space/tensor_017/users/jpacheco/QAtools/data_checker/recon_all_output_file_checker: Command not found. --- checking step order ... Running command: /autofs/space/tensor_017/users/jpacheco/QAtools/data_checker/recon_all_status_log_checker -subjid Dykens_2250_3_1_freesurfer --- /autofs/space/tensor_017/users/jpacheco/QAtools/data_checker/recon_all_status_log_checker: Command not found. /autofs/space/tensor_017/users/jpacheco/QAtools/data_checker/recon_all_status_log_checker: Command not found. --- *making snapshots ...* *Running command: /autofs/space/tensor_017/users/jpacheco/QAtools/data_checker/jlp_snapshots3.csh -subjid Dykens_2250_3_1_freesurfer -o QA.html* *---* */autofs/space/tensor_017/users/jpacheco/QAtools/data_checker/jlp_snapshots3.csh: Command not found.* ___ Freesurfer mailing list 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.
