Freesurfer

freesurfer@nmr.mgh.harvard.edu

19 participants
30132 discussions

Freesurfer v5.0.0 longitudinal processing error
by Simmons, Andy 31 Aug '10

31 Aug '10

Dear All, I have run into problems with a longitudinal analysis using v5.0.0 (freesurfer-Linux-centos4_x86_64-stable-pub-v5.0.0) that seemed to work fine under v4.5.0. For both analyses I processed the raw data from scratch since they were run on different clusters. Following the instructions at http://surfer.nmr.mgh.harvard.edu/fswiki/LongitudinalProcessing I initially processed all images using the cross sectional stream, eg recon-all -s PATIENT016_TIMEPOINT1 -i PATIENT016_TIMEPOINT1 then created a template from all time points for each subject, eg recon-all -base PATIENT016 -tp PATIENT016_TIMEPOINT1 -tp PATIENT016_TIMEPOINT2 -tp PATIENT016_TIMEPOINT3 -all Finally I tried to run the longitudinal processing stream, eg recon-all -long PATIENT016_TIMEPOINT1 PATIENT016 -all where I ran into the following error message "ERROR: longitudinal base ID cannot be the same as a timepoint subject ID (in /home/asimmons/images/FREESURFER/PATIENT016/base-tps) Find more info at: http://surfer.nmr.mgh.harvard.edu/fswiki/LongitudinalProcessing" The longitudinal base ID is however not the same as any of the timepoints in /home/asimmons/images/FREESURFER/LNDMCI016/base-tps which just contains a list of the time points as expected - PATIENT016_TIMEPOINT1 PATIENT016_TIMEPOINT2 PATIENT016_TIMEPOINT3 Best wishes, Andy Simmons ---- Dr Andy Simmons Reader in Neuroimaging & Consultant Clinical Scientist Centre for Neuroimaging Sciences and NIHR Biomedical Research Centre Institute of Psychiatry, Box P089 Kings College London De Crespigny Park London, SE5 8AF, UK Email - andy.simmons(a)kcl.ac.uk Webpage - http://www.iop.kcl.ac.uk/staff/profile/default.aspx?go=10338 Directions - http://www.iop.kcl.ac.uk/virtual/?path=/about/how-to-find-the-institute-of-… ResearcherID - http://www.researcherid.com/rid/B-8848-2008 Fax +44 (0)203 228 2116

3 2

make_average_surface error?
by Jeff Sadino 31 Aug '10

31 Aug '10

Hello, I issued this command to make an average subject: make_average_subject --subjects 2101 2102 2103 --out uh3 I wanted to verify the average thickness file is what it sounds like. I used the recon-all -qcache on each subject individually, read the fwhm0 thickness files into matlab, and averaged vertex #100. However, when I look at vertex #100 from the uh3 surf folder, the numbers don't match. What is the reason for this? I am using freesurfer 4.3.1. Thank you, Jeff Sadino

3 2

Notes on CUDA Acceleration
by Richard G. Edgar 31 Aug '10

31 Aug '10

Greetings, I've been asked to provide some extra information about GPU support in Freesurfer (being the one guilty of mri_em_register_cuda...). Firstly, there are no immediate plans for OpenCL support. It would be very nice to have - with ATI, NVIDIA _and_ x86 multicore backends. However, it's far less mature than CUDA. The good news is that the really 'hard' bit is restructuring the algorithms to fit well on a GPU. The syntax of CUDA and OpenCL is very similar (strange that....), but OpenCL is more verbose. As for cards..... for what is in the current release, any GeForce GTX-200 series or Tesla 10 series (i.e. C1060 and S1070) card should work (I don't know the Quadro model numbers - CUDA architecture 1.3 is the key feature). I think that everything should actually work on somewhat older cards, but the compile flags will have to be tweaked. So long as that threshold is reached, the only issue is the amount of RAM needed. Currently, I expect that any card with at least 1 GiB of RAM will have plenty, and the threshold for mri_em_register_cuda will be much lower than that. Going forward, I would strongly recommend purchasing 'Fermi' class cards. These are the GTX 400 series, and Tesla 20 series. The new architecture lifts some hardware limits on GPU kernels which are crippling for portions of mri_ca_register. With a more accelerated mri_ca_register, RAM limits may also come into play, until I can come up with a suitably cunning GPU implementation of the Gaussian Classifier Array (right now, I'm going to burn around 2 GiB on a single GCA, to make implementation simple). However, I have bigger fish to fry first. One final thing: Nick and I found last week that the accelerated mri_em_register_cuda doesn't seem to work prior to skull stripping. I'm going to work on this this week, but if you want to continue using the GPU accelerated binary, you'll have to turn off the FAST_TRANSLATION and FAST_TRANSFORM flags in mri_em_register.c, and recompile. This will increase the runtime to around 4 minutes on ernie, but will give results identical to the CPU code. I hope this is helpful, Richard

5 9

autorecon2
by Mareen Kussatz 30 Aug '10

30 Aug '10

> Hi to all, > > there are still correction problems after recon-all! > > After recon-all not all of the corrections are visible??????? > > I corrected e.g. 10 slices. I deleted some voxels in wm.mgz as aux volume, non-white matter classified as white matter. I saved the aux volume and i startet recon-all! > After running without errors, i checked in tkmedit. There were 5 of 10 slices corrected, but not the others???? With means there are still 5 slices of the previous corrected including some non-white matter classified as white matter! When i open the cor files for these slice, the corrections are visible!! > > > please help to find the bug > > Best Mareen > > > > -------- Original-Nachricht -------- >> Datum: Fri, 13 Aug 2010 11:38:01 -0400 (EDT) >> Von: Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> >> An: Mareen Kussatz <mareenkussatz(a)gmx.de> >> CC: freesurfer(a)nmr.mgh.harvard.edu >> Betreff: Re: [Freesurfer] autorecon2 > >> Hi Maureen, >> >> if you exit tkmedit and reload the wm.mgz before rerunning recon-all are >> your edits in it? It shouldn't matter whether you edit/save in the main or >> aux volume. >> >> cheers >> Bruce >> >> On Wed, 11 Aug 2010, Mareen Kussatz wrote: >> >>> Hi to all, >>> >>> after correcting white matter problems, we saved the wm as aux volume >> and we tried also to save it as main volume. And than, we started recon-all >> -autorecon2-wm -subjid (subject file name). The process ends without any >> error for both conditions but after checking the tkmedit, there weren´t any >> corrections visible and actually there were no change at all.??? >>> >>> We just want to know if it is a syntax problem or if there is something >> wrong with the freesurfer itself. >>> >>> thanks and best regards. >>> >>> Mareen Kussatz >>> > > 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. -- GMX DSL SOMMER-SPECIAL: Surf & Phone Flat 16.000 für nur 19,99 ¿/mtl.!* http://portal.gmx.net/de/go/dsl

3 2

FS5 Longitudinal broken
by Martin Reuter 30 Aug '10

30 Aug '10

Dear FreeSurfer user, we are sorry to let you know that the longitudinal stream in FreeSurfer Release 5.0 is broken due to some last minute improvements to mri_robust_register. It shares some of it's code with mri_robust_template, where the 'improvements' break the processing, which leads to blurry average images in some cases. We are working on a fix and will let you know immediately when it is ready. Until then you can keep processing your longitudinal data with 4.5 which does not have the bug. Best regards, Martin Reuter -- Dr. Martin Reuter Assistant in Neuroscience - Massachusetts General Hospital Instructor in Neurology - Harvard Medical School MGH / HMS / MIT A.A.Martinos Center for Biomedical Imaging 149 Thirteenth Street, Suite 2301 Charlestown, MA 02129 Phone: +1-617-724-5652 Web : http://reuter.mit.edu

1 0

Re: [Freesurfer] PALS-B12-based ROIs in fsaverage in v5.0.0
by Nick Schmansky 30 Aug '10

30 Aug '10

yes, it can be used with subjects processed prior to v5. there is nothing v5 specific about the rois (it just happened that they became available in this release). the fsaverage subject is the same as v4. n. On Mon, 2010-08-30 at 09:37 -0700, Wayne Su wrote: > Hi Nick, > > Can I use this atlas on subjects processed by the earlier version? > > Regards, > Wayne > > > On 27/08/10 9:42 AM, "Nick Schmansky" <nicks(a)nmr.mgh.harvard.edu> wrote: > > > there is one new feature in the new v5.0.0 which was missing from the > > early release notes, but that which some people might have an interest. > > the Van Essen Lab created some ROIs on their PALS-B12 atlas, and then > > mapped them to the freesurfer fsaverage subject. some basic info is > > here: > > > > http://surfer.nmr.mgh.harvard.edu/fswiki/PALS_B12 > > > > it will take a bit of freesurfer expertise on your part to make use of > > these, as you would need to: > > > > 1) identify which labels (ROIs) are of interest to you (by viewing > > the .annot file on fsaverage) > > 2) use mri_annotation2label to extract the labels > > 3) use mri_label2label to map from fsaverage to your subject > > 3) optionally use mri_anatomical_stats to get stats about those labels > > > > n. > > > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer(a)nmr.mgh.harvard.edu > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > > 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. > > > > >

1 0

Suggestions for ways to present brain images of FreeSurfer results in a manuscript?
by Max Gunther 29 Aug '10

29 Aug '10

Hi all, I am relatively new to FreeSurfer and I am wondering if people have suggestions for how to display images of brains in my sample that will be meaningful to reviewers and readers? Right now the most meaningful results are depicted using scatter plots and regression lines, etc. but I would definitely like to put some actual images of the sample's brain's in the paper. It is about 90 brains with old patient with significant atrophy. I am just not familiar enough with the FreeSufer options to know what kinds of tools A) are available and B) would be appropriate for communicating the effect of a clinical variable on brain atrophy. Many thanks for your time and suggestions! Sincerely, Max Gunther Max Gunther, PhD Vanderbilt University Medical Center Departments of Psychiatry and Medicine Center for Health Services Research Nashville, TN www.ICUdelirium.org

2 1

iPhone and IPad FreeSurfer based atlas
by Pedro Paulo de Magalhães Oliveira Junior 28 Aug '10

28 Aug '10

Some weeks ago Bruce announced the first version of the free brain atlas app for IPhone using FreeSurfer aseg. Today we have a major upgrade and now the app has a native IPad interface. Also Bruce provided high resolution mri segmented so IPhone and IPod touch users will benefit too http://itunes.apple.com/br/app/isurf-brainview/id381072423?mt=8 Suggestions for the upcoming version ate welcome. Cheers Pedro Paulo Jr. -- via iPhone iOS4

3 3

PALS-B12-based ROIs in fsaverage in v5.0.0
by Nick Schmansky 27 Aug '10

27 Aug '10

there is one new feature in the new v5.0.0 which was missing from the early release notes, but that which some people might have an interest. the Van Essen Lab created some ROIs on their PALS-B12 atlas, and then mapped them to the freesurfer fsaverage subject. some basic info is here: http://surfer.nmr.mgh.harvard.edu/fswiki/PALS_B12 it will take a bit of freesurfer expertise on your part to make use of these, as you would need to: 1) identify which labels (ROIs) are of interest to you (by viewing the .annot file on fsaverage) 2) use mri_annotation2label to extract the labels 3) use mri_label2label to map from fsaverage to your subject 3) optionally use mri_anatomical_stats to get stats about those labels n.

1 0

freesurfer 5.0 in ubuntu 10.04
by Guang Zeng 27 Aug '10

27 Aug '10

Hi, there, I just downloaded and installed freesurfer 5.0 under Ubunto 10. The version I am downlaoded is freesurfer-Linux-centos4-stable-pub-v5.0.0.tar.gz I ran a subject, but it failed at the first step, the error message I got is: talairach_avi --i nu.mgz --xfm transforms/talairach.auto.xfm ERROR: mpr2mni305 failed, see transforms/talairach_avi.log Linux guangzeng-desktop 2.6.32-24-generic-pae #41-Ubuntu SMP Thu Aug 19 02:43:57 UTC 2010 i686 GNU/Linux I checked the talairach_avi.log, and I found this: gauss_4dfp: error while loading shared libraries: libg2c.so.0: cannot open shared object file: No such file or directory ERROR: 'gauss_4dfp talsrcimg 1.1' failed! status=127 ERROR: mpr2mni305 execution aborted So, how can I fix this problem? Thanks a lot! Guang

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