Freesurfer

freesurfer@nmr.mgh.harvard.edu

12 participants
30060 discussions

"-atlas" argument and help with multiple errors running recon-all
by Rona Haker 13 Sep '23

13 Sep '23

External Email - Use Caution Dear Free Surfer developers, I have several subjects that are not successful with recon-all. In most cases, the log file looks something like the one attached, with errors in "inflating to sphere" and in "validation": *********************VALIDATION********************* curvature mean = -0.010, std = 0.009 curvature mean = 84.153, std = 7.183 No Rigid alignment: -atlas Mode Off (basic atlas / no registration) before rotation: sse = 11.66, sigma = 23.42 after rotation: sse = 11.66, sigma = 23.42 Localization of inacurate regions: Erosion-Dilation steps the sse mean is 19.34, its var is 27.07 before Erosion-Dilatation 24.37% of inacurate vertices after Erosion-Dilatation 37.82% of inacurate vertices 58.52% of 'positive' inacurate vertices 41.48% of 'negative' inacurate vertices The surface validation has detected a possible Error If the final segmentation is not valid, try using the option '-atlas' Scaling of atlas fields onto current surface fields ********FINAL ITERATIVE TEMPLATE DEFORMATION******** Compute Local values csf/gray Fine Segmentation...40 iterations mri_strip_skull: done peeling brain Brain Size = 2625362 voxels, voxel volume = 1.000 mm3 = 2625362 mmm3 = 2625.362 cm3 the /mri output directory is missing aparc+aseg and looks like this: [image: image.png] I tried running the recon-all command with the option '-atlas' as suggested in the log with this command: export FREESURFER_HOME=/usr/local/freesurfer source $FREESURFER_HOME/SetUpFreeSurfer.sh export SUBJECTS_DIR=<path_to_subject> cd $SUBJECTS_DIR recon-all -s 00_FSseg -i 8_t1_mp2rage_sag_p3_iso_UNI_Images/004933_t1_mp2rage_sag_p3_iso_UNI_Images_1.dcm -openmp 8 -all -atlas but: 1. I could not find any documentation on this option, what it means and what arguments to give it. 2. I get the following error: 'ERROR: Flag -atlas unrecognized. -s 00_FSseg -i 8_t1_mp2rage_sag_p3_iso_UNI_Images/004933_t1_mp2rage_sag_p3_iso_UNI_Images_1.dcm -openmp 8 -all -atlas Linux nbelab 4.15.0-206-generic #217-Ubuntu SMP Fri Feb 3 19:10:13 UTC 2023 x86_64 x86_64 x86_64 GNU/Linux recon-all -s 00_FSseg exited with ERRORS at Mon Sep 4 17:02:23 IDT 2023 I would greatly appreciate some help!

2 3

Problem with T1 pial adherence to skull and T1+T2 poor estimation of cortex.
by Jonas Østerhaug Andersen 13 Sep '23

13 Sep '23

External Email - Use Caution Hello FreeSurfer Developers, I'm attempting to run recon-all -i $workdir/$t1folder/${subj}.nii.gz -subjid ${subj} -all -gcut -clean-bm -3T -mprage -T2 $workdir/$t2folder/${subj}.nii.gz -T2pial -all I have added some pictures to highlight my issue. The issue that I am experiencing it that the T1 (red) adheres to what remains of the skull, while the T1+T2 (blue) underestimates the surface of the cortex. Are thee any solutions to this? And if not, would you recommend to use the T1 alone pr the T1+T2 when proceeding further? In advance I'd like to inform that I have tried to run the multistrip with watershed threshholds ranging from 0.1 to 30, but the gcut just worked better for us rather than trying different watershed threshold levels. best, Jonas Østerhaug Andersen

1 0

invalid license
by 黄俊彬 13 Sep '23

13 Sep '23

External Email - Use Caution i ran qdec and clicked on analyze, error occurred. it said the license is invalid. the version is 5.3.0. how to solve this?

1 0

Re: [Freesurfer] ScLimbic issue
by fsbuild 12 Sep '23

12 Sep '23

External Email - Use Caution  If you are getting an “illegal instruction” error running Freesurfer on Linux,  then the hardware (CPU’s) do not have those instructions available in their instruction set to execute.   As far as I know that error only happens with Freesurfer binaries compiled with AVX instructions.  So either you are running on new ARM based processors or you are running on older Intel processors (approx. pre-2011) that do not implement AVX.  There is a list of Intel processors supporting AVX instructions at https://secure-web.cisco.com/1uW45KoTvgWNrFJTk9Lu8MiuKA56yspFlAr2_S…; For Linux machines, the resolution is to run use Intel processors that can execute those instructions. - R. On Sep 12, 2023, at 16:27, Douglas N. Greve <dgreve(a)mgh.harvard.edu> wrote:        External Email - Use Caution        what problem? There is nothing else in your email and I don't have the previous threads.On 9/12/2023 10:51 AM, Glass, John wrote:        External Email - Use Caution        Hello, I am running into the exact same problem at my local site running version 7.4.1 on a centos 7 machine with a build stamp of: freesurfer-linux-centos7_x86_64-7.4.1-20230613-7eb8460. Has this issue been resolved? Thank you, John O. Glass, M.S.Signal Processing SupervisorDepartment of Diagnostic ImagingSt. Jude Children's Research Hospital262 Danny Thomas Place, Mail Stop 220Memphis, TN 38105-3678john.glass(a)stjude.org(901) 595-3276MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be http://secure-web.cisco.com/1zIIZtAoXKf8myf-KWBMwne7yPoUAd7Qy1jEcPW… Disclaimer: MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be http://secure-web.cisco.com/1Q1uNU-pDdKZt3c2gJvRAX-e_HCj8f2TfRXbDL5… Disclaimer: MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be http://secure-web.cisco.com/1YLtpOgLUGV6rBo4lpwcQb-p3mwycbu6cy2hqQt… Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://secure-web.cisco.com/1banHDx6NgdG-lM1NRwrxZmZ6Z41zC38nEpucEeSW4wG4k… mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

2 1

Re: [Freesurfer] ScLimbic issue
by Glass, John 12 Sep '23

12 Sep '23

External Email - Use Caution Hello, I am running into the exact same problem at my local site running version 7.4.1 on a centos 7 machine with a build stamp of: freesurfer-linux-centos7_x86_64-7.4.1-20230613-7eb8460. Has this issue been resolved? Thank you, John O. Glass, M.S. Signal Processing Supervisor Department of Diagnostic Imaging St. Jude Children's Research Hospital 262 Danny Thomas Place, Mail Stop 220 Memphis, TN 38105-3678 john.glass(a)stjude.org<mailto:john.glass@stjude.org> (901) 595-3276 http://secure-web.cisco.com/1cDTV5tT9Oa6ZugGCMbS5sM9mmuOcH5ETeAFbpyv_6rsfu-…<http://secure-web.cisco.com/1BpeOmGNdiCKRYBgOZ6T6GstDeTtB_1HTpS5klyKFrwc5_Q…> ________________________________ Email Disclaimer: http://secure-web.cisco.com/1uykVz0BTSeYpAi1ACN5eHA5oADlYO8HITenLBX1I7NWhN-… Consultation Disclaimer: http://secure-web.cisco.com/18gCvDjdTqEs3ScUYn27xadymDMR0ucfW9MF2xyg_dkrN2c…

2 1

Neuroimaging data analyst position at MGH / Harvard
by Jacobs, Heidi I.,PHD 12 Sep '23

12 Sep '23

External Email - Use Caution Neuroimaging data analyst position: The Gordon Center for Medical Imaging (GCMI) in the Department of Radiology at Massachusetts General Hospital (MGH) and Harvard Medical School (HMS) in Boston, Massachusetts, has an opening for highly qualified individuals to work as neuroimaging data analyst with Dr. Heidi Jacobs. The Jacobs lab is part of the Gordon Center for Medical Imaging at MGH and focused on improving the early detection and early treatment of Alzheimer’s disease. The lab focuses on the neuromodulatory subcortical nuclei, in particular the locus coeruleus, using a variety of approaches, including 7T MRI, PET imaging, pupil measurements, physiological recording, blood-based markers, cognitive assessments and non-invasive vagus nerve stimulation. Do you love working with 3T MRI, 7T MRI and PET imaging, do you enjoy the challenge of integrating the acquisition and analyses of imaging data with other modalities (physiology, eye-tracking, neurostimulation,...), do you like to build new methods, imaging pipelines and integrate them with existing ones, and finally: do you have interest in the brainstem and Alzheimer' s disease? Then apply!!! This position is also open to individuals at the MSc level or at the PhD level. Most of the work in this project will be performed at the Athinoula A. Martinos Center for Biomedical Imaging, Charlestown Navy Yard. The candidate will be part of ongoing collaborations and be able to work in a stimulating and inspiring environment. The Department of Radiology at MGH is equipped with the first mobile PET/CT, the first brain PET/MRI, the first whole-body PET/MRI in the USA and several MRI scanners, including two 7T ultra-high-field scanner. It is equipped with a large-scale shared memory computing facility for parametric image analysis, tomographic reconstruction, Monte Carlo simulation, and other computationally intensive research applications. Our research group values open communication, motivation, optimism, mutual respect, teamwork, and innovative thinking. This is a lab-wide position, working in all aspects of acquiring, analyzing data from various projects, including interventions, observational studies and helping collaborators. More information: shorturl.at/mNVY6<http://secure-web.cisco.com/13GmZQEx2maK4u83hKCu53H9eVNGlKOO9A7HOihvmR4SWQJ…> [cid:image001.png@01D9E576.D629B720] Dr. Heidi Jacobs Associate Professor of Radiology Massachusetts General Hospital Harvard Medical School Department of Radiology Gordon Center for Medical Imaging 149 13th Street Charlestown, MA 02129 hjacobs(a)mgh.harvard.edu http://secure-web.cisco.com/1kLcCyBUNPIuWdfUzSthYBDZN1FF-w-Cb_JVPpxTA0xmZ4u…<http://secure-web.cisco.com/1kDMQzfTNRb5ravA9353bYWyUpVvZYUg5vdPw-lfPGyjN07…> twitter: @HeidiJacobsLab Linkedin: https://secure-web.cisco.com/12G8DNTNXVnwx9VZSaMFkLGtedcma9jdGyfKu6M6IjKYs_…

1 0

lme and single random effect estimates
by Antonio Napolitano 12 Sep '23

12 Sep '23

2 1

Atlas Parcellation error
by Junxia Wang 12 Sep '23

12 Sep '23

External Email - Use Caution Hello All, I used the default freesurfer command (recon-all) to generate the annotated surface file for subjects. However, the results in some subjects seem to have an obvious parcellation error. As you can see in the below graph, the area pointed by the red arrow is labelled as S_precentral-inf-part; however, we think it should be S_central. (In this particular subject, the parcellation is totally fine on the left hemisphere. The problem is only on the right hemisphere as you can see below) We adopted a solution from this answer: https://secure-web.cisco.com/1qxgC1JMOwKWxmSccucR1CmKcgaAUMcy4N4o0VjYQs9ezR… We specified three manual labels: S_central, S_temperal_sup, and S_pericallosal, to align with atlas labels and generate a new registered surface file. Adding -nonorm option made the result even better. S_central.label S_temperal_sup.label S_pericallosal.label Command #1: mris_register -L S_central.label <atlas_gcsa_file> S_central -L S_temperal_sup.label <atlas_gcsa_file> S_temperal_sup -L S_pericallosal.label <atlas_gcsa_file> S_pericallosal -curv -nonorm sub-xxxxxx/surf/rh.sphere /freesurfer/7.3.2/average/rh.average.curvature.filled.buckner40.tif rh.sphere.reg.new <atlas_gcsa_file> here is rh.destrieux.simple.2009-07-29.gcs Command #2: mris_ca_label sub-xxxxxx rh rh.sphere.reg.new <atlas_gcsa_file> rh.new.aparc.a2009s.annot The parcellation looks a lot better now but it is still not perfect (for example, look at the area pointed by the red arrow) Now, my questions are: 1. Does our solution make sense? 2. Are there any other better methods to correct the parcellation error? Thank you! Best wishes, Junxia

1 0

Password for FS Ubuntu virtual machine
by sapere-aude＠tuta.io 11 Sep '23

11 Sep '23

External Email - Use Caution Hi, I would like the password for the user "developer" in the FreeSurfer 7.2.0 Ubuntu virtual machine. Thanks! Regards, Sapere-aude

2 1

voxel-specific opacity
by Proulx, Jean Sebastien 11 Sep '23

11 Sep '23

External Email - Use Caution Dear Freesurfers, Is it possible to input an alpha channel to freeview? Otherwise said, can one obtain a voxel-specific opacity? I would see something like freeview underlay.mgz overlay.mgz:opacity=opacity.mgz where the single opacity value is replaced with a file containing the desired voxel-specific opacities. Thanks for your help and Have a very good day! Sebastien

2 1

Jump to page:

2026

2025

2024

2023

2022

2021

2020

2019

2018

2017

2016

2015

2014

2013

2012

2011

2010

2009

2008

2007

2006

2005

2004

Freesurfer