Freesurfer

freesurfer@nmr.mgh.harvard.edu

17 participants
30099 discussions

Question about how to get Talairach step to work on brains with bright scalp areas
by David M. Perlman 16 Apr '14

16 Apr '14

Hello, I have a question about how to get freesurfer to work correctly with images that have problematic contrast. We have a bunch of images that were taken with a new 32-channel head coil. For some of these images, the contrast value for the scalp cutaneous fat is dramatically higher than the contrast value for the brain tissue itself. (See one attached image) Many of the images that look like this are processed just fine, but some of them fail. When they fail, it looks like this in the log (see pasted log text below). I looked at the link that it told me to check but it was an invalid page in the wiki: http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Talairach I tracked down this page instead: http://surfer.nmr.mgh.harvard.edu/fswiki/FreeSurferTalairach On that page it suggests: When you see a big bright neck region, an option is to edit the volume to erase the bright neck region and run mritotal on the edited volume. It usually works by a simple editing, setting all the region to zero where y > certain value (around 170). This worked better than using "brain" volume. I thresholded one of my trouble images with this command: poblano:/study/gates/data/mri/preprocessed/VIPR_IR/MPRAGE$ 3dcalc -a 1221_2_MPRAGE_reorient.nii.gz -expr 'step(a-1000)*1000 + step(1000-a)*a' -prefix 1221_2_MPRAGE_reorient_clip1000.nii.gz ++ 3dcalc: AFNI version=AFNI_2011_12_21_1014 (Mar 31 2014) [64-bit] ++ Authored by: A cast of thousands ++ Output dataset ./1221_2_MPRAGE_reorient_clip1000.nii.gz The image certainly looked better after that. (See other attached image) I tried it again with the command: poblano:/study/gates/data/mri/preprocessed/VIPR_IR/MPRAGE/freesurfer_nu_test$ recon-all -i /study/gates/data/mri/preprocessed/VIPR_IR/MPRAGE/1221_2_MPRAGE_reorient_clip1000.nii.gz -subject 1221_2_clip1000 -all but the result was the same. The talairach.xfm matrix is this: Transform_Type = Linear; Linear_Transform = 0.755387127399445 -0.110331535339355 -0.538617014884949 -24.9059925079346 0.544680178165436 0.0255524087697268 0.75865626335144 15.3778610229492 -0.0748601630330086 -0.927396953105927 0.0849819406867027 -111.666954040527; which definitely doesn't look right. We tried turning up the --nuiterations option to a much higher value, but this step doesn't run until after the Talairach transform so it is unable to help that process. (Wouldn't it make more sense to swap that order?) I was wondering if you could give me any advice on other steps I could try, to get this brain to process with recon_all? Thanks! INFO: Attempting MINC mritotal to perform Talairach align #-------------------------------------------- #@# Talairach Mon Apr 14 10:54:57 CDT 2014 /study1/gates/data/mri/analysis/SA/freesurfer/test_mprage_fail/1221_2/mri mri_nu_correct.mni --n 1 --proto-iters 1000 --distance 50 --no-rescale --i orig.mgz --o orig_nu.mgz talairach --i orig_nu.mgz --xfm transforms/talairach.auto.xfm /study1/gates/data/mri/analysis/SA/freesurfer/test_mprage_fail/1221_2/mri /apps/x86_64_sci6/freesurfer-latest/bin/talairach --i orig_nu.mgz --xfm transforms/talairach.auto.xfm $Id: talairach,v 1.7 2011/03/02 20:16:40 nicks Exp $ Linux c114.keck.waisman.wisc.edu 2.6.32-431.5.1.el6.x86_64 #1 SMP Tue Feb 11 13:30:01 CST 2014 x86_64 x86_64 x86_64 GNU/Linux Mon Apr 14 10:55:50 CDT 2014 tmpdir is transforms/tmp.talairach.30831 /study1/gates/data/mri/analysis/SA/freesurfer/test_mprage_fail/1221_2/mri mri_convert orig_nu.mgz transforms/tmp.talairach.30831/src.mnc mri_convert orig_nu.mgz transforms/tmp.talairach.30831/src.mnc $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from orig_nu.mgz... TR=4.55, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, 0) j_ras = (0, 0, -1) k_ras = (0, 1, 0) writing to transforms/tmp.talairach.30831/src.mnc... -------------------------------------------- mritotal -verbose -debug -clobber -modeldir /apps/x86_64_sci6/freesurfer-latest/mni/bin/../share/mni_autoreg -protocol icbm transforms/tmp.talairach.30831/src.mnc transforms/talairach.auto.xfm Mon Apr 14 10:56:11 CDT 2014 talairach done cp transforms/talairach.auto.xfm transforms/talairach.xfm #-------------------------------------------- #@# Talairach Failure Detection Mon Apr 14 10:56:12 CDT 2014 /study1/gates/data/mri/analysis/SA/freesurfer/test_mprage_fail/1221_2/mri talairach_afd -T 0.005 -xfm transforms/talairach.xfm ERROR: talairach_afd: Talairach Transform: transforms/talairach.xfm ***FAILED*** (p=0.0000, pval=0.0000 < threshold=0.0050) Manual Talairach alignment may be necessary, or include the -notal-check flag to skip this test, making sure the -notal-check flag follows -all or -autorecon1 in the command string. See http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Talairach -- -dave------------------------------------------------------------------------ "Let us work without theorizing... 'tis the only way to make life endurable." - Voltaire, Candide, Chapter 30

1 0

Units of Flat-Patch Coordinates
by Sam Norman-Haignere 16 Apr '14

16 Apr '14

I assume that the units of the surface vertex coordinates in the flattened patches (e.g. in "rh.cortex.patch.flat.asc") correspond approximately to millimeters on the cortical surface. I was hoping someone could confirm this, because I couldn't find a definite answer searching online. Thanks, Sam Norman-Haignere BCS, MIT

2 1

TRACULA lesions
by Florian Borsodi 16 Apr '14

16 Apr '14

Dear Freesurfer TRACULA Experts, We are trying to run TRACULA on patients with lesions and found out, that TRACULA had problems tracking streamlines trough the lesions, which is understandable. The problem is, if TRACULA gets lost in the lesions, the whole streamline is not considered, even if the streamline until the lesion might be correct! Is there any possibility to hand TRACULA lesionmasks, so that the regions with lesions are ignored? If not, is there a possibility to maintain the lost streamlines, or at least parts of it? Thank you in advance for your help. With kind regards, Florian Borsodi, Lukas Pirpamer Department of Neurology Medical Universtiy of Graz

2 1

ask question about freeview
by kangchengwang0808＠gmail.com 16 Apr '14

16 Apr '14

Dear professors, I have installed freesurfer according to the description online. However, when display the a result by freeview, it did not show like usual. The detailed information was followed. First, I convert SPM result into the format that freeview can read. The following was command I use: mri_vol2surf --mov ${AC}.nii.gz --mni152reg --hemi lh --o surf/lh.${AC}.z.fsaverage.nii.gz --trgsubject fsaverage --interp nearest --noreshape --cortex mri_vol2surf --mov ${AC}.nii.gz --mni152reg --hemi rh --o surf/rh.${AC}.z.fsaverage.nii.gz --trgsubject fsaverage --interp nearest --noreshape --cortex Second, I open freeview and then load surface with the lh.white/rh.white of "$FREESURFER_HOME/ subjects/fsaverages5/surf". However, when I overlay the result, which was in the attachment, and click configure overlay. It shows like this : I don't know what to do now. Please guide me! Wang Kangcheng Faculty of Psychology, Southwest University, China Email: kangchengwang0808(a)gmail.com / wangkangcheng.001(a)163.com Address: No.2 Tiansheng Road, BeiBei District, Chongqing, 400715,P.R.China Welcome to our team: http://www.qiujlab.com/code/page/

2 1

QDEC error
by Saurabh Thakur 16 Apr '14

16 Apr '14

Hello Freesurfer Expert, I am getting some error while loading file in QDEC. Error in Analyze: command failed: mri_glmfit --y /home/saurabh/Desktop/saurabh_freesurfer/qdec/lh-thickness-age-fwhm-10-164/y.mgh --fsgd /home/saurabh/Desktop/saurabh_freesurfer/qdec/lh-thickness-age-fwhm-10-164/qdec.fsgd dods --glmdir /home/saurabh/Desktop/saurabh_freesurfer/qdec/lh-thickness-age-fwhm-10-164 --surf fsaverage lh --label /home/saurabh/Desktop/saurabh_freesurfer/fsaverage/label/lh.aparc.label --C /home/saurabh/Desktop/saurabh_freesurfer/qdec/lh-thickness-age-fwhm-10-164/contrasts/lh-Avg-Intercept-thickness.mat --C /home/saurabh/Desktop/saurabh_freesurfer/qdec/lh-thickness-age-fwhm-10-164/contrasts/lh-Avg-thickness-age-Cor.mat --C /home/saurabh/Desktop/saurabh_freesurfer/qdec/lh-thickness-age-fwhm-10-164/contrasts/lh-Diff-Female-Male-Intercept-thickness.mat --C /home/saurabh/Desktop/saurabh_freesurfer/qdec/lh-thickness-age-fwhm-10-164/contrasts/lh-Diff-Female-Male-Cor-thickness-age.mat Thanks in advance, Saurabh Thakur,

1 0

error in -base of FS longitudinal stream
by L. Koenders 16 Apr '14

16 Apr '14

Dear FreeSurfer people, I posted this question before, but I am a bit further as to where the problem lies. I have a question regarding the longitudinal pipeline. In FS v5.3.0, I ran all scans through the Cross pipeline, and made brainmask.mgz pial edits where necessary. So far so good. Subsequently, I ran all the scans (all the edited scans) through the Base pipeline. However, something is going wrong with the creation of the templates. We went through the logs, and found the following error in the logs of the failed scans: ====================== TP 2 to TP 1 ============================== Register TP 2 ( /data/home/shahand/test/104/104_FU/mri/norm.mgz ) to TP 1 ( /data/home/shahand/test/104/104_BL/mri/norm.mgz ) * WARNING: TP 2 to 1 did not converge !! computing coord of TP 2 ( /data/home/shahand/test/104/104_FU/mri/norm.mgz ) wrt to TP 1 ( /data/home/shahand/test/104/104_BL/mri/norm.mgz ) computing mean coord of TP 1 ( /data/home/shahand/test/104/104_BL/mri/norm.mgz ) mapping back to rot, err = 2.86707e-08 computing mean coord of TP 2 ( /data/home/shahand/test/104/104_FU/mri/norm.mgz ) mapping back to rot, err = 2.86707e-08 mapping movs and creating initial template... using median Writing final template: /data/home/shahand/long/104/104_template/mri/norm_template.mgz Writing final transforms (warps etc.)... Determinant( lta[ 0 ]) : 1 Determinant( lta[ 1 ]) : 1 registration took 4 minutes and 7 seconds I tried to find some more information on this warning in the FreeSurfer Mailinglist archives, but did not find anything useful. Can you tell me WHY this convergence didn't take place and more importantly - how to fix it?? Looking forward to hearing your thoughts on this. Have a good weekend! Best regards, Laura Koenders ________________________________ AMC Disclaimer : http://www.amc.nl/disclaimer ________________________________

2 2

long.qdec.table.dat
by Harry Hallock [hhal5293＠uni.sydney.edu.au] 16 Apr '14

16 Apr '14

Hi all, I am currently doing longitundal processing. I have gone through the turtoial but still cannot find the answer. When creating a long.qdec.table.dat, should the first column entitled "fsid" be long or cross data? Cheers, Harry Harry Hallock | MPhil Candidate Regenerative Neuroscience Group | Brain & Mind Research Institute THE UNIVERSITY OF SYDNEY Room 408, Level 4, M02K | 94 Mallett St Camperdown | NSW | 2050 | Australia T +61 2 9114 4138 F +61 9351 0930 E hhal5293(a)uni.sydney.edu.au | W www.rng.org.au

2 2

mri_glmfit matrix error
by Johnson, Eileanoir 16 Apr '14

16 Apr '14

Hi all, I am getting an error with my matrix when running mri_glmfit (ERROR: matrix is ill-conditioned or badly scaled, condno = 37799.3). I have tried both DODS and DOSS to counteract this, and I have also checked the correlation between variables (the highest was about .65). I have 8 classes (2 gender and four data collection sites) and 5 continuous variables. I want to examine the relationship between thickness and the last continuous variable (performance on a cognitive task) regressing out class and the other 4 continuous variables. Attached are my fsgd file, contrast files for DODS and DOSS and matrix files for DODS and DOSS. My command line is: mri_glmfit --y cognitive_correlations/lh.thickness10.mgh --fsgd sdmttest.fsgd --C sdmt_DODS.mtx --surf hdaverage_final lh --cortex --glmdir cognitive_correlations/lh Any help would be greatly appreciated!! Thanks, Eli Johnson

1 0

Surface-based label to a mask
by Reza Rajimehr 15 Apr '14

15 Apr '14

Hi, Is there an easy way to convert a surface-based label to a mask without going to Matlab? Thanks, Reza

2 1

Re: [Freesurfer] hippocampal subfield segmentation
by Mike Strupp-Levitsky 15 Apr '14

15 Apr '14

To whom it may concern, I'm writing in regard to the thread below about using the sum of the hippocampal subfield volumes (excluding the hippocampal fissure). I'm finding that they are moderate-highly correlated with the hippocampal volumes from ASEG (~.75-.85). Do you have a sense of which of these measures would be more reliable than the other? Thanks so much for your help!! Best, Mike On Wed, 2013-06-05 at 10:54 +0200, Claudia Dacquino wrote: > Thank you for your response. Would you suggest a reference I can refer > to? > > > > 2013/6/4 Juan Eugenio Iglesias <iglesias at nmr.mgh.harvard.edu> > I would probably leave out the fissure, but not the fimbria... > Cheers, > /Eugenio > > On Tue, 2013-06-04 at 14:33 +0200, Claudia Dacquino wrote: > > Hi guys! > > I have a dataset including hippocampal subfields obtained > through the > > -hippo-subfields flag. I want to have a measure of total > hippo volume > > and I'm not sure which structures should I include in the > sum. I was > > thinking to exclude fimbria and fissure and sum the others. > Am I > > right? Or should I simply sum all the structures? > > Any help is more than welcome > > Cheers, > > Fabrizio > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer at nmr.mgh.harvard.edu > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > -- > Juan Eugenio Iglesias, PhD > http://www.jeiglesias.com > iglesias at nmr.mgh.harvard.edu > Athinoula A. Martinos Center for Biomedical Imaging > 149 Thirteenth Street, Suite 2301 > Charlestown, Massachusetts 2129 > U.S.A. > > > > > > 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. > > -- Juan Eugenio Iglesias, PhD http://www.jeiglesias.com iglesias at nmr.mgh.harvard.edu Athinoula A. Martinos Center for Biomedical Imaging 149 Thirteenth Street, Suite 2301 Charlestown, Massachusetts 2129 U.S.A. ----------------------------------------------------------------------- Mike Strupp-Levitsky, BA Data Manager & Image Analyst Molecular Imaging & Neuropathology Division Columbia University, Department of Psychiatry New York State Psychiatric Institute, Suite 3920 (W): 646-774-7531 (C): 607-227-8811 Email: ms4637(a)columbia.edu

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