Freesurfer February 2019

freesurfer@nmr.mgh.harvard.edu

114 participants
196 discussions

Data Analyst / Research Assistant Position at Child Mind Institute, New York {Disarmed}
by Ting Xu 21 Feb '19

21 Feb '19

External Email - Use Caution *The Autism Center of the Child Mind Institute **is inviting applications **for a Data Analyst position. The Data Analyst’s role is to assist and support the acquisition, manipulation, and analysis of data, as well as the reporting of brain imaging results. For more information click below.* The Child Mind Institute makes use of innovative MRI-imaging approaches to characterize brain maturation in typical and atypical development in childhood with an explicit focus on understanding the impact of psychiatric illnesses on maturational processes. Additionally, the Child Mind Institute is dedicated to the support of open science projects such as the International Neuroimaging Datasharing Initiative ( http://fcon_1000.projects.nitrc.org/ <https://workforcenow.adp.com/mascsr/default/mdf/recruitment/recruitment.htm…> ) and the Configurable Pipeline for the Analysis of Connectomes ( http://fcp-indi.github.com) With this background a pplications are currently being invited for Data Analyst position in the Autism Center. The Data Analyst’s role is to assist and support the acquisition, manipulation, and analysis of data, as well as the reporting results. In particular, our work includes: 1) support the preprocessing of large fMRI dataset in developing population, 2) maintain databases and imaging processing pipeline 3) test and develop new features (e.g., denoising, segmentation, etc.). 4) implement quality assurance protocols for imaging datasets. Reporting to the Director of the Autism Center (*Director: Adriana Di Martino*), this is an exempt, full-time positions located in our NYC headquarters. Responsibilities: - Implementation, execution and maintenance of fMRI imaging analysis pipelines - Exploration of novel software packages and problem-solving for issues with current and planned software packages - Develop graphs, reports, and presentations of project results - Mentoring of junior research staff in data analysis theory and implementation - Perform basic statistical analyses for projects and reports Qualifications: - Master’s degree in neuroscience, computer science, mathematics, statistics or related areas. - Extensive neuroimaging experience in fMRI analysis and proficiency with one or more packages (e.g. FreeSurfer, AFNI, FSL, Workbench or SPM) - Programming experience in one or more languages (e.g., Python, Matlab, R or similar platforms is required). - Significant prior neuroimaging experience with more imaging and/or simulation modalities (e.g., DTI, EEG, MEG, TMS etc.) is a plus, but not required. - A passion for the Child Mind Institute mission To apply: * https://workforcenow.adp.com/mascsr/default/mdf/recruitment/recruitment.htm… <https://workforcenow.adp.com/mascsr/default/mdf/recruitment/recruitment.htm…>*

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mris_preproc error: dimension mismatch
by Peters, Douglas G 21 Feb '19

21 Feb '19

External Email - Use Caution Hi Everyone, I'm trying to prepare my Cerebral blood flow surface data for mri_glmfit group analysis (qdec doesn't allow you to choose your own subject surface files to analyze, so I figured mri_glmfit is my only option). Quick summary of what I did and where I get stuck: ########## I made a vol2surf conversion for some subject perfusion images hoping to evaluate CBF as if it were cortical thickness. The original CBF volumes were registered and normalized in SPM and saved as CBF.nii all in same T1 space. I made them into surface files using : mri_vol2surf --mov CBF.nii--regheader SubjectID --hemi rh --projfrac 0.5 --fwhm 10 --o CBF.mgh I then tried to run: mris_preproc --fsgd CBF.fsdg \ --cache-in CBF.fwhm10 \ --target fsaverage \ --hemi rh \ --out rh.CBF.10.mgh\ scans through all the subject .mghs ninputs = # subjects Checking inputs "ERROR: dimension mismatch between" the first two surface files in my subject fsdg file ########## Please help. What should I do to get around this? Thanks, DP

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mri_convert
by john Anderson 21 Feb '19

21 Feb '19

External Email - Use Caution hi FS experts. I would like to inquire about the command mri_ convert I use this command to convert fMRI and PET 4D volumes from dicom format to nifti. Are there any flags that can be used in mri_convert command line to enable it to extract a text file contain each series time in seconds? thanks John

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Sections of Temporal Lobe not included
by John Mc Fadden 21 Feb '19

21 Feb '19

External Email - Use Caution Hi, I have processed two subjects data twice, once using T1w only and once including FLAIR. I haven't been able to achieve good coverage of the temporal lobe (see images) with either method for one patient, slightly better performance with the other. Is there anything else I could do to avoid manual segmentation? Thanks for any help. All the best John [cid:image001.png@01D4C466.65698730] [cid:image002.png@01D4C466.E0378430]

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CAT12 surfaces on tkregister2 and Freeview
by Loucao, Ricardo 21 Feb '19

21 Feb '19

External Email - Use Caution Dear FS experts and users, I’m having some troubles with CAT surfaces visualisation in tkregister2 and Freeview. Context: I’ve generated some surfaces with CAT12 and I’ve double checked them with Freeview [see attachment1]. Since they looked reasonable, I wanted to project some quantitative MRI data onto the surface, for visualisation purposes only. I used bbregister to register the qMRI brain to the anatomy brain and I’ve checked the results with Freeview, which seemed quite good. Finally, I used mri_vol2surf to get the projection I wanted onto the CAT surface. My problem is when I add the surface overlay the results seem very off, as if the surface from which the overlay is derived is not in the proper space. When I check the registration using tkregister2 I discovered the source of the problem [see attachment2]. It seems to me like the CAT surface is loaded into tkregister2 with a different transform than in Freeview, and, I guess, mri_vol2surf is doing the same as tkregister2. My question is: is there any way to force mri_vol2surf to load the surfaces like Freeview does? Any help is highly appreciated! Here’s a rundown of the commands I ran after the CAT12 .gii file is created: mris_convert ?h.CATsurface.gii ?h.central bbregister --s $subjid --mov qMRImap.nii --init-fsl --reg register.dat --t2 mri_vol2surf --mov qMRImap.nii --ref orig.mgz --reg register.dat --hemi ?h --surf central --o qMRIsurf.mgz Thank you very much in advance! Ricardo [cid:DF7E5FDA-18D1-4CC3-89E2-B246C6F996AA@wlan.fz-juelich.de][cid:F2FBAB4F-193B-462C-8139-93571B066156@wlan.fz-juelich.de] ------------------------------------------------------------------------------------------------ ------------------------------------------------------------------------------------------------ Forschungszentrum Juelich GmbH 52425 Juelich Sitz der Gesellschaft: Juelich Eingetragen im Handelsregister des Amtsgerichts Dueren Nr. HR B 3498 Vorsitzender des Aufsichtsrats: MinDir Dr. Karl Eugen Huthmacher Geschaeftsfuehrung: Prof. Dr.-Ing. Wolfgang Marquardt (Vorsitzender), Karsten Beneke (stellv. Vorsitzender), Prof. Dr.-Ing. Harald Bolt, Prof. Dr. Sebastian M. Schmidt ------------------------------------------------------------------------------------------------ ------------------------------------------------------------------------------------------------

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clusters annotation file in surface
by Barletta, Valeria 21 Feb '19

21 Feb '19

Dear Freesurfers, I have a 3D volume mask of cortical lesions with 8 different clusters (8 cortical lesions). I projected this mask to the cortex and obtained a .mgh file with the command vol2surf: mri_vol2surf --src $path_to_lesion/$subj/combined-$lesion.nii.gz --out $path_to_output/$subj/surf/$hemi".surf_combined-"$lesion".mgh" --projfrac-avg -0.1 1 0.05 --hemi $hemi --regheader $subj Now I need to extract label files from this surface file, one label for each cluster, and then an annotation file summarizing all the label files. How can I do this? Thanks, Vale

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White matter volume from aseg
by Mehndiratta, Ambica 21 Feb '19

21 Feb '19

Hello, I am trying to extract the white matter volume based off the aseg.stats. I noticed the text includes "total cortical white matter volume" and I was wondering if that is the same as overall white matter volume in the brain? Thank you, Ambica Mehndiratta Clinical Research Coordinator Massachusetts General Hospital 149 13th Street, Charlestown MA 02129 amehndiratta1(a)mgh.harvard.edu (617)-724-8823

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Fwd: segmentation error
by mara alves 21 Feb '19

21 Feb '19

External Email - Use Caution Hi there, I ran the recon -all command in two samples, one of young participants and another of older subjects. The segmentation worked well for young participants, however it seems that for older participants the white.pial segmentation it is being done incorrectly. I believe it is segmenting the gray matter instead (please see the pics attached). Best, Mara

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dpath folder size too big
by d mc 20 Feb '19

20 Feb '19

External Email - Use Caution Hello FreeSurfer Developers, I'm attempting to compute trac-all of two times im dti longitudinal study, patients in time PA and the same subject one year after (time PB). Let PA01 the first subject (group have 19 subjects). So PB01 is the same subject 1 year after first acquisition. So, trac-all of PA01 generates a folder of 2,68 GB and trac-all of PB01 creates a folder of 13,78 GB. More than 5 times the size of the same subject. I need to know if this is ok because I have 19 subjects to process and each subject use almost 3 days of computer processing. And i'm afraid of lose all this time if something is wrong. Could you help me to know what is happening with this processing? Thank you Best Regards David 1) FreeSurfer version: freesurfer-Darwin-OSX-stable-pub-v6.0.0.dmg 2) Platform: OSX High Sierra 10.13.6 3) uname -a: Darwin mbp.local 17.7.0 Darwin Kernel Version 17.7.0: Fri Nov 2 20:43:16 18; root:xnu-4570.71.17~1/RELEASE_X86_64 x86_64 4) recon-all.log: see attached (subjects PA01 and PB01) 5) trac-all.log: see attached (subjects PA01 and PB01) PS> PB01 trac-all.log have 138 MB and don't fit mailing list file size limit even compressed

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dtrecon
by john Anderson 20 Feb '19

20 Feb '19

External Email - Use Caution Hi FS experts, I would like to inquire about the command "dtrecon" in Freesurfer. Is this command able to process multishell diffusion data? if not would you recommend any method? Thanks in advance John

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Freesurfer February 2019