Freesurfer

freesurfer@nmr.mgh.harvard.edu

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30099 discussions

license file not working
by Saemann Philipp 06 Aug '14

06 Aug '14

Hello users or support team, after using FS successfully for some time, now, after a trivial command such as mri_convert -it analyze T1.img -ot mgz 001.mgz an error appears as follows: $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from T1.img... -------------------------------------------------------------------------- ERROR: Invalid FreeSurfer license key found in license file /net/PE1/raid1/enigma-mdd/freesurfer/.license If you are outside the NMR-Martinos Center, go to http://surfer.nmr.mgh.harvard.edu to get a valid license file (it's free). If you are inside the NMR-Martinos Center, make sure to source the standard environment. -------------------------------------------------------------------------- I re-applied for a license file which was the EXACT one I already had at the specified location, and it still does produce the error message. What makes this licence "invalid" here? Is there some problem with C-compiler versions? (though I would not this should appear right now) Thanks for any ideas, Philipp Saemann Facharzt für Nervenheilkunde Arbeitsgruppe Neuroimaging Max-Planck-Institut für Psychiatrie Kraepelinstr. 2-10 80804 Munich Mail: saemann(a)mpipsykl.mpg.de Phone: 0049-89-30622-413

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Post-hoc test failure by ROI extraction after successful group analysis with FreeSurfer
by Yunxin Wang 06 Aug '14

06 Aug '14

Hi folks, I tried to extract the thickness/volume value of the ROI labels transferred from the annot files that're generated automatically by FreeSurfer after a succesful group analysis with corrected significant results. However, the thickness/volume values are no longer correlated with the independent variable that I used in the group analysis model earlier and even the direction of group difference seems to be inconsistent with the group analysis results as well. I have no idea how it went wrong and wondered maybe there's something wrong with my scripts. Have any of you run into such kind of problem? My script for ROI value extraction goes like this: #annot2label: mri_annotation2label --subject fsaverage --annotation onsetage_thickness --hemi rh --labelbase /expdata/wangyunxin/reconall_lj/fsaverage/labels/onsetage_thickness for i in sub* do #label2label: mri_label2label --srclabel fsaverage/labels/onsetage_thickness-001.label --srcsubject fsaverage --trglabel ./$i/labels/onsetage_thickness-001.label --trgsubject $i --regmethod surface --hemi rh #label2stats: mris_anatomical_stats -l $i/labels/onsetage_thickness-001.label -t $i/surf/rh.thickness -f $i/stats/rh.onsetage_thickness-001.stats -nsmooth 10 $i rh done #stats2table aparcstats2table --subjectsfile /expdata/wangyunxin/reconall_lj/music/sublist48 --hemi rh --meas thickness --parc onsetage_thickness-001 --tablefile music/onsetage_thickness-001_rh.txt Any suggestion would be great! Thanks! Best, Yunxin ------ Yunxin Wang Visiting PhD Student Gabrieli Lab McGovern Institute for Brain Research at MIT Office: 46-5107 Tel: 617-955-2809 http://gablab.mit.edu/index.php/gablab/people/14-sample-data-articles/220

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mri_cor2label: volume --> .label vectors
by Krieger, Donald N. 06 Aug '14

06 Aug '14

mri_cor2label does work for extracting vectors with FreesurferColorLUT.txt label numbers from .mgz volumes. The documentation at http://surfer.nmr.mgh.harvard.edu/fswiki/mri_vol2label states: --id labelid 0-255 value in COR volume The attached pdf shows the number of vectors which were extracted from each of 5 volumes for labels 1-255. You can see that volumes aseg, aparc+aseg, and wmparc yield nearly identical results. I ran several file pairs through spot checks and the vectors were identical in the ones I checked. Volume filled.mgz contains vectors for only 3 labels while volume T1.mgz contained vectors for all of them and in most cases, the numbers were higher. Questions: 1. Can mri_cor2label handle labelIDs > 255? 2. Is there a tool determining which labelIDs are represented in a .mgz volume? 3. Are there other volumes which I should be using for vector extraction for these labels. 4. Is there a way to extract labels with ids > 255? I assume that mri_cor2label is an older tool and the new approach is generate .annot files and then use mri_annotation2label. 5. How are .annot files created? I have been unable to find this even though it must be staring me in the face. Thanks, Don

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Crossing Segments
by Isaiah C. Smith 06 Aug '14

06 Aug '14

Hello All, Thank you for the help. I looked at my surface images in free view and they are crossing. The crossing seems to be taking place between the the brain and inner skull crossing over outer skull and outer skin. I believe that this is because the data that we have only goes down so far in the original mr images (Below). And when the individual surfaces are created they cross towards the posterior part of the head (Next Image). I attached the surfaces just in case to allow you to see. Would it be possible to extend outer skull and skin when using freesurfer, or get around this some other way. And lastly we are getting a very bumpy skin (Last Photo). Will this be a problem when creating the head model, finding the lead field matrix, etc. with MNE because the crossing sections prevent me from proceeding? Isaiah [cid:27A0E365-2791-4E78-879D-1A3490B5A655@host.ucla.edu][cid:42061E47-0F8E-43CF-B35C-AD40D52C02E9@host.ucla.edu][cid:10EB4B44-6FF2-4C08-9D07-7291D89BA9A2@host.ucla.edu]_______________________________________________

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Available post doc position
by Anders Martin Fjell 06 Aug '14

06 Aug '14

At the Research Group for Lifespan Changes in Brain and Cognition, University of Oslo, Norway, we have an available post doc position for an excellent candidate, on the project Inflammation, Amyloid and Atrophy in the Aging Brain: The Borders between Healthy Brain Aging and Neurodegeneration. Please see more info here: http://oslobrains.no/images/stories/docs/UiO_post_doc_August_2014.pdf NB. We will extend the deadline from to August 19th, not August 10th as it says in the add. Interested candidates are wellcome to contact me if they have questions. Best whishes, Anders M Fjell

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Re: [Freesurfer] Fwd: Jacobian mri_cvs_register
by Lilla Zollei 06 Aug '14

06 Aug '14

Hi Andre, The jacobian field is computed in the coordinate space of the moving volume so if you overlay it with brain_IBSR_01.mgz, you will see that they match. We currently do not have an executbale in 5.3 that writes out the m3z transforms in nifti format. Lilla On Tue, 5 Aug 2014, André Ribeiro wrote: > Hi, > > The Freesurfer that I am using is: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0. > > The source, target, registered, Jacobian images and deformation field are provided in attachment. > > I mean with voxel-wise that by visualizing both (overlayed) there is a shift between the Jacobian and the registered image. I used the same image as target so I would suspect that it is not a header problem (though did not used a different viewer). Additionally, by looking at the Jacobian (and assuming this is > correct) the algorithm seems to relaxed allowing really high and low jacobians. > > Further, how can I obtain the deformation fields in a nifti format? > > > > [icon_10_generic_list.png] combined_toIBSR_02_elreg_afteraseg-norm.m3z > > [icon_10_generic_list.png] brain_IBSR_02.mgz > > [icon_10_generic_list.png] brain_IBSR_01.mgz > > [icon_10_generic_list.png] reg_IBSR_01_2_IBSR_02_brain.nii.gz > > [icon_10_generic_list.png] jacobian.nii.gz > > > Regards, > Andre Santos Ribeiro > PhD Student, Imperial College London > > > > On Tue, Aug 5, 2014 at 4:24 PM, Lilla Zollei <lzollei(a)nmr.mgh.harvard.edu> wrote: > > Hi Andre, > > What do you mean by they "do not seem to match voxel-wise"? Are they of different size or are they not in a corresponding space? > > Which version of FreeSurfer are you using? > > Could you send the volumes over? I don't see anything wrong with the commands so I would like ot take a look at the files. > > Lilla > > On Tue, 5 Aug 2014, André Ribeiro wrote: > > Hi, > > Ok so most of my problems are now fixed, but there is still one problem regarding the Jacobian. > > So first of all my images were normalized as follows: > createMorph --out fullCVSmorph.tm3d --template f2/mri/brain.mgz --subject f1/mri/brain.mgz --in gcam combined_tof2_elreg_afteraseg-norm.m3z > applyMorph --template f2/mri/brain.mgz --transform fullCVSmorph.tm3d vol f1/mri/brain.mgz reg_f1_brain.nii.gz trilinear > > then for the Jacobian: > mri_jacobian -tm3d combined_tof2_elreg_afteraseg-norm.m3z f1_brain.nii.gz jacobian.nii.gz > > Now if I visualize both the reg_f1_brain.nii.gz and jacobian.nii.gz they do not seem to match voxel-wise, and therefore cannot be applied for VBM. Both the jacobian and the registered t1 brain image use the same transform and therefore should be aligned. Am I making some mistake here? > > Sorry for this question in advance. > > Regards, > Andre Santos Ribeiro > PhD Student, Imperial College London > > > > On Fri, Jul 11, 2014 at 4:11 PM, Lilla Zollei <lzollei(a)nmr.mgh.harvard.edu> wrote: > > Hi, > > First, in the mri_cvs_register I kept all the files and therefore the "combined_toIBSR_02_elreg_afteraseg-norm.tm3d" file was not removed. If I try to replicate this file through the > "createMorph --out fullCVSmorph.tm3d --template template.mgz --subject movingvol.mgz --in gcam nlalign-afteraseg-norm.m3z morph el_reg_toTEMPLATE.tm3d" the file produced is different from the one previously created by the program (and gives far worse registration results when > used with > the "applyMorph"). Is > something wrong here? > > > No, there is nothing wrong. In the above command you are just not composing the right files. I assume that you have run the default mri_cvs_register command. In that case there are two non-linear registration steps one aided by aseg info and one by intensities. In the above you are > skipping the morph > created by the former so that is why you are not getting the same combined output. Instead of "morph el_reg_toTEMPLATE.tm3d" you would need to use "morph combined*aseg.tm3d" > > Second, even if the two files gave the same results wouldn’t this fullCVSmorph.tm3d (otherwise called combined_toIBSR_02_elreg_afteraseg-norm.tm3d) have both information from *afteraseg-norm.m3z and el_reg_toTEMPLATE.tm3d, and therefore the Jacobian applied solely to the > nlalign-afteraseg-norm.m3z would not > match. > > > It is correct. The jacobians of fullCVSmorph.tm3d and nlalign-afteraseg-norm.m3z will not match. I am a bit confused about whey you think they should. > > Lastly, am I right assuming the "combined_toIBSR_02_elreg_afteraseg-norm.tm3d" is the last registration (and most accurate) performed by mri_cvs_register? > > > Yes. In the most current FS version though we use the m3z files as we are trying to phase out the tm3d format. > > Lilla > > On Fri, Jul 11, 2014 at 3:11 PM, Lilla Zollei <lzollei(a)nmr.mgh.harvard.edu> wrote: > > Hi, You should use the final m3z file. The -tm3d flag just indicates that the file was created by mri_cvs_register. > Lilla > > On Fri, 11 Jul 2014, André Ribeiro wrote: > > I got an error using the mri_jacobina. > The function returns: > > The input morph originated from a tm3d (mri_cvs_register file). > GCAMread(/home/afs13/Documents/data/test_freesurfer_reg/combined_toIBSR_02_elreg_aseg.tm3d): invalid version # 0.000 > > mri_jacobian: could not read input morph /home/afs13/Documents/data/test_freesurfer_reg/combined_toIBSR_02_elreg_aseg.tm3d > > > The command is provided below: > mri_jacobian -tm3d /home/afs13/Documents/data/test_freesurfer_reg/combined_toIBSR_02_elreg_aseg.tm3d /home/afs13/Documents/data/test_freesurfer_reg/brain.mgz /home/afs13/Documents/data/test_freesurfer_reg/test_jac.nii.gz > > Regards, > Andre Santos Ribeiro > PhD Student, Imperial College London > > > > On Fri, Jul 11, 2014 at 11:09 AM, André Ribeiro <afs13(a)imperial.ac.uk> wrote: > Thank you! Didn't realized that function existed. > > Regards, > Andre Santos Ribeiro > > On Thu, Jul 10, 2014 at 4:59 PM, Lilla Zollei <lzollei(a)nmr.mgh.harvard.edu> wrote: > > Hi Andre > > You can run: > > mri_jacobian -tm3d <3d morph> <template volume> <output volume> > > --Lilla > > On Thu, 10 Jul 2014, André Ribeiro wrote: > > Dear Freesurfer Community, > > How can I obtain the Jacobian of the deformation field estimated through mri_cvs_register for further use like VBM analysis? > > > Regards, > Andre Santos Ribeiro > > > > _______________________________________________ > 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. > > > > > > _______________________________________________ > 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. > > > > > _______________________________________________ > 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. > > > > > _______________________________________________ > 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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Dealing with missing clinical variables in lme analysis and test model fit between two models with the same number of random effects.
by Knut J Bjuland 06 Aug '14

06 Aug '14

Dear FreeSurfer experts, In my dataset, I am missing some of the clinical variable for some of the subjects. How do I represent missing variables to the linear mixed model? Should I use zero or use the mean? It is possible to test the model fit of intercept compared to time with lme_mass_LR. Both models have one random effect. Your sincerely Knut J Bjuland

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Postdoctoral Fellow Position on High Angular Resolution Diffusion Imaging
by Anqi Qiu 06 Aug '14

06 Aug '14

Job description: National University of Singapore (NUS) is a leading global university centre in Asia. It offers a global approach to education and research, with a focus on Asian perspectives and expertise. Computation functional anatomy laboratory at NUS (http://www.bioeng.nus.edu.sg/cfa) focuses on mathematical modeling of anatomy and function of the brain from medical images. We are looking for candidate who is interested in the development of fundamental mathematical tools for handling HARDI data and new data-driven biological discoveries brought about by such novel modeling and analysis methods, that are otherwise unattainable in vivo. Requirements: Ph. D or MD Research background on manifold, manifold learning is preferable Good communication and writing skills in English language If you are interested in the jobs listed above, please send your CV to Associate Prof. Anqi QIU Department of Biomedical Engineering National University of Singapore Email: bieqa(a)nus.edu.sg Phone: +(65) 6516 7002

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Postdoctoral Fellow in Multivariate Analysis, Machine Learning and Classification
by Anqi Qiu 06 Aug '14

06 Aug '14

Job description: Computation functional anatomy laboratory at National University of Singapore focuses on the development of medical image analysis methods, including image segmentation, registration approaches, multivariate statistical analysis, machine learning, and classification algorithms. Our group is particularly working on multi-modal magnetic resonance imaging of the brain and derives mathematical/statistical models for characterizing variations of the brain anatomy and function and their associations with clinical phenotypes and/or genetics. We are seeking for research fellows who are interested in developing and employing data mining approaches for understanding high dimensional brain image and/or genetic data. The candidate with experience on high dimensional data or 3D image analysis will be seriously considered. Requirements: Ph. D on computer vision, statistics, electrical engineering, or biomedical engineering Good communication and writing skills in English language If you are interested in the jobs listed above, please send your CV to Associate Prof. Anqi QIU Department of Biomedical Engineering National University of Singapore Email: bieqa(a)nus.edu.sg Phone: +(65) 6516 7002

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Postdoctoral Fellow in Multivariate Analysis, Machine Learning and Classification
by Anqi Qiu 06 Aug '14

06 Aug '14

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Freesurfer