Freesurfer

freesurfer@nmr.mgh.harvard.edu

19 participants
30088 discussions

running recon -all and trac -all from different FreeSurfer home
by Costanza Gianni' 17 Jun '19

17 Jun '19

External Email - Use Caution Hello, FreeSurfer Developers, I'm trying to run trac -all (I prepared the configuration file following the instructions from v. 5.3) on a set of subjects already processed with recon -all in another computer with a different FREESURFER HOME, and I'm getting this error: Too many ('s. INFO: SUBJECTS_DIR is /home/costanza/extra/PET/PET INFO: Diffusion root is /home/costanza/extra/PET/PET Actual FREESURFER_HOME /home/costanza/freesurfer INFO: FreeSurfer build stamps do not match Subject Stamp: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 Current Stamp: freesurfer-Linux-centos4_x86_64-stable-pub-v5.3.0 /home/costanza/freesurfer/bin/dmri_motion: Command not found. /home/costanza/freesurfer/bin/dmri_group: error while loading shared libraries: libnetcdf.so.6: cannot open shared object file: No such file or directory INFO: current FREESURFER_HOME does not match that of previous processing. Current: /home/costanza/freesurfer Previous: /autofs/cluster/mscat/users/caterina/3T/freesurfer-stable5_3_0-05152013 dcmlist: Subscript out of range. I've searched the list and I couldn't find any similar error. Do you think the main problem is running commands from different FREESURFER HOME? 1) FreeSurfer version: freesurfer-Linux-centos4_x86_64-stable-pub-v5.3.0 2) Ubuntu 14.04.5 LTS 3) umane -a Linux wks4 3.13.0-166-generic #216-Ubuntu SMP Thu Feb 7 14:07:53 UTC 2019 x86_64 x86_64 x86_64 GNU/Linux Thanks a lot for your help, Costanza -- Costanza Giannì, MD Radiologist PhD student Sapienza University, Rome +39 348 711 8987 -- ___________________________________________ *Il tuo 5 diventa 1000* Fai crescere la tua università Dona il 5 per mille alla Sapienza Codice fiscale: *80209930587* https://www.uniroma1.it/it/pagina/fai-crescere-la-tua-universita-con-il-cin… <https://www.uniroma1.it/it/pagina/fai-crescere-la-tua-universita-con-il-cin…>

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Aligning structural and fMRI data
by Wenzhen Zhao 17 Jun '19

17 Jun '19

External Email - Use Caution Dear whom it may concern, I have a structural image (orig.mgz) that has 256 * 256 * 256 dimension, c_r: 0 c_a: 0 c_s:0, and a functional file that has 64*58 * 48* 200, c_r = -0, c_a = 11.9, c_s = 2.7. Two files have different start and end time, too. I have went through processing steps, but the output does not overlap with orig.mgz. tkregister-sess —bbr-sum value is 0.95. How can I overlap these two brain images with different dimensions, start/end times, geometry? I appreciate your help! Thanks, Wenzhen

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Re: [Freesurfer] hippocampal subfields error
by Iglesias Gonzalez, Eugenio 17 Jun '19

17 Jun '19

External Email - Use Caution Dear Angelika, Can you please send us a screenshot of the inaccurate T1 segmentation? Cheers, /Eugenio -- Juan Eugenio Iglesias Senior research fellow CMIC (UCL), MGH (HMS) and CSAIL (MIT) http://www.jeiglesias.com From: <freesurfer-bounces(a)nmr.mgh.harvard.edu> on behalf of "Mennecke, Angelika" <Angelika.Mennecke(a)uk-erlangen.de> Reply-To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> Date: Monday, 17 June 2019 at 06:36 To: "freesurfer(a)nmr.mgh.harvard.edu" <freesurfer(a)nmr.mgh.harvard.edu> Subject: [Freesurfer] hippocampal subfields error External Email - Use Caution Hi all, I’m doing hippocampal subfields analysis with freesurfer 6.0 with T1 and high resolution T2 data from a 7T MRT. With at least one of my datasets Matlab throws an error during the hippocampal-subfields-T2 –pipeline: Making Unknown map to reduced label 14 Computing hyperparameters for estimation of Gaussians of T2 data Error using | Inputs must have the same size. Error in segmentSubjectT2_autoEstimateAlveusML (line 1064) With other patients, the pipeline on the T2 images is correctly working without errors. I’m wondering what is causing this error and whether there is something I can do to avoid it? As far as I can see, the only difference between the “error” dataset and the others is that hippocampal subfields-T1 is also not calculated correctly. It finishes without errors, but the final result does not cover the hippocampus correctly (probably due to a T1-hypointense cyst in the hippocampus of that patient). Best regards, Angelika

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ExploreDTI Workshop in December 9-11 2019@Costa Rica
by Szabolcs David 17 Jun '19

17 Jun '19

External Email - Use Caution More info: http://www.exploredti.com/workshop/ [image: EDTI_flyer.jpg]

1 0

(no subject)
by Erik Lindberg 17 Jun '19

17 Jun '19

External Email - Use Caution Post-doc position for MRI-research on dementia and normal aging available at Karolinska institute. We are looking for a Post-doc researcher for a 1-year scholarship (with a possibility for an extension to 2-year) at our section at the NVS-department at Karolinska institute. For further information see: https://ki.mynetworkglobal.com/se/what:job/jobID:273493/type:job/where:4/ap…

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hippocampal subfields error
by Mennecke, Angelika 17 Jun '19

17 Jun '19

External Email - Use Caution Hi all, I'm doing hippocampal subfields analysis with freesurfer 6.0 with T1 and high resolution T2 data from a 7T MRT. With at least one of my datasets Matlab throws an error during the hippocampal-subfields-T2 -pipeline: Making Unknown map to reduced label 14 Computing hyperparameters for estimation of Gaussians of T2 data Error using | Inputs must have the same size. Error in segmentSubjectT2_autoEstimateAlveusML (line 1064) With other patients, the pipeline on the T2 images is correctly working without errors. I'm wondering what is causing this error and whether there is something I can do to avoid it? As far as I can see, the only difference between the "error" dataset and the others is that hippocampal subfields-T1 is also not calculated correctly. It finishes without errors, but the final result does not cover the hippocampus correctly (probably due to a T1-hypointense cyst in the hippocampus of that patient). Best regards, Angelika

1 0

Segmenting internal capsule
by Chinappen, Dhinakaran Maheswaran 16 Jun '19

16 Jun '19

Dear Freesurfer community experts, We're looking to segment the internal capsule using T1 data. We found documentation in the FreeSurfer white matter segmentation atlas that states that the right and left anterior and posterior portions of the internal capsule are segmented as regions 155-158, but they don't actually appear in any of the output parcellations. We've seen this question appear in previous email threads, <https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2016-August/047133.h…>, but can't find the script "intcapseg" that Doug mentioned here: <https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2011-October/020985.…>. If anyone could send us this script it would be much appreciated. Thanks! Lauren and Dhinakaran.

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fsaverage error with recon-all
by chen 16 Jun '19

16 Jun '19

External Email - Use Caution Dear All, I ran recon-all using single MPRAGE data set, but batching exited with an error. According to recon-all.log, there is no such a file or directory (INFO:trgsubject = srcsubject). It could not read fsaverage/surf/lh.white. I was able to run a subject before without any error not sure why all the subjects I ran now over the weekend ended up with same error. The detail information please see the attachments.Thanks in advance.Jiachen ------------------

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Postdoc position opening at Brown University in cognitive aging and Alzheimer’s disease
by Hwamee Oh 16 Jun '19

16 Jun '19

External Email - Use Caution We are seeking a highly motivated postdoctoral researcher to study behavioral and neuroimaging markers of preclinical Alzheimer’s disease in the Warren Alpert Medical School of Brown University. The primary performance site for this postdoctoral fellowship is in the Butler Hospital Memory and Aging Program (MAP). Brown University has a strong commitment to brain science and research in neurodegenerative disorders. This commitment is united under The Carney Institute for Brain Science and the new Center for Translational Neuroscience (CTN). The mission of the Carney Institute and CTN is to promote the discovery and innovation in brain science by supporting a diverse community of experimentalists, theorists, engineers, and clinicians. The MAP, one of the leading clinical trial centers for Alzheimer’s disease (AD) in the United States, is committed to accelerating drug and biomarker development for AD and to training young investigators for careers in AD research. The successful candidate will join a team of experts in Aging, Alzheimer’s disease, and related dementia research. This postdoctoral position is primarily focused on the area of the cognitive system in aging and preclinical Alzheimer’s disease and will work on developing early behavioral and neuroimaging markers of Alzheimer’s disease and integrating structural and functional MRI, PET, cognitive, genetic, and biofluid measures from ongoing or completed projects. Fellows will have ample opportunities to explore and gain experience with multidisciplinary and clinical research in aging and Alzheimer’s disease and to interact with core faculty members in the MAP and the Carney Institute of Brain Science at Brown University. Applicants with a Ph.D. degree in cognitive neuroscience, neuropsychology, biomedical engineering, electrical engineering, computer science, physics or a relevant field are encouraged to apply. Prior experience with human neuroimaging (e.g., task fMRI, rsfMRI, MRI, DTI, ERP, PET), a strong background in cognitive neuroscience and experimental design, and familiarity with programming in relevant languages (e.g., Python, MATLAB, C) are desirable. The successful candidate is expected to demonstrate communication skills, motivation and interest in the area of cognitive and brain aging, Alzheimer’s disease, and/or neuroimaging, and the ability to independently develop research questions and work in collaboration with other team members. The MAP is part of the Department of Psychiatry and Human Behavior at the Warren Alpert Medical School of Brown University, which is located in Providence, Rhode Island. Providence is within one hour from Boston and 3 hrs from New York City by train/subway and provides an intellectually and culturally rich environment with a reasonable living cost. Please note that this postdoctoral position is research-centered and prior clinical experience is not required. Pursuing licensure for a clinical neuropsychologist is optional. The postdoctoral position is supported by the fellowship program up to 2 years, with a possibility of support in year 3 depending on funding. The expected start date is late Summer 2019. Review of applications will begin immediately and continue until the position is filled. Interested persons can find more information on the position in the websites listed below. This postdoctoral fellowship is administered though the Research Fellowship Program within *The Alpert Medical School of Brown University, Clinical Psychology Training Programs at Brown: A Consortium of the Providence VA Medical Center, Lifespan, and Care New England. * The program’s website is located here: https://www.brown.edu/academics/medical/about/departments/psychiatry-and-hu… A full description of the fellowship position can be found in the link below under the section “Alzheimer’s Research – Neuroimaging” in “Neuropsychology Track” under “Research Fellowship Program (RFP): https://www.brown.edu/academics/medical/about/departments/psychiatry-and-hu… Details regarding application, are located here under “Application Details”: https://www.brown.edu/academics/medical/about/departments/psychiatry-and-hu… NOTE: As explained on the application page of our website, applications are submitted through the APPA CAS portal. Instructions are located on the webpage. For more information about the research and the position, please contact Dr. Hwamee Oh, the Director of Imaging Research in the MAP, at hwameeoh(a)gmail.com.

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How do I get FreeSurfer to use a custom Talairach target.
by Aaron Tanenbaum 16 Jun '19

16 Jun '19

External Email - Use Caution I am wondering if there is any documentation about getting FreeSurfer to use a custom Talairach target.

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