Freesurfer June 2020

freesurfer@nmr.mgh.harvard.edu

91 participants
130 discussions

Fw: Hard Error Troubleshooting
by McManus, Peter 02 Jul '20

02 Jul '20

?Hello, I'm emailing for assistance regarding 6 hard-failed FS subjects (out of 1000) that were re-processed and still prematurely terminated at different pre-processing stages (using FS 7.1). The job was completed on a SLURM computing cluster affiliated with Boston Children's Hospital's E2 server, and I've attached the recon-all.logs for clarity, although none of the logs report an "exit with errors" but rather simply stop running. Do you have any idea what the issue(s) might be? Hopefully this is enough information to work with, as I'm not the one who actually ran the commands and am a new RA trying to get acclimated to the computational environment at BCH. Thanks for the help. Best, Peter

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Recon-all 5.3.0 failing and I can't see the error message
by Ian 02 Jul '20

02 Jul '20

External Email - Use Caution I have attached the log - is there any chance you could tell me what the problem is? Thanks, Ian --

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Re: [Freesurfer] How can I create a grey matter volume in Matlab?
by Franziska Klein 02 Jul '20

02 Jul '20

External Email - Use Caution Hello again, unfortunately, nobody is responding. . Until now I am able to create meshes from the freesurfer output files with the isosurface() and read_surf() functions from a MATLAB based toolbox . However, I still do not know with which combinations of the outputs of recon-all I could create a grey matter only mask. My goal is to get subject specific channel MNI coordinates projected onto the cortex (grey matter). My solution at the moment is to simply use the pial surfaces (rh.pial and lh.pial), however, I am not sure if this is sufficient. Any thoughts or ideas maybe? Thanks, Franziska ________________________________ Von: Franziska Klein Gesendet: Mittwoch, 27. Mai 2020 11:05 An: freesurfer(a)nmr.mgh.harvard.edu Betreff: How can I create a grey matter volume in Matlab? Dear freesurfer user, due to the Covid 19 situation I am working in home office with a windows computer and can not run any freesurfer functions (installing a virtual box is not really an option). For all my subjects I do already have all output files from recon all. In the output, I found a wm.mgz but unfortunately there is no gm.mgz. Is it somehow possible to create a grey matter volume by using the recon all output in combination with Matlab? Thank you and kind regards, Franziska ------------------------------------------ Franziska Klein, M.Sc. Neurocognition and Functional Neurorehabilitation Group Neuropsychology Lab Department of Psychology University of Oldenburg D-26111 Oldenburg Germany Office: A7 0-066 Phone: +49-441-798-4947 Fax: +49-441-798-5522

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Longitudinal Stream Problem
by Danielian, Laura (NIH/NINDS) [E] 01 Jul '20

01 Jul '20

External Email - Use Caution Hi, I’ve finished processing a data set that included longitudinal data and I’m having a problem with a small percentage of the longitudinal timepoints. To review what I’ve done, I edited all of the individual (cross-sectional) timepoints until the wm and pial surfaces were correct, then created the base and edited that until it looked good, and then created the longitudinal files for each cross-sectional timepoint. Most of these did not need editing and some needed slight edits to either wm or brainmask which corrected the longitudinal surfaces. However, in a small handful of cases, the wm/pial surfaces were so distorted that editing would not fix the problem. In these cases, longitudinal surfaces were very different from both the original cross-section and base. I’ve tried to attach a file that shows an example – it might only affect a small portion of the brain but in these cases I don’t think I could edit it to improve the surfaces. In the example I attached, red/blue are from the long file and pink/lt blue are from the base. Do you have any suggestions for why this might be happening and how to fix it? I’m running v6.0. Thanks! Laura Danielian

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Sub-cortical areas and other atlases
by Martin Juneja 01 Jul '20

01 Jul '20

External Email - Use Caution Hello experts, I am following these instructions https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis to analyze the association between IQ and whole brain cortical thickness of brain areas (which by default uses Desikan atlas of 34 regions). I was wondering how: (1). To do the similar analysis to identify sub-cortical regions which show significant association between thickness and IQ. (2). To use other atlases here i.e., replace Desikan atlas with 7 or 17 network Yeo atlas to identify which network shows the association with IQ. I know how to extract thickness etc from sub-cortical areas (i.e., aseg stats) and use Yeo atlas outside these instructions, but I am not sure how to do this in above described instructions i.e., replace Desikan with sub-cortical and Yeo atlases etc. Any help would be really appreciated. Thanks !

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Discrepancy in volume calculated for thalamic nuclei in FreeSurfer
by Corinna Bauer 30 Jun '20

30 Jun '20

External Email - Use Caution Hello all, We are working on calculating the volume of thalamic nuclei in our participants and noticed that there is often a discrepancy in measured volume in the ThalamicNuclei.v12.T1.volumes.txt and the volume calculated for the same thalamic nucleus using fslstats -V. (Note that the nuclei are all created in FreeSurfer, just extracted to individual .nii files afterwards). For example: in one control subject, the volume of the right VPL was measured in FreeSurfer as 264.650938 mm^3, but the same extracted label in fslstats shows a volume of 242 mm^3. What could be causing this discrepancy? Thanks Corinna

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Error recon-all mri_cc
by Yann Quidé 29 Jun '20

29 Jun '20

External Email - Use Caution Hi there, I am using Freesurfer v7.1.0 and encounter an error for few of my subjects only. Recon-all finishes with errors, and it seems this occurs during the segmentation. What can I do to fix this? I attached the recon-all log for one of my subject. Thanks, Yann

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Question regarding MRIread
by Franziska Klein 29 Jun '20

29 Jun '20

External Email - Use Caution Hello, I am using the isosurface() function in order to create a mesh based on the T1.mgz and on the ribbon.mgz. I need those meshes for the coregistration of some channels. After coregistration I do project the channels onto the cortex and extract the corresponding voxel coordinates. Until here, everything works fine. Next, I am using MRIwrite in order to save the T1.mgz as *.nii.mgz which I am using to generate a deformation field with SPM12 to transform the voxel coordinates to normalized MNI coordinates. However, when I put the voxel coordinates (not normalized yet) into SPM12 while displaying my generated *.nii image it happens that the coordinates on the right hemisphere (MNI space) are slightly outside of the cortex which is of course not the case on my cortex mesh after projection. Now I am wondering whether there is a mismatch between the mesh and the *.nii image (one voxel maybe)? And whether that is introduced by MRIwrite? If so, do I have to shift all points of the meshes by +1 in order to get correct results the way I want to? If not, any ideas on where that mismatch could come from? Thank you and kind regards, Franziska

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Re: [Freesurfer] mri_vol2surf for NIFTI to GIFTI conversion
by Glasser, Matthew 29 Jun '20

29 Jun '20

External Email - Use Caution Your command below is missing the <surface> argument: wb_command -volume-to-surface-mapping <volume> - the volume to map data from <surface> - the surface to map the data onto <metric-out> - output - the output metric file [-ribbon-constrained] - use ribbon constrained mapping algorithm <inner-surf> - the inner surface of the ribbon <outer-surf> - the outer surface of the ribbon Which can be a repeat of one of the other surfaces I think, though we typically use the midthickness surface here. Matt. From: <freesurfer-bounces(a)nmr.mgh.harvard.edu> on behalf of Mason Wells <WellsMT1(a)cardiff.ac.uk> Reply-To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> Date: Monday, June 29, 2020 at 11:20 AM To: "freesurfer-bounces(a)nmr.mgh.harvard.edu" <freesurfer-bounces(a)nmr.mgh.harvard.edu>, Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> Subject: [Freesurfer] mri_vol2surf for NIFTI to GIFTI conversion External Email - Use Caution Dear experts, I posted a message last week about converting NIFTI files into GIFTI format, then GIFTI to CIFTI, whilst keeping these functional data in the same space as the subjects FS surface. I got some information RE usign the HCP workbench, but I wondered if running mri_vol2surf could achieve the same thing as running the wb_command? For example, is it advisable to run the following command for each hemisphere and then merge them into a single GIFTI/CIFTI in the next steps? * mri_vol2surf --src filtered_func_data.nii.gz --out movie_surface.gii --srcreg partial-to-struct.lta --hemi lh --projfrac 0.5 --out_type gii I have also tried the wb_command option but this has been unsuccesful: I first ran the mris_convert to convert the relevant surf files into .gii format (from FS format) * e.g. mris_convert lh.pial lh.pial.surf.gii I then applied the transformation to align the filtered_func to the T1 * mri_vol2vol --mov filtered_func_data.nii.gz --reg partial-to-struct.lta --fstarg --o movie_t1_space.nii.gz I then tried to run the following wb command * wb_command -volume-to-surface-mapping /home/masontwells/Documents/Data/MovPPT_001/MovPPT_001.feat/movie_t1_space.nii.gz /home/masontwells/Documents/Data/freesurfer/subjects/MovPPT_001/surf/lh.inflated.surf.gii /home/masontwells/Documents/Data/MovPPT_001/lh_movie.gii -ribbon-constrained /home/masontwells/Documents/Data/freesurfer/subjects/MovPPT_001/surf/lh.white.surf.gii /home/masontwells/Documents/Data/freesurfer/subjects/MovPPT_001/surf/lh.pial.surf.gii Which resulted in this subsequent error. ERROR: NAME OF FILE: movie_t1_space.nii.gz PATH TO FILE: /home/masontwells/Documents/Data/MovPPT_001/MovPPT_001.feat Unable to allocate memory for reading the file. File Size: 3.24 Gigabytes Note: The amount of memory required to read a data file may be substantially larger than the size of the file due to the way the file's data is organized in memory or compression of data within the file. Any advice on how to convert NIFTI to GIFTI and then GIFTI to CIFTI whilst keeping the data in the subjects space would be really appreciated. Best wishes, Mason Mason T Wells, MSc PhD student School of Optometry and Vision Sciences & Cardiff University Brain Research Imaging Centre (CUBRIC), School of Psychology Cardiff University Cardiff CF24 4HQ UK Email: WellsMT1(a)cardiff.ac.uk<mailto:WellsMT1@cardiff.ac.uk> Tel: 02920 879628 Web: Cardiff University webpage<https://www.cardiff.ac.uk/people/research-students/view/974214-> Mason T Wells, MSc Myfyriwr PhD Yr Ysgol Optometreg a Gwyddorau’r Golwg & Canolfan Ymchwil Delweddu’r Ymennydd Prifysgol Caerdydd (CUBRIC), Yr Ysgol Seicoleg Prifysgol Caerdydd Heol Maindy Caerdydd CF24 4HQ DU E-bost: WellsMT1(a)caerdydd.ac.uk<mailto:WellsMT1@caerdydd.ac.uk> Ffôn: 02920 879628 ________________________________ The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail.

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freesurfer 7.1.0 mris_sphere failure, "singular matrix in quadratic form"
by Malone, Ian 29 Jun '20

29 Jun '20

External Email - Use Caution Hello, We've run into an issue with freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b (on Rocks release 7.0, kernel 3.10.0-957.12.2.el7.x86_64). It appears some runs are failing at the mris_sphere stage, but not producing any very informative errors, just repeated "singular matrix in quadratic form" at the end of mris_sphere as below. I was wondering if anyone had any suggestions for further troubleshooting please? recon-all is being invoked in two stages, with a manual brain mask replacing /scratch0/wcoath/2217885.100/sub-11233210_ses-followup/mri/brainmask.mgz in between them. This is being managed by a python script, but I think the sequence being executed is the following: $ recon-all -i /SAN/medic/insight46/analysis/gradwarp/sub-11233210/ses-followup/anat/sub-11233210_ses-followup_T1w_run-1_desc-gradwarp.nii.gz -T2 /SAN/medic/insight46/analysis/gradwarp/sub-11233210/ses-followup/anat/sub-11233210_ses-followup_T2w_run-1_desc-gradwarp.nii.gz -autorecon1 -noskullstrip -noT2pial -cw256 -cubic -3T -openmp 4 -s sub-11233210_ses-followup -status /SAN/medic/insight46/analysis/freesurfer7/status/sub-11233210_ses-followup_recon_all_status.log -log /SAN/medic/insight46/analysis/freesurfer7/log/sub-11233210_ses-followup_recon_all.log $ mri_convert /SAN/medic/insight46/analysis/drc_brain/sub-11233210/ses-followup/anat/sub-11233210_ses-followup_T1w_run-1_space-orig_desc-drc-brain-mask.nii.gz /scratch0/wcoath/2217885.100/sub-11233210_ses-followup/mri/drcmask.mgz --cw256 --conform -rt nearest $ mri_mask -T 1 /scratch0/wcoath/2217885.100/sub-11233210_ses-followup/mri/T1.mgz /scratch0/wcoath/2217885.100/sub-11233210_ses-followup/mri/drcmask.mgz /scratch0/wcoath/2217885.100/sub-11233210_ses-followup/mri/brainmask.mgz $ recon-all -autorecon2, -autorecon3 -cw256 -cubic -T2pial -openmp 4 -s sub-11233210_ses-followup -status /SAN/medic/insight46/analysis/freesurfer7/status/sub-11233210_ses-followup_recon_all_status.log -log /SAN/medic/insight46/analysis/freesurfer7/log/sub-11233210_ses-followup_recon_all.log The first recon-all (autorecon1) completes okay, the autorecon2,3 stage fails on occasion (this works for most scans). Its last output looks like this (full copy attached): @#@FSLOADPOST 2020:06:17:02:37:18 mris_curvature N 12 1.14 1.51 1.48 #-------------------------------------------- #@# Sphere lh Wed Jun 17 02:37:18 BST 2020 /state/partition1/scratch0/wcoath/2217885.100/sub-11233210_ses-followup/scripts mris_sphere -rusage /state/partition1/scratch0/wcoath/2217885.100/sub-11233210_ses-followup/touch/rusage.mris_sphere.lh.dat -seed 1234 ../surf/lh.inflated ../surf/lh.sphere setting seed for random number genererator to 1234 7.1.0 7.1.0 == Number of threads available to mris_sphere for OpenMP = 4 == reading original vertex positions... scaling brain by 0.309... projecting onto sphere... surface projected - minimizing metric distortion... MRISunfold() max_passes = 1 ------- tol=5.0e-01, sigma=0.0, host=fry-6, nav=1024, nbrs=2, l_area=1.000, l_dist=1.000 using quadratic fit line minimization complete_dist_mat 0 rms 0 smooth_averages 0 remove_neg 0 ico_order 0 which_surface 0 target_radius 0.000000 nfields 0 scale 1.000000 desired_rms_height -1.000000 momentum 0.900000 nbhd_size 7 max_nbrs 8 niterations 25 nsurfaces 0 SURFACES 3 flags 0 (0) use curv 0 no sulc 0 no rigid align 0 mris->nsize 2 mris->hemisphere 0 randomSeed 1234 singular matrix in quadratic form singular matrix in quadratic form singular matrix in quadratic form singular matrix in quadratic form singular matrix in quadratic form singular matrix in quadratic form singular matrix in quadratic form singular matrix in quadratic form singular matrix in quadratic form singular matrix in quadratic form @#@FSTIME 2020:06:17:02:37:18 mris_sphere N 6 e 256.90 S 2.38 U 723.85 P 282% M 2286104 F 0 R 931286 W 0 c 79152 w 33537 I 0 O 0 L 1.14 1.51 1.48 @#@FSLOADPOST 2020:06:17:02:41:35 mris_sphere N 6 2.62 2.15 1.75 Linux fry-611-142.local 3.10.0-1062.9.1.el7.x86_64 #1 SMP Fri Dec 6 15:49:49 UTC 2019 x86_64 x86_64 x86_64 GNU/Linux recon-all -s sub-11233210_ses-followup exited with ERRORS at Wed Jun 17 02:41:35 BST 2020 For more details, see the log file /SAN/medic/insight46/analysis/freesurfer7/log/sub-11233210_ses-followup_recon_all.log To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting Thanks for your time, Ian

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Freesurfer June 2020