Freesurfer

freesurfer@nmr.mgh.harvard.edu

22 participants
30073 discussions

Re: [Freesurfer] fsaverage for a Left vs Right hemisphere Longitudinal
by Wang, Xiaoyu 04 Sep '18

04 Sep '18

External Email - Use Caution Thanks Martin, Yes, I did mean to have the right hemisphere added to the left hemisphere as a new time point. Can you explain on what you mean by run every subject only once? Do you mean to run xhemi for all of the subjects and then run a paired analysis? Xiaoyu

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NIFTI to pial.vtk space
by M. Jordan 04 Sep '18

04 Sep '18

External Email - Use Caution Hello, I have a CT NIFTI coregistered to the MRI NIFTI used for reconAll. When I export the .pial files to .vtk using mris_convert, they are shifted with respect to the MRI. Is there a way to process the CT NIFTI in such a way that it will match the .vtk pial files? Thank you!

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MNI to native space using mri_cvs_register and applyMorph
by Ehsan Tadayon 04 Sep '18

04 Sep '18

External Email - Use Caution Hi, I'm tyring to transform a bunch of MNI coordinates to subject's space using mri_cvs_register and applyMorph. I have run the mri_cvs_register but could'nt find detailed description of applyMorph. I appreciate any input on what command should be run to transform an MNI152 coordinate back to subject's space. thanks Ehsan.

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Tools for FreeSurfer QC based on quality metrics?
by ts+ml＠rcmd.org 04 Sep '18

04 Sep '18

External Email - Use Caution Dear FreeSurfer experts, Which tools would you recommend to compute quality metrics for FreeSurfer 6 output? I would like to complement visual QC of the FreeSurfer segmentation output for structural images with automated metrics, e.g., outlier detection for the volume or CNR of certain subcortical structures or surface-based measures. Are there any tools for this? I guess I'm looking for something similar to the QATools for FreeSurfer 5 but for the latest FreeSurfer version. All the best, -- Tim Schäfer

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error using -taskreg
by Addison Wu 03 Sep '18

03 Sep '18

External Email - Use Caution Dear List, I'm trying to use an external regressor to analyze fs-fast tutorial data. I understand a paradigm file would be the sane way to do it, but I'm just trying to understand how external regressors work. I first created a Extreg.dat file for each run of sess01, which contains a 142*5 matrix, saved it in the "00x" run folder. Then I ran mkanalysis-sess command: mkanalysis-sess \ -fsd bold -stc up -surface fsaverage rh \ -fwhm 5 -notask -TR 2 -taskreg Extreg.dat 1 \ -nskip 4 -analysis test.rh -force -per-run And a selxavg3-sess command: selxavg3-sess -s sess01 -analysis test.rh But I got an error report of this: Extension format = nii.gz INFO: key nSliceGroups unrecognized, line 11, skipping Error using basename Too many input arguments. Error in fast_ldanaflac (line 437) taskregevname = basename(taskreg,'dat'); % remove .dat Error in fast_selxavg3b (line 107) flac0 = fast_ldanaflac(analysis); 437 taskregevname = basename(taskreg,'dat'); % remove .dat K>> ------------------------------------------ ERROR: fast_selxavg3() failed\n I've tried a bunch of things, including removing the ".dat" manually for the file, or in the command lines, or changing the "taskreg" to -1 or 5, but none of them worked. Is there anyway I can solve the problem and use external regressors for the tutorial data? Thank you! Addison

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Problem downloading tutorial_data
by Andrea Mendez 03 Sep '18

03 Sep '18

External Email - Use Caution Hello, We seem to have some problems downloading the bucker tutorial data: ftp://surfer.nmr.mgh.harvard.edu/pub/data/buckner_data-tutorial_subjs.tar.gz We have already tried it repeated times with different computers etc, and problem persists. Any help?? BW Andrea Méndez Torrijos Institut für Pharmakologie und Toxikologie (FAU) Pharmakologische Bildgebung und Bildanalyse, AG Hess <+49%201515%200658828>

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FTP downloads not working
by christoph.dinh＠mne-cpp.org 03 Sep '18

03 Sep '18

External Email - Use Caution Hi FreeSurfer Team, during my attempt to download the FreeSurfer binaries for installation I noted that the ftp files are not accessible for me: ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/6.0.0/freesurfer-Linux- centos6_x86_64-stable-pub-v6.0.0.tar.gz Also an installation via GitHub is not working since the 3rd party dependency download is also not working for me: ftp://surfer.nmr.mgh.harvard.edu/pub/dist/fs_supportlibs/prebuilt/centos6_x8 6_64/centos6-x86_64-packages.tar.gz Exists there a workaround/backup archive to download the binaries? Best Christoph

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A Question about Estimating the Cortical Thickness for Each Subregion
by Maedeh Khalilian 01 Sep '18

01 Sep '18

External Email - Use Caution Dear Dr.Bruce Fischl, Thanks for helping me, actually in other words, i am gonna make my brain network based on the graph theory, the nodes of my graph are the parcels and for the edges between the nodes i am gonna compute the cortical thickness or maybe another measurment of the subregions and correlate them for each pair to find the edges and their weights. Hope I've explained clearly. Kind regards, Maedeh,

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Neuroimaging Research Engineer Position
by Florence M 31 Aug '18

31 Aug '18

External Email - Use Caution Title : Neuroimaging Research Engineer No. of Position(s) : One (1) position Location : Paris, France Starting date : November 2018 JOB DESCRIPTION The successful applicant will work in the Group of Clinical Research on Alzheimer Precision Medicine (GRC-APM) at the site of Pitié-Salpêtrière Hospital of Sorbonne University under the supervision of Prof. Harald Hampel, holder of AXA Research Fund & Sorbonne University Chair « sur le dépistage de la maladie d’Alzheimer». The GRC-APM has as main objective the advancements in detecting, treating, and preventing Alzheimer’s disease (AD) by the implementation of a Precision Medicine (PM) strategy. The successful applicant will be tasked with coding in efficient ways analytical methods and build internal capabilities and gears for these methods. He/she would also be responsible for setting up and running statistical and neuroimaging analysis pipelines for scientific studies. It would be expected for the Biomedical Research Engineer to regularly monitor and assess data quality for on-going projects and provide feedback to collaborators. Duties include: To develop MRI pipelines and data analyses in particular DTI data and their integration with structural MRI and functional MRI To support researchers in the team during the scientific writing process To manage the internal database, which may include the development of new user interfaces. Desired qualifications: Experienced in processing structural MRI and DTI neuroimaging data Demonstrated high level capacity for scripting with different languages, such as Python, R, MATLAB Familiarity with system administration, project and neuroimaging data management Familiarity with neurological concepts and/or experience with Alzheimer’s disease is desirable Ability to integrate multimodal data, including neuroimaging data, biological markers and genetic data will be appreciated. Education & experience Master's degree Biomedical Research Engineer or related field. Two years of relevant experience is highly desirable though not necessary Knowledge, skills and abilities: Strong analytical and organizational skills. Ability to learn and utilize relational databases, data integration, and statistics. Strong written and oral English communication skills. Ability to understand scientific literature, experimental procedures and their limitations, and current needs of the research community, as applied in clinical neuroscience and neuroimaging research. Position length: The position is supported for 4 years. However, candidates will be appointed for 1 year, with an extension possible based on progress Salary: 2,183 € gross / month Please send a brief letter of motivation and your detailed CV as one pdf (<2MB) to patrizia.chiesa(a)icm-institute.org

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hippocampus subfields with T2
by Alexopoulos, Dimitrios 31 Aug '18

31 Aug '18

External Email - Use Caution We have a cohort of 10yo subjects for which we have acquired a 0.85mm isotropic T1-mprage and a 1mm isotropic T2-space. Is it possible or even recommended to try and generate better hippocampal segmentation in fressurfer 6.0 using both the T1 and T2, or does the T2 need to be of equal or better resolution than the T1? Jim ________________________________ 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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