Freesurfer June 2023

freesurfer@nmr.mgh.harvard.edu

75 participants
107 discussions

how to manipulate values in m3z file
by Proulx, Jean Sebastien 17 Jul '23

17 Jul '23

External Email - Use Caution Hello, I produced an m3z warp file with mri_gradunwarp. Now I need to 0 out all displacement in the z direction, while keeping everything else the same since I need to combine multiple warps from images with different geometries. I see two strategies: (1) working directly on the m3z file I could not get mri_convert or mris_calc to do the trick. I thought I nailed it by manually editing the m3z file in freeview, but freeview saves the results in mgz format :-( Is there anything else I missed? (2) converting to mgz or nii timeseries, manupulate those and convert back to m3z mri_convert produced a nii file that freeview could not read and a single-frame mgz file that looks like some mishmash of the original 3-frame m3z. Any idea on how I can acheive my goal? A word on why would I want to do this silly thing. I have single-slice EPI and fov-matched higher-inplane-resolution single-slice GRE images. They have different within-slice gradient-non-linearity-related distortions. I want to undistort the GRE image then distort it to the EPI space. I need to zero out through-plane distortions to avoid displacing signal outside the imaging grid. Ignoring through-plane distortions should not be a problem for overlaying my GRE and EPI since, unlike within-plane distorsions, through-plane distortions are matched. Thanks a lot for the help and Have a very good day! Sebastien

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re-running recon-all after aseg.presurf.mgz edits
by Alexopoulos, Dimitrios 17 Jul '23

17 Jul '23

External Email - Use Caution A few quick questions FS experts. I made manual edits on subcortical structures in outputs from FS6.0. Specifically, I made the edits on the aseg.presurf.mgz file. I then reran using: recon-all -s neo267e_nil -autorecon2-noaseg -autorecon3 Do the updated stats files aseg.stats and ?h.aparc.stats incorporate these changes? I ask b/c the mri_segstats cmdline below uses the aseg.mgz not aseg.presurf.mgz # Title Segmentation Statistics # # generating_program mri_segstats # cvs_version $Id: mri_segstats.c,v 1.121 2016/05/31 17:27:11 greve Exp $ # cmdline mri_segstats --seg mri/aseg.mgz --sum stats/aseg.stats --pv mri/norm.mgz --empty --brainmask mri/brainmask.mgz --brain-vol-from-seg --excludeid 0 --excl-ctxgmwm --supratent --subcortgray --in mri/norm.mgz --in-intensity-name norm --in-intensity-units MR --etiv --surf-wm-vol --surf-ctx-vol --totalgray --euler --ctab /usr/local/pkg/freesurfer6.0/ASegStatsLUT.txt --subject neo267f_nil ________________________________ 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] Talairach Failure Detection
by Krystal Xiwing Yau 12 Jul '23

12 Jul '23

External Email - Use Caution Dear Freesurfer experts, I would like to seek for help regarding talairach error. I have browsed through the forum about it but still not solving my problem... The following steps are the solutions I have tried: * Re-run recon-all with -notal-check * Re-run recon-all with -notalairach * The above flags gave the same error message as follow: * WARNING2: gca.c::GCAhistoScaleImageIntensities: h_mri->nbins=100, mri_peak=108 after smoothing, mri peak at 0, scaling input intensities by inf error: Numerical result out of range error: GCAhistoScaleImageIntensities: could not find wm peak Command exited with non-zero status 252 * Ran the command to fix the registration: tkregisterfv --s Sub-108 --fstal --no-surfs * The view for this subject is weird because it shows the axial view when the coronal view is selected * [cid:49cf1b63-a35e-4003-8f38-a1def3b7bd64] * The correct view showed up when the coronal view is selected * [cid:abd68344-6bc3-489a-9eef-20569a419c02] When I viewed 001.mgz in Freeview, there was no such problem. However, some artifact (i.e. the weird lines) occurred in certain slices, as circled in pink: [cid:0c0b2ea4-3b3e-4361-ad0c-c5dec191c85c] [cid:eadbe192-c57a-48db-b429-b162b0154d0f] [cid:229941cf-2005-44c6-a979-0bf60c03da18] I am not sure how to fix it with tkregisterfv and what are the standards for it. It would be so much appreciated if someone could help out with this issue. Regards, Krystal Tel.: +852 2255 5024 Fax: +852 2872 5828 Address: Room 304, 3/F, New Clinical Building, 102 Pokfulam Road, Hong Kong.

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recon-all-clinical Longitudinal workflow
by Andrew Dedinas Geoly 10 Jul '23

10 Jul '23

External Email - Use Caution Hello Freesurfer experts! I am conducting a longitudinal GMV and CT analysis of mTBI participants who received an experimental single-dose pharmacological treatment. We collected GE Bravo (0.9mm isotropic) T1w data pre, immediately after (~ 4 days after intervention) and 1-month following the intervention. I have been working with the recon-all longitudinal pipeline stream (7.1.1) but have noticed pretty significant errors in terms of skull stripping and segmentation (participants are veterans with somewhat random lesion / atrophy patterns). I have tested your new recon-all-clinical program (7.4.0) on some of my worst cases and it is performing remarkably well. I am doing some more digging into the various synth segmentation packages available in FS newest versions and was wondering what the best course of action would be for integrating recon-all-clinical or synthseg into a longitudinal workflow. 1.Could I use the recon-all-clinical outputs as the "cross" for later base and long template construction? 2. SynthSeg and SCLimbic seem to have very good test-retest reliability-- would it be feasible to use the independent segmentation extractions from those and bypass the longitudinal stream entirely (not saying I would want to but I am curious)? Any and all help here would be greatly appreciated, and I thank you very much for your time. Warmest regards, Andrew --- Andrew D. Geoly, MS Research Data Analyst 1 Brain Stimulation Lab Department of Psychiatry and Behavioral Sciences Stanford University School of Medicine http://secure-web.cisco.com/1QSBlrn3-LhYcwEz_Sjst4ZqWKpoVeamcijnxImhD8Wxefq… [cid:40f0dd9c-7a7e-4ec0-83d1-c42f63d1a100]

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dcmunpack: Issues with the -run argument
by Sara Teso Cuesta 03 Jul '23

03 Jul '23

External Email - Use Caution Hello FreeSurfer Developers, I am trying to use dcmunpack to transform dicom images to a nifti format inside a FSFAST formatted directory ( https://secure-web.cisco.com/1JV-FemocV4fiLoKofgFHZ2hQTt_nlpR8LAqJEXvFr3d88…) however I am having issues understanding how to use properly the -run argument. This is the command I am trying to use: dcmunpack -src fMRI_dir -targ sessionid -fsfast -run 2 rest nii.gz f.nii.gz I assume I am making some mistakes with the command, specially with the run arguments since this is the error that I got in the terminal: ERROR: could not find run 2 in data My directory contains fMRIs downloaded directly from the ADNI database and grouped in folders following this structure: /fMRI_dir/subject_id/Axial_rsfMRI/date/image_uid/dicom images I've searched the list and no similar errors have been reported. Does anyone have any thoughts on how to solve this? 1) FreeSurfer version: freesurfer_ubuntu20-7.4.0_amd64.deb 2) Platform: Ubuntu 20.04 in WSL Thanks for your help.

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Re: [Freesurfer] mris_label2annot
by Maria Czarnecka 02 Jul '23

02 Jul '23

External Email - Use Caution Dear Yujing, Thank you so much for your answer. My ctab looks like this: 11100 Unknown 0 0 0 0 11102 G_and_S_occipital_inf 0 0 0 0 11111 G_cuneus 0 0 0 0 11119 G_occipital_middle 221 60 60 0 11120 G_occipital_sup 0 0 0 0 11121 G_oc-temp_lat-fusifor 0 0 0 0 11122 G_oc-temp_med-Lingual 0 0 0 0 11130 G_precuneus 0 0 0 0 11143 Pole_occipital 221 60 60 0 11145 S_calcarine 221 60 60 0 11158 S_oc_middle_and_Lunatus 0 0 0 0 11160 S_occipital_ant 0 0 0 0 11161 S_oc-temp_lat 20 180 140 0 11162 S_oc-temp_med_and_Lingual 0 0 0 0 11166 S_parieto_occipital 221 60 60 0 a sample of one of my label files: #!ascii label , from subject fsaverage vox2ras=TkReg 1630 139 -4.532 -75.888 20.953 0.0000000000 300 -15.423 -72.840 16.348 0.0000000000 301 -15.452 -76.689 23.049 0.0000000000 571 -15.631 -67.683 9.887 0.0000000000 573 -4.258 -84.880 12.147 0.0000000000 version of FreeSurfer: freesurfer-linux-centos7_x86_64-7.3.2-20220804-6354275

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Excellent results from recon-all-clinical
by Michael Mc Laughlin 30 Jun '23

30 Jun '23

External Email - Use Caution Hi, I just wanted to say how impressed I am by the Freesurfer brain analysis software in general and to share some results of a comparison of the new *recon-all-clinical *option with various contrast types and resolutions. This is only one subject, a healthy 62 year old male, so it's a very small study indeed, but the recon-all clinical does a great job in finding the correct volume of gray and white matter with some very low resolution clinical MRIs with non-ideal contrast MRI settings. As you can see below, the T2 and T2 FLAIR gray and white volumes results with 0.72mm x 0.72mm x 6.5mm get very close to the correct volumes as measured by recon-all on the T1-MPRAGE scan. When I look at the actual detail of the slices it looks good too. Obviously it can't do magic and it has to basically "guess" where the information is completely missing when there is 6.5mm between slices. The cortex tissue volumes for the T1 headscout, which is 1.6mm cubic voxels and has very low contrast between white and gray is also very good, considering the data it has to work with. The standard recon-all is not designed to work with a clinical T1 SE scan and naturally, does a much poorer GM/WM segmentation job. Here are the results I got: [image: image.png] [image: image.png] [image: image.png] [image: image.png] So, well done to the whole Freesurfer crew and especially to the volunteers who devote so much time to this support list. Michael McLaughlin, 2019 Parsons Medal Holder

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recon-all ends with error
by Justin Kasowski 29 Jun '23

29 Jun '23

External Email - Use Caution Writing masked volume to brain.finalsurfs.mgz...done. @#@FSTIME 2023:06:28:16:19:10 mri_mask N 5 e 0.51 S 0.01 U 0.44 P 89% M 74240 F 0 R 2972 W 0 c 3 w 760 I 0 O 0 L 0.13 0.04 0.01 @#@FSLOADPOST 2023:06:28:16:19:11 mri_mask N 5 0.13 0.04 0.01 #-------------------------------------------- #@# Fill Wed Jun 28 16:19:11 PDT 2023 /mnt/c/Users/BigBrain/documents/Subjects/sub-049/mri mri_fill -a ../scripts/ponscc.cut.log -xform transforms/talairach.lta -segmentation aseg.presurf.mgz -ctab /usr/local/freesurfer/7.2.0/SubCorticalMassLUT.txt -auto-man filled.auto.mgz filled.mgz ../tmp/filled.edits.txt wm.mgz filled.mgz logging cutting plane coordinates to ../scripts/ponscc.cut.log... INFO: Using transforms/talairach.lta and its offset for Talairach volume ... using segmentation aseg.presurf.mgz... error: volume size must be greater than 0 in every dimension Command exited with non-zero status 1 The error implies aseg.presurf.mgz or talairach.lta have a 0 dimension, but neither do. mri_info for aseg.presurf is below, I've attached the log and talairach.lta files: bigbrain@DESKTOP-EDQPTKK:/mnt/c/Users/BigBrain/Documents/Subjects/sub-049/mri$ mri_info aseg.presurf.mgz Volume information for aseg.presurf.mgz type: MGH dimensions: 256 x 256 x 256

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Longitudinal structural analysis in FreeSurfer ???
by Hamied Haroon 29 Jun '23

29 Jun '23

External Email - Use Caution Hello, I've run recon-all on patient T1s acquired at different timepoints after a neurological insult, in FreeSurfer v7.3.2 I want to analyse any change in the volume, surface area and average thickness of specific regions across time in each patient. Can I do this in FreeSurfer? Many thanks. Best wishes, Hamied Dr Hamied A Haroon, MSc, PhD, MInstP Research Associate in Biomedical Magnetic Resonance Imaging The University of Manchester

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Re: [Freesurfer] Freesurfer Digest, Vol 232, Issue 12 - data not displayed
by Haley O Higginbotham 28 Jun '23

28 Jun '23

External Email - Use Caution I've re-enabled the gpu and updated the drivers, and now glxgears runs properly and freeview opens and displays data. I am still unable to click on anything in the popup editing menus though, and the cursor appears greyed out when hovering over these popup windows. I also tried MobaXterm with the same results. (Interestingly the device manager and Intel Driver and Support Assistant incorrectly suggested that the graphics driver was up-to-date and I had to manually search the Intel driver database to find the actual most current driver: 31.0.101.4502) Update: I have also had to switch to a new computer and am running Ubuntu 22.04.2 with freesurfer-linux-ubuntu22_x86_64-7.4.1-20230614-7eb8460 through wsl2 Thanks, Haley

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Freesurfer June 2023