Freesurfer February 2021

freesurfer@nmr.mgh.harvard.edu

98 participants
118 discussions

Re: [Freesurfer] Different results on same MRI in different space ?
by Funk, Quentin 12 Feb '21

12 Feb '21

External Email - Use Caution I used the SPM default coregistration settings -- which it calls "4th degree B-spline". From: "Douglas N. Greve" <dgreve(a)mgh.harvard.edu> Subject: Re: [Freesurfer] Different results on same MRI in different space ? To: <freesurfer(a)nmr.mgh.harvard.edu> Message-ID: <ebbb0121-2744-472e-a726-9578d4b5570b(a)mgh.harvard.edu> Content-Type: text/plain; charset="windows-1252" When you mapped to the new space, what kind of interpolation did you use? Houston Methodist. Leading Medicine. Houston Methodist is ranked by U.S. News & World Report as the No. 1 hospital in Texas for patient care and safety and one of the top 20 hospitals in the nation. In addition, we are nationally ranked in 11 specialties, the most in the state, and have been national leaders throughout the COVID-19 pandemic in research, offering innovative treatments and surpassing CDC safety standards. For more than 100 years, Houston Methodist has provided the best — and safest — clinical care, advanced technology and patient experience. That is our promise of leading medicine. houstonmethodist.org twitter.com/MethodistHosp facebook.com/HoustonMethodist ***CONFIDENTIALITY NOTICE*** This e-mail is the property of Houston Methodist and/or its relevant affiliates and may contain restricted and privileged material for the sole use of the intended recipient(s). Any review, use, distribution or disclosure by others is strictly prohibited. If you are not the intended recipient (or authorized to receive for the recipient), please contact the sender and delete all copies of the message. Thank you.

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cortical thickness values for each point in a ctx label file
by Krieger, Donald N. 12 Feb '21

12 Feb '21

External Email - Use Caution Dear freesurfer group, I wish to measure a cortical thickness value for each entry in a label file, e.g. SubNo/wmparc/ctx-lh-lateraloccipital_1011.label . Is there a function in the freesurfer distribution which includes this capability? Also, is there a function in the distribution that produces regional label files from the surf/[lr]h.pial files? Thanks - Don [cid:image003.jpg@01D70075.1EC687E0] Don Krieger, Ph.D. Research Scientist Department of Neurological Surgery University of Pittsburgh

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LME model
by Víctor Leiva 12 Feb '21

12 Feb '21

External Email - Use Caution Dear Freesurfer experts,I'm using the LME model for longitudinal study and I'm running the part of parameter estimation but MATLAB "told me" than the file "libgeodesic.so" is not available or does not exist. So check in FreeSurfer' folder and it's not there. So I don't know where to find it because I can't found it on the internet Thanks for your help Best, -- Víctor Leiva Ormeño

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fslregister - WARNING: possible left-right reversal (image-heavy e-mail)
by S.R. Poortman 12 Feb '21

12 Feb '21

External Email - Use Caution Dear sir/madam, When running fslregister as part of our data (pre)processing steps, it consistently outputs the following warning: [cid:c2cf64e3-2dc8-4cea-a89b-0bbff6f0119b] This the mri_info --orientation output: raw T1-weighted image: [cid:2d90ae0c-c61f-473c-b0f5-37211a901743] orig.mgz: [cid:6e8edb77-9aa2-4b11-8c61-34cfd759fde2] However, when I look at all the images, raw and processed, I see no discrepancies with respect to orientation. See the images below. For reference, encircled in red, is the vitamin pill we stuck to the right side of the participant's forehead. Apologies for the image-heavy e-mail. I want to be thorough in providing enough information. [cid:dfd9e777-ad5e-46a3-8096-1968257e6ca9] [cid:4f4f38b4-3353-4afc-ab02-af4effb80a67] [cid:909b14ff-eea8-4312-af13-fe370ed77c17] [cid:a6b00c8d-6e6d-441d-b672-6f634302cf63] [cid:52d8b847-f6b4-45b6-bb9e-fd1e954f66e6] [cid:bc692c0b-8622-447d-832b-7cad3e44c4e2] [cid:bb6248c0-55e3-405a-883d-07a3ef218b2f] [cid:6f190870-8379-4583-adaf-c8e019738b2a] Am I overlooking something, perhaps? Or does this warning also appear when nothing is wrong with the orientation(s) (the "possible" does seem to imply so)? Is there another way for me to make absolutely sure the orientations are correct and consistent? Thank you for considering my questions. Kind regards, Simon Poortman (Erasmus MC, Rotterdam)

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Call for submissions: Frontiers Research Topic on “Neuroinformatics of Large-Scale Brain Modelling”
by John Griffiths 11 Feb '21

11 Feb '21

External Email - Use Caution Dear all, We are excited to announce an upcoming Research Topic, jointly within Frontiers in Neuroinformatics and Frontiers in Computational Neuroscience, on “Neuroinformatics of Large-Scale Brain Modelling”. This Research Topic will document the various ways in which neuroinformatics approaches are being applied in large-scale brain modelling, informing readers on both established practices and emerging techniques. We seek Original Research, Review, Mini-Review, Hypothesis and Theory, Perspective, and Opinion articles that cover, but are not limited to, the following topics: - Ontologies, systems, and tools for definition and specification of large-scale neural models - New approaches to parameter optimization, parameter space exploration, and systematic tracking of simulation behaviour across parameter combinations - Informing neural models with genetic and multi-omic data from large-scale databases and individual patients/subjects - Systematic computational modelling studies on large numbers of subjects, and/or using large-scale open-access datasets (HCP, ABCD, etc.) - ‘Hybrid’ modelling schemes that combine mean-field with spiking network models - ‘Hybrid’ approaches to defining connectivity in large-scale brain models (e.g. supplementing tractography with microscopy data for higher-resolution subcortical connectivity structure) - Simulations using high-resolution neuroanatomical data from initiatives such as BigBrain, Allen Institute, etc. - ‘High-density’ (large number of regions; small parcels) connectome-based neural mass modelling - Other neuroinformatics challenges and solutions in large-scale brain simulations - Comparisons between detailed spiking/morphological simulations and neural mass model simulations - Comparisons between models based on high-resolution and low-resolution Allen atlas connectivities Full details can be found on the research topic webpage at: http://secure-web.cisco.com/1hZHhtpRj8gVeM6_xqJvzBhQrTxasC-rAndyi5BIYUI9fpW… If you are considering submitting, please submit an abstract by Fri 26 Feb 2021. Deadline for submission of full manuscripts is Fri 30th July 2021. We look forward to your hearing from you and sharing this exciting work with the community. Your Research Topic co-editors, John Griffiths Padraig Gleeson Kelly Shen -- Dr. John D. Griffiths Independent Scientist @ Krembil Centre for Neuroinformatics, CAMH, Toronto Assistant Professor @ Department of Psychiatry & Institute of Medical Sciences, University of Toronto http://secure-web.cisco.com/1pwPAJXsEnOnQ39gT0nUnGh5e4p1g6W7ky5JGDbxtq9fwTo… ~~~ Frontiers in Neuroinformatics & Frontiers in Computational Neuroscience joint Research Topic: “Neuroinformatics of Large-Scale Brain Modelling” *Eds. John Griffiths, Kelly Shen, Padraig Gleeson* *Now accepting submissions! * Abstract deadline 26 Feb 2021. Manuscript deadline 30 July 2021. See topic page here <https://secure-web.cisco.com/19SFFzRdJ8-1loA4fh3BCp7VXmgONFiJKfNWqjmJYsKgf2…> for more info

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Different results on same MRI in different space ?
by Funk, Quentin 11 Feb '21

11 Feb '21

External Email - Use Caution Freesurfer experts, I have two MRIs for a patient separated by 5 years. I would like to look at progression of atrophy. These MRIs are different, however, firstly in terms of resolution (new one is 1x1x1, old one is 1.05x1.05x1.2), and secondly just in terms of general contrast, as they are different protocols from different scanners. First I ran Freesurfer 6.0.0 on both MRIs; but the results I obtained didn't make much sense -- when I compared to a group of controls, the thickness values were much lower in the old MRI than in the new one. This could, of course, be due to variance in contrast / type of scanner, etc. Reviewing the surfaces, in both cases (old and new), all surfaces looked very good with no major errors. I wanted to see how well the surfaces lined up over time -- so I wanted them in the same space. To get this, I co-registered the new MRI to the old one (via SPM), and re-ran recon-all on it. Now, when I compare to a group of controls, the new MRI has much more expected results -- e.g. lower thickness than the old one. Again, surfaces looked very good. All that changed is the space the MRI was in when I fed it into FS -- some slight variance from voxel resolutions aside, this gave very different results. I looked at the lh.aparc.stats files and computed some percent differences and was pretty surprised by what I saw. For example, GrayVol values were different by 20% in the precentral, thickaverage was off by 17% in the precuneus. obviously I made an error somewhere that caused this type of variance but I can't find it -- is there any advice for comparing this type of longitudinal data ? thank you for any help you can provide! Quentin Funk, PhD Houston Methodist Research Institute 713-363-9003<tel:713-363-9003> Houston Methodist. Leading Medicine. Houston Methodist is ranked by U.S. News & World Report as the No. 1 hospital in Texas for patient care and safety and one of the top 20 hospitals in the nation. In addition, we are nationally ranked in 11 specialties, the most in the state, and have been national leaders throughout the COVID-19 pandemic in research, offering innovative treatments and surpassing CDC safety standards. For more than 100 years, Houston Methodist has provided the best — and safest — clinical care, advanced technology and patient experience. That is our promise of leading medicine. houstonmethodist.org twitter.com/MethodistHosp facebook.com/HoustonMethodist ***CONFIDENTIALITY NOTICE*** This e-mail is the property of Houston Methodist and/or its relevant affiliates and may contain restricted and privileged material for the sole use of the intended recipient(s). Any review, use, distribution or disclosure by others is strictly prohibited. If you are not the intended recipient (or authorized to receive for the recipient), please contact the sender and delete all copies of the message. Thank you.

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Installing anither Freesurfer version - lincese not working
by Fernanda Hansen P. de Moraes 11 Feb '21

11 Feb '21

External Email - Use Caution Dear Freesurfer experts, I installed another Freesurfer version on my computer and used the same license of the version installed before. But, it is not working. How should I proceed? Best regards, Fernanda Hansen P. de Moraes fernandahmoraes(a)gmail.com Doutoranda em Ciências Médicas | Instituto D'Or de Pesquisa e Ensino (IDOR), Rio de Janeiro, Brazil

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Compute geometric mean of 32 b1000 images (DTI)
by Mateus Aranha 11 Feb '21

11 Feb '21

External Email - Use Caution Dear all, I have 32 directions DTI images and I need to compute DWI and ADC maps from these images. As far as I know the DWI is obtained by calculating the geometric mean of the 32 b1000 images. Can it be done with mri_concat --gmean Ng? Many thanks, Mateus

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For multiple comparisons
by Kim, Gwang-Won 11 Feb '21

11 Feb '21

Hi there, First, I ran "mri_glmfit" using a mask (subcortical regions) as follows: mri_glmfit --glmdir g1v1.wls --y ces.nii.gz --wis cesvar.nii.gz --fsgd g1v1.fsgd --C age.mtx --mask brain.mni305.2mm.nii.gz --fwhm 5. Second, I'm going to process "mri_glmfit-sim" to perform a cluster-wise correction for multiple comparisons. Which I select the comment? 1) mri_glmfit-sim -glmdir g1v1.wis -3spaces -grf 2 abs 2) mri_glmfit-sim -glmdir g1v1.wis -perm 1000 2.0 abs -cwp 0.05 -3spaces -bg 16 Especially, I use the mask the subcortical regions, not cortical regions. Should I remove “-3spaces” in the commend or what do I do instead of “-3spaces”? Thank you, Gwang-Won

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Recon error
by Bohorquez Montoya, Luisa 11 Feb '21

11 Feb '21

External Email - Use Caution Hello Freesurfer I have been trying to run this subject 3 times (with different walltime) and I am having the same error. Would you mind please to explain me what I am doing wrong? Thank you subject="$1" echo $subject cd /scratch/global/lbohorquez/Freesurfer/"$subject" export SUBJECTS_DIR=/scratch/global/lbohorquez/Freesurfer/"$subject" ANATDIR=/scratch/global/lbohorquez/Freesurfer/ OPENMP=12 export OMP_NUM_THREADS=12 recon-all \ -autorecon2 -autorecon3 -subject "$subject" \ -no-isrunning -parallel -openmp 12 \ ####SUMA-ize with AFNI echo "Before Suma" @SUMA_Make_Spec_FS -NIFTI \ -fspath ${SUBJECTS_DIR}/"$subject" \ -sid "$subject" echo "After Suma" ######## registration TO MNI cd ${SUBJECTS_DIR}/"$subject"/SUMA/ @SSwarper -input "$subject"_SurfVol.nii -base MNI152_2009_template_SSW.nii.gz -subid ssWarp Luisa Bohorquez, PhD. Department of Psychiatry, Medical College of Wisconsin.

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Freesurfer February 2021