Freesurfer

freesurfer@nmr.mgh.harvard.edu

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30063 discussions

Re: [Freesurfer] Creating cached versions of Xhemi registrations
by Mehta, Chintan 10 Nov '17

10 Nov '17

Dear Doug, I think that is essentially what I figured. Based on remarks in other posts, my steps for evaluating laterality index entail applying: (1). Apply mri_preproc for each subject $SUB and $meas (area or thickness) individually using -xhemi flag but without any paired differences via: > mris_preproc --target fsaverage_sym --hemi lh --xhemi --srcsurfreg fsaverage_sym.sphere.reg --meas $meas --out ${SUB}_out.mgh --s $SUB Result is a surface file with two volumes (lh and xhemi-lh) called ${SUB}_out.mgh for each subject. (2). Smooth the two volumes in ${SUB}_out.mgh at a given $fwhm (5, 10, 15...): > mris_fwhm --s fsaverage_sym --hemi lh --cortex --smooth-only --fwhm $fwhm --i ${SUB}_out.mgh --o ${SUB}_out-sm${fwhm}.mgh to create a surface file with two volumes whose values are smoothed at fwhm = $fwhm. (3). Compute laterality index over the surface for each subject via paired-diff-norm: > mri_concat ${SUB}_out-sm${fwhm}.mgh --paired-diff-norm --o ${SUB}_latIndex-sm${fwhm}.mgh where ${SUB}_latIndex-sm${fwhm}.mgh is the surface file with laterality index for subject $SUB (after smoothing measures over left and right hemispheres). (4). Stack laterality indices for each subject in sample G (of n subjects) into a single mgh, > mri_concat --i SUB1_latIndex-sm${fwhm}.mgh --i SUB2_latIndex-sm${fwhm}.mgh ....... --i SUBn_latIndex-sm${fwhm}.mgh --out --i sampleG_latIndex-sm${fwhm}.mgh. (5) Run glm with designed matrix sampleG_design.txt containing n rows of covariates for SUB1, SUB2, ..., SUBn (in order) via: > mri_glmfit --y sampleG_latIndex-sm${fwhm}.mgh --X $sampleG_design.txt --no-rescale-x --glmdir glm_sampleG --C con1.mat --surf fsaverage_sym lh The whole purpose of this exercise + question was that I need to fit the GLM over subsets of the sample for sensitivity analysis to determine whether significance for the contrast in con1.mat (say slope of an IV, such as age) depends on patterns of based on demographics groups (such as gender). I suppose alternatively, I could just as well fit another GLMs with a design matrix modeling interactions between age and gender to make my evaluation, over the same set of stacked surfaces for the full sample. Thank you. Best, Chintan 1.

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Re: [Freesurfer] dt_recon and Tracula
by Mehta, Chintan 10 Nov '17

10 Nov '17

Dear FreeSurfer users, Sorry for adding the questions, I found most of my answers at https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/DiffusionV6.0#dMRIData… I used FreeView and found that registrations of the lowb.nii, orig.mgz, lh.white, and rh.white aligned very nicely. Alignments of lowb.nii with wmparc.mgz and aparc+aseg.mgz are also very nice. However, I'm finding that resampling wmparc.mgz to diffusion space via mri_vol2vol (inverse of dti/register.dat with nearest neighbor interpolation) yields poor alignments with the white surfaces and lowb.nii. Is this inevitable if there is a difference in resolutions between DWI and T1-weighted MRI? Thank you. Best, Chintan

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Optseq and de convolution for rapid designs
by Aser A 10 Nov '17

10 Nov '17

Hi all I used Optseq to optimize rapid event designs with multiple conditions . I have a theortical question : how it is possible to distingwoh the close by trials ? Is it by de convoution ? How is it possible to deal with overallped trials ? Is it because the conditions are random so that when averaging them the distingwoh is possible? Many thanks Aser

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dt_recon and Tracula
by Mehta, Chintan 10 Nov '17

10 Nov '17

Dear FreeSurfer users, I've been using FreeSurfer and Tracula versions 6.0. I've run Tracula on DWI scans, and now I am seeking to run dt_recon on them as well. As a new user, it seems both programs follow similar initial pre-processing steps (eddy current & motion correction), which the documentation says can take 1-2 hours. I'd imagine that these steps not need be repeated for running dt_recon if Tracula has already been run. I have a few questions: Q1: I ran dt_recon per documentation and the full process finished without error within 20 minutes for several initial DWI scans I ran. This is concerning since the documentation estimates eddy current & motion correction by itself to take 1-2 hours. Is 20 minutes reasonable? Q2: Is there a way to compare outputs from dt_recon & Tracula to ensure consistency in both processes? For example, can I compare stats in the fa.nii.gz file? I compared snapshots (attached) of wmparc (from recon-all of T1-weighted MRIscan), fa.nii.gz (from dt_recon), and dtifit_FA.nii (from Tracula) at the same slice. There are clear differences between dt_recon and Tracula that also hold at other slices. I believe Tracula registers DWI data to subject's anatomical space from recon-all of T1-weighted scans. That explains why higher fractional anisotropy values (white) in dtifit_FA.nii lined up more nicely with white matter in wmparc.nii than that of fa.nii.gz from dt_recon. I want to use mri_segstats on the fa.nii from dt_recon (along lines of https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg37032.html) Does this require first registering fa.nii to subject's native space to create a "fa-anat.nii" file? If so, how can I do that? Do I apply an inverse transform from the talairach registration of this data (fa-tal.nii.gz) to native space via ${SUB}/mri/transforms/talairach.lta? Q3: One post on the FreeSurfer Forum suggests that, if dt_recon is run first, then Tracula should still be run from the start because trac-all --preproc prepares data in an orientation that FSL's bedpostx is expecting. https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2012-March/023081.ht… However, does the inverse also hold? If I've run TRACULA (all three steps), is there a way to run dt_recon in a way that can allow using the output TRACULA's initial steps? Thank you. Best, Chintan

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comparing sphere and sphere.reg
by tony han 10 Nov '17

10 Nov '17

Hi, I'm trying evaluating the distortion for each subject from their native space to fsaverage atlas space. Is it a appropriate measure to compare ?h.sphere and ?h.sphere.reg? I assume that by comparison, I may get the how each vertex warped during the registration? Thanks! Best, Tony

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Compare longitudinal evolution of two vertex-wise data
by Matthieu Vanhoutte 10 Nov '17

10 Nov '17

Dear experts, Do you know if there would be a mean to compare longitudinal evolution of two vertex-wise data (i.e. kind of longitudinal correlation) with LME tools or others ? Best regards, Matthieu

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Re: [Freesurfer] mris_preproc srcsurfreg Freesurfer 6.0
by M del Mar Velasco 10 Nov '17

10 Nov '17

Thanks you for your reply. I have used surfreg script and now it runs correctly. However, my subject list is very long, I have 100 subjects and running surfreg with all subject takes 13 hours (using all my cpus in a parallel way). Is there any option to reduce this long time? Any cuda file? Thanks in advance, M del Mar

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localGI issues
by Nillo, Ryan Michael R 09 Nov '17

09 Nov '17

Hello experts, I am using FreeSurfer version 6 and am trying to run recon-all -localGI. Each time I run it, it fails on make_roi_paths. Below is an excerpt of the recon-all.log file. Any help is much appreciated. #@# Local Gyrification Index lh Thu Nov 9 14:06:42 PST 2017 mris_compute_lgi --i lh.pial ================= rm -Rf /data/sugrue2/NF1_qdec/sub_0015/surf/tmp-mris_compute_lgi-lh.pial ================= ================= mkdir -p /data/sugrue2/NF1_qdec/sub_0015/surf/tmp-mris_compute_lgi-lh.pial ================= ================= mris_fill -c -r 1 lh.pial /data/sugrue2/NF1_qdec/sub_0015/surf/tmp-mris_compute_lgi-lh.pial/lh.pial.filled.mgz ================= reading surface from lh.pial... writing filled volume to /data/sugrue2/NF1_qdec/sub_0015/surf/tmp-mris_compute_lgi-lh.pial/lh.pial.filled.mgz... conforming output volume setting resolution for intermediate calculations to 1.0000 ================= make_outer_surface('/data/sugrue2/NF1_qdec/sub_0015/surf/tmp-mris_compute_lgi-lh.pial/lh.pial.filled.mgz',15,'/data/sugrue2/NF1_qdec/sub_0015/surf/tmp-mris_compute_lgi-lh.pial/lh.pial-outer'); exit ================= < M A T L A B (R) > Copyright 1984-2015 The MathWorks, Inc. R2015b (8.6.0.267246) 64-bit (glnxa64) August 20, 2015 For online documentation, see http://www.mathworks.com/support For product information, visit www.mathworks.com. Academic License >> reading filled volume... closing volume... morphological closing done. writing outer surface... ================= mris_extract_main_component /data/sugrue2/NF1_qdec/sub_0015/surf/tmp-mris_compute_lgi-lh.pial/lh.pial-outer /data/sugrue2/NF1_qdec/sub_0015/surf/tmp-mris_compute_lgi-lh.pial/lh.pial-outer-main ================= counting number of connected components... 76848 voxel in cpt #1: X=2 [v=76848,e=230538,f=153692] located at (-26.925182, 5.953999, 4.185574) For the whole surface: X=2 [v=76848,e=230538,f=153692] One single component has been found nothing to do done ================= mris_smooth -nw -n 30 /data/sugrue2/NF1_qdec/sub_0015/surf/tmp-mris_compute_lgi-lh.pial/lh.pial-outer-main ./lh.pial-outer-smoothed ================= smoothing for 30 iterations smoothing surface tessellation for 30 iterations... smoothing complete - recomputing first and second fundamental forms... ================= mris_euler_number ./lh.pial-outer-smoothed ================= euler # = v-e+f = 2g-2: 76848 - 230538 + 153692 = 2 --> 0 holes F =2V-4: 153692 = 153696-4 (0) 2E=3F: 461076 = 461076 (0) total defect index = 0 ================= mris_convert -n lh.pial-outer-smoothed /data/sugrue2/NF1_qdec/sub_0015/surf/tmp-mris_compute_lgi-lh.pial/lh.pial-outer-smoothed-normals.asc ================= ================= find_corresponding_center_FSformat('lh.pial','lh.pial-outer-smoothed',100,'/data/sugrue2/NF1_qdec/sub_0015/surf/tmp-mris_compute_lgi-lh.pial','/tmp/mrc_8510_.m'); exit ================= < M A T L A B (R) > Copyright 1984-2015 The MathWorks, Inc. R2015b (8.6.0.267246) 64-bit (glnxa64) August 20, 2015 For online documentation, see http://www.mathworks.com/support For product information, visit www.mathworks.com. Academic License >> FREESURFER_READ_SURF [v 1.2 ] ...reading surface file: lh.pial ...reading triangle file ...adding 1 to face indices for matlab compatibility. ...done ( 0.07 sec) FREESURFER_READ_SURF [v 1.2 ] ...reading surface file: lh.pial-outer-smoothed ...reading triangle file ...adding 1 to face indices for matlab compatibility. ...done ( 0.01 sec) deltaT = 10.1400 ================= make_roi_paths('lh.pial','lh.pial-outer-smoothed',25,100,'/data/sugrue2/NF1_qdec/sub_0015/surf/tmp-mris_compute_lgi-lh.pial','/tmp/mrp_8510_.m'); exit ================= < M A T L A B (R) > Copyright 1984-2015 The MathWorks, Inc. R2015b (8.6.0.267246) 64-bit (glnxa64) August 20, 2015 For online documentation, see http://www.mathworks.com/support For product information, visit www.mathworks.com. Academic License >> loading datas ... FREESURFER_READ_SURF [v 1.2 ] ...reading surface file: lh.pial ...reading triangle file ...adding 1 to face indices for matlab compatibility. ...done ( 0.07 sec) FREESURFER_READ_SURF [v 1.2 ] ...reading surface file: lh.pial-outer-smoothed ...reading triangle file ...adding 1 to face indices for matlab compatibility. ...done ( 0.02 sec) preparing outer mesh structure ... face 5000 / 153692 face 10000 / 153692 face 15000 / 153692 face 20000 / 153692 face 25000 / 153692 face 30000 / 153692 face 35000 / 153692 face 40000 / 153692 face 45000 / 153692 face 50000 / 153692 face 55000 / 153692 face 60000 / 153692 face 65000 / 153692 face 70000 / 153692 face 75000 / 153692 face 80000 / 153692 face 85000 / 153692 face 90000 / 153692 face 95000 / 153692 face 100000 / 153692 face 105000 / 153692 face 110000 / 153692 face 115000 / 153692 face 120000 / 153692 face 125000 / 153692 face 130000 / 153692 face 135000 / 153692 face 140000 / 153692 face 145000 / 153692 face 150000 / 153692 mesh_outer = vertices: [76848x3 double] faces: [153692x3 double] facesOfVertex: [76848x1 struct] preparing pial mesh structure ... ...searching for mesh edges...done (189.57 sec). ... creating path file for vertex 1 / 76848 area file for outer ROIs saved at 1 In 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! Linux andaman.radiology.ucsf.edu 3.10.0-693.2.2.el7.x86_64 #1 SMP Sat Sep 9 03:55:24 EDT 2017 x86_64 x86_64 x86_64 GNU/Linux recon-all -s sub_0015 exited with ERRORS at Thu Nov 9 14:11:33 PST 2017 For more details, see the log file /data/sugrue2/NF1_qdec/sub_0015/scripts/recon-all.log To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting Thank you for your time, Ryan Nillo

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Re: [Freesurfer] mris_preproc srcsurfreg Freesurfer 6.0
by Mehta, Chintan 09 Nov '17

09 Nov '17

<https://www.mail-archive.com/search?l=freesurfer@nmr.mgh.harvard.edu&q=from…> Thank you for the insight; that is very interesting. I'm performing tests of continuous independent variables over a single sample of normally developing children (ages uniformly distributed from 8 to 15 along with 50/50 gender split). The IV is, for example, age-normed cognitive scores falling in a normal distribution. Since there is only one group, I suppose creating my own template from all samples could introduce significant bias; especially if there are hidden sources of heterogeneity I'm unaware of. Thank you. Best, Chintan On 11/09/2017 07:07 AM, Greve, Douglas wrote: > It might capture specific anatomical features that are unique to your > data set. It can be tricky though as you need to make sure to include an > equal mix of all your groups. Eg, if you have 20 ADs and 10 controls, > you'd need to make an atlas with 10 ADs and 10 controls.

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longitudinal base error. (not a netCDF file)
by miracle ozzoude 09 Nov '17

09 Nov '17

Hello FreeSurfer, While running base step of the longitudinal pipeline, i got the following error (please see the rec-all.log file for more details). How do i solve this problem? Thank you Best, Paul

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