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30132 discussions

Run the recon-all -all pipeline on structural T1w images in pediatric sample
by Mohn, Johannes 09 Jul '18

09 Jul '18

External Email - Use Caution Dear FS Experts and Community, we would like to run the recon-all -all pipeline on structural T1w images in a pediatric sample ages 6-9. We intend to assess cortical thickness, surface area, and subcortical volume in both ROIs and for whole brain analyses with Freesurfer and are aware that using the available adult template and atlases may lead to misspecifications. Therefore, we hope you can answer these questions: 1) Are you aware of a pediatric template brain that is compatible with the Freesurfer CT and SA pipeline? 2) Are you aware of a pediatric template brain that comes with a ROI atlas that is compatible with the Freesurfer CT and SA pipeline? 3) If we build a study-specific template brain (potentially with an atlas), what are the technical requirements to be compatible with the recon-all -all pipeline? Do you know which programs for study-specific template brains are compatible with Freesurfer? We look forward to your response Thank you, Laurel and Johannes Jacobs Entwicklungsstudie Max-Planck-Institut für Bildungsforschung Max Planck Institute for Human Development Lentzeallee 94 14195 Berlin Tel.: 030-824 06 371 E-Mail: jacobs-studie(a)mpib-berlin.mpg.de<mailto:jacobs-studie@mpib-berlin.mpg.de>

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Deep Learning Scientist for Medical Imaging
by shi yao wang 08 Jul '18

08 Jul '18

External Email - Use Caution Deep learning Scientist for Medical Imaging YIWEI Medical Inc. www.drbrain.net Locations: Atlanta, GA, USA / Shenzhen, China We are looking for talented, driven and autonomous candidates who are professional for deep learning develop for medical imaging such as Alzheimer’s diseases (AD), Parkinson's disease (PD), stroke, Autism, attention deficit hyperactivity disorder (ADHD) etc. You will work in a multidisciplinary team, helping to review, maintain, design, and develop AI algorithm for medical imaging analysis. Our team consists of world leading radiologists, scientists and engineers dedicated to revolutionizing medical imaging with significantly improved image quality, safety and efficiency. *Job* *r**esponsibilities* l Design and implement AI powered models for medical diagnosis. l Combine medical imaging models into traditional big data analysis for healthcare. l Translate new technologies into product solutions for improved clinical care l Collaborate with clinicians and customers to address unmet clinical needs *Requirement* l Master's degree or above in Math/Statistics/Computer Science or related fields with working experience. Fresh Ph.D. graduates are welcomed to apply. l Candidates with solid background in image processing /computer vision or related areas are preferred. l Strong experience in deep learning and computer vision, including designing and implementing deep convolutional neural networks l Knowledge of Linux programming in python, familiar with at least one of the popular deep learning frameworks, such as tensorflow, keras and caffe. l Experience of parallel programming, GPU programming, especially in CUDA, is a plus. l Experience of medical imaging processing with deep learning is preferred. l Good communication skill and strong team player. *Interested candidates should forward your CV to:* Mrs. Mak : yuly.mak(a)szdrbrain.com Dr. Lawrence Wang: lawrence.wang(a)szdrbrain.com

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Learning which data derivatives matter most
by Chris Gorgolewski 07 Jul '18

07 Jul '18

External Email - Use Caution Dear all, To learn which neuroimaging data derivatives (intermediate or final analysis outputs) matter most to people conducting analyses and reusing data we have put together a survey: https://goo.gl/forms/5ghpVbiiPHd8BN153 Please take a moment and fill it and most importantly share it with your colleagues - this feedback is extremely helpful and will help to focus BIDS Derivatives <https://docs.google.com/document/d/1Wwc4A6Mow4ZPPszDIWfCUCRNstn7d_zzaWPcfcH…> standardization work. I know the survey is not exhaustive (for example does not include very important modalities such as EEG, MEG, iEEG or PET). I hope we will be able to perform followup surveys in the near future to fill in those gaps. Best, Chris

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Hippocampal Subfields Logitudinal Processing Error
by Maksimovskiy, Arkadiy 06 Jul '18

06 Jul '18

Dear Experts, I am attempting to initiate a longitudinal portion of the hippocampal subfield module and am getting an error. I was wondering if someone might have a suggestion for troubleshooting. I am using the following version of freesurfer: freesurfer-Darwin-OSX-ElCapitan-dev-20180124-2459312abf I have the Matlab runtime installed using the following command: curl "https://surfer.nmr.mgh.harvard.edu/fswiki/MatlabRuntime?action=AttachFile&d…" -o "runtime.tar.gz" Here is the command I use to initiate the stream: segmentHA_T1_long.sh SILVA008_Template Here is the error message: [arkadiysnewimac:Freesurfer/Freesurfer_Files_with_Freesurfer_Masks/Post_Manual_Edits] arkadiy% segmentHA_T1_long.sh SILVA008_Template #-------------------------------------------- #@# Longitudinal Hippocampal Subfields processing (T1) left Fri Jul 6 12:43:59 EDT 2018 ------------------------------------------ Setting up environment variables --- DYLD_LIBRARY_PATH is .:/Applications/freesurfer_Dev_El_Capitan//MCRv84//runtime/maci64:/Applications/freesurfer_Dev_El_Capitan//MCRv84//bin/maci64:/Applications/freesurfer_Dev_El_Capitan//MCRv84//sys/os/maci64:/Applications/freesurfer_Dev_El_Capitan/lib/gcc/lib:/Applications/freesurfer_6.0/lib/gcc/lib:/opt/X11/lib/flat_namespace dyld: Library not loaded: @loader_path/libmwmclmcrrt.8.0.dylib Referenced from: /Applications/freesurfer_Dev_El_Capitan/bin/SegmentSubfieldsT1Longitudinal.app/Contents/MacOS/SegmentSubfieldsT1Longitudinal Reason: image not found /Applications/freesurfer_Dev_El_Capitan/bin/run_SegmentSubfieldsT1Longitudinal.sh: line 37: 58577 Abort trap: 6 "${exe_dir}"/SegmentSubfieldsT1Longitudinal.app/Contents/MacOS/SegmentSubfieldsT1Longitudinal $args Darwin arkadiysnewimac.mclean.harvard.edu 17.6.0 Darwin Kernel Version 17.6.0: Tue May 8 15:22:16 PDT 2018; root:xnu-4570.61.1~1/RELEASE_X86_64 x86_64 longitudinal subfields exited with ERRORS at Fri Jul 6 12:43:59 EDT 2018 For more details, see the log file /Volumes/silverilab/Arkadiy/Freesurfer/Freesurfer_Files_with_Freesurfer_Masks/Post_Manual_Edits/SILVA008_Template/scripts/long-hippocampal-subfields-T1.log I would love to hear if anyone has suggestions for fixing this. Thanks, arkadiy -- Arkadiy L. Maksimovskiy, Ph.D. Postdoctoral Research Fellow McLean Imaging Center, McLean Hospital Department of Psychiatry, Harvard Medical School

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POSTDOCTORAL FELLOWSHIP IN NEUROIMAGING (MRI and DTI)
by Meaghan Perdue 06 Jul '18

06 Jul '18

External Email - Use Caution *POSTDOCTORAL FELLOWSHIP IN NEUROIMAGING (MRI and DTI)* The LandiLab (PI: Nicole Landi, PhD *https://landi.lab.uconn.edu/ <https://urldefense.proofpoint.com/v2/url?u=https-3A__landi.lab.uconn.edu_&d…>*) at Haskins Laboratories *https://haskinslabs.org/ <https://haskinslabs.org/>* (which is closely affiliated with Yale and the University of Connecticut) is seeking to hire a postdoctoral research fellow. This postdoc will join a project investigating the neurobiological basis (brain structure, genetics) of reading. The successful applicant will be responsible for conducting and interpreting analyses of neuroimaging data (structural and diffusion imaging data). This position is part of a multi-site project (Haskins Laboratories, University of Houston, Baylor College of Medicine) that is aggregating and analyzing neuroimaging and genotyping data from multiple locations to explore gene-brain-behavior relationships. Applicants must have a background conducting research using MRI. The ideal candidate will also have experience with diffusion weighted imaging (DWI) and experience with advanced statistical analysis of imaging data (e.g. imaging-genetic analyses, Bayesian methods, machine learning). *For details regarding required qualifications and application procedure, please visit: https://haskinslabs.org/postdoctoral-fellowship-neuroimaging-mri-and-dti <https://haskinslabs.org/postdoctoral-fellowship-neuroimaging-mri-and-dti>*

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Polar retinotopy using FSFAST
by Paul Scotti 05 Jul '18

05 Jul '18

External Email - Use Caution Hello, I am trying to use FSFAST to map polar angle retinotopy and wanted to make sure I am following the right steps as well as understanding the final visualization. These are the current list of commands I am using, after already making a flattened occipital patch: preproc-sess -sf sessid -df SUBJ01 -surface self lhrh -fwhm 0 -fsd bold > -per-session > mkanalysis-sess -a rtopy.self.lh -surface self lh -TR 2 -retinotopy 24 > -paradigm rtopy.par -per-session -fsd bold -fwhm 0 -ngroups 3 > selxavg3-sess -a rtopy.self.lh -sf sessid > fieldsign-sess -a rtopy.self.lh -patch lh.occip.patch.flat -sf sessid > rtview --s s101 --hemi lh --polar --real polar/real.nii.gz --imag > polar/imag.nii.gz --fsig polar/fsig.nii.gz --flat 1. Am I correct in saying that to do retinotopy with only polar mapping runs, I have to make a fake folder with eccentricity data (otherwise selxavg3 will error)? 2. After rtview, I am using this color wheel <http://t.sidekickopen08.com/e1t/c/5/f18dQhb0S7lC8dDMPbW2n0x6l2B9nMJW7t5XX45…> after changing the color scheme from "color wheel" to "RYGB colors" in tksurfer. However, I am not even sure this is the right color wheel to be looking at. (If it is, do I need to flip it horizontally when looking at the left hemisphere -- the stripes seem to follow the same color pattern across l and r hemispheres for me?) 3. Is the color wheel represented in radians? If so, how can I figure out what radian a certain color is? 4. I specified -ngroups 3 because I used multiband with a factor of 3, but I also tried running this all without -ngroups specified and everything seemed to come out the same. Is ngroups necessary if we collected slices using multiband or no? Thanks very much for any assistance, Paul Scotti

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mri_vol2surf: dACC/Insula clusters on surface not found
by srishti goel 05 Jul '18

05 Jul '18

External Email - Use Caution Hello, I am using mri_vol2surf to project my volume maps on to the surface. There is a dACC/insula cluster visible in my volume maps that doesn't show up when I project it on the surface. Is that because dACC/insula is not included in surfaces on Freesurfer? Thanks! Best, Srishti Social/Clinical Research Specialist Child Imaging Research and Life Experiences Lab University of North Carolina at Chapel Hill email (W): srishtig(a)email.unc.edu skype: srishti.goel12

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Longitudinal processing in v6.0 using manual edits from v5.3.0 - recon-all.log
by KALEY E ELLIS 04 Jul '18

04 Jul '18

External Email - Use Caution Hello FreeSurfer experts, I previously emailed regarding processing longitudinal data in v6.0 using bases with manual edits that had been completed in v5.3. I went ahead and ran recon-all -all on the base of a subject (originally generated in v5.3) in v6.0, but it looks like the header of the recon-all.log still indicates v5.3. Looking at the /stats output, all files indicate v6.0. Below is the head of the log from running recon-all -all on this subject. Is this what you would expect if you ran recon-all -all on a subject_base in v6.0 that was generated in v5.3? If so, is this okay? Recon-all log: setenv SUBJECTS_DIR /study1/nccam3/data/mri/freesurfer_v6/subjects FREESURFER_HOME /apps/x86_64_sci7/freesurfer-latest Actual FREESURFER_HOME /apps/freesurfer-5.3.0/x86_64_sci6 build-stamp.txt: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 Linux c139.keck.waisman.wisc.edu 3.10.0-514.6.1.el7.x86_64 #1 SMP Tue Jan 17 11:12:41 CST 2017 x86_64 x86_64 x86_64 GNU/Linux Thank you! Kaley Ellis Associate Research Specialist Center for Healthy Minds Waisman Center for Brain Imaging and Behavior University of Wisconsin-Madison

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Longitudinal processing: cannot find input volume error
by Arsenije Subotic 04 Jul '18

04 Jul '18

External Email - Use Caution Dear Freesurfer experts, I’m having problems with one of my participants when I am trying to create the base template for my longitudinal analysis. I get an error saying that the input volume (norm.mgz) for my followup time-point cannot be opened, even though the volume is not missing and loads perfectly fine in Freeview. Is this a bug or is something wrong with my norm.mgz volume by any chance? Please let me know. Thank you, Arsenije

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Longitudinal analysis of multiple scanner acquisitions
by zalewk 04 Jul '18

04 Jul '18

External Email - Use Caution Good afternoon Freesurfer team, I want to run the longitudinal pipeline on multiple groups of subjects, the problem is we are at the mercy of the scanners available to us at the various time-points. We have two different Siemens 1.5 scanners (same type of scanner, there was an effort made to match them) at time point 1 and 2 with a Phillips 3T at time point 3. Is it worth the time to attempt a longitudinal analysis on this cohort? Best, Kody Zalewski

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