Freesurfer April 2018

freesurfer@nmr.mgh.harvard.edu

118 participants
177 discussions

freeview problem on Linux RHEL 7-4 libGLU.so.1
by Avner Meoded 01 Oct '18

01 Oct '18

Hello all, I installed the latest version for Linux I get this message when trying to run an example: "freeview.bin: error while loading shared libraries: libGLU.so.1: cannot open shared object file: No such file or directory" I installed the missing library and now it is in /usr/local/fsl/bin/FSLeyes/libGLU.so.1 any idea ho to solve this problem Thanks avner

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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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-qcache in recon-all commnd
by Alexopoulos, Dimitrios 07 Jun '18

07 Jun '18

Is it recommended to use the -qcache flag in the basic recon-all -all command? What does it do and what are the advantage of using it? 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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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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Re: [Freesurfer] FSGD design for multi-centre study
by C.P.E. Rollins 01 Jun '18

01 Jun '18

External Email - Use Caution I thought that I could not remove the class since this would mean that the contrast positive and negative values would no longer add up to 0. For instance if I remove only class "patient_centre2_female", then my contrast would have 11 (-1) and 12 (1) as opposed to 12 and 12. Could you please clarify? Thanks again, Colleen -------- Original Message -------- Subject: Re: [Freesurfer] FSGD design for multi-centre study Date: 2018-04-20 11:19 From: "C.P.E. Rollins" <cper2(a)cam.ac.uk> To: Freesurfer <freesurfer(a)nmr.mgh.harvard.edu> Thanks a lot for the explanation. The issue is that I don't think Freesurfer will run a design for which there are no subjects for a given class. So if I keep the classes (24 classes since 6 centres x 2 gender x 2 groups (patient vs. control), and have the contrast with 12 (-1) and 12 (1), -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 1 1 1 1 1 1 1 1 1 1 1 1 0 I get the error: -------------------------------- ERROR: matrix is ill-conditioned or badly scaled, condno = 1e+08 -------------------------------- Possible problem with experimental design: Check for duplicate entries and/or lack of range of continuous variables within a class. I'm assuming this is because there are no participants in, for example, patient_centre2_female Is there any way to get around this issue, or should I remove those centres from my analysis (since I can't only remove "patient_centre2_female", as this would make the contrast unbalanced (positives and negatives would not add to the same number). I hope this was clear but please let me know if it was not. Thanks again, Colleen

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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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Freesurfer April 2018