Freesurfer

freesurfer@nmr.mgh.harvard.edu

1 participants
30089 discussions

Re: [Freesurfer] cortical parcellation question
by Daniel Ferreira 30 Oct '12

30 Oct '12

Hello again, Thanks for all the information Bruce. Is it not possible to back-project the regions defined in the 2D surface-based spherical coordinate system onto the mean_intensity.nii image? As those regions in the 2D surface-based coordinate system would have been initially defined on a 3D volume(s) and transformed (inflated) to the 2D spherical surface? Daniel ---------- Forwarded message ---------- From: Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> Date: 2012/10/11 Subject: Re: [Freesurfer] cortical parcellation question To: Daniel Ferreira <daniferp(a)gmail.com> Cc: freesurfer(a)nmr.mgh.harvard.edu Hi Daniel, no, sorry. The gca is not a cortical atlas. Those labels are stored in the .gcas file and aren't in the same space (in fact, they are in a surface-based spherical coordinate system and not in the volume at all, so not easily combinable). Bruce On Thu, 11 Oct 2012, Daniel Ferreira wrote: Thanks for the detailed information. > > The mean intensity image (mean_intensity.nii) generated from frame #1 is > almost exactly what I need. This image has all the sub-cortical regions > assigned a discrete integer number (i.e. all the voxels in the left > cerebelllar grey matter = 8 and right = 47). However the whole of the > neocortex is defined as left (intensity = 3) and right (intensity = 42) > only, there are no cortical sub-divisions. > > Is it possible to have the individual neocortical regions assigned a > discrete integer number; (obviously not one already assigned to the other > regions in the mean_intensity.nii image)? For example all inferior temporal > voxels = 9; middle temporal voxels = 10; superior temporal voxels = 11. So > each of the regions defined in the "colortable_desikan_killiany.**txt" > file > found in the FREESURFER_HOME/average/ directory are also defined in the > mean_intensity.nii image? > > Thanks > > > 2012/10/6 Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> > Hi Daniel > > it's in .gca format, and includes information that wouldn't fit > in a nifti file (e.g. markov relationships). You can use > mri_convert to extract some of the basic info though (e.g. the > most likely class at each location and the mean intensity of the > most likely class) using mri_convert. For example: > > mri_convert $FREESURFER_HOME/average/RB_**all_2008-03-26.gca#0 > ./labels.nii > mri_convert $FREESURFER_HOME/average/RB_**all_2008-03-26.gca#1 > ./mean_intensity.nii > > > where the #<n> syntax mean extract the nth frame from the 4D gca > volume. Frame 0 is the most likely label and frame 1 is the mean > intensity. Note however that there is lots more info in the .gca > that this doesn't capture such as the MRF parameters I mentioned > above, class variances, other class probabilities, etc.... > cheers > Bruce > > > > > On Thu, 4 Oct 2012, Daniel Ferreira wrote: > > Thanks Bruce, > When you say the atlas itself is included in the > Freesurfer distribution, do > you mean there is a 3D version of it available in > the download? > Also, I am not looking for the individual subjects' > images, I just want a > copy of the final atlas as a 3D image in > analyze/nifti format. (i.e. in the > same format as the Harvard-Oxford atlas that is > downloaded with FSL). > > Thanks a lot. > > Daniel Ferreira > > > > 2012/10/3 Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> > Hi Daniel, > > 1. Do you mean the atlas or the parcellation > of your subjects? > We cannot distribute the individual subjects > in the atlas as the > data was collected under an IRB long ago that > didn't include > this. The atlas itself (summary statistics > derived from those > subjects) is included in the FreeSurfer > distribution. > > 2. The subcortical areas are the same, but not > the cortical > ones. That cortical parcellation is quite > coarse, and while we > did implement it we were never given > permission to distribute > the automated version, so it is not part of > FreeSurfer. The > boundaries that we define are thus different > than that one (and > since the Harvard-Oxford one is based on > volumetric labeling of > folding patterns we found that it contained a > bunch of errors in > which e.g. the wrong side of a sulcus was > labeled) > > cheers > Bruce > > > On Wed, 3 Oct 2012, Daniel Ferreira wrote: > > Dear experts, > I have a couple of questions regarding > the cortical > parcellation atlas that > is used in Freesurfer: > > 1) I would like to know if it is > possible to obtain > the Desikan-Killiany > atlas in 3D analyze/nifti format. With > each region > of the brain assigned a > discrete integer number (for example the > all of the > voxels of the left > inferior temporal lobe have an intensity > = 1, or > the whole of the left > hippocampus = 2). > > 2) Are the Harvard-Oxford cortical and > subcortical > atlases that can be > downloaded with FSL the same as the > cortical > parcellation atlas that is used > in Freesurfer? (i.e. are the > neuroanatomical > boundaries the same; does the > left inferior temporal cortex in the > Freesurfer > cortical parcellation = the > left inferior temporal cortex in the > Harvard-Oxford > atlas downloaded with > FSL) > > Many thanks > > Daniel Ferreira > > > > > > > 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. > > > > > >

2 2

which version of FS to use?
by Chunhui Chen 29 Oct '12

29 Oct '12

Dear Freesurfers, I just read this paper about freesurfer version and operating system matters: Gronenschild EHBM, Habets P, Jacobs HIL, Mengelers R, Rozendaal N, et al. (2012) The Effects of FreeSurfer Version, Workstation Type, and Macintosh Operating System Version on Anatomical Volume and Cortical Thickness Measurements. PLoS ONE 7(6): e38234. doi:10.1371/journal.pone.0038234 http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0038234 I am running freesurfer on linux system, and installed both version 4.5 and 5.1, and currently using 5.1. So which version is most recommended? should I use other versions like 5.0 or the coming 5.2? Any suggestion is appreciated

2 4

Problems to create my own template
by Bernd Merkel 29 Oct '12

29 Oct '12

Dear all, just having started using Freesurfer, I have the following question which has also been touched by other people but I couldn't find a solution for my problem. I have about 100 subjects from which I want to create my own template to be used by Freesurfer. These have been my steps: 1. recon-all (on all my subjects) 2. make_average_subject --subjects (list of all subjects) 3. I wanted to use the code provided on the Wiki: for subject in 'subjectList.txt'; do cd $SUBJECTS_DIR/subject mris_register -curv surf/lh.sphere $SUBJECTS_DIR/newtemplate/lh. reg.template.tif surf/lh.sphere.reg.newtemplate end The first two steps went fine. But I do not know how to handle that template.tif-File, because that hasn't been created as a result during my second step. Have I missed something ? Furthermore there is this other command mris_make_template but I do not know whether (and where in my processing) I should use that (perhaps instead of make_average_subject) ? Thanks for any help, Bernd

2 1

error: 'fast_contrastmtx' undefined near line 25 column 21
by Garlinghouse, Matthew 29 Oct '12

29 Oct '12

Dear Surfers, I was running mkcontrast-sess with Matlab and having good success. Then wanted to try Octave for ease of use on a cluster I have access to, and after browsing the listserv set the following: export FS_USE_OCTAVE=1 export FS_OCTAVE_LIB=/usr/lib64/octave export FS_OCTAVE_BIN=/usr/bin/octave However when I run mkcontrast-sess now (on the cluster and a VB ubuntu machine, both without Matlab), it runs through launching Octave and then errors out as noted below. I'm new to using Octave and wasn't sure what else I might need to set up for it to run properly? Any thoughts would be much appreciated. Best Regards, Matthew brain@neurodebian:/usr/local/freesurfer/subjects$ mkcontrast-sess -analysis test.08.lh -contrast faces_gt_objects -a 2 -c 3 INFO: Found 3 Non-Null Conditions INFO: Found 1 Delays Condition Weights: 0 1.00000000000000000000 -1.00000000000000000000 mkcontrast -anadir test.08.lh -wcond 0 1.00000000000000000000 -1.00000000000000000000 -sumconds -o test.08.lh/faces_gt_objects.mat -wdelay 1 -octave $Id: mkcontrast,v 1.10 2010/07/16 16:20:10 greve Exp $ cmtxfile test.08.lh/faces_gt_objects.mat nconds 3, wcond 0 1.00000000000000000000 -1.00000000000000000000 ndelays 1, wdelay 1 ndelays 1, wpsa sumconds 1 sumdelays 0 nircorr 0 TER 0.050000 rdelta rtau GNU Octave, version 3.2.4 Copyright (C) 2009 John W. Eaton and others. This is free software; see the source code for copying conditions. There is ABSOLUTELY NO WARRANTY; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. For details, type `warranty'. Octave was configured for "i486-pc-linux-gnu". Additional information about Octave is available at http://www.octave.org. Please contribute if you find this software useful. For more information, visit http://www.octave.org/help-wanted.html Report bugs to <bug(a)octave.org> (but first, please read http://www.octave.org/bugs.html to learn how to write a helpful report). For information about changes from previous versions, type `news'. error: `fast_contrastmtx' undefined near line 25 column 21 ________________________________ The Nebraska Medical Center E-mail Confidentiality Disclaimer The information in this e-mail may be privileged and confidential, intended only for the use of the addressee(s) above. Any unauthorized use or disclosure of this information is prohibited. If you have received this e-mail by mistake, please delete it and immediately contact the sender.

2 1

Different steps of RecommendedRecontruction on different operating systems possible?
by Thomas Fink 28 Oct '12

28 Oct '12

Dear Freesurfers, I know that differences in FS versions and operating systems can lead to different results. Thus my question: Would it be possible/advisable to run different steps of the RecommendedRecontruction on different operating systems? I would like to do talairach and control points for all my healthy subjects on a Linux based computer (Suse) and then switch to a Mac (OS X Mountain Lion) for further steps and use 5.1 on both machines. Thank you very much for your time. Thomas

3 2

make_face_parcellation ambiguous color table
by Franz Liem 26 Oct '12

26 Oct '12

Dear Freesurfers, I have performed make_face_parcellation on fsaverage (with ic5) (Darwin-leopard-i686-stable-pub-v5.1.0). I read_annotation ed the parcellation into matlab an noticed that while colortable.table has 10242 rows (as expected), length(unique(colortable.table(:,5))) produces 9834 => some entries are in the list more than once. If I grasped the procedure correctly, the entries in label are determined by colortable.table(:,5) and colortable.table(:,5) is determined by: % Column 5 is the structure ID, calculated from % R + G*2^8 + B*2^16 + flag*2^24 One example for this problem is colortable.table(43,:) and colortable.table(86,:) both read: 0 0 170 0 11141120 How are Rm G, B determined? I guess one quick fix would be to introduce flags >0. Would that affect anything else? Or, is there a way to force my own indices onto colortable.table(:,5)? (if I change this entry, save the annot and load the annot, the entry is at R + G*2^8 + B*2^16 + flag*2^24 again (I already encountered the effects of this problem a couple of months ago (2. in this post http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg21189.html).) Thank you so much for your help, Franz

2 4

Retinotopy: Group map on fsaverage
by Andreas Schindler 26 Oct '12

26 Oct '12

Dear freesurfers Have you ever tried to get an average retinotopic map across all subjects on freesurfer's standard surface (fsaverage)? I obtained an individual map for each subject using the fsfast stream (mkanalysis-sess, selxavg3-sess) and plotted the results using rtview: e.g. rtview.sh --s subj1 --lh --polar --real polar/real.nii.gz --imag polar/imag.nii.gz --fsig polar/fsig.nii.gz Now for the group map, my initial idea was to sample each subject's real and imaginary component to the fsaverage surface and average them separately across subjects. However, I am not sure how I would threshold such an average map on fsaverage using rtview (i.e. what would I use as fsig.nii) given that averaging log p-values is probably not a good idea. Within each subject's rtopy.self.?/polar(or /eccen) folder the following files (and few more but probably not important here) exist: fsig.nii -> I understand this contains the unsigned log p values probably obtained via an F-test (frequency of interest) / (noise frequencies) sig.nii -> this might then be the signed counterpart of fsig.nii imag.nii -> this must contain the imaginary component of the polar angle or eccen map real.nii -> this must contain the real component of the polar angle or eccen map mag.nii -> I suppose this might contain the amplitude of the signal at the frequency of interest (i.e. the frequency the wedge / ring is traveling) However, I don't quite know what the remaining files are good for iminsig.nii minsig.nii cwmap-imag.nii cwmap-real.nii ces.nii cesmag.nii cesmagpct.nii cespct.nii cesvar.pct cesvarpct.nii For the ces* files I understand that they generally contain effect sizes / variances and are used for group analyses. However, I am not quite sure what effects they correspond to in the case of retinotopy. When browsing the web for similar problems I found the following post: > Hi Michelle, try this: > > isxconcat-sess -sf sessidlist -a rtopy.fsaverage.lh -call -o retgroup > > cd retgroup/rtopy.fsaverage.lh > > mri_glmfit --y eccen/ces.000.nii.gz --osgm --o eccen/glm.real --surface > fsaverage lh > mri_glmfit --y eccen/ces.001.nii.gz --osgm --o eccen/glm.imag --surface > fsaverage lh > mri_glmfit --y polar/ces.000.nii.gz --osgm --o polar/glm.real --surface > fsaverage lh > mri_glmfit --y polar/ces.001.nii.gz --osgm --o polar/glm.imag --surface > fsaverage lh > > mri_fieldsign --fs lh.fieldsign.mgh \ > --eccen eccen/glm.real/osgm/gamma.mgh eccen/glm.imag/osgm/gamma.mgh \ > --polar polar/glm.real/osgm/gamma.mgh polar/glm.imag/osgm/gamma.mgh \ > --s fsaverage --hemi lh --sphere --old > > tksurfer fsaverage lh inflated -aparc -ov lh.fieldsign.mgh -fthresh .5 However, as mentioned above I wonder what effect sizes are used here and why (different to rtview) there is no significance map needed to plot the data. Is there a way to use rtview for the result of a group analysis? And if yes how would I get a fsig.nii file for that? I really appreciate your help! many thanks & best wishes Andreas

2 1

Cannot save edited label
by Jürgen Hänggi 26 Oct '12

26 Oct '12

Dear FS experts I used mri_annotation2label to extract the superior frontal gyrus label from the aparc annotation. I edited (cut plane) this label in tksurfer and then tried to save it using Save Selected Label. However, the whole label is saved including also the part that I have cut away. Any idea what is going wrong here? Thanks in advance Regards Jürgen ---------------------------------------------------------------------------- Jürgen Hänggi, Ph.D. Division Neuropsychology Institute of Psychology University of Zurich Binzmuehlestrasse 14, PO Box 25 8050 Zurich, Switzerland 0041 44 635 73 97 (phone office) 0041 76 445 86 84 (phone mobile) 0041 44 635 74 09 (fax office) BIN 4.D.04 (office room number) j.haenggi[at]psychologie.uzh.ch (email) http://www.psychologie.uzh.ch/neuropsy/ (website) http://www.juergenhaenggi.ch (private website) This e-mail (and any attachment/s) contains confidential and/or privileged information. If you are not the intended recipient (or have received this e-mail in error) please notify the sender immediately and destroy this e-mail. Any unauthorised copying, disclosure or distribution of the material in this e-mail is strictly forbidden. ----------------------------------------------------------------------------

2 3

recon-all crash
by Jesse Bledsoe 25 Oct '12

25 Oct '12

Hello experts, Wonder if you could help me with the following error after running "recon-all -all -subjid BT6403 -qcache": ---------- unfolding failed - restoring original position -------------------- 0581: dt=0.112000, rms=0.602 (0.000%), neg=0, invalid=766 writing output transformation to transforms/talairach.m3z... GCAMwrite GCAMwrite:: m3z loop GCAMwrite:: the command is: gzip -f -c > transforms/talairach.m3z registration took 2 hours, 50 minutes and 30 seconds. /var/local/scratch/bledsoe1/ Desktop/Braintumor/BT_6403/touch/ca_register.touch: No such file or directory. bledsoe1 @ivan:~/Desktop/Braintumor/BT_6403$ Build stamp: freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0 Any suggestions are much appreciated, Jesse

1 0

znzTAGskip error using mri_em_register
by Kim, Daniel 25 Oct '12

25 Oct '12

Hello FreeSurfer users, I was finally able to compile mri_em_register successfully from source and trying to test the build with subject 'bert', I ran into this error ~/freesurfer/bin# ./mri_em_register -uns 3 -mask $SUBJECTS_DIR/bert/mri/brainmask.mgz $SUBJECTS_DIR/bert/mri/nu.mgz $FREESURFER_HOME/average/RB_all_2008-03-26.gca $SUBJECTS_DIR/bert/mri/transforms/talairach.lta aligning to atlas containing skull, setting unknown_nbr_spacing = 3 using MR volume /usr/local/freesurfer/subjects/bert/mri/brainmask.mgz to mask input volume... reading 1 input volumes... logging results to talairach.log reading '/usr/local/freesurfer_4_5_0/freesurfer/average/RB_all_2008-03-26.gca'... average std = 6.9 using min determinant for regularization = 4.7 0 singular and 1812 ill-conditioned covariance matrices regularized reading '/usr/local/freesurfer/subjects/bert/mri/nu.mgz'... znzTAGskip: tag=-8454144, failed to calloc 4286513152 bytes! Cannot allocate memory Has anyone had similar error before? I'm using Ubuntu 10.04 LTS- 64 bit and I've built mri_em_register from scratch using CVS public checkout "-P dev" The test subject was through installing freesurfer 5.1.0 and also same has happened with freesurfer 4.5.0 Any help with this would be again greatly appreciated! Cheers! Danny Kim

2 2

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