Freesurfer

freesurfer@nmr.mgh.harvard.edu

15 participants
30064 discussions

Labels from Pial surface
by Fereshte 26 Aug '17

26 Aug '17

Hello FreeSurfer developers, Is it possible to have the segmentation labels after the pial surface is done in FreeSurfer? I mean once you do the topology correction and expand the inner cortical boundary to make the pial surface ; is it possible to have the inner and outer cortical boundaries as labels from pial surface? Looking forward to hearing from you Sincerely, Fereshte Ramezani

2 4

Change the template in Freesurfer
by YQ Chen 26 Aug '17

26 Aug '17

Hi, I want to change the template when doing recon-all. Is it possible? If it can, how can I do? Tell me, please! Thanks a lot! YQ

2 1

dividing cortex into equal patches
by Aniqa Dalowr 26 Aug '17

26 Aug '17

Hi All, I want to divide the cortex into patches that have the ~ same surface area. Is there a quick way to do that ? Please let me know, Thanks Ani

2 5

Re: [Freesurfer] Pial surface editing
by Michelle VanTieghem 25 Aug '17

25 Aug '17

Hi, Yes, I am trying to use skull stripping from another package, since -gcut option did not work on our data for appropriate skull stripping, and as a result there is too much pial matter included as white matter. a) Is brainmask.mgz an appropriate input file for recon-all -all? for example, should I run "recon-all -all -i brainmask.mgz -s SB001" ? or, am I still using the original .dcm file as input, and merely putting a copy of my skull stripped brain into the SUB/mri directory that was created in the previous processing attempt? b) I am not understanding why i will still run skull stripping in the script here, if it is already done. Is the brainmask.auto.mgz generated just another duplicate copy that will be ignored for the actual segmentations? Will this still perform intensity normalization and other auto-recon1 steps normally? Thank you, Michelle On Tue, Jul 18, 2017 at 12:44 PM, Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> wrote: > Hi Michelle > > can you cc the list so others can answers? I'm also no longer sure which > thread this is - were you trying to use the skull stripping from another > package? If so, convert that file to be named brainmask.mgz, then do *not* > include the -noskullstrip in your command line. Let us do the skull > strippping, which will create a brainmask.auto.mgz, but should preserve the > brainmask.mgz (since it is different than the .auto file) > > cheers > Bruce > > > > On Tue, 18 Jul 2017, Michelle VanTieghem wrote: > > >> Hi Bruce, >> >> >> Thanks for the information. Sorry I had changed my mail settings so I >> wasn’t >> seeing your responses until now. I had tried to run all, but just >> skip skull >> strip step, as well as the talaraich check step since we saw errors with >> that too. >> >> The command I used is follows: >> >> recon-all -all -3T -mprage -notal-check -noskullstrip >> -i/vega/psych/users/mrv2115/fsdata/ORIG_AFNI_SKULLSTRIP/SB00 >> 1/mprage_deobliqu >> e_brain.nii -s SB001 >> >> However, I am getting the following error during the registration step >> (see >> below). It looks like the mask volume brainmask.mgz hasn't been generated, >> but i don't know why. You suggested to convert my afni skull stripped >> brain >> to brain mask.mgz and place in the MRI folder. but am I still going to run >> the steps of autorecon-1 ? (intensity normalization, etc)? Does recon-all >> take inputs of already existing mri/brainmask.mgz files? It seems like it >> just needs one file and then re-generates a new directory with mri, >> scripts, >> ect. I would appreciate more detail on how to implement this! >> >> Thank you, >> >> Michelle >> >> >> ERROR: >> >> >> >> ======= NUMBER OF OPENMP THREADS = 1 ======= >> >> aligning to atlas containing skull, setting unknown_nbr_spacing = 3 >> >> using MR volume brainmask.mgz to mask input volume... >> >> reading 1 input volumes... >> >> logging results to talairach.log >> >> reading '/vega/psych/app/freesurfer/average/RB_all_2008-03-26.gca'... >> >> average std = 6.9 using min determinant for regularization = 4.7 >> >> 0 singular and 1812 ill-conditioned covariance matrices regularized >> >> reading 'nu.mgz'... >> >> mghRead(/vega/psych/users/mrv2115/fsdata/processed/SB001/ >> mri/brainmask.mgz, >> -1): could not $ >> >> mri_em_register: could not open mask volume brainmask.mgz. >> >> >> Linux bogota.cc.columbia.edu 2.6.32-696.el6.x86_64 #1 SMP Tue Feb 21 >> 00:53:17 EST 2017 x86_$ >> >> >> recon-all -s SB001 exited with ERRORS at Tue Jul 18 11:50:24 EDT 2017 >> >> >> —— >> >> >> >> >> >> > > 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 Partners Compliance > HelpLine at > http://www.partners.org/complianceline . 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. > -- Michelle VanTieghem PhD student in Psychology Developmental Affective Neuroscience Lab Columbia University mrv2115(a)columbia.edu

2 12

cudadetect fails: wrong amount of memory and number of cores detected
by Markus.Mertens＠evkb.de 25 Aug '17

25 Aug '17

Hello FreeSurfer Developers, I would like to use recon-all with the option "-use-gpu" so I ran cudadetect first to see whether the nvidia card on my system will be detected. But at least the values for total amount of memory and number of cores are wrong (should be 8GB and 2304 cores). $ cudadetect Detecting CUDA... There are 0 devices supporting CUDA: Device 0: "Quadro K5200" CUDA Driver Version: 8.0 CUDA Runtime Version: 6.50 CUDA Capability Major revision number: 3 CUDA Capability Minor revision number: 5 Total amount of global memory: 4224450560 bytes Number of multiprocessors: 12 Number of cores: -2109039396 Total amount of constant memory: 65536 bytes Total amount of shared memory per block: 49152 bytes Total number of registers available per block: 65536 Warp size: 32 Maximum number of threads per block: 1024 Maximum sizes of each dimension of a block: 1024 x 1024 x 64 Maximum sizes of each dimension of a grid: 2147483647 x 65535 x 65535 Maximum memory pitch: 2147483647 bytes Texture alignment: 512 bytes Clock rate: 0.77 GHz Concurrent copy and execution: Yes Run time limit on kernels: Yes Integrated: No Support host page-locked memory mapping: Yes Compute mode: Default (multiple host threads can use this device simultaneously) $ What could I try? Thank you. FreeSurfer: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0.tar.gz uname -a: Linux cortex 4.4.74-server-1.mga5 #1 SMP Mon Jun 26 08:34:35 UTC 2017 x86_64 x86_64 x86_64 GNU/Linux _______________________________________________________________ Evangelisches Klinikum Bethel gGmbH Akademisches Lehrkrankenhaus der Universität Münster Sitz der Gesellschaft Kantensiek 11 | 33617 Bielefeld Amtsgericht Bielefeld HRB 30169 Geschäftsführer Dr. Rainer Norden (Vorsitz) Dr. Matthias Ernst Dr. Maren Thäter Vorsitzender des Aufsichtsrates Pastor Ulrich Pohl 150 Jahre Bethel - Für Menschen da sein

2 3

Please unsubscribe me
by Micah Rhodes 25 Aug '17

25 Aug '17

Please unsubscribe me to this email list. Thanks.

2 1

nuiterations question
by Floris van Vugt 25 Aug '17

25 Aug '17

Dear Freesurfer developers and community, I am using recon-all as part of a pipeline and I am wondering about how to control the non-uniform intensity correction. When I run `recon-all -help` I get: -nuiterations Number of iterations in the non-uniform intensity correction. Default is 1. However, when I run `recon-all -i structural.nii -subjid foo -sd . -nuiterations 7` I get: ERROR: Flag -nuiterations unrecognized. -nuiterations 7 Linux colossus 4.4.0-92-generic #115-Ubuntu SMP Thu Aug 10 09:04:33 UTC 2017 x86_64 x86_64 x86_64 GNU/Linux recon-all -s exited with ERRORS at Wed Aug 23 15:27:55 EDT 2017 For more details, see the log file To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting I am running this version of Freesurfer: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c Is this option deprecated? But then why is it still listed under freesurfer -help? Thanks, Floris -- Floris van Vugt, Ph.D. Motor Control Lab, Psychology Dept. McGill University 1205 Dr. Penfield Ave Stewart Biology Building Montreal QC Canada H3A 1B1 www.florisvanvugt.com

2 1

Tracula - QA for Forceps Minor
by Abigail Waters 25 Aug '17

25 Aug '17

Hello - We've processed approximately 500 DTI scans using Tracula and are in the process of visually inspecting the forceps minor for errors. For subjects with dramatic errors (see image 1) we will be redoing the -path step of Tracula with control points set to 7 and reinit = 1. Is this an appropriate solution? In order to generate the fminor_PP_avg33_mni_bbr_cpts_7 files, would we need to redo the whole pipeline, or just parts of it? We would also like to know if any of the following issues described below are errors or normal variation in white matter tracts: 1. Spread of white matter at the ends of the curve (see image 2) 2. Overlapping of the white matter across hemispheres in the prefrontal region (see image 3) 3. Non-smooth surfaces with small protrusions along the length of the forceps minor (see image 4_1 and 4_2) 4. Slightly larger single protrusions of white matter (see image 5) And if so, would increasing the number of control points to 7 increase the quality of the reconstruction? Please let me know if you need any additional information. Best Abby

1 0

recon-all
by John Anderson 25 Aug '17

25 Aug '17

Dear FS experts, Attached is a snapshot for orig.mgz overlayed by wm.mgz for one of my recons which finished with no errors. I am reviwing the data and I see a lot of holes in the brain stem, Are these needs to be filled manually. Do you recommend to fill this type of holes or just the ones in the hemispheric white matter? Thanks in advance John

2 5

Skull striping problems
by MATEUS ROZALEM ARANHA 25 Aug '17

25 Aug '17

Hi! When I run recon-all on my data, some skull and dura is left behind and affects the surfaces and the parcellation. I re-run the data using a lower watershed (I tried 20, 15, 10 and 05). The brainmask changed, but the remaining skull still affects the parcellation and surfaces. My doubt is: when I re-run my data using a lower watershed value, does it automatically create new surfaces and volumes or not? If not, how can I reset it? Best Mateus

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