Freesurfer

freesurfer@nmr.mgh.harvard.edu

30132 discussions

MRI Signal Dropout
by Victor Yee 17 May '11

17 May '11

Hello, We have some signal dropout at the top of the brain in some scans, possibly similar to Rutvik Desai's 02/18/10 post. However, in our case, FreeSurfer is not including any of the regions affected by the dropout in both its subcortical segmentation and cortical parcellation. Instead, FreeSurfer essentially begins to treat the gray/white boundary as the CSF/gray surface, and classifies white matter as gray matter. The severity of this issue seems to correlate with how severe the dropout is. I have tried running nu_correct (normalization) for up to 256 iterations. This produces a noticeable effect when visualizing the volumes in tkmedit, but has no effect on FreeSurfer's output. I can upload a sample subject, if desired. We are using FreeSurfer 5.0 x64 on a Sun Grid Engine operating servers running CentOS 4.5. Thank you, Victor Yee

2 2

No inflated brain...
by jim kroger 17 May '11

17 May '11

Hello, I am following the sequence in the "FreeSurfer Troubleshooting Reconstruction Work Flow" instructions, and am at step 8, FsTutorial/WhiteMatterEdits. It looks like the thalamus and corpus callosum are included as white matter, and the pial surface surrounds some subcortical structures. Assuming this is not correct, I decided to look at the inflated surface as suggested in the referenced page " Making Edits to the White Matter." Unfortunately when I issue: tksurfer wm1_edits_before rh inflated I only see what looks like a very small fraction of an egg shell for the rh, and nothing for lh. Can I check somehow to see why I have almost no inflated brain? Thanks, Jim -- Cell: 575-571-8274 Email: jkk251(a)gmail.com

2 9

ERROR: mpr2mni305 failed, see transforms/talairach_avi.log
by Pedro Paulo de Magalhães Oliveira Junior 17 May '11

17 May '11

I'm having this error in the recon-all #-------------------------------------------- #@# Talairach Mon May 16 16:38:01 EDT 2011 /usr/local/freesurfer/subjects/GAGRICOLA/mri talairach_avi --i orig.mgz --xfm transforms/talairach.auto.xfm ERROR: mpr2mni305 failed, see transforms/talairach_avi.log I've uploaded to the ftp at surfer.nmr.mgh.harvard.edu the talairach_avi.log, the orig.mgz (as ppj_orig.mgz) and the original nifti image as ga_2010.nii Any hints?

2 3

different V1 sizes for same subject in two different sessions
by Ritobrato Datta 17 May '11

17 May '11

Hello All, I have estimated V1 using Hinds and Fischl method for some subjects scanned on two different days. I've been going through the V1 surface area data for these. One thing that concerns me is that is seems that very different V1 sizes are reported for the same subject when scanned on different dates and each run through the cross sectional stream. I am trying to check the test-re-test values for these. Any idea why this is so and whats a better method to do the comparison ? Thanks Ri

2 1

Re: [Freesurfer] Question about volumetric group analysis
by Michael Harms 17 May '11

17 May '11

For subcortical structures, you could consider using a covariate measure that itself includes subcortical gray matter. Not sure if the latest FS version has such a measure automatically constructed or not. In the past, we have used "whole brain volume" as a covariate for analysis of both cortical and subcortical structures, with "whole brain volume" defined as the volume contained within the pial surface (obtained using mris_volume) minus the volume of the lateral ventricles (contained within the aseg). cheers, -MH On Tue, 2011-05-17 at 10:19 -0300, Fernanda Palhano wrote: > Thanks, Michael. > > I have a follow up question. > If I understood, I should use the total cortical gray matter volume to > control for a global change > in cortical brain volume, so for exemple, if I'm interested in the > volume of parahippocampal gyrus, > I can normalize this way. And, once I have the measures for both the > hemispheres separately, I have to use the total cortical gray matter > of each one > to normalize? > But for other structures like hippocampus or amigdala it makes sense > to control using volume of gray matter? Or, I continue using the ICV? > > Thanks again, > > > On Tue, May 17, 2011 at 9:57 AM, Michael Harms > <mharms(a)conte.wustl.edu> wrote: > > Hi Fernanda, > The choice between ICV vs a measure of total "brain volume" or > total > cortical gray matter volume depends on whether you want to > control for > potential overall brain atrophy. Using ICV will control for > overall > "head size", but not for potential overall brain atrophy > (e.g., with > age, or related to dementia). Using total cortical gray > matter will > control for overall brain atrophy and thus would allow you to > say that > changes in a given structure were "above and beyond" any > existing global > atrophy. > > Personally, I find it more informative to control for > potential global > atrophy, and thus use total cortical gray matter rather than > ICV. After > all, if a structure is decreased in size, but the overall > brain is > decreased as well, you have not established anything regarding > the > specificity of that change to the structure of interest if you > use ICV > as the covariate. > > cheers, > -MH > > > On Tue, 2011-05-17 at 09:19 -0300, Fernanda Palhano wrote: > > Hello, > > > > I have two questions about volumetric analysis: > > First: Are the volume measures in the files aseg.stats or ? > > h.aparc.stats (Gray Matter Volume) already normalized by > ICV? Or > > should I divide > > all the structure volumes which I want to compare between > subjects by > > the ICV of each subject? > > Second: When comparing gray matter volumes the correct is > use the ICV > > or the total cortical gray matter volume to normalize? And > if I have > > to use the total cortical gray matter volume, how can I > obtain it? I > > know that this information is in the aseg.stats file, but I > was > > wondering if I can use asegstats2table to extract it. > > > > > > Thank you very much, > > > > Fernanda > > > > > _______________________________________________ > > 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

Question about volumetric group analysis
by Fernanda Palhano 17 May '11

17 May '11

Hello, I have two questions about volumetric analysis: First: Are the volume measures in the files aseg.stats or ?h.aparc.stats (Gray Matter Volume) already normalized by ICV? Or should I divide all the structure volumes which I want to compare between subjects by the ICV of each subject? Second: When comparing gray matter volumes the correct is use the ICV or the total cortical gray matter volume to normalize? And if I have to use the total cortical gray matter volume, how can I obtain it? I know that this information is in the aseg.stats file, but I was wondering if I can use asegstats2table to extract it. Thank you very much, Fernanda

4 3

Segmentation Fault
by Chindhuri Selvadurai 17 May '11

17 May '11

Hi all, We are trying to run individual analyses on several subjects, and we keep getting a 'Segmentation Fault.' We have run other subjects with the same command a while ago, and the command worked fine at that time. Do you have any idea what would be causing this error? The output is included below: Command: selxavg3-sess -analysis mandyrh3 -fwhm -s PBMCT15 Subjects Dir: /cluster/manoach/milton/subjects FreeSurfer v. Stable 5 Session: /autofs/cluster/manoach/milton/subjects/PBMCT15 ---------------- Fri May 13 12:21:58 EDT 2011 Run: 012 ---------------- Fri May 13 12:21:58 EDT 2011 Update not needed Fri May 13 12:21:58 EDT 2011 register-sess completed PBMCT15 MC ----------------------------- mc-sess -fstem f -fmcstem fmcpr -s PBMCT15 -d /autofs/cluster/manoach/milton/subjects -fsd bold -rlf task -per-run -nolog -update Logfile is /dev/null ------------------------------------------- /autofs/cluster/manoach/milton/subjects/PBMCT15 RunList: 012 ------- ************************** ----------- ------- Motion Correcting Run 012 ----------- ------- ************************** ----------- sess = PBMCT15 Fri May 13 12:21:58 EDT 2011 mc-afni2 --i 012/f.nii --t 012/template.nii --o 012/fmcpr.nii.gz --mcdat 012/fmcpr.mcdat /autofs/cluster/manoach/milton/subjects/PBMCT15/bold mri_info --nframes --o /tmp/mriinfo.3377 012/template.nii log file is 012/fmcpr.nii.gz.mclog mcdat file is 012/fmcpr.mcdat tmp dir is 012/tmp.mc-afni2.3377 #@# -------------------------------- /autofs/cluster/manoach/milton/subjects/PBMCT15/bold mri_convert 012/template.nii 012/tmp.mc-afni2.3377/tempvol.nii.gz --nskip 0 --ndrop 0 -odt float mri_convert 012/template.nii 012/tmp.mc-afni2.3377/tempvol.nii.gz --nskip 0 --ndrop 0 -odt float nskip = 0 ndrop = 0 $Id: mri_convert.c,v 1.179.2.1 2011/03/22 16:37:02 nicks Exp $ reading from 012/template.nii... TR=3000.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-0.998297, -0.0395807, 0.0428535) j_ras = (0.0411249, -0.998513, 0.0357732) k_ras = (0.0413739, 0.0374746, 0.998441) changing data type from short to float (noscale = 0)... writing to 012/tmp.mc-afni2.3377/tempvol.nii.gz... #@# -------------------------------- /autofs/cluster/manoach/milton/subjects/PBMCT15/bold mri_convert 012/f.nii 012/tmp.mc-afni2.3377/invol.nii.gz -odt float mri_convert 012/f.nii 012/tmp.mc-afni2.3377/invol.nii.gz -odt float Segmentation fault Thanks! Best, Chindhuri Selvadurai Psychiatric Neuroimaging, Manoach Lab Martinos Center for Biomedical Imaging, MGH Phone: (617)726-0307

3 4

missing tutorial data for Longitudinal Processing - Tutorial
by Knut J Bjuland 17 May '11

17 May '11

Hi I am trying to follow the Longitudinal Processing - Tutorial but it appear that the tutorial data is missing at the server? Has the file been rename or moved to another place? Knut J Bjuland

2 1

Re: [Freesurfer] freeview: creating ROIs, measuring volume
by Lynette Silva 16 May '11

16 May '11

Thanks Ruopeng, I tried tracing the outline with the freehand tool, and I also tried setting waypoints around the surface area of my ROI. What tools would you recommend? Thanks again! Lynette On Mon, May 16, 2011 at 3:46 PM, Ruopeng <rpwang(a)nmr.mgh.harvard.edu> wrote: > When you say tracing an ROI by hand in freeview, did you fill it or just > traced the outline? In any case, you will need to do this on each slice > by hand. However, there're various options and tools in freeview that > may help speed up the process dramatically. > > Ruopeng > > On 5/16/11 5:12 PM, Lynette Silva wrote: >> Hello All, >> >> I think I am missing a key step in creating an ROI in freeview. I have >> been tracing an ROI by hand in freeview, and saving as a label. Then I >> use mri_label2vol followed by mri_label_volume, and this works >> GREAT... except the output has far too few voxels to be the whole >> volume of my ROI. >> >> How can I select my ROI in three planes in freeview so that I can >> eventually get a volume output in mm^3? Someone here suggested I >> trace by hand on every slice in every view, but that can't be the way >> it's done, is it (please say it isn't)? >> >> Thanks! >> Lynette >> > > _______________________________________________ > 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. > > -- Lynette M. Silva, M.S. Doctoral Candidate Department of Psychology University of New Mexico

2 1

freeview: creating ROIs, measuring volume
by Lynette Silva 16 May '11

16 May '11

Hello All, I think I am missing a key step in creating an ROI in freeview. I have been tracing an ROI by hand in freeview, and saving as a label. Then I use mri_label2vol followed by mri_label_volume, and this works GREAT... except the output has far too few voxels to be the whole volume of my ROI. How can I select my ROI in three planes in freeview so that I can eventually get a volume output in mm^3? Someone here suggested I trace by hand on every slice in every view, but that can't be the way it's done, is it (please say it isn't)? Thanks! Lynette -- Lynette M. Silva, M.S. Doctoral Candidate Department of Psychology University of New Mexico

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