Freesurfer April 2019

freesurfer@nmr.mgh.harvard.edu

99 participants
136 discussions

correlation analysis
by TMS lab 10 Apr '19

10 Apr '19

External Email - Use Caution Dear Freesurfer team, I'm running a correlation analysis where I'd like to corelate myelination and a clinical parameter (NHPT) regressing out the effect of age. My contrast.mtx: 0 0 0.5 0.5 This is my FSGD FILE: GroupDescriptorFile 1 Title Myelin Class Main Variables Age NHPT Input fs_CGa Main 19 18.2 ....... Is the matrix ok? Thanks Rafael

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The mystery of the missing mcprextreg file
by Mcnorgan, Christopher 10 Apr '19

10 Apr '19

External Email - Use Caution Hello, I’ve been trying to get to the bottom of why selxavg3-sess is failing for lack of a mcprextreg motion correction parameters file for one or more of the functional runs. I have 6 runs of BOLD data, and following the last failed attempt, we cleared out the run folders to start again from scratch with preprocess on the f.nii volumes. We are running preproc-sess on a per-run basis: preproc-sess -s SUBJECTNAME -per-run -surface fsaverage lhrh -mni305 -fsd bold -fwhm 4 -sliceorder up After doing this, we find that the folders for runs 1,2,3,4 and 6 contain the file mcprextreg, but run 5 does not. Consequently, selxavg3-sess throws an error and aborts when it fails to find this file for run 5. Prior to our do-over, we had the same issue, so it appears that this file is reliably not being generated only for run 5. To further the mystery, a second dataset (different participant) was recently preprocessed and also is missing this file for runs 1 and 5. I notice that the runs with the missing motion correction parameter each contain a tmpdir.mcdat2extreg.##### folder, which suggests that the process might have not completed, though it’s odd that it would have completed for runs 1-4 and 6, but not 5. I was hoping someone might have some suggestions for debugging why this file might not be getting generated, as well as what steps might be taken to force its creation. I’m going to start by deleting the tmpdir folders. Thanks, Chris /********************************************** * Chris McNorgan * Assistant Professor * Department of Psychology * University at Buffalo, * The State University of New York * http://ccnlab.buffalo.edu/ * Office: 716.645.0236 * Lab: 716.645.0222 **********************************************/

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web page library to show freesurfer data (mesh and axial, coronal, sagital slices)
by Gonzalo Rojas Costa 10 Apr '19

10 Apr '19

External Email - Use Caution Hi: Do you know any library to show freesurfer data (mesh and axial, coronal, sagittal slices) embedded a web page? Sincerely, Gonzalo Rojas Costa

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regions of Yeo 17 networks in fast
by stdp82＠virgilio.it 10 Apr '19

10 Apr '19

External Email - Use Caution Hi list, I'd like to use the regions included in Yeo 17 networks (https://github.com/ThomasYeoLab/CBIG/tree/master/stable_projects/brain_parc…) in FS-FAST. Which is the command line to be used to create a segmentation in $SUBJECTS_DIR/$subject/mri in the same format as aseg.mgz? (I'd like to use it to run fcseed-config, specify -seg yourseg.mgz -segid). Thanks Stefano

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Image Analyst Position at the Yale Alzheimer's Disease Research Unit
by Adam Mecca 10 Apr '19

10 Apr '19

External Email - Use Caution The Yale University Alzheimer’s Disease Research Unit at Yale University School of Medicine has an opening for a highly qualified and motivated individual to work on research involving the development of analysis techniques integrating human imaging data including PET and fMRI for NIH-funded studies and clinical trials in Alzheimer’s disease. Applicants must have obtained a Master’s Degree or a Bachelor’s Degree with significant experience in neuroimaging analysis. Qualifications: Strong analytical, and programming skills are essential. Experience in fMRI, image analysis, algorithm development, and biological applications is highly desirable. The selected candidate will work under the direction of Drs. Christopher van Dyck and Adam Mecca. The successful candidate should have a Master’s Degree or a Bachelor’s Degree with at least three years of experience in fMRI and/or PET imaging. Application Instructions: Interested individuals should email a CV to adam.mecca(a)yale.edu. Adam Mecca, M.D. Ph.D. Yale School of Medicine, Department of Psychiatry Geriatric Psychiatry and the Alzheimer's Disease Research Unit Tel: (203) 764-8100 Fax: (203) 764-8111

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freesurfer longitudinal issue
by maxime GUILLAUME 10 Apr '19

10 Apr '19

External Email - Use Caution Dear freesurfer experts, I am performing a longitudinal study (2 time points, 1 year apart) in patients with Multiple Sclerosis using freesurfer 6.0. After following the tutorial for the CROSS, the BASE (where I only performed few manual edits of the surfaces) and the LONG steps, I am facing a problem with the results of the longitudinal pipeline: If I overlay the final surfaces of the different time points (the white and pial surfaces of the LONG step) on the BASE template, there are major differences between the two time points (see figure attached). This happened only on a subset of my subjects. One of our collaborators in this study suggested that this might be because the patient was positioned differently in the two time points, in particular with respect to the z axis (and indeed the major differences between the two surfaces are in the topmost area of the brain). Does anybody have experienced the same problem? And how can I correct for it? Thank you in advance for your help. (*in the capture surfaces of the first visit are in yellow and in green for the second visit)

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Creating anatomical ROI's
by Daniel Callow 09 Apr '19

09 Apr '19

External Email - Use Caution Hello, I am trying to create ROI volumes from the hippocampal subfields I get from mri_vol2vol --mov /Volumes/DANIEL/dti_freesurf/dtrecon/${cond}.${subj}/lowb.nii.gz --targ /Volumes/DANIEL/dti_freesurf/diffusion_recons/${subj}.${cond}/mri/lh.hippoAmygLabels-T1.long.v21.HBT.FSvoxelSpace.mgz --inv --interp nearest --o /Volumes/DANIEL/dti_freesurf/dtrecon/${cond}.${subj}/lhipp2diff.nii.gz --reg /Volumes/DANIEL/dti_freesurf/dtrecon/${cond}.${subj}/register.dat --no-save-reg so that I can merge specific hippocampal subfields I want together into a single ROI (like --id 231 and --id 232). However, when looking through the freesurfer options like mri_vol2vol there isn't an option to index to specific segments of the lh.hippoAmygLabels-T1.long.v21.HBT.FSvoxelSpace.mgz volume I have converted into dti space. My plan is to combine the head and body segments and extract average diffusion information from the combined mask. Anything that can help get me in the right direction would be greatly appreciated! *Daniel Callow* *PhD Student, Neuroscience and Cognitive Science* Exercise for Brain Health Lab University of Maryland, College Park *ddcc2442(a)gmail.com <ddcc2442(a)gmail.com>* 443-254-6298

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Post-doctoral Research Position at the Yale Alzheimer's Disease Research Unit
by Adam Mecca 09 Apr '19

09 Apr '19

External Email - Use Caution The Yale University Alzheimer’s Disease Research Unit and the Yale PET Center has an opening for a highly qualified and motivated individual at the post-doctoral level to work on research involving the development of analysis techniques integrating human imaging data including PET and fMRI for NIH-funded studies and clinical trials in Alzheimer’s disease. Applicants must have obtained a Ph.D. in neuroscience, biomedical engineering, or a related field. Qualifications: Strong experimental, analytical, and programming skills are essential. Experience in fMRI, image analysis, algorithm development, and biological applications is highly desirable. The selected candidate will work under the direction of Drs. Christopher van Dyck and Adam Mecca. The successful candidate should have a Ph.D. or an M.D./Ph.D. with at least three years of experience in fMRI and/or PET imaging. Application Instructions: Interested individuals should email a CV to adam.mecca(a)yale.edu. Adam Mecca, M.D. Ph.D. Yale School of Medicine, Department of Psychiatry Geriatric Psychiatry and the Alzheimer's Disease Research Unit Tel: (203) 764-8100 Fax: (203) 764-8111

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Paired Analysis Questions
by brain health 09 Apr '19

09 Apr '19

External Email - Use Caution Dear Dr. Greve: Thank you so much for your time and help. I am working on the Paired Analysis that you suggested. Very appreciated! I am interested if there are different within-group changes in brain structure for an Intervention (PA) and Control (C) group. Does the paired-diff.fsgd file (peek below) look correct? PAC Groups Class Main Variables Group Input sub107 Main PA Input sub112 Main PA Input sub113 Main C Input sub118 Main PA Input sub131 Main C Input sub132 Main C Input sub136 Main C What would be the contrast of interest to include for my question? Just want to make sure I am running the correct model. I am also reading the guide about how to interpret the results of the mri_glmfit commands (e.g., https://surfer.nmr.mgh.harvard.edu/fswiki/mri_glmfit) Is there another guide to follow regarding the output of the Paired Analysis? I appreciate your guidance!

2 1

Problem with calculating significant clusters' values
by Georgina Angelopoulou 09 Apr '19

09 Apr '19

External Email - Use Caution Hello FreeSurfer Developers, I have compared two groups in area, volume and thickness (using mri_glmfit and mri_glmfit-sim) and I want to extract the total value from each significant cluster so that I can run analysis with behavioural variables in SPSS. I have found some previous posts with the following command: mri_segstats --i <pathway to rh.volume.Study.10.mgh> --seg cache.th13.abs.sig.ocn.mgh --excludeid 0 --sumwf ClusterVolumeValues.dat –accumulate. but also the alternative option in --seg cache.th13.abs.y.ocn.dat. Could you please tell me: 1. Which is the correct option for -- seg and what is their difference? 2. I tried to run both option and I get the exact same error: mri_read(): couldn't determine type of file lh.SexStudy_area.glmdir/MN-FM/cache.th13.abs.y.ocn.dat ERROR: loading lh.SexStudy_area.glmdir/MN-FM/cache.th13.abs.y.ocn.dat Any ideas of how to resolve that? 3. Is that command the right one for volume, area and thickness? Thank you in advance, Best, Georgina

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Freesurfer April 2019