Freesurfer

freesurfer@nmr.mgh.harvard.edu

30132 discussions

Re: [Freesurfer] use of --a2009s flag
by Douglas N Greve 21 Nov '11

21 Nov '11

does that file exist? LAOUCHEDI MAKHLOUF wrote: > hi doug > i am using the v5.0.0 version, the massage i have when > running "mri_aparc2aseg --s ctr12 --a2009s" is : > ( SUBJECTS_DIR makh_free > subject ctr12 > outvol makh_free/ctr12/mri/aparc.a2009s+aseg.mgz > useribbon 0 > baseoffset 10100 > RipUnknown 0 > > Reading lh white surface > makh_free/ctr12/surf/lh.white > > Reading lh pial surface > makh_free/ctr12/surf/lh.pial > > Loading lh annotations from makh_free/ctr12/label/lh.aparc.a2009s.annot > could not read annot file makh_free/ctr12/label/lh.aparc.a2009s.annot > No such file or directory > ERROR: MRISreadAnnotation() failed > makh_free/ctr12/label/lh.aparc.a2009s.annot) > > same thing when using : --annot aparc.a2009s > > thanks for your help > > > --- En date de : *Lun 21.11.11, Douglas N Greve > /<greve(a)nmr.mgh.harvard.edu>/* a écrit : > > > De: Douglas N Greve <greve(a)nmr.mgh.harvard.edu> > Objet: Re: [Freesurfer] use of --a2009s flag > À: "LAOUCHEDI MAKHLOUF" <laoumakhl(a)yahoo.fr> > Cc: Freesurfer(a)nmr.mgh.harvard.edu > Date: Lundi 21 novembre 2011, 18h18 > > What version are you using? You can accomplish the same thing with > --annot aparc.a2009s > doug > > LAOUCHEDI MAKHLOUF wrote: > > hi everyone > > > > i am trying to use the mri_aparc2aseg command with > the > > --a2009s flag to have the aparc.a2009s labels and i have the > following > > message " Option --a2009s unknown" > > > > thanks > > > > > ------------------------------------------------------------------------ > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer(a)nmr.mgh.harvard.edu > </mc/compose?to=Freesurfer(a)nmr.mgh.harvard.edu> > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > greve(a)nmr.mgh.harvard.edu </mc/compose?to=greve(a)nmr.mgh.harvard.edu> > Phone Number: 617-724-2358 > Fax: 617-726-7422 > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html > > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu > </mc/compose?to=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. > -- Douglas N. Greve, Ph.D. MGH-NMR Center greve(a)nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html

1 0

reg-feat2anat
by Michelle Umali 21 Nov '11

21 Nov '11

Dear Freesurfers, I've previoiusly run reg-feat2anat on some fsl feat data, but now my advisor things i should re-preprocess my fsl data with a larger kernel size. Since it's the same dataset , do I have to re-run reg-feat2anat on this or can I just copy the registration folder from the old analysis? Thanks. Michelle

2 1

control points didn't work
by Tetiana Dadakova 21 Nov '11

21 Nov '11

Dear FreeSurfer list, I was trying to edit wm surface by adding control points. After saving them and re-running recon-all -autorecon2-cp -autorecon3, the control points are still there, but wm is not edited (although cp worked in other places for the same brain). The intensity there is around 95-98 depending on slice. Could you please suggest what could go wrong? Thank you, Tanja.

2 1

T1 mapping, mri_ms_fitparms and flip angle map
by Dr.med. Johannes C. Klein 21 Nov '11

21 Nov '11

Dear all, For a structural study, I would like to determine cortical T1 values. T1 map generation from two FLASH images works like a charm, and I would like to add B1 correction now. I have acquired flip angle maps for my subjects (using the Yarnykh method with interleaved FLASH and two TRs), and would like to correct my T1 maps accordingly. Looking at the online help of mri_ms_fitparms, I think the parameter -afi should do the trick. However, I'm not sure about the properties of the flip angle map that I need to supply to mri_ms_fitparms. Does that programme expect absolute flip angle values? Or can I feed in my two AFI FLASH volumes in some way? If anyone can point me in the right direction, that would be great! Thanks for you help, Johannes

2 3

when to invoke reg-feat2anat in fsl ppi
by Michelle Umali 21 Nov '11

21 Nov '11

Dear Freesurfers, I am using seeds based on Freesurfer masks to run a PPI analysis and am wondering if I am using reg-feat2anat at the right fsl feat registration step. First, I ran an fsl analysis to generate a feat directory. Then I ran reg-feat2anat using that feat directory. Next I ran aseg2feat and fslmaths to generate binary masks Next I extracted the timeseries by using the filtered func of the feat and the binary masks from aseg2feat. So now I want to do another feat analysis, but this time using the extracted timeseries But this timeseries is based on the first feat and associated masks from the reg-feat2anat registration. 1) Is it still valid to use this timeseries in this new feat since FSL will be running another registration? 2) Do I have to run reg-feat2anat again? Thanks. Michelle

2 1

use of --a2009s flag
by LAOUCHEDI MAKHLOUF 21 Nov '11

21 Nov '11

hi everyone i am trying to use the mri_aparc2aseg command with the --a2009s flag to have the aparc.a2009s labels and i have the following message " Option --a2009s unknown" thanks

2 1

mri_nu_correct error
by Baris Demiral 21 Nov '11

21 Nov '11

Hello everybody, I am trying to use mri_nu_correct.mni function in freesurfer on the XUbuntu system installed on the VirtualBox on a Windows 7 machine. I converted Siemens IMA into analyze format .img (with function; mri_convert -i input_file_name.IMA -ot analyze -o output_file_name.img), then when I called the function mri_nu_correect for the inhomogeneity correction, it gave me an error message (see below). What is wrong? Cheers, Baris FreeSurfer:~/Documents/EEGLAB/NFT/MPRAGE/7031> mri_nu_correct.mni --i S1.img --o S1inh.img --n 2/home/virtualuser/Documents/EEGLAB/NFT/MPRAGE/7031/home/virtualuser/freesurfer/bin/mri_nu_correct.mni--i S1.img --o S1inh.img --n 2nIters 2$Id: mri_nu_correct.mni,v 1.18 2011/03/02 20:16:39 nicks Exp $Linux FreeSurfer 2.6.28-11-generic #42-Ubuntu SMP Fri Apr 17 01:57:59 UTC 2009 i686 GNU/LinuxMon Nov 21 10:53:06 EST 2011Program nu_correct, built from:Package MNI N3, version 1.10, compiled by nicks@fishie (i686-pc-linux-gnu) on 2010-02-20 at 20:19:13tmpdir is ./tmp.mri_nu_correct.mni.3086/home/virtualuser/Documents/EEGLAB/NFT/MPRAGE/7031mri_convert S1.img ./tmp.mri_nu_correct.mni.3086/nu0.mnc -odt floatmri_convert S1.img ./tmp.mri_nu_correct.mni.3086/nu0.mnc -odt float $Id: mri_convert.c,v 1.179.2.1 2011/03/22 16:37:02 nicks Exp $reading from S1.img...TR=2400.00, TE=0.00, TI=0.00, flip angle=0.00i_ras = (-0.0286335, -0.999213, 0.0274527)j_ras = (-0.00717244, -0.0272578, -0.999603)k_ras = (-0.999564, 0.028819, 0.00638633)changing data type from short to float (noscale = 0)...writing to ./tmp.mri_nu_correct.mni.3086/nu0.mnc... --------------------------------------------------------Iteration 1 Mon Nov 21 10:53:10 EST 2011nu_correct -clobber ./tmp.mri_nu_correct.mni.3086/nu0.mnc ./tmp.mri_nu_correct.mni.3086/nu1.mnc -tmpdir ./tmp.mri_nu_correct.mni.3086/0/[virtualuser@FreeSurfer:/home/virtualuser/Documents/EEGLAB/NFT/MPRAGE/7031/] [2011-11-21 10:53:11] running: /home/virtualuser/freesurfer/mni/bin/nu_estimate_np_and_em -parzen -log -sharpen 0.15 0.01 -iterations 50 -stop 0.001 -shrink 4 -auto_mask -nonotify -b_spline 1 -distance 200 -quiet -execute -clobber -nokeeptmp -tmpdir ./tmp.mri_nu_correct.mni.3086/0/ ./tmp.mri_nu_correct.mni.3086/nu0.mnc ./tmp.mri_nu_correct.mni.3086/nu1.imp Assertion failed at line 827 in file templates/CachedArray.ccnu_estimate_np_and_em: crashed while running volume_stats (termination status=256)nu_correct: crashed while running nu_estimate_np_and_em (termination status=256)ERROR: nu_correct -- Ş. Barış Demiral, PhD. Department of Psychiatry Washington University School of Medicine 660 S. Euclid Avenue Box 8134 Saint Louis, MO 63110 Phone: +1 (314) 7477 1603

1 0

gcut memory requirements
by Michael Harms 19 Nov '11

19 Nov '11

Hello, Approximately how much memory does one need when using the -gcut option with FS 5.1? I had submitted 30+ recons to a cluster that alloted a default of 2.5 GB for processes submitted under this particular queue, and all of them aborted with a bad_alloc error at the gcut stage of skull stripping. Should 4 GB be sufficient? thanks, -MH -- Michael Harms, Ph.D. -------------------------------------------------------------------- Conte Center for the Neuroscience of Mental Disorders Washington University School of Medicine Department of Psychiatry, Box 8134 Renard Hospital, Room 6604 Tel: 314-747-6173 660 South Euclid Ave. Fax: 314-747-2182 St. Louis, MO 63110 Email: mharms(a)wustl.edu --------------------------------------------------------------------

2 1

Errors with recon-all -autorecon2
by Linda Zhang 19 Nov '11

19 Nov '11

Hi, I'd been having trouble with "recon-all -all -subjid [mysubject]", so I broke it down with -autorecon1 and -autorecon2. -autorecon1 worked fine, it seems that the problem is somewhere in -autorecon2. I've included the system information below, as well as the error message I got, and the recon-all log. I've tried this with another subject as well and the same error occurs. It'd be great if someone could tell me what the problem is and how I can fix it. --------------------------------------------------------------------- FREESURFER_HOME: /home/virtualuser/freesurfer Build stamp: freesurfer-Linux-centos4-stable-pub-v5.1.0 Debian version: squeeze/sid Kernel info: Linux 2.6.31-23-generic i686 --------------------------------------------------------------------- The command line: FreeSurfer:~/freesurfer/subjects> recon-all -subjid avo0260 -autorecon2 The error message: GCAMwrite(transforms/talairach.m3z): gzip encountered error. writing output transformation to transforms/talairach.m3z... GCAMwrite GCAMwrite:: m3z loop GCAMwrite:: the command is: gzip -f -c > transforms/talairach.m3z GCAMwrite:: the popen error code is: 12 mri_ca_register: GCAMwrite(transforms/talairach.m3z) failed ERROR: mri_ca_register with non-zero status 252 but continuing despite the error #-------------------------------------- #@# CA Reg Inv Fri Nov 18 11:23:25 EST 2011 /home/virtualuser/freesurfer/subjects/avo0260/mri mri_ca_register -invert-and-save transforms/talairach.m3z Loading, Inverting, Saving, Exiting ... Reading transforms/talairach.m3z ERROR: cannot find or read transforms/talairach.m3z ERROR: mri_ca_register with non-zero status 0 Linux FreeSurfer 2.6.31-23-generic #75-Ubuntu SMP Fri Mar 18 18:08:39 UTC 2011 i686 GNU/Linux recon-all -s avo0260 exited with ERRORS at Fri Nov 18 11:23:26 EST 2011 The recon-all.log and recon-all.error files are attached. Thanks for your time and help! Regards, Linda Zhang University of Hong Kong

2 1

Corpus Callosum Volume
by Alan Francis 18 Nov '11

18 Nov '11

Hi Bruce et al, Thanks for the stimulating discussion on the Hippocampal subfields. I have a question. How exactly does FS segment and parcellate the Corpus Callosum volume ? thanks again, Alan

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