Freesurfer December 2017

freesurfer@nmr.mgh.harvard.edu

107 participants
172 discussions

extra brain tiussue
by John Anderson 15 Dec '17

15 Dec '17

Dear FS experts, I want to extra the extra brain tissue. Is it correct to subtract orig.mgz from aparc+aseg? Is this provide accurate estimates forrhe space between the brain tissue and the skull. Kindly, do you suggest me better solution? Thanks for any advice! J

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how to get intrinsic/gaussian curvature in custom FMRI ROI?
by Russell Butler 15 Dec '17

15 Dec '17

Hi, i would like to use an FMRI ROI as a label from which to extract some curvature metrics in single subjects. all my FMRI ROIs are in nifti volume format, in the same space as my freesurfer segmentations. i've tried this tutorial: https://surfer.nmr.mgh.harvard.edu/fswiki/VolumeRoiCorticalThickness? and it works for cortical thickness, but don't know how to use it to get the other metrics like curvature. thanks, Russell?

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Issue with Freesurfer installation
by Pruett, Scott 15 Dec '17

15 Dec '17

I just recently followed the steps to install Freesurfer on my Mac. The installation initially seems to have gone fine, but when I try to test the installation by using the listed "Example 1: Convert the sample-001.mgz to nifti format," I get the following error: -------- freesurfer-Darwin-OSX-stable-pub-v6.0.0-2beb96c -------- Setting up environment for FreeSurfer/FS-FAST (and FSL) FREESURFER_HOME /Applications/freesurfer FSFAST_HOME /Applications/freesurfer/fsfast FSF_OUTPUT_FORMAT nii.gz SUBJECTS_DIR /Applications/freesurfer/subjects MNI_DIR /Applications/freesurfer/mni scott-pruetts-computer:~ scottpruett$ cp $FREESURFER_HOME/subjects/sample-001.mgz usage: cp [-R [-H | -L | -P]] [-fi | -n] [-apvX] source_file target_file cp [-R [-H | -L | -P]] [-fi | -n] [-apvX] source_file ... target_directory scott-pruetts-computer:~ scottpruett$ mri_convert sample-001.mgz sample-001.nii.gz mri_convert.bin sample-001.mgz sample-001.nii.gz $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ reading from sample-001.mgz... mghRead(/Users/scottpruett/sample-001.mgz, -1): could not open file scott-pruetts-computer:~ scottpruett$ Any ideas about what I should do to remedy this? Thanks, Scott -- Scott Pruett, M.D., Ph.D. General Psychiatry and R25 Research Track Resident, PGY4 Department of Psychiatry and Human Behavior Warren Alpert Medical School of Brown University

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surface/volume conversion
by Strebl, Martin Georg 15 Dec '17

15 Dec '17

Hi all, Is there an existing matrix that I could use to transform the surface files (white/pial) back into the volume coordinate system so that they're registered with the fsaverage volume in another visualization tool like AMIRA? Currently they seem to be in totally different spaces. Best, Martin Martin G. Strebl-Bantillo, Ph. D. Laboratory of Prof. Jacob Hooker, Ph.D. Martinos Center for Biomedical Imaging Massachusetts General Hospital http://hookerlab.martinos.org

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local Gyrification Index
by Gonzalo Rojas Costa 15 Dec '17

15 Dec '17

Hi: To compute local Gyrification Index is necessary Matlab... Complete installation or only runtime? Sincerely, Gonzalo Rojas Costa Laboratory for Advanced Medical Image Processing Department of Radiology Clínica las Condes Lo Fontecilla 441, Las Condes, Santiago, Chile. Tel: 56-2-2105170 Cel: 56-9-97771785 www.clc.cl http://www.aribrain.info https://scholar.google.com/citations?user=LO7LZ3oAAAAJ https://www.researchgate.net/profile/Gonzalo_Rojas2 https://cl.linkedin.com/in/gonzalorojascosta

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hemisphere analysis
by lanbo Wang 15 Dec '17

15 Dec '17

Dear experts, I have two questions about hemisphere analysis: 1) When I run left-right hemisphere paired t-test, can I add age as covariate? If use fsgd to add covariate, to this paired t-test analysis, how to make the fsgd table? 2) I want to reorganize the hemisphere from left-right to symptom-nosymptom according to body symptom side record and compare different between symptom hemisphere and nosymptom hemisphere. Can I use freesurfer to do it? Thanks for your patient and help. All best, Lanbo Wang

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extract surface area for singe vertex
by Clara Kühn 15 Dec '17

15 Dec '17

Dear Freesurfer experts, I've run a longitudinal two stage model of 2 time points to look at the rate of change in surface area and whether my two groups change differently. I find a superior parietal cluster in the right hemisphere. So far I've already run the mri_glmfit-sim to get the values of rate of change in this cluster for each subject. Now I would like to extract the peak vertex that I get the coordinates of from mri_glmfit-sim for each subject from each time point. I have tried to use mri_convert mris_convert -c $SUBJECTS_DIR/WL8K_1.long.WL8K.base/surf/lh.thickness.fwhm10.81kids_template.mgh $SUBJECTS_DIR/001/WL8K_1.long.WL8K.base/lh.orig $SUBJECTS_DIR/WL8K_1.long.WL8K.base/lh.thickness.fwhm10.81kids_template.vertices.asc however, I get this error message: ERROR: number of vertices in /nobackup/etsch2/kids/prepost-61kids/WL8K_1.long.WL8K.base/surf/lh.thickness.fwhm10.81kids_template.mgh does not match surface (97361,109356) I've read in other threads that I'm supposed to use mri_surf2surf to map it to my template (81kids_template). I thought I had already done that before the analysis when running long_mris_slopes --qdec ./qdec/long.qdec.table.dat --meas thickness --hemi lh --do-avg --do-rate --do-pc1 --do-spc --do-stack --do-label --time years --qcache 81kids_template Could you tell me what I need to do to extract the values of the peak vertex in my significant cluster for each subject and each time point? Thank you so much! Clara -- Clara Kühn, Phd Candidate Max-Planck-Institute for Human Cognitive and Brain Science Department of Neuropsychology Stephanstrasse 1A 04103 Leipzig, Germany Phone: +49 341 - 9940 2271 Fax: +49 341 - 9940 2260 Web: www.cbs.mpg.de E-Mail: ckuehn(a)cbs.mpg.de

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Finding correlation between Cth and clinical data
by Shatil, Anwar Shahadat 15 Dec '17

15 Dec '17

Dear Experts: I am very new to freesurfer glmfit and this post may seem dumb. I want to find the correlation between Cth and Education for each of HC and RRMS group regressing out the effect of gender and (demeaned) age. My fsgd file is something like below. GroupDescriptorFile 1 Title Group-Edu-Correlation MeasurementName thickness Class FemaleHC Class FemaleRRMS Class MaleHC Class MaleRRMS Variables Age Education Input 1 FemaleRRMS -7.97 0.243 Input 2 MaleRRMS -2.97 -1.300 Input 3 FemaleHC -12.97 -0.914 Input 5 Male HC 4.03 -1.686 ………………….. I used DODS method. For HC, I set the correlation matrix as: 0 0 0 0 0 0 0 0 0.5 0 0.5 0 And for RRMS, I set the matrix as: 0 0 0 0 0 0 0 0 0 0.5 0 0.5 1. Are my DODS contrasts correct? 2. To get better DOF, should I create two different FSGD file for each group (i.e. one for HC and one for RRMS)? 3. If I create two different FSGD file for each group then can I use DOSS method and use the contrast: 0 0 0 1 ? Thanks, Anwar 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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Job Posting: Research Methods Specialist for Psychiatry Neuroimaing Lab, Toronto
by Erin W. E. Dickie 14 Dec '17

14 Dec '17

The Kimel Family Translational Imaging-Genetics Laboratory is a large multidisciplinary research laboratory dedicated to discovering the causes of severe mental illness and advancing treatments for severe mental illness. The focus of the laboratory is on combining brain imaging and genetics, brain imaging and brain stimulation, and brain imaging and clinical trials. The laboratory is located in the Research Imaging Centre, Toronto, Canada. The Research Methods Specialist’s primary responsibility will be to collaborate and support laboratory members and subject matter experts in design, development and implementation of analyses and new methods, as well as provide guidance, technical advice and training. The successful candidate will also be involved in the maintenance of different analysis pipelines and will help users migrate existing software to high performance computing infrastructures (such as the SciNet facilities). Additionally, the Research Methods Specialist will be involved in the system administration of a computing cluster that is used in the daily research endeavours of scientists, fellows, and trainees. In this role you will manage both user access and hardware of the cluster. You will support a healthy workplace that embraces diversity encourages teamwork and complies with all applicable standards and requirements. This position will be located at 250 College Street. *Salary range:* $35.77 – $48.24 per hour For full posting and application instructions see: *http://www.recruitingsite.com/csbsites/camh/JobDescription.asp?SuperCategoryCode=15233&JobNumber=816025&lang=en <http://www.recruitingsite.com/csbsites/camh/JobDescription.asp?SuperCategor…>* *Contact erin.w.dickie(a)gmail.com <erin.w.dickie(a)gmail.com> with inquiries.*

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mri_cnr with mask
by Kathy L. Pearson 14 Dec '17

14 Dec '17

Is it possible to get CNR info on a masked region? I have tried these commands but see only unexpected tiny values or NaN for results: mri_binarize --i $SUBJECTS_DIR/$subj/mri/aseg.mgz --match $mndx --o $tmpmask mri_mask $SUBJECTS_DIR/$subj/mri/norm.mgz $tmpmask $norm_tmpmask mri_cnr $SUBJECTS_DIR/$subj/surf $norm_tmpmask I have used the --match $mndx for each of the 45 regions listed in the aseg stats report. For hippocampus, for example: --match 17 -- match 53 but all give NaN or values <= .003 for total CNR. Thanks for any suggestions. Kathy Pearson

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Freesurfer December 2017