Freesurfer March 2018

freesurfer@nmr.mgh.harvard.edu

115 participants
161 discussions

FreeSurfer 6.0.0 CentOS 7 compatibility
by Vanzo, Davide 25 Sep '18

25 Sep '18

Hello, According from few messages in this mailing list, FreeSurfer 6.0.0 should be compatible with CentOS 7. However in the official documentation I cannot find any related statement. Moveover, the download web page still shows only CentOS 6 as supported platform. Could you please clarify if the current stable release works correctly on CentOS 7 or not? Thank you. Best regards -- Davide Vanzo, PhD Application Developer Adjunct Assistant Professor of Chemical and Biomolecular Engineering Advanced Computing Center for Research and Education (ACCRE) Vanderbilt University - Hill Center 201 www.accre.vanderbilt.edu

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Histogram analysis capability via mri_segstats or other command-lines in Freesurfer?
by Yash Patel 22 Aug '18

22 Aug '18

Dear all, I am using mri_segstats to obtain intensity values from each of the 34 cortical parcellations in the Desikan-Killiany Atlas; this provides metrics such as mean, min, max, range, and standard deviation. Is there a way to extract information such as the *mode*, or information to create a histogram for each of the particular regions? Thank you, Yash

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Custom color map in Freeview
by Anna Mynick 11 Jul '18

11 Jul '18

Hi all, I’m wondering whether there’s a way to create a custom color map in Freeview that would operate as a alternative to the preset Greyscale, Heatmap, NIH, PET, Jet and GE Color options. Ideally, I could assign each number value a given color, e.g. every “0” value in an .nii file is black, every “1” value is red, every “2” value is blue, every “3" is green and so on. I already have the RGB values worked out for each number value; I just need to know how to format this information and where to put it so that I can my custom colormap as an option in Freeview. For my purposes, there would be no need to adjust the assigned colors based on the overall range of values. For instance, there would be no need to assign a different color value to a “1” value depending on whether the highest value in the overall .nii file is 1 or 100. I did try reading the related conversation here<https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2017-April/051277.ht…> but I can’t seem to find the file it references, annotval2surfoverlay.m, in the Freesurfer directory. Thanks very much for your help! Anna

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ROI extraction using functional masks
by Yann Quidé 06 Jun '18

06 Jun '18

Dear FS experts, I am trying to extract values for cortical thickness, surface area and volumes, from different functional ROIs. These cortical ROIs have been defined using SPM tools, and are in .nii format. My scans have been processed using FS v5.3. Although the conversion seems to go well, the “end product” does not really look good, some of the extracted ROI for some subjects are empty. Does anyone have a clue of why? Here is what I have done: 1) transform .nii file to .mgz file $FREESURFER_HOME/bin/mri_convert $MASKS_DIR/ROI.nii $MASKS_DIR/L_ROI.mgz $FREESURFER_HOME/bin/mri_convert $MASKS_DIR/ROI.nii $MASKS_DIR/R_ROI.mgz 2) to make sure our masks from SPM will match fsaverage templates, I did tkmedit -f $MASKS_DIR/avg152T1.mgz -overlay $MASKS_DIR/L_ROI.mgz -fthresh 0.5 tkmedit -f $MASKS_DIR/avg152T1.mgz -overlay $MASKS_DIR/R_ROI.mgz -fthresh 0.5 It was fine. 3) I created a .dat file containing the registration matrix from avg152T1 onto fsaverage cd $SUBJECTS_DIR/fsaverage/surf spmregister --s fsaverage --mov $MASKS_DIR/avg152T1.nii --reg $REG_DIR/avg152T1_to_fsaverage.dat 4) Visualisation of the registration tkregister2 --mov $MASKS_DIR/avg152T1.nii --targ $SUBJECTS_DIR/fsaverage/mri/brainmask.mgz --reg $REG_DIR/avg152T1_to_fsaverage.dat --surf orig The registration was bad, so… I manually relocate the TAL template onto the fsaverage template and saved a new avg152T1_to_fsaverage.dat file called avg152T1_to_fsaverage_edited.dat. This file is used for the next steps. 5) Visualisation of the registration of our mask onto fsaverage T1 cd $SUBJECTS_DIR/fsaverage/surf tkmedit fsaverage T1.mgz \ -overlay $MASKS_DIR/L_ROI.mgz \ -overlay-reg $REG_DIR/avg152T1_to_fsaverage_edited.dat \ -fthresh 0.5 \ -surface lh.white -aux-surface rh.white tkmedit fsaverage T1.mgz \ -overlay $MASKS_DIR/R_ROI.mgz \ -overlay-reg $REG_DIR/avg152T1_to_fsaverage_edited.dat \ -fthresh 0.5 \ -surface lh.white -aux-surface rh.white Up to this sep, everything looks good. 6) Transformation of the ROI mask to surface and thickness mri_vol2surf --src $MASKS_DIR/L_ROI.mgz --reg $REG_DIR/avg152T1_to_fsaverage_edited.dat --hemi lh --o $MASKS_DIR/L_ROI.mgh mri_vol2surf --src $MASKS_DIR/R_ROI.mgz --reg $REG_DIR/avg152T1_to_fsaverage_edited.dat --hemi rh --o $MASKS_DIR/R_ROI.mgh mri_cor2label --i $MASKS_DIR/L_ROI.mgh --surf fsaverage lh --id 1 --l $MASKS_DIR/L_ROI.label mri_cor2label --i $MASKS_DIR/R_ROI.mgh --surf fsaverage rh --id 1 --l $MASKS_DIR/R_ROI.label 7) Extraction of the ROI surface and thickness for analyses mris_anatomical_stats -l $MASKS_DIR/L_ROI.label -f $OUT_DIR/results_L_ROI_SubjID SubjID lh mris_anatomical_stats -l $MASKS_DIR/R_ROI.label -f $OUT_DIR/results_R_ROI_SubjID SubjID rh Thanks to anyone who will be able to help me with that! Yann

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Freesurfer6.0 failure
by Naka Beguedou 22 May '18

22 May '18

Hello, I allow myself to send you this mail in order to have some informations. we have a problem concerning the segmentation of FREESURFER6.0 Indeed for T1image of one subject, the surface segmentation(figure1) is accurate but there is failure on the cortical segmentation(figure2) of the right hemisphere for the free surfer 6.0. For that subject, we relaunched the free surfer6.0 , but still the same problem. Here is the command we used to relaunch the free surfer6.0 for that subject: recon-all -all -FLAIR FLAIR/FLAIR_585.nii.gz -i T1/T1_585.nii.gz -brainstem-structures -3T -contrasurfreg -qcache -subjid SHARE0585_2 -sd /scratch/alaurent006/freesurfer_end -FLAIRpial What can we do about it? Thanks

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Longitudinal data from different sequences and scanners
by James Gullickson 15 May '18

15 May '18

All, Our lab is working with longitudinal (two time points) data from a cohort of around 130 individuals. We are attempting to make comparisons between time points 1 and 2 on measures like total brain volume, ventricular volume, ventricle-brain-ratio, and cortical thickness. However, we have run into an issue--we are seeing net increases in cortical thickness and total brain volume over time (which seems biologically implausible, given our age range of ~30-60 yrs old). We think it may have something to do with the fact that the T1w data from each time point was acquired with slightly different parameters and on different scanners, possibly leading to a rounding error in quantification of volumes/thickness. Timepoint 1 data are 1.0mm isotropic and were acquired on a 3T Siemens Tim Trio with 12ch headcoil. Timepoint 2 data are 0.8mm isotropic and were acquired on the same scanner, but which went through an upgrade to a Prisma Fit between timepoints, using a 32ch coil. Currently we have been comparing data from the cross sectional stream. We would like to use the longitudinal stream if that would improve results, but we saw this post that cautioned against it: https://www.mail-archive.c om/freesurfer(a)nmr.mgh.harvard.edu/msg52992.html What would be your recommendation for comparing this data longitudinally? Any thoughts on why we are seeing net increases in volume/thickness, and how to avoid that? One idea we had was perhaps degrading each image by rigid co-registration and then bringing each image into the halfway space between the two (as FSL's SIENA does). Thanks, James

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Neuroimaging postdoc position available at the University of Michigan
by Martijn Muller 15 May '18

15 May '18

*Research Fellow - Multimodal neuroimaging of Parkinson’s disease* A Research Fellow position is available immediately at the Functional Neuroimaging, Cognitive, and Mobility Laboratory, Department of Radiology, University of Michigan, Ann Arbor, MI, USA. Our laboratory specializes in clinical, mobility, cognition, and multimodal neuroimaging studies of Parkinson's disease and is directed by Drs. Nicolaas Bohnen, MD, PhD (Director) and Martijn Muller, PhD (Co-director). We are looking for a post-doctoral candidate to conduct and interpret multimodal and voxel-based imaging analyses of structural, functional MRI and PET datasets to address clinical research questions in patients with Parkinson’s disease. The applicant will also participate in the development of a new neuroimaging and clinical database with incorporated imaging analysis pipeline processing routines. Applicants must have completed a graduate degree (PhD) with relevant experience in multimodal imaging. The applicant must have experience in radiology/radiological sciences, signal processing, functional MRI and diffusion tensor imaging, the use of neuroimaging software packages such as SPM, Freesurfer, Matlab, and FSL. Experience in network-based methods, such as graph theory, would be highly desirable. Additional roles include leadership and active participation in project management activities including the administration of research projects, as well as some teaching sessions and supervision of students. Fluency in English conversation and team work skills to work in a multidisciplinary environment are important. This position will require self-initiative and the ability to work independently without close supervision. Send a brief letter of interest that describes how current skills fit with the required skills for this position, current curriculum vitae, names and contact information of three references to: Dr. Martijn Muller at mtmuller at umich.edu. Compensation of this limited term position will be commensurate with experience and includes health benefits. The University of Michigan is an equal opportunity/affirmative action employer. If applicable, this offer is contingent on your securing valid immigration status and work authorization before your expected start date and maintaining your valid immigration status and work authorization throughout your employment. University of Michigan Health System conducts background screening and pre-employment drug testing on job candidates upon acceptance of a contingent job offer and may use a third party administrator to conduct background screenings. Background screenings are performed in compliance with the Fair Credit Report Act.

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POST-DOCTORAL FELLOWSHIP IN NEUROIMAGING
by Xiaosong He 28 Apr '18

28 Apr '18

POST-DOCTORAL FELLOWSHIP IN NEUROIMAGING THOMAS JEFFERSON UNIVERSITY/ SIDNEY KIMMEL MEDICAL COLLEGE, PHILA., PA. The Department of Neurology at Thomas Jefferson University/Jefferson Medical College has an opening for a Two-Year Postdoctoral Research Fellowship in Neuroimaging focusing on both clinical brain mapping and primary cognitive neuroscience investigations. The emphasis in our neuroimaging program is on cognitive and behavioral network organization and plasticity in neurologic disorders such as epilepsy. The lab focuses on the use of advanced network neuroscience measures to understand seizure networks and cognitive reorganization in epilepsy, and has had recent publications in Brian, Neurology, and Epilepsia, with some also prompting complimentary peer reviews. The lab is part of the Jefferson Comprehensive Epilepsy Center, an internationally-known epilepsy surgery program. Presurgical brain mapping studies are undertaken (MRI volumetrics, task-fMRI, resting state functional connectivity, diffusion imaging, neuropsychological assessment, electrophysiology/electrocortical stimulation) as well as post-surgical neuroimaging studies investigating clinical, cognitive, and behavioral outcomes. The pre-surgical brain mapping studies are conducted on a regular basis, utilized in image-guided surgery, and then made available for research. Studies in brain recovery and the cognitive reorganization of language and memory functions are emphasized, utilizing rich multi-modal datasets for the investigation of both cognitive and pathologic (e.g., seizure) networks. Thomas Jefferson University provides a high-level interdisciplinary research environment with grand rounds, seminars, case conferences, and opportunities to collaborate with faculty across departments such as neurosurgery and radiology. Successful applicants must have a strong background in image processing and analysis using programs such as MATLAB, SPM, Freesurfer, and FSL with a strong interest in clinical neuroimaging and cognitive neuroscience. Applicants must have a Ph.D. or MD in neuroscience, biomedical engineering, statistics, neurology, neuropsychology, radiology, or related field. Interested applicants should send a CV and cover letter stating experience and interests, 2-3 peer-reviewed publications. Anticipated start date is 7/1/18, but is flexible. Contact: Joseph I. Tracy, Ph.D., ABPP(CN). Director, Cognitive Neuroscience and Brain Mapping Laboratory, Thomas Jefferson Univ./Sidney Kimmel Medical Coll., Jefferson Hospital for Neuroscience, 901 Walnut Street, Suite #447, Phila., PA 19107, phone:#215-955-4661, e-mail: joseph.tracy(a)jefferson.edu. Thomas Jefferson University and Hospitals is an Equal Opportunity Employer. Jefferson values diversity and encourages applications from women, members of minority groups, LGBTQ individuals, disabled individuals, and veterans.

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resting state motion censoring
by Adam Martersteck 24 Apr '18

24 Apr '18

Hi Freesurer experts, I’m looking to censor (drop volumes) from my resting state fMRI time series that violate a predetermined motion and signal threshold (FD and DVARS). I've already determined which volumes violate X and Y criteria. Is there a way to to tell FS to "ignore" these time points in the analysis such as in preproc-sess or mkanalysis-sess? If there is not and if I were to drop the volumes directly from the 4D file before starting any pre-processing and analysis – would that be a problem for finding and regressing the auto-correlation in the time series? Thanks! Adam

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Re: [Freesurfer] using T2 for hippo subfields
by Iglesias Gonzalez, Eugenio 20 Apr '18

20 Apr '18

Hi Jim, In the end it’s an empirical question, but my gut feeling is that the T1 with hi-res flag will be best. Cheers, /E -- Juan Eugenio Iglesias ERC Senior Research Fellow Translational Imaging Group University College London http://www.jeiglesias.com http://cmictig.cs.ucl.ac.uk/ From: <freesurfer-bounces(a)nmr.mgh.harvard.edu> on behalf of "Alexopoulos, Dimitrios" <dimitriosalexopoulos(a)wustl.edu> Reply-To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> Date: Friday, 23 March 2018 at 16:00 To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> Subject: [Freesurfer] using T2 for hippo subfields Hi. We are acquiring sequences on a pediatric cohort that include a T1-mprage (0.8mm isotropic) and a T2-space (1mm isotropic), and I’d like to run the hippocampal subfields module on the subjects using FS 6.0. Is it recommended/useful to run the multispectral segmentation mode with the additional lower resolution T2 sequence? I read that you really only benefit if the T2 is of similar or better resolution than the T1. If that’s the case, would it be best to just run with the single T1 but with the hi-res flag in the recon-all command? Thanks. 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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Freesurfer March 2018