Freesurfer June 2018

freesurfer@nmr.mgh.harvard.edu

105 participants
154 discussions

Fwd: Correcting defect issue
by Julian Macoveanu 07 Jun '18

07 Jun '18

External Email - Use Caution Hi all, I have a subject that is stuck here for days (fs60): CORRECTING DEFECT 8 (vertices=18549, convex hull=3089, v0=69938) XL defect detected... The inflated.nofix surface looks like attached. What can I do to make to analysis go through? This is my first analysis so please take it easy :) Best, Julian [image: Screenshot 2018-06-07 19.27.47.png]

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Postdoctoral fellowship: fMRI in OCD at Nathan Kline Institute
by ROBERT CARY WELSH 07 Jun '18

07 Jun '18

External Email - Use Caution Post-doctoral Fellowship in Neuroimaging in Obsessive-Compulsive and Related Disorders Psychiatric NeuroCognition Lab The Nathan S. Kline Institute for Psychiatric Research The Psychiatric NeuroCognition laboratory, under the direction of Dr. Emily Stern at the Nathan S. Kline Institute for Psychiatric Research, is seeking a post-doctoral fellow to work on projects investigating brain function and structure in obsessive-compulsive disorder (OCD) using task-based fMRI, resting-state functional connectivity, and diffusion imaging approaches. Broadly speaking, the lab’s work uses a cognitive neuroscience approach to investigating brain function in psychiatric disorders, with a focus on using fMRI to tap into core constructs relevant for OCD and related disorders including interoception, rumination, decision-making, and reward processing. The person in this position will primarily work on two ongoing NIMH funded projects using fMRI to investigate neural mechanisms of sensory and other key symptoms in OCD, including a clinical trial in OCD and Tourette’s Disorder testing the effects of a novel treatment on symptoms and brain function. In addition to working on these funded studies, there will also be opportunity for the fellow to develop new studies and/or analyses relevant to the lab’s work and to obtain pilot research funding offered through the institute. NKI is a research facility of the New York State Office of Mental Health, one of only two state-funded research institutes in the U.S. dedicated entirely to investigating biological mechanisms and treatments for psychiatric disorders. NKI was founded in 1952 by Dr. Nathan Kline, whose pioneering research into psychopharmacological management of schizophrenia and major depression revolutionized treatments for serious mental illness. The Psychiatric NeuroCognition lab is part of the Clinical Research Department at NKI, which contains several investigators, trainees, and staff working on studies examining treatments and biomarkers in a variety of disorders (depression, schizophrenia, autism spectrum disorder). Research facilities at NKI include a 3T Siemens MRI scanner for human neuroimaging, an MRI-compatible EEG system, and equipment for advanced neuromodulation techniques including transcranial magnetic stimulation and transcranial direct current stimulation. NKI also has an active animal research program with a 7T small animal scanner. For the past 30 years, NKI’s academic affiliate has been the New York University School of Medicine (NYUSoM) located in midtown Manhattan, and investigators and trainees at NKI have access to many of NYUSoM’s research tools and resources. Approximately 20 miles north of Manhattan, NKI is located in suburban Rockland County, home to many beautiful hiking and cycling trails overlooking the Hudson River. Although several towns in Rockland County are accessible to Manhattan via public transportation on New Jersey Transit, a driver’s license and access to a car is highly recommended for anyone considering this position. Interested candidates should meet the follow criteria: Required: • Ph.D. in experimental psychology, clinical psychology, or cognitive neuroscience • Moderate or better proficiency with functional MRI data analysis and presentation Other desirable qualifications: • Strong interest in psychiatric disorders and applying cognitive neuroscientific techniques to OCD and related disorders • Track record of publishing and presenting fMRI data • Experience with 2 or more standard fMRI packages for data processing (SPM, FSL, AFNI, Conn, Freesurfer, DPABI/DPARSF, C-PAC) and/or experience with both task-based and resting-state functional connectivity methods • Experience with task programing software such as EPrime, Presentation, or PsychoPy • Good knowledge of basic statistical concepts and approaches • Experience with (or desire to learn) basic programming in MATLAB, bash, and/or python • Knowledge or experience in psychiatric/psychological assessment and diagnosis would be a plus but is not required Duties of the position include: • Managing and analyzing task-activation and functional connectivity data, programming fMRI and behavioral experiments, running subjects through experimental protocols • Reading the literature and publishing behavioral and neuroimaging findings in top tier journals • Presenting results at conferences and seminars • Developing new studies or analyses relevant for the ongoing work in the lab and applying for pilot and post-doctoral grants to support this work • Assisting with grant applications, NIH progress reports, and IRB applications • Assisting in the training of junior lab members including research coordinators and interns Salary is competitive and commensurate with experience. Fellows would be employed by the Research Foundation for Mental Health (RFMH), which offers a full benefits package with medical and dental benefits. The position is for 1 year initially, with the opportunity to extend based on performance. Applications should be emailed to fmripostdocnki(a)gmail.com<mailto:fmripostdocnki@gmail.com> (‘fmri’ and ‘postdoc’ and ‘nki’) and include a cover letter, CV, and the names and contact information for two referees.

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connectivity between two ROIs
by Eryilmaz, H. Hamdi 07 Jun '18

07 Jun '18

Dear all, I would like to use the fsfast functional connectivity pipeline to compute connectivity between two binarized ROIs. One of the ROIs is a surface ROI, the other is a hippocampal subfield. Based on the tutorial on http://surfer.nmr.mgh.harvard.edu/fswiki/FsFastFunctionalConnectivityWalkth…, I created the time courses for the two ROIs. However, in order to regress out the signal from the ventricles, CSF, and white matter as well as the motion parameters, it seems that I need to run a whole-brain analysis (or at least one hemisphere). Is that correct? Would it be possible to compute connectivity just between two given ROIs without needing to run the analysis on the hemisphere? Thanks a lot! Best, Hamdi

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Python Developer Study
by Lussier,Desiree 07 Jun '18

07 Jun '18

External Email - Use Caution Dear Freesurfer community, We are currently interested in recruiting Python developers for a study. Information can be found below. Thank you, Désirée Lussier, MS Graduate Student Department of Psychology University of Florida [1509730522218_github]<https://github.com/dllussier> [1509730529145_linkedin-icon-14small.png] <https://www.linkedin.com/in/desiree-lussier/> [1509730538655_twitter-icon] <https://twitter.com/desiree_lussier> <http://www.psych.ufl.edu/ebnerlab/> <https://people.clas.ufl.edu/desireelussier/> [1509730546740_website] <https://people.clas.ufl.edu/desireelussier/> From: Oliveira,Daniela Sent: Thursday, June 7, 2018 12:25 PM To: Natalie Ebner; Myers,Elisha M Subject: Recruiting text (for email distribution) Subject: Recruiting Python Developers for User Study Hello All, Our lab at the University of Florida is recruiting Python developers for a research study on developer's perceptions while programming. Please help us advance Science! Compensation in US dollars (Amazon gift card): $50 for professionals working with software development and testing (employed) and $20 for senior undergrads and graduate students from Universities. Graduate students with internship experience in the industry can qualify for enrollment as professional developer. English fluency is required. Tasks: 1) Complete a multiple-choice survey about programming. 2) Complete a short questionnaire on personality and cognition. For more information and to enroll please contact: psy-ebnerlab(a)psych.ufl.edu This study has been funded by the National Science Foundation and is approved by the University of Florida Institutional Review Board (IRB). Please share our ad and/or tag someone you know will be interested! Thanks [cid:259d6abc-ad88-443e-a825-5705f49dc7db] :) _______________________________________________________________ Daniela Oliveira, PhD IoT Term Professor Associate Professor University of Florida Department of Electrical and Computer Engineering MAE 208 Gainesville, FL 32611 http://www.daniela.ece.ufl.edu/ 352.392.6618| daniela(a)ece.ufl.edu<mailto:daniela@ece.ufl.edu> Note: Under Florida Law, e-mail communications are public records. Therefore, you should have limited expectations of privacy. If you do not want your e-mail address or e-mail contents released in response to a public records request, please contact me so I can provide you with an alternate non-UF email address.

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E-TIV and Linux version: Some quick questions
by Jeff Crawford 07 Jun '18

07 Jun '18

External Email - Use Caution Dear Freesurfer Experts, I have two questions that I hope are easy to answer. 1. Would the calculation for E-TIV change if I edited the pial and reran recon-all as in this tutorial below? https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/PialEdits_freeview My understanding is that E-TIV should not change after minor edits to the pial segmentation, because the transform happens before these edits even happen. We start the at autorecon2-pial for the pial correction, which is after the Talairach transform computation. 2. I have two different windows computers with two VMware workstations running what I thought were the same versions of CentOS. They are both CentOS 6, but one is 6.5 and the other is 6.9. If both VMware workstations run the exact same versions of Freesurfer 6 (freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c), is it a problem if the CentOS versions are slightly different? I know the FS wiki says "it is essential to process all your subjects with the same version of FreeSurfer, on the same OS platform and vendor, and for safety, even the same version of the OS.", but would there be enough of a difference between CentOS 6.5 and 6.9 to cause major discrepancies in Freesurfer T1 processing? Thanks so much, Jeff

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poor anterior lobe surfaces
by Meaghan Perdue 07 Jun '18

07 Jun '18

External Email - Use Caution Hello Freesurfer experts, I have come across a problem with several subjects in which the pial surface fails to adequately capture the anterior temporal lobes. This occurs despite accurate brainmask and wm volumes. I have included a screen shot below, in this case, the wm surface is also affected, but this is not always the case. This is pediatric data that was acquired on a 1.5T scanner and processed in Freesurfer v 5.3. The following expert options have been employed to try to improve surface rendering: mris_make_surfaces -max_gray_at_csf_border 80 -max_csf 30 -min_gray_at_csf_border 35 Please let me know how I can solve this issue. As a second question, I've heard that segmentation and surface rendering is improved with v 6.0, and I'm wondering if subjects that have been initially run through v. 5.3 and had manual edits made can then have autorecon run through v 6.0 for improvement of surfaces? Please let me know if this would be a reliable/recommended approach to improving surfaces. Thank you, Meaghan Perdue -- Meaghan Perdue PhD Student Developmental Psychology Neurobiology of Language University of Connecticut Bousfield A302

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Matrix ill-conditioned
by Guillaume Bellanger 06 Jun '18

06 Jun '18

External Email - Use Caution Hello Freesurfer people, I am having an issue with my matrix using QDEC (ERROR: matrix is ill-conditioned or badly scaled, condno = 10880.8), I have 2 discrete variables (Sex, Cognition) and I want to regress against 2 continuous variable (Age, Education). My outcome: is there a relation between cortical thickness and Cognition (yes/no), accounting for Sex, Age and Education. I attached my FSGD file and matrix. Thanks a lot. Guillaume

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issue merging label files
by Nicholas Blauch 06 Jun '18

06 Jun '18

External Email - Use Caution Hello freesurfer experts, I wrote some matlab functions for merging surfaces, overlays, curvature, annotations, and curvature across hemispheres for easier viewing in Freeview and in preparation for multiple comparisons correction. It all works with the exception of merging the labels. It is odd, because out of 4 labels I've tried, 1 worked perfectly, and the others did not work at all. I cannot see any reasons why this would be the case. I wanted to see if anybody might have some insight as to what's going wrong. The function is below. x_shift is so that the hemispheres do not overlap (not sure why its necessary since when plotted separately the hemispheres do not overlap, but it is). I also attached two output merged label files, one working (mh.STS.label), and one not working (mh.FFA.label), along with a surface to view on (apologies if it is too big and doesn't send; it is just a merged partially inflated fsaverage with x_shift = 90 applied to right hemisphere). When the label function is fixed, I'd be happy to share the collection of functions with others who are interested. thanks for any help, Nick function merge_fs_hemi_labels( exp, subname, labname) %MERGE_FS_HEMI_LABELS( exp, subname, labname) % % merge freesurfer labels across hemispheres % requires freesurfer % % inputs: % % exp: experiment name under bids/ directory % subname: subject name % labname: base label name, e.g., 'OFA'. hemis will be preprended to this % using standard format, e.g. 'lh.OFA', 'rh.OFA', 'mh.OFA' % % x_shift = 90; bids_dir = get_bids_dir(exp); setenv('SUBJECTS_DIR',[bids_dir,'/derivatives/freesurfer']) fs_sub_dir = [bids_dir,'/derivatives/freesurfer/',subname]; surf_L = read_surf([fs_sub_dir,'/surf/lh.white']); n_nodes_L = length(surf_L); %check for which hemispheres label exists try lab_L = read_label(subname, ['lh.',labname]); use_L = 1; catch use_L = 0; end try lab_R = read_label(subname, ['rh.',labname]); use_R = 1; catch use_R = 0; end % determine how to create lab_M and do it if use_L && use_R lab_R(:,1) = lab_R(:,1) + n_nodes_L; lab_R(:,2) = lab_R(:,2) + x_shift; lab_M = [lab_L;lab_R]; elseif use_L && ~use_R lab_M = lab_L; elseif ~use_L && use_R lab_M = lab_R; lab_M(:,1) = lab_R(:,1) + n_nodes_L; lab_M(:,2) = lab_R(:,2) + x_shift; end %first two lines standard for FS label files line_1 = ['#!ascii label , from subject ',subname,' vox2ras=TkReg coords=white']; line_2 = num2str(length(lab_M)); %create file, write first two lines fname_M = [fs_sub_dir,'/label/mh.',labname,'.label']; if exist(fname_M) delete(fname_M) end fid = fopen(fname_M,'w'); fprintf(fid,'%s\n%s\n', line_1, line_2); fclose(fid); %write the tab delimited data dlmwrite(fname_M,lab_M,'-append','delimiter','\t','precision','%10.5f','newline','unix'); end

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Re: [Freesurfer] pcc.mgh file missing
by jahanvi patel 06 Jun '18

06 Jun '18

External Email - Use Caution Hello, thank you, we are using FS 5.3 virtual box, is there a version of 6.0 for the virtual box too? About the correlation, we meant to obtain the r-value (pearson correlation coef) from each significant cluster we got after running Monte Carlo simulation. So we didn't want to correlate only one cluster because we had correlate the whole brain thickness with the scores first, and we got the results from freesurfer, but it shows only the p-value, there was no r-value shown in the files. Hope it is correct to do in this way? Best, Jahanvi > Message: 2 > Date: Tue, 5 Jun 2018 12:55:23 -0400 > From: Douglas Greve <dgreve(a)mgh.harvard.edu> > Subject: Re: [Freesurfer] pcc.mgh file missing > To: <freesurfer(a)nmr.mgh.harvard.edu> > Message-ID: <4a311f78-3567-8817-f500-8bac737fa1af(a)mgh.harvard.edu> > Content-Type: text/plain; charset="utf-8" > Which version of FS are you using? I don't think it was in 5.3, so you > might have to use 6.0 version of mri_glmfit. Also, before you compute > and report the mean correlation inside of a significant cluster, you > might want to read this paper: > Puzzlingly High Correlations in fMRI Studies of Emotion, Personality, > and Social Cognition > https://www.google.com/url?sa=t&rct=j&q=&esrc=s&source=web& > cd=2&cad=rja&uact=8&ved=0ahUKEwj6wuqb_rzbAhVnslQKHa4tAAkQFggzMAE& > url=https%3A%2F%2Fwww.edvul.com%2Fpdf%2FVulHarrisWinkielmanPashler- > PPS-2009.pdf&usg=AOvVaw0C6XKQkj4hypGKRIaZFLc0 On 6/5/18 10:24 AM, jahanvi patel wrote: > > > Hello together, > > We used the following command to perform correlation analysis. But we > didn't obtain the "pcc.mgh" file which we want to extract the > correlation coefficient?from the significant cluster. > > Is there a command or way to generate the pcc.mgh file? > > Thank you in advance > > > > mri_glmfit \ > --glmdir GLM_dir_corr_behavior_lh_CT_tp1_tp2_plus_FFMQ_f1_f2 \ > --y lh.testretest_only_TP2.thickness-pc1.stack.fwhm15.mgh \ > --label lh.testretest.fsaverage.cortex.label \ > --fsgd GLM_dir_corr_behavior_lh_CT_tp1_tp2_plus_FFMQ_f1_f2/TP1_TP2.fsgd \ > --C > GLM_dir_corr_behavior_lh_CT_tp1_tp2_plus_FFMQ_f1_f2/contrasts/main.mtx \ > --C > GLM_dir_corr_behavior_lh_CT_tp1_tp2_plus_FFMQ_f1_f2/ contrasts/Delta_age.mtx > \ > --C > GLM_dir_corr_behavior_lh_CT_tp1_tp2_plus_FFMQ_f1_f2/ contrasts/Delta_CesD_score.mtx > \ > --C > GLM_dir_corr_behavior_lh_CT_tp1_tp2_plus_FFMQ_f1_f2/ contrasts/Delta_STATI_state.mtx > \ > --C > GLM_dir_corr_behavior_lh_CT_tp1_tp2_plus_FFMQ_f1_f2/ contrasts/Delta_STATI_trait.mtx > \ > --C > GLM_dir_corr_behavior_lh_CT_tp1_tp2_plus_FFMQ_f1_f2/ contrasts/Delta_total_medi_min.mtx > \ > --C > GLM_dir_corr_behavior_lh_CT_tp1_tp2_plus_FFMQ_f1_f2/ contrasts/Delta_FFMQ_f1.mtx > \ > --C > GLM_dir_corr_behavior_lh_CT_tp1_tp2_plus_FFMQ_f1_f2/ contrasts/Delta_FFMQ_f2.mtx > \ > --surf fsaverage lh > > > Best, > Jahanvi > > > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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Correction for multiple comparisons
by Yann Quidé 06 Jun '18

06 Jun '18

External Email - Use Caution Dear all, Using Freesurfer 5.3, I would like to limit my whole-brain analyses to a mask I already defined (ie, small volume correction-like analysis). To correct for multiple comparisons, I want to use the mri_glmfit-sim option. As I am looking within my own mask, I understand I need to run my own Monte-Carlo simulation. Would 10,000 permutations be sufficient? Also, I am a bit confused on what is best practice when setting the cluster forming threshold. Should I use the mc-z=3 (that is p=0.001) or mc-z=1.3 (that is p=0.05)? Here is an exemple of what I’m doing so far: mri_glmfit-sim \ --glmdir $STATS_DIR/lh.my_analysis.glmdir \ --sim mc-z 10000 3 mc-z.abs.3 \ --sim-sign abs Thanks for your time. Yann

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Freesurfer June 2018