Freesurfer

freesurfer@nmr.mgh.harvard.edu

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30076 discussions

hippocampal subfield question
by Maksimovskiy, Arkadiy 29 Nov '18

29 Nov '18

Dear Experts, I was wondering if it is important to wait for the manual edits to be done on a dataset before running hippocampal subfield analyses. I believe that recon-all processing is sufficient, and edits can be done in parallel. But wanted to make sure that they will not affect the nuclei/subfield segmentation. Thank you for your help, Arkadiy -- Arkadiy L. Maksimovskiy, Ph.D. Postdoctoral Research Fellow McLean Imaging Center, McLean Hospital Department of Psychiatry, Harvard Medical School

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Pial surface error
by Miguel Ángel Rivas Fernández 29 Nov '18

29 Nov '18

External Email - Use Caution Hi Freesurfer devs, I´m doing a visual quality control of my pial and white matter segmentation using freeview and I noticed that several subjects could present an error in pial surface segmentation. I have attached two images. Is this an pial surface error? in that case, How can I fix it? maybe adding control points in order to extend the pial surface limit? Thanks Cheers, -- *Miguel Ángel Rivas Fernández*

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Neuroimaging staff scientist position
by bryon mueller 29 Nov '18

29 Nov '18

External Email - Use Caution The Department of Psychiatry at the University of Minnesota is seeking an experienced MR Neuroimaging Analyst to join our Discovery Program initiative. The successful candidate will join a team that will use MR brain imaging and other methods to advance the understanding of and improve treatment in mental health conditions such as psychosis, depression, and addiction. The Neuroimaging Analyst will be involved in all aspects of neuroimage, including collection of MRI data, assembly of comparison MRI data, development of computer modeling, creation of processing workflows and development of statistical analysis and report generation that produces quantitative metrics from computational models of the brain. Required Qualifications Include: • BA/BS plus at least 4 years of experience or advanced degree plus 2 years of experience. Will also accept a combination of related education and work experience to equal 8 years. • Demonstrated/documented excellent analytical and statistical skills • Ability and willingness to work safely within the MR environment • Experience with scientific neuroimaging data processing using standard packages (HCP, FSL, AFNI, etc) • Proficiency in at least one programming language (Python, MATLAB, Java, C++, etc) • Proficiency with the Linux operating system See https://hr.myu.umn.edu/jobs/ext/327198 for additional details on the position.

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lack of convergence when analyzing tbss-data with FreeSurfer's lme code
by Knut J Bjuland 29 Nov '18

29 Nov '18

External Email - Use Caution Dear Freesurfer Experts I used the FreeSurfer univariate lme_fit_FS.m on longitudinal DTI data (FA) from tbss, converted from the skeleton to a matlab matrix so as to be able to use the FreeSurfer lme code. However, the model fit converges in only 20 % of the cases, which is too low for me to be able to use these data. I would appreciate any suggestion as to how I can rectify this situation. How do I troubleshoot this in order to increase the convergence? Can I adjust the convergence epsilon (gradient's norm) in order to increase the number of iterations, is that possible and would that help? Best regards Knut J Bjuland PhD

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Volume, area and thickness external analysis
by Miguel Ángel Rivas Fernández 28 Nov '18

28 Nov '18

External Email - Use Caution Hi FreeSurfer devs, Is there any difference bet I ran the recon-all several participants (using the command recon-all -subjid -all) and I want to out an external analysis using the volume, area and thickness measures of the Destrieux and Desikan-Killiany atlas. *Do these measures suffer any change if I add the qcache flag to the command* (i.e recon-all -subjid -all -qcache) or by contrary this flag is only necessary when the analysis is made using QDEC? I have this doubt because I saw that when I used the -qcache flag, Freesurfer make a smoothing of the images using a FWHM filter of 5,10,12. Thanks in advance, Cheers, -- *Miguel Ángel Rivas Fernández*

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[PETSurfer] MGX and RBV Correction
by Matthieu Vanhoutte 28 Nov '18

28 Nov '18

External Email - Use Caution Dear Freesurfer's experts, I tried to use PETSurfer to correct partial volume effect on my FDG PET images, testing both Muller-Gartner and RBV corrections. I ran the commands specified in PETSurfer website and used the two following commands for both MGX and RBV corrections respectively: mri_gtmpvc --i PET.nii.gz --reg register.dof6.lta --psf-col 5.51 --psf-row 5.51 --psf-slice 5.9 --seg gtmseg.mgz --default-seg-merge --auto-mask PSF .01 --mgx .01 --o ./gtmpvc.output mri_gtmpvc --i PET.nii.gz --reg register.dof6.lta --psf-col 5.51 --psf-row 5.51 --psf-slice 5.9 --seg gtmseg.mgz --default-seg-merge --auto-mask PSF .01 --rbv --o rbv.output.orig 1) However, I found that cortical output mgx.ctxgm.nii.gz of MGX correction encompass more than just GM and values at the boundaries of mgx.ctxgm.nii.gz seem to me very high or aberrant. 2) Concerning RBV correction, output rbv.nii.gz seems to me following more precisely the GM ribbon. However contrary to what is said in PETSurfer website, rbv.nii.gz seems to be in the anatomical space (not in native PET) at the resolution of gtmseg.mgz. How then map rbv.nii.gz to the anatomical space when mapping the volume to the surface ? 3) What are the advantages/inconveniences of RBV vs GMX ? 4) Would it be beneficial to upsample native PET to the anatomical resolution before launching gtmpvc in order to preserve the high resolution of the anatomical tissues during partial volume correction ? Thank you. Best, Matthieu

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Freesurfer tutorial datasets v5.1/5.3
by Amy Barzgari 28 Nov '18

28 Nov '18

External Email - Use Caution Hello FreeSurfer Experts, I'm following the longitudinal FreeSurfer tutorial using v5.1 to become acquainted with stream prior to analyzing our own data. I was able to follow the QDEC tutorial using this version on the Buckner data, however, I kept getting error messages in the QDEC when using the longitudinal data. I created the cross-sectional .dat file using: long_qdec_table --qdec ./qdec/long.qdec.table.dat --cross --out ./qdec/cross.qdec.table.dat The longitudinal measures (i.e. long.thickness-avg) did not appear in the QDEC, and I've tried to look at thickness alone, and got an error message after hitting 'Analyze'. I assumed these issues were arising due to the fact I downloaded the tutorial dataset for v6, when FreeSurfer v5.1 was installed. I then tried to download the datasets for versions 5.1/5.3, but the files seem to be missing. Can these links be updated? (https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Data#FreeSurferTutoria…) Thank you, Amy

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average of surfaces
by john Anderson 28 Nov '18

28 Nov '18

External Email - Use Caution Dear Freesurfer experts, I have multiple PET volumetric images in MNI standard space. I can average (or get the Tmean) of these images using fslmerge then fslmaths. I would like to do something similar on surfaces images. I registered the images from native space to Freesurfer space using spmregister as follows: spmregister ---s $subject -mov PET.nii.gz --reg reg.dat --o PET_T1.mgh Then I used mris_preproc with the flag --mean to register the volumetric images to fsaverage, then concatenate the surfaces and average it as follows: mris_preproc --target fsaverage --hemi lh --projfrac 0.5 --iv PET_T1_subj1 reg_subj1.dat --iv PET_T1_subj2 reg_subj2.dat . ...... .--iv PET_T1_subjN reg_subjN.dat --mean --o lh.mgh the final output "lh.mgh" is an empty image. I am not sure what I am doing wrong here. Any guidance to average the surfaces images in fsaverage would be highly appreciated. john

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GM and WM intensity thresholds (Manual Edits)
by David S Lee 27 Nov '18

27 Nov '18

External Email - Use Caution Hello FreeSurfer Experts! I currently supply inhomogeneity-corrected (via N4 biascorrection) 3T T1w scans through recon-all pipeline. The correction has solved many segmentation errors which reduced the time spent on manual editing. I have several questions related to this: 1. I am aware of the "3T" flag that can be supplied to recon-all command. It seems redundant to use this flag for already-bias-corrected 3T scans (testing from my end also confirms this), but do you recommend any other bias-correction steps? 2. What are the minimum and maximum intensity thresholds set for GM and WM during recon-all? In the official control point tutorial <https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/ControlPointsV6.0>, it suggests that WM should be "close" to intensity of 110, but I wanted to know the exact thresholds to perform more accurate manual editing. 3. If these GM and WM intensity parameters can be changed from default, do you recommend doing so? If there is a documentation I can refer to find answers (I've failed to find one so far), please let me know. Thank you for your time as always, -- David S. Lee Research Specialist Center for Healthy Minds University of Wisconsin - Madison (608) 890-1115

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re-run fsaverage only
by Ryan Wales 27 Nov '18

27 Nov '18

External Email - Use Caution Hello, I accidentally renamed my fsaverage directory when I was renaming my subjects' directories. Since I was still in the process of running subjects, a new fsaverage directory was automatically created. Now I have two fsaverage directories that each have a different subset of my participants, but I'd like there to be one directory that has all my participants. Is there any command that I could run that would generate a new fsaverage from subjects in the same output directory? Thanks, Ryan Wales -- Ryan Wales Graduate Student Cognition and Motor Control Neuroscience Laboratory Integrative Neuroscience Psychology Department Stony Brook University E-mail: ryan.wales(a)stonybrook.edu <ryanwales(a)stonybrook.edu>

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