Freesurfer May 2018

freesurfer@nmr.mgh.harvard.edu

117 participants
167 discussions

gcs and gca to coordinates
by Tim Hahn 18 May '18

18 May '18

External Email - Use Caution Dear all, thanks for building and maintaining freesurfer. It's really a great tool. My question is very simple: I have three Freesurfer Atlas files (lh and rh curvature.buckner40.filled.desikan_killiany.2010-03-25.gcs and RB_all_2008-03-26.gca) and would like to either get all coordinates in a given area and/or a nifti/img. I realize that the gcs and gca files contain much more information. However, I just need the location information and ROI name for a meta-analytic approach based on the literature. Is there any way to get this information? Thanks a lot! Cheers, Tim

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LGI trouble with Matlab
by subin oh 18 May '18

18 May '18

External Email - Use Caution Hello, I downloaded the Freesurfer ver 5.3.0 and installed it on Mac OS. I run *"recon-all -s <subject> -local GI" *for my subject.. And I run *Matlab Script* about "*Start up" , "make_outer_surface", "make_roi_paths" , "find correspoding center" *as follows: But it exited with same *errors* as follows: Please Could you tell me the way for correcting that error and to calculate the LGI? *the error message is..* Thank you very much. Best Regards, Subin =====================[Mac OS Error]====================== -------- freesurfer-Darwin-lion-stable-pub-v5.3.0 -------- Setting up environment for FreeSurfer/FS-FAST (and FSL) FREESURFER_HOME /Applications/freesurfer FSFAST_HOME /Applications/freesurfer/fsfast FSF_OUTPUT_FORMAT nii.gz SUBJECTS_DIR /Applications/freesurfer/subjects MNI_DIR /Applications/freesurfer/mni FSL_DIR /usr/local/fsl Chans-iMac:subjects roh$ recon-all -s test01_t1 -localGI Subject Stamp: freesurfer-Darwin-lion-stable-pub-v5.3.0 Current Stamp: freesurfer-Darwin-lion-stable-pub-v5.3.0 INFO: SUBJECTS_DIR is /Applications/freesurfer/subjects/test01_t1 Actual FREESURFER_HOME /Applications/freesurfer -rw-rw-r-- 1 roh staff 468188 May 18 16:01 /Applications/freesurfer/subjects/test01_t1/test01_t1/scripts/recon-all.log Darwin Chans-iMac.local 13.4.0 Darwin Kernel Version 13.4.0: Mon Jan 11 18:17:34 PST 2016; root:xnu-2422.115.15~1/RELEASE_X86_64 x86_64 /Applications/freesurfer/subjects/test01_t1/test01_t1/surf #-------------------------------------------- #@# Local Gyrification Index lh Fri May 18 17:36:00 KST 2018 \n mris_compute_lgi --i lh.pial \n ERROR: Matlab is required to run mris_compute_lgi! Darwin Chans-iMac.local 13.4.0 Darwin Kernel Version 13.4.0: Mon Jan 11 18:17:34 PST 2016; root:xnu-2422.115.15~1/RELEASE_X86_64 x86_64 recon-all -s test01_t1 exited with ERRORS at Fri May 18 17:36:00 KST 2018 For more details, see the log file /Applications/freesurfer/subjects/test01_t1/test01_t1/scripts/recon-all.log To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting =============================================================== *the Matlab Scripts are..* =================[Matlab Script: StartUp]====================== % freesurfer start fshome = getenv('FREESURFER_HOME'); fsmatlab = sprintf('%s/matlab',fshome); if (exist(fsmatlab) == 7) path(path,fsmatlab); end clear fshome fsmatlab; =================[Matlab Script: make_outer_surface]================ function make_outer_surface (filled_volume, se_diameter, output_surface) % Original Author: Marie Schaer % Date: 2007/11/14 % % This function takes as an input the binary volume resulting of the % filling of the any surface (usually the pial one) using mris_fill, and % will close the sulci using morphological operation, with a sphere as the % structural element. % % Parameters: % se_diameter is the diameter of the sphere (in mm), use 15mm by default % to close the sulci. % % Utilities to write the surface to the freesurfer format are modified from % "freesurfer_write_surf" (from Darren Weber's bioelectromagnetism toolbox), % according to a suggestion by Don Hagler in FreeSurfer's mailing list on % August 3, 2007. % % Example: make_outer_surface('lh.pial.mgz',15,'lh.outer-pial') fprintf('reading filled volume...\n'); vol=MRIread(filled_volume); volume=vol.vol; volume(volume==1)=255; fprintf('closing volume...\n'); % first apply a very soft gaussian filter, with sigma = 1mm, in order to % facilitate the closing Gaussian = fspecial('gaussian',[2 2],1); image_f=zeros(256,256,256); for slice=1:256 temp = double(reshape(volume(:,:,slice),256,256)); image_f(:,:,slice) = conv2(temp,Gaussian,'same'); end image2=zeros(size(image_f)); image2(image_f<=25)=0; image2(image_f>25)=255; se=strel('ball',se_diameter,se_diameter); BW2=imclose(image2,se); thresh = max(BW2(:))/2; i=find(BW2<=thresh); BW2(i)=0; i=find(BW2>thresh); BW2(i)=255; [f,v] = isosurface(BW2,100); v2=[129-v(:,1) v(:,3)-129 129-v(:,2)]; % in order to cope with the different orientation v=v2; fprintf('morphological closing done.\n'); fprintf('writing outer surface...\n'); fname=output_surface; vert = v; face = f - 1; vnum = size(vert,1); fnum = size(face,1); % open it as a big-endian file fid = fopen(fname, 'wb', 'b'); TRIANGLE_FILE_MAGIC_NUMBER = 16777214; fwrite3(fid, TRIANGLE_FILE_MAGIC_NUMBER); % Ouput a couple of text lines with creation date str = sprintf('created from matlab on %s\n',datestr(now)); fwrite(fid, str,'char'); fwrite(fid, vnum,'int32'); fwrite(fid, fnum,'int32'); % reshape vert into column array and write vert = reshape(vert',size(vert,1)*size(vert,2),1); fwrite(fid, vert,'float32'); % reshape face into column array and write face = reshape(face',size(face,1)*size(face,2),1); fwrite(fid, face,'int32'); fclose(fid) ; return end =================[Matlab Script: make_roi_paths]=============== function make_roi_paths(pial, outersmoothed, radius, stepsize, outdir, flagf) % Original Author: Marie Schaer % Date: 2007/11/15 % % This function creates multiple circular regions of interest on the outer % surface, measures their area (saved in matlab format) and save path file % containing a set of % corresponding points on the pial surface. The path files are required as % an input to the mri_path2label function % % Parameters: % radius: radius of the circular region of interest on the outer surface. % Most appropriate values between 20 and 25 mm, further documentation % available in the validation publication: "A surface-based approach to % quantify local cortical gyrification" by Schaer M, Bach Cuadra M, % Tamarit L, Eliez E, Thiran JP, IEEE Transactions on Medical Imaging, 2007 % % Utilities to transfer points on the pial surface calls "mesh_vertex_nearest", % a function written by Darren Weber. Utilities to compute matrix adjacency % for the pial surface calls "mesh_adjacency", a program first written by % Darren Weber, then modified by G. Peyre (source: toolbox_graph on % mathworks) % % Example: make_roi_paths('lh.pial','lh.outer-pial-smoothed',25,100,/tmp) t0 = cputime; disp('loading datas ...') [mesh_total.vertices, mesh_total.faces]=freesurfer_read_surf(pial); [mesh_outer.vertices, mesh_outer.faces]=freesurfer_read_surf(outersmoothed); disp('preparing outer mesh structure ...') mesh_outer = createMeshFacesOfVertex (mesh_outer.vertices, mesh_outer.faces) disp('preparing pial mesh structure ...') A = mesh_adjacency(mesh_total); % Keep track of the area for each individual region of interest on the % outer surface: nbVertices = size(mesh_outer.vertices,1); areasOuterROI = zeros(nbVertices,1); areasOuterROI = sparse (areasOuterROI); clear nbVertices % Circular regions of interest are defined each 100 vertex on the outer % surface. Due to the high resolution of the outer mesh (average face area % of ~0.3mm2), calculations are computed each 1 on 100 vertex, to avoid % high redundancies and optimize calculation time. for iV = 1:stepsize: length(mesh_outer.vertices) disp(['... creating path file for vertex ',num2str(iV),' / ' ,num2str(length(mesh_outer.vertices))]) % ------ Part 1: find the ROI on the enveloppe -------------- [verticesInROI, facesInROI] = getVerticesAndFacesInSphere(mesh_outer, iV, radius); % In rare case, the intersection of the enveloppe with the sphere result % in two regions of interest: the one that we expect, circular and % centered in iV; and an aberrant one at the bottom of the sphere % (e.g. near the superior sagittal vault). The next step is used to % control for that and keep only the radial region centered at iV. facesListOuterGeo = MakeGeodesicOuterROI (mesh_outer, iV, facesInROI); % Find the perimeter of the outer ROI verticesOuterGeo=unique(facesListOuterGeo(:)); perim=setdiff(verticesOuterGeo,verticesInROI); % Measure its area areaOuterROI = getFacesArea(mesh_outer,facesListOuterGeo); areasOuterROI(iV) = areaOuterROI; if (mod(iV,50*stepsize) == 1) fname = [outdir '/' pial '.area_intermed.mat']; save(fname, 'areasOuterROI') ; disp(['area file for outer ROIs saved at ',num2str(iV)]) end clear verticesInROI facesInROI facesListOuterGeo verticesOuterGeo areaOuterROI % ----- Part2: Define the corresponding set of points on the pial surface: % Transfer a few points of the perimeter of the hulls ROI from % the envelope to the pial surface, and save them as path file. step = 7; [verticeslist] = SearchProjectionOnPial(mesh_total, mesh_outer, perim, step); % reorganize the set of points in the right order to input them to % mri_path2label reorglist = reorganize_verticeslist (mesh_total, A, mesh_outer, perim, verticeslist, step); lindex = reorglist'; lxyz = mesh_total.vertices(lindex,:); lindex= lindex-1; p = sprintf ('%06d', iV); write_path(lxyz, lindex,[outdir '/' pial '.' p '.path']); clear verticeslist lindex lxyz end disp(['saving area file in matlab format... ']) fname = [outdir '/' pial '.outer_ROIs_area.mat']; save(fname, 'areasOuterROI') disp('DONE.') deltaT = cputime - t0 % indicate successful completion by deleting flagfile delete(flagf); =======================[find corresponding_center_FSformat]========================= t0 = cputime; [mesh_pial.vertices, mesh_pial.faces] = freesurfer_read_surf(pial); [mesh_outer.vertices, mesh_outer.faces] = freesurfer_read_surf(outersmoothed); fidv = fopen([outdir '/' pial '.center.vertices'], 'w') ; for iV = 1 :stepsize: length(mesh_outer.vertices) centerSeed=mesh_vertex_nearest(mesh_pial.vertices,mesh_outer.vertices(iV,:)); centerSeed = centerSeed - 1; %FreeSurfer-s vertex are 0-based p = sprintf ('%06d', iV); fid = fopen([outdir '/' pial '.' p '.center'], 'w') ; fprintf(fid,'%d\n',centerSeed); fclose(fid) ; fprintf(fidv,'%s\n',p); end fclose(fidv) ; deltaT = cputime - t0 % indicate successful completion by deleting flagfile delete(flagfile); ===================================================================================

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Getting stats file from nii.gz Yeo atlas for FEF
by Catherine Joe 17 May '18

17 May '18

External Email - Use Caution Hello everyone, I am having a bit of trouble extracting stats data (such as gray matter volume etc) from a particular FEF nifti file I generated from the Yeo Atlas 17 networks. I tried using mri_convert --in_stats <in volume><out volume> but the information given is really just the TE, TR, TI etc and not actually the information such as gray matter volume, surface area, number of voxels etc. What would be your advice to proceed from here? Is there another type of command I should be looking at? Thank you all in advance. Kind regards, Catherine

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FS Longitudinal Two Stage Model
by Evelyn Medawar 16 May '18

16 May '18

External Email - Use Caution Dear FS community, I got a question about the Longitudinal Two Stage Model for the following command put into Freesurfer v 6.0: long_mris_slopes --qdec ./qdec/long.qdec.table.dat --meas thickness --hemi lh --do-avg --do-rate --do-pc1 --do-spc --do-stack --do-label --time years --qcache fsaverage The first subject is running smoothly, but then the following ERROR message pops up: =============================================================================== SUBJECT template_09440.22 Intersecting Within-Subject Cortex Label cp /data/pt_nro186_lifeupdate/preprocessing/FREESURFER/FREESURFER_long/09440.22_VERIO.long.template_09440.22/label/lh.cortex.label /data/pt_nro186_lifeupdate/preprocessing/FREESURFER/FREESURFER_long/template_09440.22/label/lh.long.cortex.label mris_label_calc intersect /data/pt_nro186_lifeupdate/preprocessing/FREESURFER/FREESURFER_long/09440.22_SKYRA.long.template_09440.22/label/lh.cortex.label /data/pt_nro186_lifeupdate/preprocessing/FREESURFER/FREESURFER_long/template_09440.22/label/lh.long.cortex.label /data/pt_nro186_lifeupdate/preprocessing/FREESURFER/FREESURFER_long/template_09440.22/label/lh.long.cortex.label mris_label_calc: malloc.c:2394: sysmalloc: Assertion `(old_top == initial_top (av) && old_size == 0) || ((unsigned long) (old_size) >= MINSIZE && prev_inuse (old_top) && ((unsigned long) old_end & (pagesize - 1)) == 0)' failed. ERROR -6 : mris_label_calc intersect did not work? It seems that the labelling step at the intersection does not work (the result of the copying is an empty file). Has anybody any idea why that would be the case? Thank you a lot! Evelyn Medawar

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FS_Fast preproc-sess - bbregister misalignment
by Patrycja Naumczyk 16 May '18

16 May '18

External Email - Use Caution Hi All, I'm running FS v. 5.3 on Gentoo Linux. I made a study, where all subjects during one session had T1, resting-state and task-based fMRI. I processed all anatomical data through standard recon-all (it worked well), and the task-based fMRI through FS-FAST - which also generated fine results. Now I wanted to look into the rs-fMRI with functional connectivity. I made a separate directory tree for this purpose (in order not to mess task and rest data), and unfortunately the bbregister doesn't handle the registration during preproc-sess properly. Misalignment is big and covers all runs. BBR-sums of all of participants (N=39) exceed 0.8 (some of them exceed 1.0). What's interesting is that bbregister previously managed the task-based fMRI data well (with no BBR-sum exceeding 0.8). I double checked the data for any i.e. conversion/orientation faults, but found none. The command for preprocessing was identical in rs-fMRI and task-based fMRI: preproc-sess -sf <sessid> -d <ProjectDirectory> -surface fsaverage lhrh -mni305 -fwhm 5 -per-run -fsd bold I attach exemplary register log file from rs-fMRI subject registration (BBRsum=0.9704). This subject's task-based fMRI BBR-sum was 0.55. My question is - what may be the cause of such a discrepancy between registration of two functional runs taken one by one (the rs-fMRI preceded the task based)? Does anyone have an idea how to fix the problem? Best regards, Patrycja

3 7

Problem with template longitudinal pipeline
by Binnewies, Julia 16 May '18

16 May '18

External Email - Use Caution Dear FreeSurfer experts, We are trying to run FreeSurfer v5.3 on our longitudinal imaging data using the longitudinal pipeline. We first processed both time points cross-sectionally. The output of this step looks fine for both time points. We then performed step 2: creation of a template from both time points and step 3: longitudinally processing both time points. All steps run without errors, but the output of steps 2 and 3 look abnormal (please see images attached), so there appears to be something wrong in the creation of the template. We also have some subjects with data from only one timepoint and ran the longitudinal pipeline for these subjects as well (as was recommended on the wiki) and the output of steps 2 and 3 look fine for these subjects, so there appears to be an issue in creating the template based on both time points. The acquisition parameters at both time points are the same as far as we know. There is nine years between both measurements, and most of our subjects are between 50 and 60 years old at the second measurement. We have attached the recon.all.log file for one of our subjects. We hope you have some suggestions what the problem might be and how we could check this. Many thanks in advance for your help! Kind regards, Julia Binnewies & Laura van Velzen Dit e-mailbericht is uitsluitend bestemd voor de geadresseerde. Als dit bericht niet voor u bestemd is, wordt u verzocht dit aan de afzender te melden en het bericht te vernietigen. Het is niet toegestaan de inhoud van dit bericht verder te verspreiden of te gebruiken. Voor meer informatie over GGZ inGeest: www.ggzingeest.nl. Denk aan het milieu voordat u deze e-mail print.

1 0

ICV adjustment of volumes in longitudinal pipeline
by Tamir Eisenstein 15 May '18

15 May '18

External Email - Use Caution Hello Freesurfer experts, If I want to analyze the volume difference of regions (2 time points) after performing all the 3 steps of the longitudinal pipeline, do I need to adjust each volume in the "long" directories to its specific "tp.long" ICV or are the data of the two "long" directories already "adjusted" to the template and there is no need for the specific time-point ICV adjustment? Thanks! Tamir

2 1

Longitudinal LME cluster value extraction
by Emmanuel Nwosu 15 May '18

15 May '18

External Email - Use Caution Dear FreeSurfer experts, Am analysing longitudinal structural data with the LME model algorithm. I will like to map the significant cluster after analysing the data to all subjects at all time points, extract the values for all and perform further statistical analyses. Please how do I go about extracting the cluster value from all subjects at all time points? Any help will be appreciated. Kind regards Emmanuel

2 1

Problem with template longitudinal pipeline
by Laura van Velzen 15 May '18

15 May '18

2 1

Longitudinal data from different sequences and scanners
by James Gullickson 15 May '18

15 May '18

All, Our lab is working with longitudinal (two time points) data from a cohort of around 130 individuals. We are attempting to make comparisons between time points 1 and 2 on measures like total brain volume, ventricular volume, ventricle-brain-ratio, and cortical thickness. However, we have run into an issue--we are seeing net increases in cortical thickness and total brain volume over time (which seems biologically implausible, given our age range of ~30-60 yrs old). We think it may have something to do with the fact that the T1w data from each time point was acquired with slightly different parameters and on different scanners, possibly leading to a rounding error in quantification of volumes/thickness. Timepoint 1 data are 1.0mm isotropic and were acquired on a 3T Siemens Tim Trio with 12ch headcoil. Timepoint 2 data are 0.8mm isotropic and were acquired on the same scanner, but which went through an upgrade to a Prisma Fit between timepoints, using a 32ch coil. Currently we have been comparing data from the cross sectional stream. We would like to use the longitudinal stream if that would improve results, but we saw this post that cautioned against it: https://www.mail-archive.c om/freesurfer(a)nmr.mgh.harvard.edu/msg52992.html What would be your recommendation for comparing this data longitudinally? Any thoughts on why we are seeing net increases in volume/thickness, and how to avoid that? One idea we had was perhaps degrading each image by rigid co-registration and then bringing each image into the halfway space between the two (as FSL's SIENA does). Thanks, James

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Freesurfer May 2018