Freesurfer November 2017

freesurfer@nmr.mgh.harvard.edu

110 participants
198 discussions

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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Creating functional ROI
by a a 09 Nov '17

09 Nov '17

Dear FreeSurfer community, I am new to FreeSurfer and I apologize in advance if my questions are too naiive. I have some nii files for both a localizer and an experiment. I would like to find some ROIs in the localizer, get their coordinates, create a mask, and then find those regions on the experiment data and run MVPA. My main goal is to keep everything in the native space. Also, I am looking for percent signal change in selected ROIs. Here is my approach to analyze the localizer data: First, I ran the recon-all command. Then, I preprocessed the data in native space. The command that I ran was: preproc-sess -s sess01 -fsd bold -stc odd -surface self lhrh -mni305 -fwhm 5 -per-session -force Then, I configured my analyses and contrasts in each hemisphere, as well as the volume. Finally, I ran the analyses for each hemispheres and the volume. I ran this command: selxavg3-sess -s sess01 -analysis ffa.native.rh Lastly, I visualized the results by running these commands: tksurfer-sess -s sess01 -hemi rh -analysis ffa.native.rh -c faces-vs-bodies -self tkmedit-sess -s sess01 -analysis ffa.native.mni -c faces-vs-bodies -self So far, I think I have done everything correctly as am seeing the activation map where I am supposed to. Now, I would like to be able to select some of these ROIs/clusters, take their voxel coordinates/numbers and create a mask. Then, use this mask on the main experiment (non localizer) nii files and get the signal value for only those voxels. Is this possible? I have found this tutorial to create a functional ROI https://surfer.nmr.mgh.harvard.edu/fswiki/CreatingROIs but unfortunately I am not following it. I don't see these options in tksurfer. Also is it possible to create an ROI on the surface? I appreciate any help. Thank you so much Ashley Cole

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preproc-sess with symbolic links
by Tuominen, Lauri Johannes 09 Nov '17

09 Nov '17

Hi all, I’m trying to run preproc-sess using symbolic links in my SUBJECTS_DIR but the program exists with error message: could not find session XXXX. Symbolic links work fine when I run recon-all for instance. Suggestion for a fix would be greatly appreaciated. Cheers! Laurio

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Creating cached versions of Xhemi registrations
by Mehta, Chintan 09 Nov '17

09 Nov '17

Dear FreeSurfer Users, I'm using FreeSurfer version 6.0. I've processing subjects with recon-all and performed surface-based interhemispheric registration (via Xhemi at https://surfer.nmr.mgh.harvard.edu/fswiki/Xhemi) I want to run a GLM on the subjects Area and Thickness from the differences (Left minus Right). When stacking subjects asymmetry maps, I wanted to use a "--cache-only". The post at https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg27657.html seems to imply this requires running > recon-all -qcache -measure area -target fsaverage_sym -fwhm 10 -no-isrunning -s subjid -hemi lh for area at FWHM = 10. This would create files with the left hemisphere area registered to fsaverage_sym at smoothing FWHM = 10: $subjid/surf/lh.area.fwhm10.fsaverage_sym.mgh However, how do I do this also for the xhemi registration? I.e. create a file like $subjid/xhemi/surf/lh.area.fwhm10.fsaverage_sym.mgh Then, if I do this, can I stack the subjects using something like: > mris_preproc --target fsaverage_sym --hemi lh --xhemi --paired-diff \ --srcsurfreg fsaverage_sym.sphere.reg \ --cache-in area.fwhm10.fsaverage_sym \ --out lh.lh-rh.area.sm10.mgh \ --s subj1 --s subj2 ... Thank you. Best, Chintan mris_preproc --target fsaverage_sym --hemi lh --xhemi --paired-diff \ --srcsurfreg fsaverage_sym.sphere.reg \ --meas thickness \ --out lh.lh-rh.thickness.sm00.mgh \ --s subj1 --s subj2 ...

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Freesurfer November 2017