Hi Thomas
Can you check the input images? I’ve seen this happen when e.g. the skull
stripping failed and the images are blank
Cheers
Bruce
From: freesurfer-boun...@nmr.mgh.harvard.edu
<freesurfer-boun...@nmr.mgh.harvard.edu> On Behalf Of Thomas Kaufmann
Sent: Wednesday, October 9, 2024 1:37 PM
To: Freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] Error During T2/FLAIR Pial Surface Refinement
External Email - Use Caution
Hello FreeSurfer Developers,
I'm attempting to refine pial surfaces with T2/FLAIR images as described here
(MailScanner has detected a possible fraud attempt from "secure-web.cisco.com"
claiming to be
https://surfer.nmr.mgh.harvard.edu/fswiki/recon-all#UsingT2orFLAIRdatatoimprovepialsurfaces<https://secure-web.cisco.com/1AH1BRBqXr5DfxhMfqvYMi7G1gSsW58-k5PUb3k7qBej25TzL4oJZblrUDWJjsLLjcoAP23YnnERxvXNWVp31VdS7Wz1q7Z9IGsbTfDYOtXS_IS2-NhyuSgcWRvjVEcIp8Ze5ad_mIfUdHi9dSOWXrSa2ApGwk2xa-45widx5O0YJ8QeYGP7QyiMbju7dhcO71PJoQVT13M2wFZLho8E4k-PiWY01aJ40WpQIqe-_MMmdpqn9-O7dJCNKFLcHeCc3vNvfCC-KBkMRhTOSH4vTaK_dzQspzQmlaXnfywC9zdXl9bVc-EaHeonBR_hFj6XSXZgCPXHCzOr4wFvMmGZaJg/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2Frecon-all%23UsingT2orFLAIRdatatoimprovepialsurfaces>).
For some of my subjects I get the following error during the
mris_place_surface subprocess when I run recon-all:
error: MRIhistogramLabelRegion: constant image
error: MRIhistogramLabelRegion: constant image
Segmentation fault
The error occurs independent of whether I process T1 and T2 images together
with -all or if I run only -autorecon3 with the T2 or FLAIR images added.
I've searched the list and while similar errors have been reported, no
solutions have been proposed. Does anyone have any thoughts on how to
troubleshoot this one?
1) FreeSurfer version: freesurfer-macOS-darwin_x86_64-7.4.1-20230614-7eb8460
2) Platform: macOS Sonoma 14.6.1
3) uname -a: Darwin MacBook-Air-M3 23.6.0 Darwin Kernel Version 23.6.0: Mon Jul
29 21:14:04 PDT 2024; root:xnu-10063.141.2~1/RELEASE_ARM64_T8122 arm64
4) recon-all.log: relevant section below
Thank you!
Thomas
mris_place_surface --adgws-in
../surf/autodet.gw.stats.lh.dat<http://surf/autodet.gw.stats.lh.dat> --seg
aseg.presurf.mgz --wm wm.mgz --threads 8 --invol brain.finalsurfs.mgz --lh --i
../surf/lh.pial.T1 --o ../surf/lh.pial.T2 --pial --nsmooth 0 --rip-label
../label/lh.cortex+hipamyg.label --pin-medial-wall ../label/lh.cortex.label
--white-surf ../surf/lh.white --aparc ../label/lh.aparc.annot --repulse-surf
../surf/lh.white --mmvol T2.mgz T2
Reading in input surface ../surf/lh.pial.T1
Not smoothing input surface
Area 280714 0.42434 0.32508 0.000178 6.1090
Corner 842142 60.00000 30.99319 0.049953 179.7466
Edge 421071 1.04711 0.48130 0.006015 7.4374
Hinge 421071 18.87838 25.11022 0.000011 179.9979
Reading white surface coordinates from ../surf/lh.white
Reading repulsion surface coordinates from ../surf/lh.white
Reading in aparc ../label/lh.aparc.annot
[DEBUG] CTABreadFromBinaryV2(): ct->nentries=36, num_entries_to_read=36
Reading in input volume brain.finalsurfs.mgz
Reading in seg volume aseg.presurf.mgz
Reading in wm volume wm.mgz
MRIclipBrightWM(): nthresh=15378, wmmin=5, clip=110
MRIfindBrightNonWM(): 1814 bright non-wm voxels segmented.
Masking bright non-wm for pial surface mid_gray = 67.5589
MRImask(): AllowDiffGeom = 1
MRImask(): AllowDiffGeom = 1
MRImask(): AllowDiffGeom = 1
Ripping frozen voxels
Ripping vertices not in label ../label/lh.cortex+hipamyg.label
MRISripNotLabel() ripped 6543/140359 vertices (133816 unripped)
INFO: rip surface needed but not specified, so using input surface
Ripping segs (eg, WMSA, BG, frozen)
Starting MRISripSegs() d = (-2 2 0.5) segnos: 247
MRISripSegs(): -2 2 0.5 ripped 0
Reading in multimodal volume T2.mgz
using multi modal weights
vertex 70180: xyz = (-39.3637,-26.8713,28.9107) oxyz =
(-42.1603,-27.2597,31.4024) wxzy = (-42.1603,-27.2597,31.4024) pxyz =
(-39.3637,-26.8713,28.9107)
CBVO Creating mask 140359
n_averages 4
Iteration 0 =========================================
n_averages=4, current_sigma=2
Computing pial target locations using multimodal (1)
starting MRIScomputePialTargetLocationsMultiModal()
max_outward_dist = 3, sample_dist = 0.1, pix_size = 1, whalf = 7
T2_min_inside = 110, T2_max_inside 300, T2_min_outside = 130, T2_max_outside 300
inside_peak_pct = 0.1, 0.01, outside_peak_pct = 0.5, 0.5
wm_weight = 3, nlabels=0, contrast_type=1
Changed 198177 aseg cortex voxels to 0
Creating lowres distance volumes t=0.0164299
Creating white distance volumes t=0.307498
(box.dx, box.dy,
box.dz<http://secure-web.cisco.com/1mzGv4vKcrdiw8HRX0Ke8D_5_Vx8djKG-sL522y5P7XwINHKSyJz0TEqD8ZwnO4fVJPg-MoQ7ZsnfjmVQ4zqXk4YaYnQX53rUXNXpOU9suVrCJHiBsIxp1wXsLmuHukndC5Q2ARcucmjKcD5rt-4dFkkA8WfKPfJe9-nB0vIXmTgILbV3dupL1HSpQDpWkPe4U3MxyV0cN5RPsJ8qIx595cvXAfwiocufEgJyjpgpuueeVC7ui2ScGU-qV0BTLYw2vLaNpsu9Aa7cqCVf-hwr3H5bqpVH-fFo2n0NF1w8ek0jEucrnBh7283zR4UZwCfYU7uAqJGLNvgb1MoZ_YRBug/http%3A%2F%2Fbox.dz%2F>)
= (132, 242, 326)
(region->dx, region->dy, region->dz) = (132, 242, 326)
(region->dx, region->dy, region->dz) = (132, 242, 326)
Creating pial distance volumes t=0.609579
(box.dx, box.dy,
box.dz<http://secure-web.cisco.com/1mzGv4vKcrdiw8HRX0Ke8D_5_Vx8djKG-sL522y5P7XwINHKSyJz0TEqD8ZwnO4fVJPg-MoQ7ZsnfjmVQ4zqXk4YaYnQX53rUXNXpOU9suVrCJHiBsIxp1wXsLmuHukndC5Q2ARcucmjKcD5rt-4dFkkA8WfKPfJe9-nB0vIXmTgILbV3dupL1HSpQDpWkPe4U3MxyV0cN5RPsJ8qIx595cvXAfwiocufEgJyjpgpuueeVC7ui2ScGU-qV0BTLYw2vLaNpsu9Aa7cqCVf-hwr3H5bqpVH-fFo2n0NF1w8ek0jEucrnBh7283zR4UZwCfYU7uAqJGLNvgb1MoZ_YRBug/http%3A%2F%2Fbox.dz%2F>)
= (144, 256, 336)
(region->dx, region->dy, region->dz) = (144, 256, 336)
(region->dx, region->dy, region->dz) = (144, 256, 336)
locating cortical regions not in interior range [110.0 --> 300.0], and not in
exterior range [130.0 --> 300.0]
t = 0.984043
Starting loop over 140359 vertices
vno = 0, t = 0.984043
error: MRIhistogramLabelRegion: constant image
error: MRIhistogramLabelRegion: constant image
Segmentation fault
_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Mass General Brigham
Compliance HelpLine at https://www.massgeneralbrigham.org/complianceline
<https://www.massgeneralbrigham.org/complianceline> .
Please note that this e-mail is not secure (encrypted). If you do not wish to
continue communication over unencrypted e-mail, please notify the sender of
this message immediately. Continuing to send or respond to e-mail after
receiving this message means you understand and accept this risk and wish to
continue to communicate over unencrypted e-mail.
