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30088 discussions

MNI to native space using mri_cvs_register and applyMorph
by Ehsan Tadayon 06 Sep '18

06 Sep '18

External Email - Use Caution Dear Freesurfer experts, I would appreciate any help regarding my previous question: I need to transform a bunch of MNI coordinates to subject's space. I have already registered my subjects to cvs_avg35_inMNI152 using mri_cvs_register. How can I use the mri_cvs_register outputs to transform an MNI coordinate back into the subject's space? Thanks in advance. Ehsan.

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Data Analyst Position - Child Mind Institute (New York)
by Suk Jun Hong 06 Sep '18

06 Sep '18

External Email - Use Caution The Child Mind Institute is seeking a Data Analyst to support a collaborative study with Dr. Amy Roy at Fordham University. The Data Analyst’s role is to assist with the analysis of functional MRI data, as well as reporting results. In particular, the work includes: 1) preprocessing of a large fMRI dataset and implementing quality assurance protocols, 2) maintaining the database and imaging processing pipeline; 3) supporting post-doctoral researchers by implementing novel analytic methods; and 4) training graduate and undergraduate students in how to preprocess and analyze resting state and task-based functional MRI data. Reporting to Dr. Suk Jun Hong and the Director of the Center for the Developing Brain, this is a full-time position, primarily located at the CMI headquarters (101 E 56th St, New York, NY 10022). Responsibilities: Implementation, execution, and maintenance of fMRI imaging analysis pipelines Conduct neuroanatomical profile analyses as well as analyses of resting-state functional MRI data using novel software packages and neuroinformatic platforms Develop graphs, reports, and presentations of project results Training undergraduate and graduate students 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 is preferred 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 applying computational methods to understand clinical conditions. If you are interested in the positions, please apply to https://workforcenow.adp.com/mascsr/default/mdf/recruitment/recruitment.htm… Thank you! -------------------------- Suk-Jun Hong, PhD Postdoc, Center for the Developing Brain Child Mind Institute

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How to deal with different resolutions in recon all and hippocampal subfield segmentation
by Boris Rauchmann 06 Sep '18

06 Sep '18

External Email - Use Caution Hi, I'm working on data from different sites, scanned with different MRI-Scanners ans slightly different parameters (all in the range of 1x1x1 to 1.2x1.2x1). I wonder if you would recommend to run recon all and segmentation of HC sub-fields in different analysis and how comparable the results will be. Thanks, Tragus

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A Question about Estimating the Cortical Thickness for Each Subregion
by Maedeh Khalilian 06 Sep '18

06 Sep '18

External Email - Use Caution Dear Freesurfer Experts; I have a question, are there any ways in FreeSurfer to estimate the gray matter volume or cortical thickness of each region after parcellation, in order to define the edges in the brain network? Kind regards, Maedeh,

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how to dilate a mgh binary mask file in fsaverage space. The file is in .mgh format.
by Anik Dar 05 Sep '18

05 Sep '18

External Email - Use Caution Hi I have created a .mgh file which is a bunch of vertices all with a value of 1. Please see pic. [image: Screen Shot 2018-09-05 at 7.06.04 PM.png] I want to create a bigger region of interest by dilating this yellow region lets say with a radius of 10 vertices around this region. How to do it ? Thank you. Ani

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Resting-State and Brain Connectivity 2018: Early registration fee applies until September 14, 2018
by Kelvin Mok 05 Sep '18

05 Sep '18

External Email - Use Caution ---------- Forwarded message --------- *From:* Amir Shmuel, Dr. *Subject:* Resting-State and Brain Connectivity 2018: Early registration fee applies until September 14, 2018 *Resting-State and Brain Connectivity 2018: *Early registration fee applies until September 14, 2018 Educational course: September 24-25 Conference, featuring 45 world-renowned speakers: September 26-28 Satellite workshop on how to incorporate machine and deep learning in your data analysis: September 29 *http://restingstate.com/2018/ <http://restingstate.com/2018/>* *Amir Shmuel* *Chair of the organizing committee* *Resting-State and Brain Connectivity 2018* *Montreal, QC, Canada* *[image: http://restingstate.com/2018/wp-content/uploads/2017/06/resting-state-logo-…

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Mean FA values for major tracts all greater than 1
by Katherine Damme 05 Sep '18

05 Sep '18

External Email - Use Caution Hello Freesurfer Support group, I have run tracula on hundreds of subjects for a study and their primary tracts are all showing that MFA is greater than 1. Typically, I expected that MFA should be in the .3 to 1 range. Should I be suspicious that these MFA values are over the top of that range or is this common for major tracts like the forceps major? Thank you for your insights on this potential error. Kate

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mris_compute_parc_overlap average minimum distance measurement
by Zimmerman, Jared 05 Sep '18

05 Sep '18

External Email - Use Caution Hi Freesurfers, I’m using mris_compute_parc_overlap to compare the similarity between two parcellations and I’m curious about how the average minimum distance measurement is calculated. The help text for the function says “… a table of mean minimum distances between corresponding labels.” My questions are 1) what set of measurements is being meaned here, and 2) what exactly is the measurement. My current interpretation is that for every vertex in annot1 the minimum distance to a vertex in annot2 with the same label is calculated such that overlapping regions have a distance of zero. The mean is then calculated over these distance measures for all vertices in a given label. If this is true, do you recommend doing any subject level corrections? Seems like subjects with larger cortical surface areas would be biased to have larger distances. Thanks, Jared

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long_mris_slopes: error: cannot create a table with longitudinal pc1
by Shatil, Anwar Shahadat 05 Sep '18

05 Sep '18

External Email - Use Caution ?Dear Doug: I am trying to get a table containing pc1 values for each subject in a longitudinal study and failed to extract this. I use the code below: long_mris_slopes --qdec ./qdec/long.qdec.table.2.dat --meas thickness --hemi lh --do-avg --do-rate --do-pc1 --do-spc --do-stack --do-label --time years --qcache fsaverage --sd /Users/richardaviv/Desktop/Longitudinal_FS --out-pc1 out-pc1.dat It says long_mris_slopes: error: no such option: --out-pc1 However in the --help file it says: Within-Subject Output: Pass these to overwrite the default names: --out-avg=OUT_AVG filename to store temporal average in <template>/stats/<OUT_AVG> (default: long.<stats>.<meas>-avg.dat) --out-rate=OUT_RATE filename to store rate in <template>/stats/<OUT_RATE> (default: long.<stats>.<meas>-rate.dat) --out-pc1fit=OUT_PC1FIT filename to store pct. change (to tp1fit) in <template>/stats/<OUT_PC1FIT> (default: long.<stats>.<meas>-pc1fit.dat) --out-pc1=OUT_PC1 filename to store pct. change (to tp1) in <template>/stats/<OUT_PC1> (default: long.<stats>.<meas>-pc1.dat) --out-spc=OUT_SPC filename to store sym. pct. change in <template>/stats/<OUT_SPC> (default: long.<stats>.<meas>-spc.dat) --out-resid=OUT_RESID filename to store residual in <template>/stats/<OUT_RESID> (default: long.<stats>.<meas>-resid<resid>.dat), requires --resid <int> --out-stack=OUT_STACK filename to store stacked measure file <template>/stats/<OUT_STACK> (default: long.<stats>.<meas>-stack.dat) Stacked Tables: To output tables with results from all subjects --stack-avg=STACK_AVG full filename to stack temporal average tables (default no stacking) --stack-rate=STACK_RATE full filename to stack rate tables (default no stacking) --stack-pc1fit=STACK_PC1FIT full filename to stack pct. change to tp1fit tables (default no stacking) --stack-pc1=STACK_PC1 full filename to stack pct. change to tp1 tables (default no stacking) --stack-spc=STACK_SPC full filename to stack sym. pct. tables (default no stacking) --stack-resid=STACK_RESID full filename to stack residual tables (default no stacking)? Am I writing the code wrong?? I never got any long.<stats>.<meas>-pc1.dat file in <template>/stats/ folder except bunch of mgh files in <template>/surf/ folder. Thanks, Anwar -- Anwar S. Shatil Research Assistant Department of Medical Imaging Sunnybrook Health Sciences Centre Room AB204, 2075 Bayview Avenue Toronto, ON M4N 3M5 Tel: 416.480.6100 ext. 89617 Email: anwar.shatil(a)sunnybrook.ca This e-mail is intended only for the named recipient(s) and may contain confidential, personal and/or health information (information which may be subject to legal restrictions on use, retention and/or disclosure). No waiver of confidence is intended by virtue of communication via the internet. Any review or distribution by anyone other than the person(s) for whom it was originally intended is strictly prohibited. If you have received this e-mail in error, please contact the sender and destroy all copies.

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Get corresponding vertex of another subject
by Michael . 05 Sep '18

05 Sep '18

External Email - Use Caution Hi, i want to create a lookup table for the vertex correspondence between the subjects A & B (pial files). e.g verticesA(100) corresponds to verticesB(122) Of course the number of vertices is different between the subjects, e.g one vertex of A can correspond to several vertices from B. Currently, I am reading in the pial files of subject A using 'read_surf' and create two label files (lh/rh) containing all vertices. In order to get the corresponding vertices of Subject B, i use "label2label". label file A: #!ascii label, from subject 142350 0 -7.814680 -88.725967 9.598738 1.000000 1 -8.505306 -88.835274 9.457685 2.000000 2 -9.234029 -89.900490 9.420641 3.000000 resulting label file: #!ascii label , from subject cvs_avg35_inMNI152/Segmentation vox2ras=TkReg 137427 888 -7.179 -84.047 -28.333 1.0000000000 642 -7.533 -84.272 -28.382 2.0000000000 637 -7.717 -84.612 -28.118 3.0000000000 But how can I interpret the result? Can I assume that verticesA(0) corresponds to verticesB(888)? Or verticesA(0) corresponds to verticesB(888)? Or is there another way to create such a lookup table? Thank you in advance!

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