Freesurfer December 2019

freesurfer@nmr.mgh.harvard.edu

85 participants
117 discussions

Converting labels drew by freeview to volume Error: coordinate mismatch
by zorothustra 04 Dec '19

04 Dec '19

External Email - Use Caution Hello Freesurfer Developers, I'm trying to get superior colliculus' ROI mannually by freeview. I load "orig.mgz" as volumes and set the "orig.mgz" as the ROI's template then draw the ROI and save it as a label file. After that I use "mri_label2vol --label sc.label --temp T1.nii --reg register.dat --o sc.nii", "T1.nii" is my initial structure image, "register.dat" got from the code:" tkregister2 --mov T1.nii --s SUB --regheader --noedit --reg register.dat", and it worked, but the coordinate mismatch, much different from the SC's position in the T1 space( Load T1.nii as volume and SC.label as ROI in freeview, and they are matched). Can anyone help me? Thank you! 1)FreeSurfer version: freesurfer-local-build-dev-20191104 2)platform: Ubuntu 18.04

5 6

LME Contrast Question
by Hua, Jessica 04 Dec '19

04 Dec '19

External Email - Use Caution Hi FreeSurfer Experts, I had a question regarding contrasts for univariate LME models. I am interested in looking at the interaction of alcohol with change in volume across two time-points. Included in my model are covariates Gender, ICV, and Previous Drinking History. My X matrix includes 7 columns: Column 1 = 1s Column 2 = time Column 3 = alcohol Column 4 = time*alcohol Column 5 = Gender Column 6 = ICV Column 7 = Previous Drinking History My contrast is C = [0 0 0 1 0 0 0 ]. I have 4 different previous drinking history variables. However, when I change column 7 with my different previous drinking history variables, the F and P values for the interaction are the same. Am I setting up my contrasts incorrectly? Best, Jessica Hua

1 0

Re: [Freesurfer] [External] Freesurfer Digest, Vol 190, Issue 3
by Ferraro, Pilar 04 Dec '19

04 Dec '19

External Email - Use Caution Yes, absolutely, this should work! Many Thanks! I have just one last question concerning the colors in FreeView. I have a fsgd file with class 1 (patients) coming first and then class 0 (hc) after. The contrast matrix is 1 -1 0. Among the results I see blue and red regions in Freeview. Am I correct assuming that blue regions are the ones where cortical thickness is reduced in patients relative to HC (correcting for disease duration)? I just wanted to ask for a confirmation. Many thanks, Pilar > > Message: 2 > Date: Mon, 2 Dec 2019 16:06:54 +0000 > From: "Greve, Douglas N.,Ph.D." <DGREVE(a)mgh.harvard.edu> > Subject: Re: [Freesurfer] Fw: Regression Analysis accounting for one > variable > To: "freesurfer(a)nmr.mgh.harvard.edu" <freesurfer(a)nmr.mgh.harvard.edu> > Message-ID: <c8973136-8b3d-801a-9e88-2d6b8fd396be(a)mgh.harvard.edu> > Content-Type: text/plain; charset="windows-1252" > > It sounds like it would be a one-group, two-variable situation, like this > https://surfer.nmr.mgh.harvard.edu/fswiki/Fsgdf1G2V > Is that not correct? > > > On 11/28/2019 5:24 AM, Ferraro, Pilar wrote: > > External Email - Use Caution > > Hi, > > I apologize if I did not explain my issue properly. > I'm interested in looking at age-related thickness reductions in 1 group (patients), but I'd like to also account for the effect of disease duration. > We can say that in my case disease duration is the nuisance factor. > Briefly, I have the same issue reported in here (https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg32860.html) but with only one group. > How would you recommend to proceed? > > Many thanks, > > Pilar > > ________________________________ > Message: 2 > Date: Wed, 27 Nov 2019 16:56:20 +0000 > From: "Greve, Douglas N.,Ph.D." <DGREVE(a)mgh.harvard.edu><mailto:DGREVE@mgh.harvard.edu> > Subject: Re: [Freesurfer] [External] Freesurfer Digest, Vol 189, Issue > 36 > To: "freesurfer(a)nmr.mgh.harvard.edu"<mailto:freesurfer@nmr.mgh.harvard.edu> <freesurfer(a)nmr.mgh.harvard.edu><mailto:freesurfer@nmr.mgh.harvard.edu> > Message-ID: <fbb77a97-61b5-fac5-e2b3-0ee327e29ce3(a)mgh.harvard.edu><mailto:fbb77a97-61b5-fac5-e2b3-0ee327e29ce3@mgh.harvard.edu> > Content-Type: text/plain; charset="utf-8" > > what is the difference between and independent variable and a covariate? > > On 11/27/2019 6:57 AM, Ferraro, Pilar wrote: >> External Email - Use Caution >> >> Yes, I did. >> But in this case I have two factors, not only one. In particular, I have an independent variable X and a covariate I?d like to include in the model. >> How would you suggest to proceed? >> >> >> Thanks, >> >> Pilar > > > > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > >

2 3

Re: [Freesurfer] freeview parallelized binary
by Hoopes, Andrew 04 Dec '19

04 Dec '19

Hi Dustin, The freeview binaries that we ship are the same binaries installed on the cluster. You should try specifying the number of threads available to openmp by setting the OMP_NUM_THREADS env variable to something like 4 or 8 on your local machine to see if this makes a difference. Best, Andrew From: <freesurfer-bounces(a)nmr.mgh.harvard.edu> on behalf of "Clark, Dustin Christopher" <clarkdc(a)bu.edu> Reply-To: FS Help <freesurfer(a)nmr.mgh.harvard.edu> Date: Tuesday, November 26, 2019 at 9:43 AM To: FS Help <freesurfer(a)nmr.mgh.harvard.edu> Subject: [Freesurfer] freeview parallelized binary External Email - Use Caution Hello, We recently noticed freeview on the MGH cluster was using multiple cores when loading niftis, however, our local installation only uses one core when loading the same nifiti. Is it possible to get access to this freeview binary or the source code to build it for parallelization on our system? Thank you, Dustin Clark

2 1

Network license with user stats
by James Vincent 04 Dec '19

04 Dec '19

Hello Freesurfer, We would like to distribute Freesurfer through our BioGrids tool ( biogrids.org) with a license file already in place. I've read the previous message that asks individual users to obtain licenses even if using a single central license. I have requested a license ad filled in the expected number of users. Is that an acceptable alternative to asking individual to obtain licenses? Also, we can provide detailed usage statistics if there is interest. Thanks, Jim -- James Vincent, PhD BioGrids / SBGrid, Harvard Medical School vincent(a)hkl.hms.harvard.edu

1 0

Doctoral Position in Brain Microstructure Imaging Analysis using MRI and light sheet microscopy
by Matteo Bastiani 04 Dec '19

04 Dec '19

External Email - Use Caution MRC-funded Doctoral Position in Brain Microstructure Imaging Analysis using MRI and light sheet microscopy - Sir Peter Mansfield Imaging Centre, School of Medicine, University of Nottingham, UK Application Deadline: 5.00 pm Friday 17 January 2020 Applications are invited for an MRC fully funded 3.5 year PhD studentship at the University of Nottingham – UK, under the primary supervision of Dr Matteo Bastiani. The successful candidate will engage in specialist training with ex vivo and in vivo (subject to the experience and wishes of the applicant) animal handling, preclinical imaging, and data analysis techniques. The student will also acquire new computational and modelling skills as well as learn practical laboratory procedures to make a brain transparent. This will allow the student to model features of the MR images using 3D microscopy images. The research will be carried out in collaboration with the Birmingham branch of the Centre Of Membrane Proteins And REceptors (COMPARE) and the School of Life Sciences of the University of Nottingham. This project is offered through the MRC IMPACT Doctoral Training Programme. Applications should therefore be made through the IMPACT DTP website (project can be found under the University of Nottingham list): https://more.bham.ac.uk/mrc-impact/phd-opportunities/ For informal inquiries and more information feel free to contact by e-mail: matteo.bastiani(a)nottingham.ac.uk<mailto:matteo.bastiani@nottingham.ac.uk> Benefits The studentship is within the Integrated Midlands Partnership for Biomedical Training (IMPACT) Doctoral Training Program (DTP) funded by the UK Medical Research Council (MRC). Students will be supported for three years and six months on the following model: · Cohort Training Programme (3 months): additional training will take place during the programme (https://more.bham.ac.uk/mrc-impact/training-opportunities/) · PhD Research Project · The successful candidate will have their tuition fees covered and will also benefit from a standard PhD stipend, a research training support grant (up to £5k per year) and funds to cover conference attendance. Required Qualifications The PhD candidate must have a background in computer science, (applied) physics, mathematics, biomedical engineering, medical imaging, computational neuroscience or a related field from an approved program, with skills in scientific reporting/presenting, image processing or machine learning and computer programming (preferably C++/Matlab/Python). Prior (research) experience with MRI and/or medical image processing/analysis is an advantage. The candidate should be highly motivated and should be able to work in a team. Eligibility You must hold (or be about to obtain) a First or an Upper Second Class UK undergraduate degree or an equivalent degree from a recognised EU institution, in an area relevant to the projects you are applying for. Qualifications (or a combination of qualifications and experience) which demonstrate equivalent ability and attainment will also be considered. For example, a less than sufficient first degree may be enhanced to meet the requirements by the acquisition of a Distinction at Masters level or significant research experience gained from employment). These studentships are available to UK and other EU nationals ONLY. For full details on eligibility, including residence requirements, please see the MRC website. We are not currently accepting applications from overseas students. Further Information The Beacon of Excellence in Precision Imaging (University of Nottingham) has access to cutting-edge MRI scanners and hosts high-performance computing and storage facilities dedicated to imaging research. Its vibrant highly-interdisciplinary research community will provide the student with support at many different levels. The cross-institutional supervisory team is composed of researchers that are still actively doing experiments in the lab. They can provide the necessary multi-disciplinary expertise. An additional set of cross-institutional and cross-expertise collaborators will offer further support to the student. Several professional development opportunities will also be available, and there will be continuous opportunity for the student to develop communication and leadership skills via university courses, internal seminars/symposia, annual post-graduate symposia, teaching opportunities, and outreach activities. One to one mentoring, and participation in an enthusiastic and innovative research environment will provide the student with all the necessary training to complete a PhD. The full details for the position can be found at https://www.dropbox.com/s/mz8db078qzq2k0h/MRC_Impact_Bastiani_advert.pdf?dl….

1 0

-qcache and thickness questions
by Joëlle Ismay Rosanne Van Der Molen 03 Dec '19

03 Dec '19

External Email - Use Caution Dear Freesurfer experts, After running the -qcache option to extract thickness data for every subject, I tried pulling all the data together in order to get a matrix of subjects x vertices containing thickness data (for a given hemisphere) in all vertices of the brain. I noticed that for some small areas, particularly medial temporal, thickness data equals to 0 for some subjects, and has values for other subjects. May this be of concern? If so, would you have any idea why this is happening? Another, perhaps related question is: when I try to use a subject's individual thickness mgh as an overlay in tksurfer, I obtain the outputs attached to this email (I am not modifying any overlay min max or threshold values). I am wondering if these grey zones in the map (around occipital and parietal areas specifically; not for subcortical areas) are to be expected, or if they may reflect some processing problem? If so, what problem could it be? Thank you in advance for your help, Best regards, Joëlle van der Molen

2 4

Map fMRI data onto surface
by An 03 Dec '19

03 Dec '19

External Email - Use Caution Hi there, I want to map the intensities of the fMRI 4D volumes onto its surface in order to get the functional values on each vertex in each frame. I have done the following steps for achieving this: 1. ran recon-all on its anatomical volume. 2. register the fMRI series with the anatomical volume by using bbregister. 3. assign values from volumes to each surface vertex through the command mri_vol2surf. I have got a result of mapping the 4D volumes intensities onto its surfaces but there are 35.5% vertices assigned 0 value in every time frame. I am wondering is the ratio reasonable and how could I improve the result? I guess resolution would be one of reasons causing the high 0 value ratio, my fMRI data is 2mm^3 and anatomical data is 1mm^3. Many thanks for your help. Best, An

2 8

Re: [Freesurfer] Question on GLM - correlation
by Greve, Douglas N.,Ph.D. 03 Dec '19

03 Dec '19

I'm not sure those condition numbers include the pvr. Try loading the Xg.mat into matlab and computing cond(Xg'*Xg) Make sure Xg has the extra column for the pvr On 12/3/2019 10:42 AM, Barletta, Valeria wrote: Ok it worked. So I tried with a non-zero vertex and I got: Normalized matrix condition is 81.1382 Matrix condition is 30558.5 Found 149926 points in label. Found 149926 voxels in mask Saving mask to /autofs/space/lipari_001/users/valeria/NODDI/GLM//GLM_CME_ficvf_doug/rh_contrast-MS_CME_all_FIS_ICA1/mask.mgh Reshaping mriglm->mask... search space = 74490.928733 DOF = 18 Dumping voxel 1024 0 0 to /autofs/space/lipari_001/users/valeria/NODDI/GLM//GLM_CME_ficvf_doug/rh_contrast-MS_CME_all_FIS_ICA1/voxdump-1024-0-0 ...and with a zero vertex and got: Normalized matrix condition is 81.1382 Matrix condition is 30558.5 Found 149926 points in label. Found 149926 voxels in mask Saving mask to /autofs/space/lipari_001/users/valeria/NODDI/GLM//GLM_CME_ficvf_doug2/rh_contrast-MS_CME_all_FIS_ICA1/mask.mgh Reshaping mriglm->mask... search space = 74490.928733 DOF = 18 Dumping voxel 150252 0 0 to /autofs/space/lipari_001/users/valeria/NODDI/GLM//GLM_CME_ficvf_doug2/rh_contrast-MS_CME_all_FIS_ICA1/voxdump-150252-0-0 ________________________________ From: freesurfer-bounces(a)nmr.mgh.harvard.edu<mailto:freesurfer-bounces@nmr.mgh.harvard.edu> <freesurfer-bounces(a)nmr.mgh.harvard.edu><mailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Greve, Douglas N.,Ph.D. <DGREVE(a)mgh.harvard.edu><mailto:DGREVE@mgh.harvard.edu> Sent: Monday, December 2, 2019 2:56 PM To: freesurfer(a)nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu> <freesurfer(a)nmr.mgh.harvard.edu><mailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] Question on GLM - correlation oh, sorry, did not see the pvr. It could very well be the pvr that is causing the patchiness. Unfortunately, you have to debug it vertex by vertex. I would choose a few vertices (one with signal, on without) and run mri_glmfit with --voxdump vertexno 0 0 This will create a subfolder with the GLM for that vertex. I'm not sure what to tell you to look for, but I would at least check the condition numbers in each vertex. What is the nature of ficvf? On 12/2/2019 1:22 PM, Barletta, Valeria wrote: My other continuous variable is --pvr ${hemi}.ficvf.mgh Not sure about --no-prune, I found it in my script as a default... Shall I remove it? ________________________________ From: freesurfer-bounces(a)nmr.mgh.harvard.edu<mailto:freesurfer-bounces@nmr.mgh.harvard.edu> <freesurfer-bounces(a)nmr.mgh.harvard.edu><mailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Barletta, Valeria <VBARLETTA(a)mgh.harvard.edu><mailto:VBARLETTA@mgh.harvard.edu> Sent: Friday, November 29, 2019 3:08 PM To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu><mailto:freesurfer@nmr.mgh.harvard.edu> Subject: [Freesurfer] Question on GLM - correlation Dear Freesurfers, I am running glmfit to assess for correlation between y and another continue variable across the cortex (ficvf), correcting for the effect of age, using the command: mri_glmfit \ --y {surfname_cme}.mgh \ --fsgd {contrast}.fsgd \ --C {contrast}.mat \ --pvr ${hemi}.ficvf.mgh" \ --surf fsaverage $hemi \ --glmdir ${glm_dir}/${hemi}_contrast-${contrast}_${surfname_cme} \ --no-prune This is my matrix: 1 0 0 And my fsgd file: Title CME Class MS Variable age Input MS069_R01_01 MS 29 Input MS070_R01_02_R1year MS 44 Input MS072_R01_04 MS 38 Input MS073_R01_05 MS 47 Input MS075_R01_07_R1year MS 34 Input MS076_R01_08 MS 25 Input MS077_R01_09 MS 30 Input MS078_R01_10 MS 22 Input MS080_R01_12 MS 52 Input MS081_R01_13 MS 31 Input MS082_R01_14 MS 37 Input MS084_R01_16 MS 42 Input MS086_R01_18 MS 28 Input MS087_R01_19_R1year MS 39 Input MS088_R01_20 MS 44 Input MS089_R01_29 MS 44 Input MS090_R01_21 MS 32 Input MS091_R01_22 MS 32 Input MS092_R01_23 MS 36 Input MS094_R01_25 MS 47 Input MS104_R01_36 MS 52 This is the result: [cid:part5.EF2B16D0.6F355EBE@mgh.harvard.edu][cid:part6.DCB6E7A8.EAB1A47E@mgh.harvard.edu] Am I proceeding correctly? Thank you, Valeria _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

1 0

Plotting Longitudinal Data and Calculating Effect Sizes
by Hua, Jessica 03 Dec '19

03 Dec '19

External Email - Use Caution Hi FreeSurfer Experts, I used the longitudinal pipeline and analyzed my data using the univariate linear mixed effects models. I had a couple of questions: 1) The model outputted the F and p values. How do I calculate the effect size? 2) How do I plot my analyses? I would like to create a plot for change in CC volume with eBAC. Below is my model: Yij = ß1 + ß2(timeij) + ß3(eBACi) + ß4*estimated eBACi*timeij + ß5(genderi) ß6(intracranial volumei) + b1i + b2i(timeij) + eij. Thank you for your help! Jessica --- Jessica Hua, M.A. Cognitive and Emotional Control Lab Doctoral Candidate Clinical Psychology University of Missouri

2 1

2026

2025

2024

2023

2022

2021

2020

2019

2018

2017

2016

2015

2014

2013

2012

2011

2010

2009

2008

2007

2006

2005

2004

Freesurfer December 2019