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Re: [Freesurfer] convert (resample) fsaverage/mri/aseg.mgz into $FSLDIR Nifti with MNI152_T1_1mm target - aparc+aseg.mgz problem
by Roderick McColl 04 Nov '13

04 Nov '13

Hmmm, Actually using aseg.mgz works just fine (just tried this now), displays correctly on fslview. What I was really trying to do was convert aparc+aseg.mgz which does not provide the expected orientation in fslview. Does this mean aparc+aseg.mgz and aseg.mgz are in different spaces somehow? For the aparc_aseg_mni152.nii.gz output, 1) the coronal image in fslview (top left) has the S/I labels upside down compared to the coronal slice, (or the coronal slice upside down compared to the S/I labels) 2) the sagittal image (top right) has the same S/I issue 3) the axial image (bottom left) has the A/P labels the opposite of the image slice. Thanks for any advice -roddy ________________________________________ From: freesurfer-bounces(a)nmr.mgh.harvard.edu [freesurfer-bounces(a)nmr.mgh.harvard.edu] on behalf of Roderick McColl [Roderick.McColl(a)utsouthwestern.edu] Sent: Monday, November 04, 2013 3:37 PM To: freesurfer(a)nmr.mgh.harvard.edu Subject: [Freesurfer] convert (resample) fsaverage/mri/aseg.mgz into $FSLDIR Nifti with MNI152_T1_1mm target I am obviously using mri_vol2vol incorrectly but I'm stumped. Goal is to get the $SUBJECTS/fsaverage/mri/aseg.mgz file into the FSL MNI152 space to do some fslmaths. >From looking around it seemed the command to accomplish this is (inside $SUBJECTS/fsaverage/mri) mri_vol2vol --targ $FSLDIR/data/standard/MNI152_T1_1mm.nii.gz \ --mov aseg.mgz --reg transforms/reg.mni152.1mm.dat --o asegmni152.nii.gz which does execute but if I load asegmni152.nii.gz into fslview all of the orthogonal views are upside down. There is something missing regarding the co-ordinate system but I'm not sure what. Can anyone point me in the right direction? Thanks -roddy ________________________________ UT Southwestern Medical Center The future of medicine, today. _______________________________________________ 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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tkregister2 and mri_label2vol
by Zhao Jingjing 04 Nov '13

04 Nov '13

Hi Doug, I asked a question a couple days ago for how to convert .label files into .nii files in freesurfer. At the end of this email, you can see the original email from me and your response. I tried to run the function mri_label2vol by myself. However, it seems not working quite well. In order to run mri_label2vol, it seems that I have to have a registration.dat file. I search online for how to generate it and get an answer from maillinglist posted by you several years ago. That is, I need to run the function of tkregister2. Then I tried to find out how to run tkregister2 and I found out an example suggested by you, although I don't know how it works because there is no information online for this function. Your example is like this: *tkregister2 --mov rawavg.mgz --targ aseg.mgz --regheader --reg rawreg.dat --noedit* I ran it and it successfully generated a rawreg.dat file, but I don't know if it is a correct file that I should use. Below is the results that I got from the command window: *tkregister_tcl /opt/freesurfer/lib/tcl/tkregister2.tcl target volume aseg.mgzmovable volume rawavg.mgzreg file rawreg.datLoadVol 0ZeroCRAS 0$Id: tkregister2.c,v 1.117.2.1 2010/08/02 17:42:03 greve Exp $Diagnostic Level -1INFO: loading target aseg.mgz Ttarg: ---------------------1.000 0.000 0.000 128.000; 0.000 0.000 1.000 -128.000; 0.000 -1.000 0.000 128.000; 0.000 0.000 0.000 1.000;INFO: loading movable rawavg.mgzTmov: -------------------- -0.900 0.000 0.000 100.799; 0.000 0.000 0.898 -115.000; 0.000 -0.898 0.000 115.000; 0.000 0.000 0.000 1.000;mkheaderreg = 1, float2int = 0Computing reg from header (and possibly input matrix) ---- Input registration matrix (computed) ---------1.000 -0.012 -0.025 -0.000;-0.025 0.069 0.997 0.000; 0.010 -0.998 0.070 -0.000; 0.000 0.000 0.000 1.000;--------------------------------------- ---- Input registration matrix ---------1.000 -0.012 -0.025 -0.000;-0.025 0.069 0.997 0.000; 0.010 -0.998 0.070 -0.000; 0.000 0.000 0.000 1.000;Determinant -1subject = subject-unknown RegMat ----------------------------1.000 -0.012 -0.025 -0.000;-0.025 0.069 0.997 0.000; 0.010 -0.998 0.070 -0.000; 0.000 0.000 0.000 1.000;* Then I tried to run the function of mri_label2vol. I specifically referred to the example posted online in freesurfer website. It seems to me that this is a popular function that a lot of people have used. My command line is as below: *mri_label2vol --label lh.words10_10.label --temp T1.mgz --reg rawreg.dat --fillthresh .5 --o lh.words10_10.nii* However, my command line didn't run successfully to generate the nii file that I want. The error message is "segmentation flaut". Here I attached all the results from the command window after I run this function. *Number of labels: 1lh.words10_10.labelAnnot File: (null)Template Volume: T1.mgzOutut Volume: lh.words10_10.niiRegistration File: rawreg.datFill Threshold: 0.5Label Vox Vol: 1ProjType: (null) ProjTypeId: 0ProjStart: 0ProjStop: 0ProjDelta: 0.1Subject: (null)Hemi: (null)UseNewASeg2Vol: 1DoLabelStatVol 0$Id: mri_label2vol.c,v 1.32 2009/10/22 23:35:53 greve Exp $ Template RAS-to-Vox: ---------1.000 0.000 0.000 128.000;-0.000 -0.000 -1.000 128.000;-0.000 1.000 -0.000 128.000; 0.000 0.000 0.000 1.000;Template Voxel Volume: 1nHits Thresh: 0.5 Loading registration from rawreg.datRegMat: ---------1.000 -0.012 -0.025 -0.000;-0.025 0.069 0.997 0.000; 0.010 -0.998 0.070 -0.000; 0.000 0.000 0.000 1.000;Label RAS-to-Vox: -------- 1.000 0.012 0.025 128.000;-0.010 0.998 -0.070 128.000;-0.025 0.069 0.997 128.000; 0.000 0.000 0.000 1.000;Allocating Hit Volume (16777216) voxelsnlabels = 1Loading lh.words10_10.label Thesholding hit volume.Segmentation fault* I was surprised by this result, because it tells me that "the template voxel volume is 1". How strange! And finally, no nii file was generated. Can you help check whether I did something wrong? Attachment I put the files that might be used for running these two functions (I didn't put T1.mgz and rawavg.mgz in this email since it makes the file bigger than 500K, but if you need it please let me know and I will send you the link from my dropbox). I might need to specify more parameters in the functions, which I didn't how to either. If you can supervise me for how to write the functions correctly, that would be really appreciated. And after I generate nii file, how can I visualize it and see how it matches the ROI from the .label file? I tried tksurfer "subject name" lh inflated, but it doesn't work. If I can get some instructions for this command, that would be also helpful. Thanks. Best, Jingjing Date: Tue, 29 Oct 2013 10:21:59 -0400 From: Douglas N Greve <greve(a)nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] how to transfer .label file to .nii file To: freesurfer(a)nmr.mgh.harvard.edu Message-ID: <526FC487.6020601(a)nmr.mgh.harvard.edu> Content-Type: text/plain; charset=windows-1252; format=flowed You can use mri_label2vol to create a nii mask from the label. To map the label to the DTI space, register your DTI (b=0) to the anatomical using bbregsiter. You can then use mri_label2vol to transfer the label. doug On 10/28/2013 06:14 AM, Zhao Jingjing wrote: > Hi, > > Our lab have managed to generate ROIs in T1 images using Freesurfer, > which led to .label files. We succesfully measured the cortical > thickness in these ROIs for each subject in Freesurfer. Now we are > aiming to track white matter fibers from these ROIs in a tractography > software Trackvis. However, .lable files seem not be readable in > Trackvis. Thus, we are wondering if .label files can be tranferred to > .nii files easily in Freesurfer so that we can use the converted .nii > ROI files to track fibers in Trackvis. Another related question is how > can we coregister the ROIs drawn in T1 images with DTI images and make > sure that those ROIs converted from T1 images are the still in the > same regions in the DTI images? > > Thanks. > Jingjing Zhao > > Postdoc scientist > > Laboratoire de Sciences Cognitives et Psycholinguistique > > Departement d?Etudes Cognitives > > Ecole Normale Superieure > > 29 rue d?Ulm, 75230, Paris Cedex 05, France > > Tel: +33 1 44 32 26 57 > > Fax: +33 1 44 32 26 30

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convert (resample) fsaverage/mri/aseg.mgz into $FSLDIR Nifti with MNI152_T1_1mm target
by Roderick McColl 04 Nov '13

04 Nov '13

I am obviously using mri_vol2vol incorrectly but I'm stumped. Goal is to get the $SUBJECTS/fsaverage/mri/aseg.mgz file into the FSL MNI152 space to do some fslmaths. >From looking around it seemed the command to accomplish this is (inside $SUBJECTS/fsaverage/mri) mri_vol2vol --targ $FSLDIR/data/standard/MNI152_T1_1mm.nii.gz \ --mov aseg.mgz --reg transforms/reg.mni152.1mm.dat --o asegmni152.nii.gz which does execute but if I load asegmni152.nii.gz into fslview all of the orthogonal views are upside down. There is something missing regarding the co-ordinate system but I'm not sure what. Can anyone point me in the right direction? Thanks -roddy ________________________________ UT Southwestern Medical Center The future of medicine, today.

3 2

new version of mri_segstats
by Matura, Silke 04 Nov '13

04 Nov '13

Dear Freesurfer community, we are doing cortical thickness analyses with Freesurfer version 5.3.0 in a Linux environment. In order to do the autorecon-1 and autorecon-2 steps, we need to download the new version of mri_segstats. Unfortunately, the link on the Freesurfer Release Notes Webpage does not work. Also, we could not find mri_segstats on the ftp server: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mri_segstats.… Could you tell us, where we can download the new version of mri_segstats? Thank you, Silke Dr. Dipl.-Psych. Silke Matura Department of Psychiatry, Psychosomatic Medicine and Psychotherapy Laboratory of Neurophysiology and Neuroimaging Johann Wolfgang Goethe University of Frankfurt Heinrich-Hoffman-Str. 10 60528 Frankfurt Germany Tel: 069 6301 7655 email: Silke.Matura(a)kgu.de

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Which boost version is used in CVS, mris_resample
by Martin Kavec 04 Nov '13

04 Nov '13

Hi guys, When running mri_cvs_register on linux (5.3.0), I get into problem with mris_resample, which cannot find libboost_programs_options.so.5. I installed the latest version of boost-1.52.0 for my system, but there are unresolved symbols. Which version is suitable for mris_resample? Thanks, Martin Sent from my iPad

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mri_segment WM/GM limits
by Jonathan Holt 04 Nov '13

04 Nov '13

HI experts, I’m wondering how these limits work, and whether the limit numbers indicate voxel intensity. If I wanted WM to be segmented more aggressively would I plug in a higher number or a lower number? Jon

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Inaccurate white matter and pial surfaces
by Linda Zhang 04 Nov '13

04 Nov '13

Dear all, A few of my subjects end up with surfaces where the white matter surface is actually the pial surface, probably due to less than ideal contrast between the wm and cortical gm. The aseg seems to do a better job though. I've attached a few images to demonstrate what I mean. What's the best method to correct this? I'm running FS 5.1 with the -nuintensitycor-3T flag for recon-all. Cheers, Linda

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Research Felow/Postdoc: Neuroimaging in Cerebrovascular Disease
by Direktion, Institut f. Schlaganfall- und Demenzforschung 04 Nov '13

04 Nov '13

The Hospital of the University of Munich, Germany, is one of the largest and most competitive university hospitals in Germany and Europe. 45 specialized hospitals, departments and institutions harboring excellent research and education provide patient care at the highest medical level with approximately 10.000 employees. The Institute for Stroke and Dementia Research at the Ludwig Maximilian University of Munich offers: Research Fellow/Postdoc: Neuroimaging in Cerebrovascular Disease (m/f) RESEARCH FOCUS and RESPONSIBILITIES: The research fellow/postdoc will work on the mechanisms of post-stroke dementia using multimodal MRI data acquired through a prospective longitudinal study that involves repeat structural and functional MRI together with amyloid PET and detailed cognitive testing. The project is funded by the German Center for Neurodegenerative Diseases (DZNE) and embedded in an ambitious imaging program on vascular cognitive impairment. The fellow/postdoc will work in a highly dynamic neuroimaging team and is encouraged to bring in own research ideas. REQUIREMENTS: The candidate should hold a PhD, MD or equivalent degree in relevant disciplines (informatics, engineering, mathematics, neuroscience), should be familiar with state of the art structural and functional imaging techniques and should have skills in image postprocessing. Solid knowledge of programming and statistics is a plus. An enthusiastic, reliable and independent work style will provide a good fit for our team. OFFER: We offer an excellent multidisciplinary environment with expertise in neuroimaging, neuropsychology, bioinformatics, epidemiology and state of the art multimodal neuroimaging equipment (3T MRI, high-density fMRI compatible EEG, molecular PET, IT infrastructure). The research team is embedded in the Munich Cluster for Systems Neurology, which is funded by the German Excellence Initiative. The research fellow will draw on a comprehensive database and technical support to facilitate efficient work conditions. He/she will work in a friendly, highly productive team at the Institute for Stroke and Dementia Research. The Ludwig Maximilian University of Munich (LMU) (http://www.en.uni-muenchen.de/index.html) Germany, and its hospitals figure among Germany's premier and internationally competitive biomedical research sites and are funded by the government's Excellence Initiative. Salary is according to TV-L. The position is limited for two years, with a possible extension. Disabled persons will be preferentially considered in case of equal qualification. Presentation costs can not be refunded. HOW TO APPLY: Your application - preferably in electronic form - with the usual documents indicating the earliest possible starting date should be directed to: Klinikum der Universität München, Institute for Stroke and Dementia Research Prof. Dr. Martin Dichgans Marchioninistr. 15 81377 Munich | Germany Send application by email to: isd(a)med.uni-muenchen.de --------------------------- Viele Grüße Lilo Thomas Assistentin der Institutsleitung Institut für Schlaganfall- und Demenzforschung (ISD) Klinikum der Universität München Heiglhofstraße 55 D-81377 München Telefon: +49 (0)89 7095 - 7801 Fax: +49 (0)89 7095 - 8729 E-Mail: lilo.thomas(a)med.uni-muenchen.de<mailto:lilo.thomas@med.uni-muenchen.de> Internet: www.isd.klinikum.uni-muenchen.de<http://www.isd.klinikum.uni-muenchen.de/>

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Betreff: Error “mri_segstats will not calculate Supratentorial due to missing ribbon.mgz file”
by jana dinges 04 Nov '13

04 Nov '13

2 1

minimal freesurfer pieces for recon-all
by Satrajit Ghosh 04 Nov '13

04 Nov '13

hi folks, has anybody on this list: a. built or extracted the necessary pieces (binaries, libraries, atlases) for running vanilla recon-all only? b. or better still, has a package file for any linux distro? i know the neurodebian folks are building one, but that's not fully ready yet. cheers, satra

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