Freesurfer November 2011

freesurfer@nmr.mgh.harvard.edu

110 participants
165 discussions

create an annotation file
by LAOUCHEDI MAKHLOUF 28 Nov '11

28 Nov '11

hi everyone i am new in freesurfer and i want to create a masque of some color made of somme régions labels (say for ex. the post central gyrus and precentral gyrus or any combination of geri and sulcus) to put it as a layer on an a pial or inflated surface. how can i proceed? thanks

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subjects with contrast medium
by LAOUCHEDI MAKHLOUF 28 Nov '11

28 Nov '11

hi everyone i am working on traumatic brain injury and noticed that some exams i received recently (T1datasets) were conducted using à contrast medium: sometimes the whole memisphere presents hypersignal. can i run recon-all (if there is a way) on such subjects? thanks

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running recon-all after editing aseg.mgz
by Maria Jalbrzikowski 28 Nov '11

28 Nov '11

Hi, I am a relatively new user of Freesurfer and have a couple questions. I have gone through the tutorials and I am now at the point where I check the segmentation. If I open my subject in tkemdit (*tkmedit your_subject_name brainmask.mgz -surfs -aseg) * and use the edit the segmentation and then press "save *segmentation", I am editing the aseg.mgz file, correct? After doing that, what parts of recon-all would I need to run again? Thanks, Maria *-- Maria Jalbrzikowski, M.A. University of California, Los Angeles

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longitudinal processing edema from lesion causing skewed registration
by kelsi 28 Nov '11

28 Nov '11

Hi, I am doing longitudinal processing of multiple subjects (each with 3 sessions) post stroke. However, some of the lesions are so extensive in the first session that they cause edema and push the brain midline. This greatly affects the pial surface on the lesioned hemishpere after longitudinal processing with the other sessions of the same subject. Is there anyway to fix this without manually editing the area? Would it help to register each session individually to fsaverage instead of registering them first across sessions? Thank you! Kelsi

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preproc-sess error with -per-session flag
by Elisa Scariati 28 Nov '11

28 Nov '11

Dear Freesurfers, I ran into an issue while trying to preprocess some resting state data. As I wished to use the first slice to correct for motion, I typed in this command : preproc-sess -s 5167/ -fsd bold -stc down -surface fsaverage lhrh -mni305-2mm -fwhm 6 -*per-session. * The error message was the following : ...... stc-sess Done 5167 To Surface ----------------------------- rawfunc2surf-sess -fwhm 6 -s 5167 -d /Applications/freesurfer/sessions -fsd bold -stc down -update instem fmcpr.down outstem fmcpr.down.sm6.fsaverage.hemi ------------------------------ 1/1 5167 1/1 5167 007 lh --------- Fri Nov 25 09:39:53 CET 2011 ERROR: could not determine file for /Applications/freesurfer/sessions/5167/bold/007/fmcpr.down When I use the middle slice as a reference slice with the command *-per-run *I don't have any problems. Does any one know where this is coming from? I see some people already had the same issue a while ago, does any one know if a solution was found? Cheers, Elisa Scariati

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ERROR with mri_nu_correct function
by Baris Demiral 27 Nov '11

27 Nov '11

Hi, I am trying to use mri_nu_correct.mni function in freesurfer on theXUbuntu 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 -ooutput_file_name.img), then when I called the function mri_nu_correctfor the inhomogeneity correction, it gave me an error message (seebelow). What is wrong? Cheers,Baris FreeSurfer:~/Documents/EEGLAB/NFT/MPRAGE/7031> mri_nu_correct.mni --iS1.img --o S1inh.img --n2/home/virtualuser/Documents/EEGLAB/NFT/MPRAGE/7031/home/virtualuser/freesurfer/bin/mri_nu_correct.mni--iS1.img --o S1inh.img --n 2nIters 2$Id: mri_nu_correct.mni,v 1.182011/03/02 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 2110:53:06 EST 2011Program nu_correct, built from:Package MNI N3,version 1.10, compiled by nicks@fishie (i686-pc-linux-gnu) on2010-02-20 at 20:19:13tmpdir is./tmp.mri_nu_correct.mni.3086/home/virtualuser/Documents/EEGLAB/NFT/MPRAGE/7031mri_convertS1.img ./tmp.mri_nu_correct.mni.3086/nu0.mnc -odt floatmri_convertS1.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 fromS1.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 typefrom short to float (noscale = 0)...writing to./tmp.mri_nu_correct.mni.3086/nu0.mnc...--------------------------------------------------------Iteration 1Mon 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.impAssertion failed at line 827 in filetemplates/CachedArray.ccnu_estimate_np_and_em: crashed while runningvolume_stats (termination status=256)nu_correct: crashed while runningnu_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

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Re: [Freesurfer] Skull stripping and RAM
by Mahinda Yogarajah 27 Nov '11

27 Nov '11

Dear Bruce and Freesurfer Experts, Thanks for the quick answer, Bruce, to previous post. As I work my way through all the checks on output I had a couple of other quick questions 1) I noticed by skull-stripping was poor (too aggerssive at the back of the brain with part of the occipital lobe and a small part of cerebellum). I therefore tried a number of suggestions from the tutorials including using -wsthresh 35 and -no-wsgcaatlas - this worked well but could someone explain why the lack of atlas use improves things ? 2) I also tried to improve skull stripping using the talairach_with_skull_2.lta option but I did not have this file despite recon-all -all having run fine the first time around with no errors/problems reported - should this concern me ? 3) I am using Centos 64 on a Linux box with 4 cores and 12 GB of RAM - how many instances of recon-all could I have running at the same time with no problems Thank you. Mo On Thu, Nov 24, 2011 at 4:01 PM, Bruce Fischl <fischl(a)nmr.mgh.harvard.edu>wrote: > Hi Mo, > > that's not a problem. We have different normalizations for different > pieces of the recon. For subcortical we use the norm.mgz, which should > *not* be eroding borders of thalamus, pallidum, etc.... The brain*.mgz are > for cortex, where we don't care about those borders. > > cheers > Bruce > > On Thu, 24 Nov 2011, Mahinda Yogarajah wrote: > > Dear Experts, >> >> I am a beginner to the use of Freesurfer and having just installed version >> 5.1.0 (Centos 64bit) I have been going through the processing pipeline >> with >> one of our own datasets (3T GE Excite II scanner - coronal T1-weighted >> volumetric acquisition sequence with 1.1-mm thick slices). recon-all >> works >> fine and I have been looking at the outputs. >> >> I have a question regarding the subcortical segmentation especially around >> the basal ganglia - during the intensity normalisation it appears to have >> assigned similar high (110) voxel values to parts of the internal capsule, >> pallidum and thalamus (pic1- brainmask.mgz), though the actual >> segmentation >> (pic2-aseg) looks reasonable when compared with the native image (pic3-raw >> T1) (though I appreciate one is normalised and the other is not). Should >> I >> be worried about this (and if so how can I correct ?) or is this intensity >> normalisation used only in the surface stream with a different intensity >> normalisation used in the volume stream ? Or ... is it used in the volume >> stream but the other parts of the model (eg priors from atlas etc) >> compensate in some way. >> >> Thanks. >> >> Mo >> >> PS I can post screen >> >> >> > > 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<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. >

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Re: [Freesurfer] Yeo_JNeurophysiol11_FreeSurfer networks
by Thomas Yeo 26 Nov '11

26 Nov '11

Hi Yolanda, Just to understand what you are doing, you have run BASGU throughrecon-all and you are trying to project the surface parcellation intothe anatomical volume of BASGU? The annotation we are providing is actually in fsaverage space, so youneed to first project the parcellation from fsaverage space to BASGUnative surface space before running mris_annot_to_segmentation toproject the parcellation into his/her anatomical volume. To project the parcellation from freesurfer surface space to thesubject's native surface space, I think you can use mri_surf2surf,although I am not sure if there's a more specific freesurfer functionthat is specialized for transferring annotation files. --Thomas On Sun, Nov 27, 2011 at 12:40 AM, Thomas Yeo <yeoyeo02(a)gmail.com> wrote: > Hi Yolanda, > > Just to understand what you are doing, you have run BASGU through > recon-all and you are trying to project the surface parcellation into > the anatomical volume of BASGU? > > The annotation we are providing is actually in fsaverage space, so you > need to first project the parcellation from fsaverage space to BASGU > native surface space before running mris_annot_to_segmentation to > project the parcellation into his/her anatomical volume. > > To project the parcellation from freesurfer surface space to the > subject's native surface space, I think you can use mri_surf2surf, > although I am not sure if there's a more specific freesurfer function > that is specialized for transferring annotation files. > > --Thomas > > On Thu, Nov 24, 2011 at 4:11 PM, Yolanda Vives <yvives(a)pic.es> wrote: >> Dear Freesurfer experts, >> >> I would like to use the Yeo_JNeurophysiol11_FreeSurfer parcellations with my >> dataset and I am not sure what I have to do. I have used the >> mris_annot_to_segmentation command but I have the following error: >> >> mris_annot_to_segmentation BASGU lh inflated >> ./fsaverage5/label/lh.Yeo2011_17Networks_N1000.annot >> ../Yeo_JNeurophysiol11_MNI152/Yeo2011_17Networks_ColorLUT.txt test >> reading /freesurfer/BASGU/surf/lh.inflated... >> reading colortable from annotation file... >> colortable with 18 entries read (originally MyColorLUT) >> mri_read(): couldn't determine type of file /freesurfer/BASGU/mri/T1 >> (null): could not read T1 for template volume >> >> I have a T1.mgz file inside mri/. Where could be the problem? Is this >> command appropriate? >> >> Thank you in advance, >> Yolanda >> >> _______________________________________________ >> 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. >> >> >

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Bad nu_noneck
by Jeff Sadino 26 Nov '11

26 Nov '11

Hello, I am having problems creating the nu_noneck file in fs500. Using the default stream, the front and back of the brain is clipped off, which seems to be causing significantly bad surfaces downstream. I changed the radius to 45 so that all of the brain is included, but then too much neck is left over, causing bad surfaces and a bad aseg downstream. I am running now in fs510 to see if I can copy over from there. If not, are there any recommendations on how to get a useful nu_noneck file? Thank you, Jeff Sadino

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what does the tk stand for in tksurfer?
by Martina Papmeyer 24 Nov '11

24 Nov '11

Hello, I have a very simple question but couldn't find an answer yet. What does the "tk" actually stand for in tksurfer and tkmedit? Many thanks for this info, Martina -- The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336.

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Freesurfer November 2011