Freesurfer

freesurfer@nmr.mgh.harvard.edu

16 participants
30084 discussions

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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Re: [Freesurfer] Missed Module nibabel Python -- Re: Form submission from: Infant Freesurfer Download Request
by Zollei, Lilla,Ph.D. 11 Feb '21

11 Feb '21

Hi Sair, Just to make sure, could you run? fspython -m pip install nibabel Otherwise you can re-install the distribution as we have update the latest one with the missing nibabel package. Best, Lilla ________________________________ From: Carlos Sair Flores Bautista <sairfb(a)inb.unam.mx> Sent: Wednesday, February 10, 2021 8:52 PM To: Zollei, Lilla,Ph.D. <LZOLLEI(a)mgh.harvard.edu> Cc: freesurfer(a)nmr.mgh.harvard.edu <freesurfer(a)nmr.mgh.harvard.edu> Subject: Missed Module nibabel Python -- Re: Form submission from: Infant Freesurfer Download Request External Email - Use Caution Hello Freesurfer Team My Name is Sair, i have been trying to run a test subject on last dev version of freesurfer infant pipeline, however when i try to run this subject i receive the next error from infant recon all process: Reslicing using trilinear interpolation writing to /home/lain/Documents/PruebasFsInfant/test/work/mprage.nu.conf.nii.gz... CONFORMED FILE /home/lain/Documents/PruebasFsInfant/test/work/mprage.nu.conf.nii.gz Traceback (most recent call last): File "/usr/local/freesurferinfant/python/scripts/sscnn_skullstrip", line 5, in <module> import nibabel as nib ModuleNotFoundError: No module named 'nibabel' it suppose the last freesurfer infant dev version contains python 3.6 however i have made sure to check the availability of this module on the installed python version however this still happens every time, also i have made the same test on different server and pc getting the same error. i have tested it on debian and ubuntu I have attached to this mail the complete stream from my infant recon all test in order to analyze and help to receive support from your side. thanks in advance. Best regards Sair. L.C.E. Carlos Sair Flores Bautista Secretario Tecnico INB-UNAM El mié, 13 de ene. de 2021 a la(s) 15:24, Zollei, Lilla,Ph.D. (LZOLLEI(a)mgh.harvard.edu<mailto:LZOLLEI@mgh.harvard.edu>) escribió: Thank you for your interest in the infantFreesurfer pipeline. The version below is our new beta distribution (Jan 2021). Please, continue giving me feedback and asking a lot of questions along the way so that we can improve upon the user-friendliness of its use. After downloading the package, you should run the below four commands: source YOUR_FREESURFER_ENVIRONMENT setenv SUBJECTS_DIR your_data_path or export SUBJECTS_DIR=your_data_path infant_recon_all --s SUBJ --age age_in_months SUBJ is the subjectID of the subjects's whose data you are processing. The script will expect the input file to be located at $SUBJECTS_DIR/$subj/mprage.nii.gz or $SUBJECTS_DIR/ $subj/mprage.mgz by default. Unless otherwise specified, the output of this process will be saved to $SUBJECTS_DIR/$SUBJ using a FreeSurfer type directory structure. If the --masked flag is used, we recommend also running intensity normalization, for example by using: mri_nu_correct.mni --i $infile --o $nufile --n 2 Note, you can use both tcsh and bash for this distribution. Before execution, you will also need install FSL [https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/FslInstallation<https://secure-web.cisco.com/1cGp1eiz_7sOm02QhOvn3jmhR4tJTNPCAhjpNXJy9K5rBP…>]. Note, we have changed our default nonlinear registration tool. We rely on niftyreg which ships directly with this release. If you would like to use DRAMMS you will need to install it separately and use the corresponding flag. Other useful flags: --outdir (redirecting output) --kneigh (number of training examples to use) See infant_recon_all --help for more information or visit https://surfer.nmr.mgh.harvard.edu/fswiki/infantFS<https://secure-web.cisco.com/1SO4Xs7x3V6qnRb_RWiJBY343GLDSD6_eDDvRSlrhuC-wT…> * Skullstripping The current release ships with our new skullstripping tool so you will not need to skullstrip your data before running infantFS. Note, the new tool requires about 23GB of memory! At present, the error messages related to lack of sufficient memory are pretty vague, so please, check whether you have enough if you rely on this tool. Also "Your CPU supports instructions that this TensorFlow binary was not compiled to use" is just a warning not an error. It indicates that the process could be faster if you built with a more modern tensorflow, but the computations should be working even with this version. * Citation: Cite the below papers if you use our work and publish yourself: Zöllei, L, Iglesias, JE, Ou, Y, Grant, PR, Fischl,B. Infant FreeSurfer: An automated segmentation and surface extraction pipeline for T1-weighted neuroimaging data of infants 0-2 years, NeuroImage, Volume 218, September 2020, 116946 https://doi.org/10.1016/j.neuroimage.2020.116946<https://secure-web.cisco.com/1QyTKPVjpukeljrh0n5fRo7K-S_AxdepVjCQ_yydZp7OgY…>. (http://www.sciencedirect.com/science/article/pii/S1053811920304328<http://secure-web.cisco.com/124O1IxeSlJOGHpA_Mg0Tx1tyLZSHjY4vKxlkhb2cRAzqZw…>) de Macedo Rodrigues, K., et al., A FreeSurfer-compliant consistent manual segmentation of infant brains spanning the 0–2 year age range. Front. Hum. Neurosci., 2015. 9(21). * Download: https://surfer.nmr.mgh.harvard.edu/ftp/dist/freesurfer/infant/freesurfer-li…<https://secure-web.cisco.com/1tBEYaGAdDitkfPUajg7pJGKaxxzO-KQ7FVRcE-R55wnSj…> Lilla NOTE: Currently, the parcellation information (aparc) is provided only for the sake of completeness but has not been fully validated. It is a projected version of the adult atlas, so it does not originate from the infant training data set directly! ________________________________ From: webmaster(a)nmr.mgh.harvard.edu<mailto:webmaster@nmr.mgh.harvard.edu> <webmaster(a)nmr.mgh.harvard.edu<mailto:webmaster@nmr.mgh.harvard.edu>> on behalf of MGH/HST Martinos Center for Biomedical Imaging via MGH/HST Martinos Center for Biomedical Imaging <webmaster(a)nmr.mgh.harvard.edu<mailto:webmaster@nmr.mgh.harvard.edu>> Sent: Thursday, January 7, 2021 10:12 AM To: lzollei(a)nmr.mgh.harvard.edu<mailto:lzollei@nmr.mgh.harvard.edu> <lzollei(a)nmr.mgh.harvard.edu<mailto:lzollei@nmr.mgh.harvard.edu>> Subject: Form submission from: Infant Freesurfer Download Request Submitted on Thursday, January 7, 2021 - 10:12 Submitted by anonymous user: 189.128.48.80 Submitted values are: Name: Carlos Sair Flores Bautista Email Address: sairfb(a)inb.unam.mx<mailto:sairfb@inb.unam.mx> Institution: UNAM-México Operating System Used: Debian Intended use of the Pipeline: analyze the neurodevelopment between perinatal brain damage subject dataset and control subject data set during 0-8 years in a longitudinal analysis The results of this submission may be viewed at: https://www.nmr.mgh.harvard.edu/node/8319/submission/31809<https://secure-web.cisco.com/1ZLBHTi_QZ1M8KoGgrzKvLFWXqE6-zLjpsABpjUgPA4ubT…> The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Mass General Brigham Compliance HelpLine at http://www.massgeneralbrigham.org/complianceline<http://secure-web.cisco.com/1ND4Et7v64GxG61i6JVC2kcSsAjoYmzPSdgk95vYUnxp3oh…> . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.

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Permission to create directory denied
by Gabriel Mackie 11 Feb '21

11 Feb '21

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Freesurfer