Freesurfer

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Dijk.m - Freesurfer Dijkstra MATLAB function
by Sarah Lavelle 23 Jan '23

23 Jan '23

External Email - Use Caution Hi there, I'm looking to use the *Dijkstra matlab code* provided by freesurfer, titled 'dijk.m'. It calculates the *shortest path* from node 's' to node 't'. I want to use this to calculate the distance from 1 vertex to another on an inflated cortical surface( in matlab.) I currently have the surface imported into matlab in terms of 2 matrices: *vertices(V) and edges(E)*. (this was done using the 'freesurfer_read_surf' function. ) However, the input used to describe the cortical surface/graph in dijk.m is 'A'. After researching, I believe that 'A' the *weighted adjacency matrix* of the graph? Is that right? And if so, do you know how I can get 'A' using 'V' and 'E', so I can use it as an input in dijk.m? Thanks, Sarah DIJK.M: function [D,P] = dijk(A,s,t) %DIJK Shortest paths from nodes 's' to nodes 't' using Dijkstra algorithm. % [D,P] = dijk(A,s,t) % % (Note: A(i,j) = 0 => Arc (i,j) does not exist; % A(i,j) = NaN => Arc (i,j) exists with 0 weight) % s = FROM node indices % = [] (default), paths from all nodes % t = TO node indices % = [] (default), paths to all nodes % D = |s| x |t| matrix of shortest path distances from 's' to 't' % = [D(i,j)], where D(i,j) = distance from node 'i' to node 'j' % = Inf, if no path from 'i' to 'j' % P = |s| x n matrix of predecessor indices, where P(i,j) is the % index of the predecessor to node 'j' on the path from 's(i)' to % 'j',where P(i,i) = 0 and P(i,j) = NaN is 'j' not on path to % 's(i)' (use PRED2PATH to convert P to paths) % = path from 's' to 't', if |s| = |t| = 1 % % Example: % A = [0 1 3 0 % 0 0 0 2 % 0 0 0 4 % 0 0 0 0] % [d,p] = dijk(A,1,4) % (Single path) d = 3 % % p = 1 2 4 % % [D,P] = dijk(A) % (All paths) D = 0 1 3 3 % % Inf 0 Inf 2 % % Inf Inf 0 4 % % Inf Inf Inf 0 % % P = 0 1 1 2 % % NaN 0 NaN 2 % % NaN NaN 0 3 % % NaN NaN NaN 0 % p = pred2path(P,1,4) % p = 1 2 4 % % (If A is a triangular matrix, then computationally intensive node % selection step not needed since graph is acyclic (triangularity is a % sufficient, but not a necessary, condition for a graph to be acyclic) % and A can have non-negative elements) % % (If |s| >> |t|, then DIJK is faster if DIJK(A',t,s) used, where D is now % transposed and P now represents successor indices) % % (Based on Fig. 4.6 in Ahuja, Magnanti, and Orlin, Network Flows, % Prentice-Hall, 1993, p. 109.) % Copyright (c) 1994-2006 by Michael G. Kay % Matlog Version 9 13-Jan-2006 (http://secure-web.cisco.com/1cRs4G5kkiqFfc2Vy9yVEtcMD7rwIzApZJZ4z6EgLjvr3DL…) % Input Error Checking **************************************************** error(nargchk(1,3,nargin)) [n,cA] = size(A); if nargin < 2 || isempty(s), s = (1:n)'; else s = s(:); end if nargin < 3 || isempty(t), t = (1:n)'; else t = t(:); end if ~any(any(tril(A) ~= 0)) % A is upper triangular isAcyclic = 1; elseif ~any(any(triu(A) ~= 0)) % A is lower triangular isAcyclic = 2; else % Graph may not be acyclic isAcyclic = 0; end if n ~= cA error('A must be a square matrix'); elseif ~isAcyclic && any(any(A < 0)) error('A must be non-negative'); elseif any(s < 1 | s > n) error(['"s" must be an integer between 1 and ',num2str(n)]); elseif any(t < 1 | t > n) error(['"t" must be an integer between 1 and ',num2str(n)]); end % End (Input Error Checking) ********************************************** A = A'; % Use transpose to speed-up FIND for sparse A D = zeros(length(s),length(t)); if nargout > 1, P = NaN*ones(length(s),n); end for i = 1:length(s) j = s(i); Di = Inf*ones(n,1); Di(j) = 0; isLab = false(length(t),1); if isAcyclic == 1 nLab = j - 1; elseif isAcyclic == 2 nLab = n - j; else nLab = 0; UnLab = 1:n; isUnLab = true(n,1); end if nargout > 1, P(i,s(i)) = 0; end %Change from NaN to indicate no pred while nLab < n && ~all(isLab) if isAcyclic Dj = Di(j); else % Node selection [Dj,jj] = min(Di(isUnLab)); j = UnLab(jj); UnLab(jj) = []; isUnLab(j) = 0; end nLab = nLab + 1; if length(t) < n, isLab = isLab | (j == t); end [jA,kA,Aj] = find(A(:,j)); Aj(isnan(Aj)) = 0; if isempty(Aj), Dk = Inf; else Dk = Dj + Aj; end if nargout > 1, P(i,jA(Dk < Di(jA))) = j; end Di(jA) = min(Di(jA),Dk); if isAcyclic == 1 % Increment node index for upper triangular A j = j + 1; elseif isAcyclic == 2 % Decrement node index for lower triangular A j = j - 1; end end D(i,:) = Di(t)'; end if nargout > 1 && length(s) == 1 && length(t) == 1 P = pred2path(P,s,t); end

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PetSurfer - MG coregister
by Marina Fernández 23 Jan '23

23 Jan '23

External Email - Use Caution Dear experts, I am trying to do PVC on FBB-PET images using the following commands: " mri_coreg --s s_001 --mov s_001_pet_fbb.nii.gz --reg s_001_pet_fbb.reg.lta mri_gtmpvc --i s_001_pet_fbb.nii.gz --reg s_001_pet_fbb.reg.lta --psf 6 --seg gtmseg.mgz --rescale 174 --default-seg-merge --auto-mask --mgx .1 --o s_001_pet_fbb " The problem is that when overlaying the mgx.ctxgm.nii.gz file with the T1.mgz of the corresponding subject, they don't match, since the resulting MG-image is in the space of the original PET (without PVC) instead of in the space of the freesurfer subject. How can I make the MG image be in the freesurfer's subject space? Where is the error? Thank you very much in advance. Best regards, Marina

3 2

mri_segstats question: --avgwf for cross hemisphere ROI
by Bram Diamond 23 Jan '23

23 Jan '23

External Email - Use Caution Hello FreeSurfer Team, I've made a New Year's resolution to stop bothering Andrew Hoopes and instead send my questions to the FreeSurfer Mailing List. I would like to calculate a single average waveform for two surface labels on contralateral hemispheres. In essence, I would like to treat these contralateral labels as a single label. Is there a way to use freesurfer binaries (e.g., mri_segstats) with, lh.func.mgz, rh.fun.mgz, lh.ROI.label, and rh.ROI.label to write a text file with a single average waveform column? Thanks! I hope all is well in Boston! Cheers, Bram Bram R. Diamond, BSc Clinical Neuropsychology Doctoral Student Northwestern University Feinberg School of Medicine Mesulam Center for Cognitive Neurology & Alzheimer’s Disease 300 E. Superior Street | Tarry 8 | Chicago, IL 60611 http://secure-web.cisco.com/1rd9CGB1epEqWboZc37JDhl3-uOBS_KFp5wmeeP-n7zZWCM… <https://secure-web.cisco.com/1l1WxoIUCeqChdzdCLmFK4W0BM6NBQUq7Q-yena2Oie4hv…>

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Quantification of regional volume using external atlas
by Beatriz Cavendish 23 Jan '23

23 Jan '23

External Email - Use Caution Hi all, I would like to know how to quantify the regional volume using an external atlas. I already ran the recon all command and now I want to quantify the volume not with the default Freesurfer atlases, but a specific atlas that is in the MNI space. Should I transform the atlas to each subject's native space before quantifying? How should I do it? Then how do I quantify it and make sure it was done correctly? Could you provide me with command line suggestions? And if I wanted to work with everything on the MNI space, how would the code be like? Also, Best, -- Beatriz Araújo Cavendish, MSc PhD student | Psychologist University of São Paulo São Paulo/SP - Brazil

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freesufer
by David 23 Jan '23

23 Jan '23

External Email - Use Caution Hi Freesurfer experts, I'm very sorry to bother you, but I am very confused with the following questions: My experimental design includes two discrete factors: with three levels (d,m,h); gender (f, m), and two Nvariables So I can get 6 classes: df, dm,mf, mm,hf,hm. I want to perform the difference between any of the classes leves analysis with regressing out the effect of gender and two Nvariables, but I don't know the rules for setting the contrasts for the F-test. The contrast matrix I used is: 1 -1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 -1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 -1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 -1 0 0 0 0 0 0 0 0 0 0 0 0 My orders are as follows： mris_preproc --fsgd glmteach3.fsgd --target fsaverage --hemi lh --meas thickness --out lh_teach3.mgh mris_preproc --fsgd glmteach3.fsgd --target fsaverage --hemi rh --meas thickness --out rh_teach3.mgh mri_glmfit --y lh_teach3.mgh --fsgd glmteach3.fsgd --C glmteach3.mtx --glmdir group3.testA1_10sm.lh --fwhm 10 --surface fsaverage lh --eres-save mri_glmfit --y rh_teach3.mgh --fsgd glmteach3.fsgd --C glmteach3.mtx --glmdir group3.testA1_10sm.rh --fwhm 10 --surface fsaverage rh --eres-save mri_glmfit-sim --glmdir group3.testA1_10sm.lh --cache 3 abs --cwp .05 --2spaces mri_glmfit-sim --glmdir group3.testA1_10sm.rh --cache 3 abs --cwp .05 --2spaces We obtained five differential brain regions and extracted their cortical thickness. And then put the extracted cortical thickness into SPSS for general linear model analysis, but two of the brain regions were not statistically significant. Why? Is the contrast matrix I used wrong? Or other errors? Any help will be very appreciated. Best wishes

2 1

Multiple comparison correction
by David 23 Jan '23

23 Jan '23

1 0

Freesurfer TRACULA Error
by Stylianos Charalampous 23 Jan '23

23 Jan '23

External Email - Use Caution Hello FreeSurfer Developers, I am trying to apply TRACULA for the reconstruction of white matter pathways but I am getting an error when running the trac-all command which I haven’t managed to resolve. The TRACULA is applied on an MRI sample from the ADNI dataset that has been preprocessed using recon-all. I've searched the list but I was not able to found a similar error. Does anyone have any thoughts on how to trouble-shoot this one? I have also attached the trac-all.log in case it's of any use. 1) FreeSurfer version: 7.3.2 2) Platform: Ubuntu 22.04 3) trac-all.log: see attached Kind regards, Stylianos Charalampous

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FreeSurfer atlas and statistics question
by Levman, Jacob 20 Jan '23

20 Jan '23

To whom it may concern among FreeSurfer staff, My colleagues and I have performed an analysis with FreeSurfer that is under peer review. The reviewer has asked that we detail each atlas relied upon and connect that with each of the statistics that we relied upon in our analysis. The statistics that we relied upon were the .stats data from each of the following: aparc, aparc.DKTatlas40, aparc.a2009s, BA, BA.thresh, w-g.pct, curv, entorhinal_exvivo, wmparc, aseg. Obviously we use the Desikan-Killiany-Tourville atlas (and aparc.DKTatlas40 statistics were extracted from that atlas). I know there are other atlases, such as the Destrieux atlas, etc., but I'm not certain which of the above codes were extracted from Destrieux, and which ones were extracted from other atlases (and the names of those other atlases). We ran a recon-all command for this study, but we only used the statistics outlined above (aparc, aparc.DKTatlas40, etc.). We need a list of all atlases supported with recon-all, and which ones were relied upon to generate each of the statistics codes in the above list. Perhaps there is a complete list on a website somewhere of all the atlases and which of these .stats codes came from which atlas, but my searches online have not revealed the appropriate website. Could someone answer this question, or direct me to a complete website with all these details? Thanks so much for your assistance! Jacob

2 1

Re: [Freesurfer] samseg error: illegal hardware instructions
by fsbuild 20 Jan '23

20 Jan '23

External Email - Use Caution Hello Jacky, You can try the procedure listed below, which was posted to the list around Dec. 12th.  It might work for 7.3.1 release, though I have only tried it on the 7.3.2 release.  If it does not work for you on 7.3.1, then I would download and install 7.3.2. - R. - - - - - -  If you are running the Freesurfer 7.3.2 release on an Apple Silicon machine (M1/M2 processor) with MacOS BigSur (11.X) or Monterey (12.X) AND have seen the error message "illegal hardware instruction", then please read following.The "illegal hardware instruction" error can occur when running commands such as samseg and mri_synthseg.  This update is not necessary if your normal workflow does not include commands that produce this error.Please note the update should not be applied if:- Your Mac has an Intel processor.- Your Apple silicon machine (M1/M2 processor) is running a version of Freesurfer that is not the 7.3.2 release, e.g., a more recent development build.UPDATE PROCEDURE:You may not be able to run these commands without sudo/admin permissions on your machine.1) Download the tensorflow-2.4.1-py3-none-any.whl from,https://secure-web.cisco.com/1RlFRGxkPg7szXjSO-DV1PYt0XDgmWYUHtCxw8UNi…) Check the download is OK with the md5 command in the terminal window,$ md5 tensorflow-2.4.1-py3-none-any.whlMD5 (tensorflow-2.4.1-py3-none-any.whl) = fab44de8702faf65e17a22d706a525a4DO NOT PROCEED UNTIL YOU GET THE ABOVE OUTPUT FROM the md5 command.3) Setup the Freesurfer 7.3.2 environment (shown here as installed via .pkg file under /Applications) and verify the path to fspython is from the 7.3.2 release,$ export FREESURFER_HOME=/Applications/freesurfer/7.3.2$ source $FREESURFER_HOME/SetUpFreeSurfer.sh-------- freesurfer-darwin-macOS-7.3.2-20220803-878457d --------... environment variable settings output ...$ which fspython/Applications/freesurfer/7.3.2/bin/fspython4) Uninstall the existing tensorflow package with,$ sudo $FREESURFER_HOME/python/bin/python3 -m pip uninstall tensorflow... apart from any warnings you should see the output ...Successfully uninstalled tensorflow-2.4.15) Install the package downloaded above..  This command assumes the package is in the current directory where the command is run.$ sudo -H $FREESURFER_HOME/python/bin/python3 -m pip install ./tensorflow-2.4.1-py3-none-any.whl... apart from warnings and output about requirements (which should all be satisfied) ...... you should see tensorflow was updated ....Successfully installed tensorflow-2.4.1CHECK THE UPDATE:$ which fspython/Applications/freesurfer/7.3.2/bin/fspython$ fspython>>> import sys, os>>> import tensorflow>>>You should see the prompt return to ">>>" after the import of tensorflow with no errors reported.  Hit Ctrl-D to escape the python session.  The update should now be complete. On Jan 20, 2023, at 05:16, Jacky Lee <cylee10(a)gmail.com> wrote:        External Email - Use Caution        Hi FreeSurfer developers,I was trying to do lesion segmentation and calculation with FreeSurfer samseg function on my MS subjects as described here: MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://secure-web.cisco.com/1QPXcpu2aaMG6bcv5GooTisWdsTr3IYiqIFead… have performed coregistration and reformatting of my FLAIR image. I proceeded to run_samseg as follows: run_samseg --input 105_t1.nii 105_flairRegT1.nii --pallidum-separate --lesion --lesion-mask-pattern 0 1 --output samsegoutputThen I encountered this error: zsh: illegal hardware instruction  run_samseg --input 105_t1.nii 105_flairRegT1.nii --pallidum-separate --lesion1) FreeSurfer version: freesurfer-darwin-macOS-7.3.1-20220723-115e466 2) Platform: macOS Ventura 13.1 (22c65) [Apple M1 macbook pro]Please help looking into it. ThanksJacky_______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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samseg error: illegal hardware instructions
by Jacky Lee 20 Jan '23

20 Jan '23

External Email - Use Caution Hi FreeSurfer developers, I was trying to do lesion segmentation and calculation with FreeSurfer samseg function on my MS subjects as described here: https://secure-web.cisco.com/1zAsxk4FzHM5NR_SkitDdzHN3p9YF3oxn6CN---kSGPRsx… I have performed coregistration and reformatting of my FLAIR image. I proceeded to run_samseg as follows: run_samseg --input 105_t1.nii 105_flairRegT1.nii --pallidum-separate --lesion --lesion-mask-pattern 0 1 --output samsegoutput Then I encountered this error: zsh: illegal hardware instruction run_samseg --input 105_t1.nii 105_flairRegT1.nii --pallidum-separate --lesion 1) FreeSurfer version: freesurfer-darwin-macOS-7.3.1-20220723-115e466 2) Platform: macOS Ventura 13.1 (22c65) [Apple M1 macbook pro] Please help looking into it. Thanks Jacky

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