Freesurfer

freesurfer@nmr.mgh.harvard.edu

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30133 discussions

creating labels from aseg.mgz
by Ladan Shahshahani 01 Jan '17

01 Jan '17

Dear experts, I'm trying to create labels for subcortical regions. I want to use these labels to extract time series from resting state fMRI data (I want all of the subcortical time series and I want them to be in mni305 space). I'm not sure if I'm doing the right thing. Here's an example of what I used: mri_cor2label --c $FREESURFER_HOME/subjects/fsaverage/mri.2mm/aseg.mgz --id 255 --l ~/Desktop/CC_Anterior.label After running this command, attached is the label file I get. The first column is all "-1"s. any ideas how I can go about doing such thing? Best, Ladan

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mri_glmfit-sim
by stdp82＠virgilio.it 31 Dec '16

31 Dec '16

Hi list, which is the correct option, please? 1- mri_glmfit-sim --glmdir my-glm.wls --cache 1.3 abs --cwpvalthresh .0166 --3spaces 2- mri_glmfit-sim --glmdir my-glm.wls --cache 1.3 abs --cwpvalthresh .05 --3spaces Thanks Best regards Stefano

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Revisiting GM ROI list
by P Taylor 30 Dec '16

30 Dec '16

Hi, Doug- I've looked more into my earlier question of identifying FS-returned regions, in particular: 1) which regions of the whole FreeSurferColorLUT.txt seem to get returned by default recon-all calls (for either the 2000- or 2009-parc+segs); and 2) which of those regions are GM and non-GM (WM/CSF/other), based both on the mri_binarize list you had posted earlier in this thread and on the names given in the LUT. I'd like to pick your brain on this. A) The main questions I have relate to the regions labeled from [0, 256], which seem have the same labelling in both the 2000 and 2009 parc+segs. >From a few different FreeSurfer recon-alls on healthy adults, below is a list of the ROIs that seem to be consistently returned by recon-all (a much sparser subset than all 256). For each, I have included the number and label, as well as put arrows by the numbers that, according to the MatchValues list in mri_binarize, should be in either the WM or Vent masks, (and hence non-arrowed regions should be GM, by how that function returns "--gm"). My main questions arise about #30, 62, 80 and 85, as they don't appear to be GM-- therefore, am I correct that I should also *exclude* those four regions from a list of GM regions? (Here, "FS_nongm*" means that it was in the list of non-GM regions in mri_binarize, as either unknown, WM, CSF or ventricle.) ------------------------------------------------------------ ----------------------------------------- 0 Unknown -> FS_nongm 2 Left-Cerebral-White-Matter -> FS_nongm_wm 4 Left-Lateral-Ventricle -> FS_nongm_vent 5 Left-Inf-Lat-Vent -> FS_nongm_vent 7 Left-Cerebellum-White-Matter -> FS_nongm_wm 8 Left-Cerebellum-Cortex 10 Left-Thalamus-Proper 11 Left-Caudate 12 Left-Putamen 13 Left-Pallidum 14 3rd-Ventricle -> FS_nongm_vent 15 4th-Ventricle -> FS_nongm_vent 16 Brain-Stem 17 Left-Hippocampus 18 Left-Amygdala 24 CSF -> FS_nongm_csf 26 Left-Accumbens-area 28 Left-VentralDC 30 Left-vessel -------> *should be in list of FS_nongm? 31 Left-choroid-plexus -> FS_nongm_vent 41 Right-Cerebral-White-Matter -> FS_nongm_wm 43 Right-Lateral-Ventricle -> FS_nongm_vent 44 Right-Inf-Lat-Vent -> FS_nongm_vent 46 Right-Cerebellum-White-Matter -> FS_nongm_wm 47 Right-Cerebellum-Cortex 49 Right-Thalamus-Proper 50 Right-Caudate 52 Right-Pallidum 53 Right-Hippocampus 54 Right-Amygdala 58 Right-Accumbens-area 60 Right-VentralDC 62 Right-vessel -------> *should be in list of FS_nongm? 63 Right-choroid-plexus -> FS_nongm_vent 72 5th-Ventricle -> FS_nongm_vent 77 WM-hypointensities -> FS_nongm_wm 80 non-WM-hypointensities -------> *should be in list of FS_nongm_wm? 85 Optic-Chiasm -------> *should be in list of FS_nongm? 251 CC_Posterior -> FS_nongm_wm 252 CC_Mid_Posterior -> FS_nongm_wm 253 CC_Central -> FS_nongm_wm 254 CC_Mid_Anterior -> FS_nongm_wm 255 CC_Anterior -> FS_nongm_wm ------------------------------------------------------------ -------------------- It seem that the new version of mri_binarize that you had sent me might still include those four flagged regions in the 'mri_binarize --gm' output. B) For the ROIs specific to the 2000aparc+aseg, I think it also seems pretty clear: + 1000 and 2000 are returned as "ctx_*_unknown"; + All ROIs in the intervals [1001, 1003] and [1005, 1035] can be returned, and these are all LH GM; + All ROIs in the intervals [2001, 2003] and [2005, 2035] can be returned, and these are all RH GM; + ROIs '1004' and '2004' are the "ctx-?h-corpuscallosum", which would be WM, but they don't seem to be returned. C) For the ROIs specific to 2009aparc+aseg, I think it also seems pretty clear: + 11100 and 12100 are returned as "ctx_*_Unknown"; + All ROIs in the intervals [11101, 11141] and [11143, 11175] can be returned, and these are all LH GM; + All ROIs in the intervals [12101, 12141] and [12143, 12175] can be returned, and these are all RH GM; + ROIs '11142' and '12142' are the "ctx_?h_Medial_wall", which would be non-GM, but they don't seem to be returned. D) And you mentioned that the regions in the interval [3000, 4035] are WM parcellations. So, in total, does that seem like a complete categorization of regions that are typically returned, as well as their classification as either GM or non-GM? And in particular, I would be happy to know your thoughts on the flagged ROIs in the interval [0, 256]. Thanks, pt

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Re-running recon-all in V6 {Disarmed}
by Kevin Aquino 30 Dec '16

30 Dec '16

Hi all, When V6 is released I'd want to re-run all my (10) subjects through recon-all again (they were processed with v6 alpha). I'd like to keep all my wm edits, mask and control points, is it as easy as just running recon-all on the same folder again? They are 0.7mm so I'd like to keep all the corrections. Cheers! *Dr Kevin Aquino* Research fellow, Sir Peter Mansfield Magnetic Resonance Center, The University of Nottingham. Honorary Research Fellow School of Physics, Faculty of Science, University of Sydney *E* Kevin.aquino(a)nottingham.ac.uk, aquino(a)physics.usyd.edu.au | *W* https://kevinaquino.github.io <http://www.physics.usyd.edu.au/~aquino/> ---------------------------------------------- The brain is a wonderful organ. It starts working the moment you get up and does not stop until you get into the office. - Robert Frost CRICOS 00026A This email plus any attachments to it are confidential. Any unauthorised use is strictly prohibited. If you receive this email in error, please delete it and any attachments. Please think of our environment and only print this e-mail if necessary.

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under estimation of white matter and pial surface
by miracle ozzoude 29 Dec '16

29 Dec '16

Hello Freesurfer, I was wondering if anyone knows how to correct an underestimation of white matter and pial surface outputs from freesurfer. I attached an image showing the error. Thanks. Best, Paul

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Fwd: localGI bug
by David Groppe 28 Dec '16

28 Dec '16

Dear FreeSurfer Developers, I think there is a bug in FreeSurfer's MATLAB code that is used to compute the local gyrification index. Specifically, when I run this command: *recon-all -s PT001 -localGI* I get the following error: *face 115000 / 118360mesh_outer = vertices: [59182x3 double] faces: [118360x3 double] facesOfVertex: [59182x1 struct]preparing pial mesh structure ......searching for mesh edges...done (171.44 sec).... creating path file for vertex 1 / 59182area file for outer ROIs saved at 1In an assignment A(:) = B, the number of elements in A and B must be the same.Error in dsearchn (line 79) [d(i),t(i)] = min(sum((x-yi).^2,2));Error in mesh_vertex_nearest (line 29)nearestIndex = dsearchn(vertices,points);Error in reorganize_verticeslist (line 28) [nextindex,nextvalue]=mesh_vertex_nearest(mesh_total.vertices(remaininglist,:),mesh_total.vertices(verticeslist(start_vertex),:)); Error in make_roi_paths (line 93) reorglist = reorganize_verticeslist (mesh_total, A, mesh_outer, perim, verticeslist, step);* *>> ERROR: make_roi_paths did not complete successfully!* I ran the command in debugging mode and *x* and *yi *are both empty variables. I am using a freshly installed version of the Lion OS X 10.7 (64b Intel) version of FreeSurfer (freesurfer-Darwin-lion-stable-pub-v5.3.0.dmg; freesurfer-Darwin-lion-stable-pub-v5.3.0) and am running on OS 10.11.6 using MATLAB version R2015b (8.6.0.267246). The recon-all.log is attached. Let me know if there is any further information I can provide and thanks for producing such a fantastic piece of freeware. -David Groppe

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recon-all Line search failed
by Ladan Shahshahani 28 Dec '16

28 Dec '16

Dear experts, I tried running recon-all for a subject and it exited with the following error: LINE SEARCH FAILED. SEE DOCUMENTATION OF ROUTINE MCSRCH ERROR RETURN OF LINE SEARCH: INFO= 3 POSSIBLE CAUSES: FUNCTION OR GRADIENT ARE INCORRECT OR INCORRECT TOLERANCESoutof QuasiNewtonEMA: 010: -log(p) = -0.0 tol 0.000010 I'm using freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 and my operating system is 14.04.1-Ubuntu. attached is the recon-all.log. Best, Ladan

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postdoc in computational neuroimaging (method development)
by Martin Reuter 28 Dec '16

28 Dec '16

Hi all, I wish everyone a successful new year 2017! Please pass along this job offer for a postdoc position in my group in Bonn, Germany, to anyone interested and feel free to contact me with any questions. Thanks, Martin Reuter The German Center for Neurodegenerative Diseases (DZNE) in Bonn, Germany is looking for a Postdoc (f/m) in Computational Neuroimaging – Code 1427/2016/12 to join the research group of Prof. Martin Reuter. Research projects will focus on developing image analysis, geometry processing and machine learning methods for the automatic analysis of multi-modal human MRI data, primarily with the aim to extract imaging biomarkers that can be leveraged to both understand or diagnose neurodegenerative disease and to provide a rational framework for targeting and monitoring therapy. Prof. Martin Reuter, has recently joined the DZNE and simultaneously holds a faculty position at the Martinos Center, MGH, Harvard Medical School, Boston, USA with an affiliation at the Massachusetts Institute of Technology CSAIL. He is the principal developer of the longitudinal processing framework of the software package FreeSurfer, providing a suite of tools for the automated analysis of brain MRI data to a world-wide user base. He and his team have, furthermore, introduced novel approaches for neuroanatomical shape analysis and computer-aided diagnosis and prognosis of neurodegenerative disease. Your profile: We seek a postdoctoral candidate with a Ph.D. in computer science, engineering or mathematics with interest in image and geometry processing and with solid programming skills in C/C++, Python, Matlab, R, shell scripting, GPU (parallelization). The ideal candidate would have knowledge in computational neuroimaging or biomedical engineering and considerable expertise in methodological development of quantitative MRI analysis, e.g. registration, segmentation, Bayesian modeling. Experience with big data analysis, cloud computing and machine learning is an asset. Knowledge of state-of-the-art data analyses techniques and neuroimaging software, including FreeSurfer, ANTS, FSL is also appreciated. Highly motivated individuals with a record of productive research are encouraged to apply. The working language is English. We offer: Integration into the computational imaging environment at DZNE and interdisciplinary interactions with other institutes in Bonn and abroad (e.g. Harvard Medical School). Recently opened DZNE Research Facilities at Bonn Venusberg, hosting a state of the art neuroimaging center with 7T and 3T MRI scanners, as well as computational infrastructure supported by experienced IT specialists and physicists. A rich set of high-quality MR data and applied research questions through collaboration with the Rhineland Study, a prospective deeply phenotyped longitudinal cohort study with up to 30.000 participants. A strong mentoring program for career development is provided. An international environment characterized by a strong focus on science and research. Bonn, located at the Rhine river in proximity to the Cologne metropolitan area, has a very high quality of life, with an international student, research and business community. The position is initially available for 2 years. Employment, payment and social benefits are determined by the Public Sector Collective Agreement (Tarifvertrag für den öffentlichen Dienst – TVöD Bund). The DZNE is an equal opportunity employer and especially welcomes and encourages disabled individuals to apply. You will obtain special skills and knowledge for your scientific qualification during your activities at DZNE. Interested candidates should send their full application documents in a single PDF with subject CODE 1427/2016/12 via email to application(at)dzne.de . Please include a CV, contact information of two referees, a brief statement describing your personal qualifications and future research interests (up to 1 page), and a list of publications highlighting up to three most important ones. Informal enquiries may be directed to Martin Reuter (martin.reuter(at)dzne.de <>). Information about previous activities of the group can be found at http://reuter.mit.edu <http://reuter.mit.edu/> Applications are due January 25 2017

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Re: [Freesurfer] Brighter image at baseline vs. follow up using longitudinal processing stream
by Tamara Tavares 28 Dec '16

28 Dec '16

Thank you for your reply Dr. Reuter. I have about 3 scans in which the acquisition parameters are slightly different between time 1 and time 2 which probably contributes to these differences. Do you recommend that I do not use these scans? For my other scans, sometimes the differences in intensity are very subtle. For example, I have one scan where the contrast between the GM and WM are more apparent at one time point vs. the other time point. In another example, the thalamus looks a bit darker at time 1 vs. time 2. Again these differences are very subtle and only noticeable if you are looking for them. I am just wondering at what point do these differences become problematic? I should also note that sometimes these differences are not readily apparent in the original T1 scan. Thank you again for your help. Best, Tamara

2 1

Defining labels and Gordon 2014 annotation file
by Ladan Shahshahani 27 Dec '16

27 Dec '16

Dear experts, I want to use ROIs from Power et al. 2011 paper (Functional network organization of the human brain). An excel file is provided with the center coordinates. I wonder if it's possible to use this file to automatically create parcels. Is there any way of getting Gordon's 2014 parcellation annotation file in fsaverage space? Best regards, Ladan

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