Freesurfer

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30132 discussions

Changing labels of aseg.mgz to {BG, CSF, GM, WM}
by Andreas Schuh 26 Oct '11

26 Oct '11

Hi FreeSurfers, The results of FreeSurfer include a subcortical segmentation and a segmentation of white matter only. However, there is no segmentation of (background), cerebrospinal fluid, gray matter, and white matter only as produced by other tools. Such segmentation is often (as in our case) required for an evaluation study. Thus, relabeling the subcortical segmentation (mri/aseg.mgz) should be an option. Find attached a C++ implementation of such program, depending only on the nifticlib library. Questions: a) Does this mapping of FreeSurfer labels to the classes BG, CSF, GM, and WM look correct? Note that it is mainly based on Table 41 on page 71 of the master thesis of Kowkabzadeh found on the web [1]. b) Is there already such tool in the FreeSurfer package actually? I have seen mentioning of mri_compute_volume_fractions on this mailing list but could not figure how to use it. (A more meaningful help output of the tools would be nice... in particular what [options] are available). Thanks, Andreas [1] K. Kowkabzadeh, Evaluations of Tissue Segmentation of brain MR Images, Master of Science Thesis in Biomedical Engineering, Department of Signals and Systems, Division of Biomedical Engineering, Chalmers University of Technology, Göteborg, Sweden, 2010 Report No. EX048/2010, http://publications.lib.chalmers.se/records/fulltext/125991.pdf

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Remote tkmedit/qdec segmentation fault
by Martijn Steenwijk 26 Oct '11

26 Oct '11

Dear all, I would like to use Freesurfer's (5.1.0, 64bit) gui interfaces remotely to inspect Freesurfer's results produced on a server. I used two setups in an attempt to realize this: 1. PuTTy with X11 forwarding and Xming 2. TightVNC with VirtualGL In both configurations, entering for example the command 'tkmedit' or 'qdec' (or in case 2 'vglrun cmd') results in a segmentation fault. In another thread I found the suggestion to 'setev QDEC_DONT_USE_HISTOGRAM_EDITOR 1', but unfortunately this doesn't help. Do you have any ideas to fix this? Thanks in advance, Martijn

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gray scale inflated surf rendering prob
by Gregory Kirk 26 Oct '11

26 Oct '11

send a question that martina asked before and we have not solved the prob. on macs when we run tksurfer xxx lh inflated for example the surf comes up looking smoother,low resolution rendered. if we load something like curvature that displays in color the surface looks fine, so the problem is only with the grayscale surfaces. this occurs on all the macs in a psychiatry dept. lab,other macs at other labs around the surfs always appear normal, i have never seen this problem before, the machines used to display the surfs normally and then all of a sudden it started happening all the time on this one group of macs, seems it must be associated with some config change or upgrade,but i am not much of a mac uses, i use linux. anybody out in freesurfer land seen something like this and can give me a clue ? thanks greg

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-notalcheck question
by Christopher McCarthy 26 Oct '11

26 Oct '11

Freesurfer Experts, I am having lots of success, and making progress, with FreeSurfer thus far. I have been able to load DICOMS into Slicer3 to reorient, and resample them, after using FSL to extract the brain. Loading these brains into FreeSurfer is straight forward, and I've run them through the entire process. However, I am still hoping to use brains that have been previously skull stripped but are unfortunately saved in analyze (.img, .hdr) format. All of the things that I've tried have led to a talairach error, and the brain being incorrectly oriented when loaded in tkmedit. Using slicer3, however, I was able to load the .img file and put the brain in ACPC space using the ACPC registration module included. It still gives me a talaraich error, but if I run recon1 with -notalcheck, the process runs without error and the brain is correctly oriented in tkmedit. Is this data usable? If I run it with notalcheck will I be unable to use volumetric analysis reliably? Thanks for your help and patience! Chris McCarthy

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CUDA Error in file '/space/freesurfer/build/minerva/stable/dev/include/ctfactory.hpp' on line 92 : invalid texture reference
by Hemant Bokil 25 Oct '11

25 Oct '11

Hi all, Here are the details of my freesurfer and linux installations FREESURFER_HOME: /usr/local/freesurfer Build stamp: freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0 RedHat release: CentOS Linux release 6.0 (Final) Kernel info: Linux 2.6.32-71.29.1.el6.x86_64 x86_64 I successfully ran autorecon2 without gpu on several datasets that we have. However, when I try to use the GPU, I get the following error message: CUDA Error in file '/space/freesurfer/build/minerva/stable/dev/include/ctfactory.hpp' on line 92 : invalid texture reference The calling sequence and all on-screen messages are listed at the end of this email. A similar error was reported a year ago by a different user ( https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2010-August/015528.h…) so I am hoping there is a simple fix. Thanks in advance, Hemant recon-all -subjid 203 -use-gpu -autorecon2 Testing for CUDA device: nvcc: NVIDIA (R) Cuda compiler driver Copyright (c) 2005-2010 NVIDIA Corporation Built on Thu_Nov__4_12:44:17_PDT_2010 Cuda compilation tools, release 3.2, V0.2.1221 Driver : 4.10 Runtime : 3.20 Acquiring CUDA device Using default device CUDA device: Quadro FX 4600 stable5 NVIDIA driver version info: NVRM version: NVIDIA UNIX x86_64 Kernel Module 285.05.09 Fri Sep 23 17:31:57 PDT 2011 Subject Stamp: freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0 Current Stamp: freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0 INFO: SUBJECTS_DIR is /home/hemant/FreeSurferSubjects Actual FREESURFER_HOME /usr/local/freesurfer -rw-rw-r--. 1 hemant hemant 226454 Oct 24 15:05 /home/hemant/FreeSurferSubjects/203/scripts/recon-all.log Linux Lab-3.intelect.local 2.6.32-71.29.1.el6.x86_64 #1 SMP Mon Jun 27 19:49:27 BST 2011 x86_64 x86_64 x86_64 GNU/Linux #------------------------------------- #@# EM Registration Mon Oct 24 15:05:52 EDT 2011 /home/hemant/FreeSurferSubjects/203/mri mri_em_register_cuda -uns 3 -mask brainmask.mgz nu.mgz /usr/local/freesurfer/average/RB_all_2008-03-26.gca transforms/talairach.lta nvcc: NVIDIA (R) Cuda compiler driver Copyright (c) 2005-2010 NVIDIA Corporation Built on Thu_Nov__4_12:44:17_PDT_2010 Cuda compilation tools, release 3.2, V0.2.1221 Driver : 4.10 Runtime : 3.20 Acquiring CUDA device Using default device CUDA device: Quadro FX 4600 aligning to atlas containing skull, setting unknown_nbr_spacing = 3 using MR volume brainmask.mgz to mask input volume... reading 1 input volumes... logging results to talairach.log reading '/usr/local/freesurfer/average/RB_all_2008-03-26.gca'... gcaAllocMax: node dims 64 64 64 gcaAllocMax: prior dims 128 128 128 gcaAllocMax: max_labels 0 average std = 6.9 using min determinant for regularization = 4.7 0 singular and 1812 ill-conditioned covariance matrices regularized reading 'nu.mgz'... freeing gibbs priors...done. bounding unknown intensity as < 14.9 or > 790.2 total sample mean = 84.4 (994 zeros) ************************************************ spacing=8, using 2772 sample points, tol=1.00e-05... ************************************************ CUDA Error in file '/space/freesurfer/build/minerva/stable/dev/include/ctfactory.hpp' on line 92 : invalid texture reference. register_mri: find_optimal_transform find_optimal_transform: nsamples 2772, passno 0, spacing 8 Abort (core dumped) Linux Lab-3.intelect.local 2.6.32-71.29.1.el6.x86_64 #1 SMP Mon Jun 27 19:49:27 BST 2011 x86_64 x86_64 x86_64 GNU/Linux recon-all -s 203 exited with ERRORS at Mon Oct 24 15:06:11 EDT 2011

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hippocampal subfields
by Lugar, Heather 25 Oct '11

25 Oct '11

If I were to run the hippocampal subfields command on data that had been previously processed using Freesurfer 5.0 (rather than 5.1), would the results be valid? Thanks, Heather

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Fwd: BEM surface generation questions
by Dan G Wakeman 25 Oct '11

25 Oct '11

Hi, I have a couple of questions about the two different ways to generate BEM surfaces available in FreeSurfer. I have done a comparison of the techniques available in mri_watershed -surf mri_make_bem_surfaces (Version 4.3.0) with another algorithm (which I know the algorithm) I have received a request from reviewers to briefly describe how each of the first two techniques develops the surfaces. I have read all of the Ségonne 2004 paper several times and while I believe I can explain how the "brain"/"inner skull" surface is generated. I cannot figure out how the other two surfaces are generated: "outer skull" and "outer skin" surfaces. Additionally, I cannot find any information about mri_make_bem_surfaces either on the wiki or in the email archives (I realize this software may be kept in as a courtesy to the MEG users: my tests suggest this is very useful). Is there anyone who can provide even a brief description of how this tool generates the surfaces? Thank You, Dan

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Diffusion tensor estimation method
by Ed Gronenschild 25 Oct '11

25 Oct '11

Hi, There are various methods to estimate the diffusion tensor, like linear-least squares, non-linear least-squares, German-McClure M-estimator..... I would like to know which method is used by FreeSurfer in the dt_recon command? Cheers, Ed

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Re: [Freesurfer] white matter volume in a ROI
by Douglas N Greve 25 Oct '11

25 Oct '11

Yes, I see what you mean. mri_aparc2aseg is hard coded to accept both hemis. The easiest way around it is just to create a dummy label for the right hemisphere. doug dolphinede(a)aol.com wrote: > Hi Doug, > > thanks a lot your advice. > > I created an annnotation of my ROI-label as called > lh.cluster1.labe.label with the command line: > > /mris_label2annot --s ZPN20 --h lh --ctab > //Users/dolphinede/Desktop/Probanden/ZPN20/label/aparc.annot.ctab --a > myaparc --l lh.cluster1.labe/.label --nhits nhits.mgh > > This works fine. After that i have used your commmand in this way: > > m/ri_aparc2aseg --s ZPN20 --labelwm --hypo-as-wm --rip-unknown > --volmask --o mri/wmparc.mgz --ctxseg aparc+aseg.mgz --annot myaparc/ > > and i get the following error, which is cause that i have no > lh.cluster1.labe.label in the right hemisphere: > > /Loading lh annotations from > /Users/dolphinede/Desktop/Probanden/ZPN20/label/lh.myaparc.annot > reading colortable from annotation file... > colortable with 36 entries read (originally > //Users/dolphinede/Desktop/Probanden/ZPN20/label/aparc.annot.ctab) > > Reading rh white surface > /Users/dolphinede/Desktop/Probanden/ZPN20/surf/rh.white > > Reading rh pial surface > /Users/dolphinede/Desktop/Probanden/ZPN20/surf/rh.pial > > Loading rh annotations from > /Users/dolphinede/Desktop/Probanden/ZPN20/label/rh.myaparc.annot > could not read annot file > /Users/dolphinede/Desktop/Probanden/ZPN20/label/rh.myaparc.annot > No such file or directory > ERROR: MRISreadAnnotation() failed > /Users/dolphinede/Desktop/Probanden/ZPN20/label/rh.myaparc.annot/ > > The question i have is if all these steps are right and/if i have to > do some more steps to get white matter volume of my annotation and > where i can find it? > > Excuse my numerous questions but I am just a freesurfer-beginner... > > Best regards > > Daniel > > > > > > > > > > -----Ursprüngliche Mitteilung----- > Von: Douglas N Greve <greve(a)nmr.mgh.harvard.edu> > An: dolphinede <dolphinede(a)aol.com>; freesurfer > <freesurfer(a)nmr.mgh.harvard.edu> > Verschickt: Mo, 24 Okt 2011 10:04 pm > Betreff: Re: [Freesurfer] white matter volume in a ROI > > It will be more involved than that. You will need to create an > annotation that contains your label (maybe in addition to other labels), > then uses mri_aparc2aseg with the --labelwm option, something like > > mri_aparc2aseg --s subject-anat --labelwm --hypo-as-wm --rip-unknown > --volmask --o mri/wmparc.mgz --ctxseg aparc+aseg.mgz --annot yourannot > > doug > > dolphinede(a)aol.com <mailto:dolphinede@aol.com> wrote: > > Hi Doug, > > > > thanks a lot for your answer. > > > > So i understand you right that i can get "exact" knowledge about the > > thickness, grey matter volume and pial surface area in my ROI, but in > > case of "the" ROI white matter volume, i have to look to which > > cortical label my ROI counts and then I use the wmparc.files for this > > label? > > > > Best regards > > > > Daniel Klein > > > > > > > > > > > > > > > > > > > > -----Ursprüngliche Mitteilung----- > > Von: Douglas N Greve <greve(a)nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> > > An: dolphinede <dolphinede(a)aol.com <mailto:dolphinede@aol.com>> > > Cc: freesurfer <freesurfer(a)nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu>> > > Verschickt: Mo, 24 Okt 2011 4:48 pm > > Betreff: Re: [Freesurfer] white matter volume in a ROI > > > > For GM area and volume, you can use mris_anatomical_stats. See the > > recent thread on how. For the WM volume, how would you define the WM > > volume that corresponds to you label? We have a routine that parcellates > > WM based on closest proximity to a cortical label. > > doug > > > > dolphinede(a)aol.com <mailto:dolphinede@aol.com> wrote: > > > Dear FreeSurfer experts, > > > > > > i have created a ROI in qdec , where i have found a significant > > > correlation between lgi and age. > > > > > > I mapped this ROI to all subjects. > > > > > > I am interested to compare in this ROI the pial-surface area, the grey > > > matter volume and if possible the white matter volume for this > > > specific region and i am not sure how to do this? > > > > > > Best regards > > > > > > Daniel Klein > > > ------------------------------------------------------------------------ > > > > > > _______________________________________________ > > > Freesurfer mailing list > > > Freesurfer(a)nmr.mgh.harvard.edu <mailto:Freesurfer@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 <mailto:greve@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 <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > > > > > > > > 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 <mailto:greve@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 <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > -- 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

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Re: [Freesurfer] roi analysis from label or annotation
by Douglas N Greve 25 Oct '11

25 Oct '11

Did you try passing --olab a full path? Knut J Bjuland wrote: > Hi > > I use mri_surfcluster -olab --subject fsaverage --in sig.mgh --hemi ?h > to produce label for the areas indicated by mri_glmfit. Then I use > label and mean follow by the python script. > > > cheers > Knut J > > I use > > > Date: Mon, 24 Oct 2011 10:43:02 -0400 > > From: greve(a)nmr.mgh.harvard.edu > > To: knutjbj(a)hotmail.com > > CC: freesurfer(a)nmr.mgh.harvard.edu > > Subject: Re: [Freesurfer] roi analysis from label or annotation > > > > It's very hard to tell what you are doing without a command-line. > > Generally, you can pass the full path of a label to surfcluster to make > > it save it in a particular location. > > doug > > > > Knut J Bjuland wrote: > > > I am working on roi analysis. I have made a label using > mri_surdcluster and used mri_label2label to > > > copy the label from fsaverage to each individual subject. The next > step would be to use > > > mris_anatomical_stats to calculate stats for each subject. I used > a Python to merge the txt file from > > > mris_anatomical_stats. > > > > > > Is it possible to force mri_surfcluster to save the label another > dir than fsaverage? > > > Can I use convert roi label to annotation and then use aparc2stats > > > or similar command to get group statics? > > > > > > > > > Cheers > > > Knut J > > > > ------------------------------------------------------------------------ > > > > > > _______________________________________________ > > > Freesurfer mailing list > > > 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 > > 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 > > > > > > > > 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

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