Freesurfer

freesurfer@nmr.mgh.harvard.edu

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Fwd: The results of your email commands
by Rob Kudyba 26 May '23

26 May '23

External Email - Use Caution does this message mean my email was rejected? Also the link to subscrobe on https://secure-web.cisco.com/1C8Ww8WKzb-WR8JygU7XB0JN4vWN1-1IzwWYF8eJpyXmp6… are broken as they should point to the https version, e.g., the link to subscribe http://secure-web.cisco.com/1Rs_mL5ODuvETF1LGNBWxqNLByNtjtuyy843X-XuQN3-Jxn… ---------- Forwarded message --------- From: <freesurfer-bounces(a)nmr.mgh.harvard.edu> Date: Fri, May 26, 2023 at 11:25 AM Subject: The results of your email commands To: <rk3199(a)columbia.edu> The results of your email command are provided below. Attached is your original message. - Results: Ignoring non-text/plain MIME parts - Unprocessed: c3RlciB3aGVyZSBGcmVlc3VyZmVyIGlzIGxvYWRlZCBhZCBob2MgYXMgYSBtb2R1bGUuIFJ1bm5p bmcgbW9kdWxlCmF2YWlsIHJlc3VsdHMgaW4gdGhlIGZvbGxvd2luZyB3YXJuaW5nczoKCi9wYXRo L3RvL2FuYWNvbmRhMy0yMDIxLjExL2Jpbi9tcGljYzogbGluZSAyODU6Cng4Nl82NC1jb25kYV9j b3M2LWxpbnV4LWdudS1jYzogY29tbWFuZCBub3QgZm91bmQKIEVSUk9SOiBFbnZpcm9ubWVudCB2 YXJpYWJsZSBGUkVFU1VSRkVSX0hPTUUgbXVzdCBiZSBkZWZpbmVkIHByaW9yIHRvCnNvdXJjaW5n IEZyZWVzdXJmZXIuCi9wYXRoL3RvL2FuYWNvbmRhMy0yMDIxLjExL2Jpbi9tcGljYzogbGluZSAy ODU6Cng4Nl82NC1jb25kYV9jb3M2LWxpbnV4LWdudS1jYzogY29tbWFuZCBub3QgZm91bmQKIEVS Uk9SOiBFbnZpcm9ubWVudCB2YXJpYWJsZSBGUkVFU1VSRkVSX0hPTUUgbXVzdCBiZSBkZWZpbmVk IHByaW9yIHRvCnNvdXJjaW5nIEZyZWVzdXJmZXIuCgpJbiBteSAuYmFzaHJjIGZpbGU6CgogPj4+ IGNvbmRhIGluaXRpYWxpemUgPj4+CgogISEgQ29udGVudHMgd2l0aGluIHRoaXMgYmxvY2sgYXJl IG1hbmFnZWQgYnkgJ2NvbmRhIGluaXQnICEhCgpfX2NvbmRhX3NldHVwPSIkKCcvcGF0aC90by9h bmFjb25kYTMtMjAyMS4xMS9iaW4vY29uZGEnICdzaGVsbC5iYXNoJyAnaG9vaycKMj4gL2Rldi9u dWxsKSIKCmlmIFsgJD8gLWVxIDAgXTsgdGhlbgoKICAgIGV2YWwgIiRfX2NvbmRhX3NldHVwIgoK ZWxzZQoKICAgIGlmIFsgLWYgIi9wYXRoL3RvL2FuYWNvbmRhMy0yMDIxLjExL2V0Yy9wcm9maWxl LmQvY29uZGEuc2giIF07IHRoZW4KCiAgICAgICAgLiAiL3BhdGgvdG8vYW5hY29uZGEzLTIwMjEu MTEvZXRjL3Byb2ZpbGUuZC9jb25kYS5zaCIKCiAgICBlbHNlCgogICAgICAgIGV4cG9ydCBQQVRI PSIvcGF0aC90by9hbmFjb25kYTMtMjAyMS4xMS9iaW46JFBBVEgiCgogICAgZmkKCmZpCgp1bnNl dCBfX2NvbmRhX3NldHVwCgoKVGhlIG1vZHVsZWZpbGUgZm9yIEZyZWVzdXJmZXIgY29udGFpbnM6 Cgptb2R1bGUtd2hhdGlzICJhZGRzIGZyZWVzdXJmZXIgdG8geW91ciBlbnZpcm9ubWVudCB2YXJp YWJsZXMiCgpzZXQgICAgICAgICAgICAgIHJvb3QgICAgICAgICAgL3BhdGgvdG8vZnJlZXN1cmZl cgoKc2V0ZW52ICAgICJGUkVFU1VSRkVSX0hPTUUiICAgICIvcGF0aC90by9mcmVlc3VyZmVyIgoK c2V0ZW52ICAgICJTVUJKRUNUU19ESVIiICAgICAgIi9wYXRoL3RvL2ZyZWVzdXJmZXIvc3ViamVj dHMiCgpwcmVwZW5kLXBhdGggICAgIFBBVEggICAgICAgICAgICAgICAgICRyb290L2JpbgoKaWYg eyBbIG1vZHVsZS1pbmZvIG1vZGUgbG9hZCBdIH0gewoKc3lzdGVtICJzb3VyY2UgL3BhdGgvdG8v - Ignored: ZnJlZXN1cmZlci9TZXRVcEZyZWVTdXJmZXIuc2giCgp9CgoKSSBzZWUgdGhhdCBTZXRVcEZyZWVT dXJmZXIuc2ggaGFzIHRoaXM6CgoKIyBDYWxsIGNvbmZpZ3VyYXRpb24gc2NyaXB0OgoKc291cmNl ICRGUkVFU1VSRkVSX0hPTUUvRnJlZVN1cmZlckVudi5zaAoKCkFmdGVyIHJ1bm5pbmcgbW9kdWxl IHVubG9hZCBmcmVlc3VyZmVyIHNldmVyYWwgZGlyZWN0b3JpZXMgcmVtYWluIGluICRQQVRIOgoK CmVjaG8gJFBBVEgKL3BhdGgvdG8vZnJlZXN1cmZlci9mc2Zhc3QvYmluOi9wYXRoL3RvL2ZyZWVz dXJmZXIvdGt0b29sczovcGF0aC90by9mcmVlc3VyZmVyL21uaS9iaW46L3BhdGgvdG8vZnJlZXN1 cmZlci9mc2Zhc3QvYmluOi9wYXRoL3RvL2ZyZWVzdXJmZXIvdGt0b29sczovcGF0aC90by9mcmVl c3VyZmVyL21uaS9iaW4KCgpTbyAkRlJFRVNVUkZFUl9IT01FIGFuZCAkU1VCSkVDVFNfRElSIGFy ZSBiZWluZyB1bnNldCBidXQgYWxsIG9mIHRoZSBvdGhlcgplbnYgdmFycyBhcmUgbm90LiBJcyB0 aGVyZSBhIHdheSB0byB1bnNldCB0aGUgdmFycyBmcm9tCkZyZWVTdXJmZXJFbnYuc2g/IEEgdGhy ZWFkCm9uIFNPCjxodHRwczovL3NlY3VyZS13ZWIuY2lzY28uY29tLzFyOC1DLWhlMlRkSWpHVUVG dnJpdjBNZUNOWVZPRlVVcW05ekhTTkN2RTg0NEpSZGNEaUgtelRvelMxTUs0WW1MWWJXVzVvd1Ju MV9qRzJwSTdhUkdNTDFWeFo2TXdQeXlYLWw2OFNWczhDTGhfT2dYYk52cXFiYkt4YzZIMndKT3JS MmxGdzg4SjdlMHVISG9oZUNwV3B0V2MxYzZUaDZaQzNXaGVucTFvTDJwMFdGcWVaOFE0RDFmem4x bFZWNFZjR3JKaWZnM21XSkFWajJhT2M5OU1TUjNyVEpfdWFMXzJrR2NmUGI4SXNlOWJ5N0wzY2Nr c21VUW5HcFZxWkxYVU9hMnl4MVFnb2tHYVNRWDA0bkpTZUVibGwxMXEtS1FOd3VYM3FybmsycmJq WlRQYUpzTEotZEhDRkl0Z1ZjNkV5MmVkalcxajFBQklTcmgtTTJJQUEvaHR0cHMlM0ElMkYlMkZz dGFja292ZXJmbG93LmNvbSUyRnF1ZXN0aW9ucyUyRjY5Mjc0MzQ3JTJGb3ZlcndyaXRlLWFuZC1y ZXN0b3JlLWVudmlyb25tZW50LXZhcmlhYmxlcy1pbi1iYXNoLXdpdGgtZW52aXJvbm1lbnQtbW9k dWxlcz4KbWVudGlvbnMgdXNpbmcgdW5zZXRlbnYgYnV0IHBlcmhhcHMgdGhlcmUncyBhbiBlbHNl aWYgdGhhdCBjYW4gYmUgYWRkZWQgdG8KdGhlIG1vZHVsZWZpbGU/Cg== - Done. 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://secure-web.cisco.com/1Ia6Ud55puWRILt2_mnFiSQklsfT7C9EDW3db8NhTcmq7V… < https://secure-web.cisco.com/1Ia6Ud55puWRILt2_mnFiSQklsfT7C9EDW3db8NhTcmq7V…> . 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. ---------- Forwarded message ---------- From: Rob Kudyba <rk3199(a)columbia.edu> To: Freesurfer-request(a)nmr.mgh.harvard.edu Cc: Bcc: Date: Fri, 26 May 2023 11:24:40 -0400 Subject: FS in a HPC cluster via module file: ERROR: Environment variable FREESURFER_HOME must be defined prior to sourcing Freesurfer External Email - Use Caution In. HPC cluster where Freesurfer is loaded ad hoc as a module. Running module avail results in the following warnings: /path/to/anaconda3-2021.11/bin/mpicc: line 285: x86_64-conda_cos6-linux-gnu-cc: command not found ERROR: Environment variable FREESURFER_HOME must be defined prior to sourcing Freesurfer. /path/to/anaconda3-2021.11/bin/mpicc: line 285: x86_64-conda_cos6-linux-gnu-cc: command not found ERROR: Environment variable FREESURFER_HOME must be defined prior to sourcing Freesurfer. In my .bashrc file: >>> conda initialize >>> !! Contents within this block are managed by 'conda init' !! __conda_setup="$('/path/to/anaconda3-2021.11/bin/conda' 'shell.bash' 'hook' 2> /dev/null)" if [ $? -eq 0 ]; then eval "$__conda_setup" else if [ -f "/path/to/anaconda3-2021.11/etc/profile.d/conda.sh" ]; then . "/path/to/anaconda3-2021.11/etc/profile.d/conda.sh" else export PATH="/path/to/anaconda3-2021.11/bin:$PATH" fi fi unset __conda_setup The modulefile for Freesurfer contains: module-whatis "adds freesurfer to your environment variables" set root /path/to/freesurfer setenv "FREESURFER_HOME" "/path/to/freesurfer" setenv "SUBJECTS_DIR" "/path/to/freesurfer/subjects" prepend-path PATH $root/bin if { [ module-info mode load ] } { system "source /path/to/freesurfer/SetUpFreeSurfer.sh" } I see that SetUpFreeSurfer.sh has this: # Call configuration script: source $FREESURFER_HOME/FreeSurferEnv.sh After running module unload freesurfer several directories remain in $PATH: echo $PATH /path/to/freesurfer/fsfast/bin:/path/to/freesurfer/tktools:/path/to/freesurfer/mni/bin:/path/to/freesurfer/fsfast/bin:/path/to/freesurfer/tktools:/path/to/freesurfer/mni/bin So $FREESURFER_HOME and $SUBJECTS_DIR are being unset but all of the other env vars are not. Is there a way to unset the vars from FreeSurferEnv.sh? A thread on SO <https://secure-web.cisco.com/1r8-C-he2TdIjGUEFvriv0MeCNYVOFUUqm9zHSNCvE844J…> mentions using unsetenv but perhaps there's an elseif that can be added to the modulefile?

1 0

Tracula dpath Missing Files
by Lauren Stephens 25 May '23

25 May '23

External Email - Use Caution Dear Freesurfer Experts, We have been working to run a test data set through tracula and have seemingly had success, however when we ran trac-all -path it completed without error but the files created did not go into a dpath folder. The files that were created went into the dmri and dlabel folders. We are specifically looking for the dpath/merged_avg<nsubj>_<inter>_<intra>.mgz file. We are using Freesurfer 7.3.2 on an iMac Pro running Ventura 13.3.1 in a bash shell. I have attached the dmrirc file. I have also attached the trac-all.log. Thank you for any help you can provide. Lauren Stephens Lauren Stephens, MS Assistant Clinical Research Coordinator Department of Psychiatry and Behavioral Science Stanford University School of Medicine E: laurenss(a)stanford.edu P: (650)-725-1716

2 1

change ants N4 bias field correction parameter in recon-all pipeline
by 刘梦醒 25 May '23

25 May '23

External Email - Use Caution Hello FreeSurfer Developers, Some T1s we collected have higher intensity in the occipital cortex. The default recon-all failed skull stripping and wm/gm segmentation in that part of the brain. After several tests, we found that doing ants N4 bias field correction with a shrink factor of 1 could fix the problem in most cases. We are aware that the same correction is included in recon-all, while with default parameters. We wonder if there is one way to specify the parameter for the bias correction in recon-all? If not, what would you recommend in this situation? A bias correction before recon-all, and still do another correction inside recon-all? The freesurfer we use is 7.1.1. Thanks! best, Mengxing

3 2

fsl fmri thresh_zstat1.nii file showing in fsaverage pial surface
by Gonzalo Rojas Costa 25 May '23

25 May '23

External Email - Use Caution Hi: I processed an fMRI task using FSL. I got the standard image coregistered result... How can I show the thresh_zstat1.nii file in fsaverage pial surface? Sincerely, Gonzalo Rojas Costa

1 0

conjunction
by Maria Czarnecka 25 May '23

25 May '23

External Email - Use Caution Dear experts, Another question: How do I do conjunction analysis? I have my contrasts on 1lvl, I have the second level, I need a conjunction of two contrasts. I would guess "mergecontrasts-sess", unfortunately, it doesn't seem to work. [image: image.png] Could you help me with that issue? Kind regards, Maria Czarnecka

2 1

fsfast percent signal change
by Maria Czarnecka 25 May '23

25 May '23

External Email - Use Caution Dear experts, I struggle with the functional analysis in Freesurfer. How can I calculate the percent signal change in a specific contrast in an ROI? I will be grateful for your suggestions (especially if you point toward a specific function). Kind regards, Maria Czarnecka

2 1

MICCAI Workshop on Machine Learning in Clinical NeuroImaging: Paper Submissions
by Vin 25 May '23

25 May '23

External Email - Use Caution Dear Researchers! We are excited to announce that the paper submissions for the #MICCAI Workshop on Machine Learning in Clinical NeuroImaging are now open! This workshop aims to bring together experts from the fields of machine learning and clinical neuroimaging to explore innovative solutions and advancements in this rapidly evolving domain - https://secure-web.cisco.com/153XVXhlclD9QnxOpu0soPhfDZvJxzhlZhJnF7G7lphKNy… If you have been working on cutting-edge research related to machine learning techniques applied to clinical neuroimaging data, we invite you to submit your work for consideration. This is a remarkable opportunity to showcase your expertise and contribute to the advancement of the field. Benefits: - Accepted papers will be presented during the workshop, providing an opportunity for valuable discussions and feedback from experts in the field. - The top 3 papers will receive recognition and prize money of 1.500 USD will be awarded to the authors of these top papers. - Accepted papers will be published in conference proceedings, Springer (MLCN 22 Proceeding: https://secure-web.cisco.com/1sY98crGbyMWOD79iNBAx2CRjs0I14tuhCQ66l3fHKjsh5…) Join us in exploring the frontiers of machine learning in clinical neuroimaging and help shape the future of this exciting field. We encourage you to spread the word among your colleagues and fellow researchers who may be interested. For more information, including the workshop schedule, submission guidelines, and important dates, please visit our workshop website - https://secure-web.cisco.com/153XVXhlclD9QnxOpu0soPhfDZvJxzhlZhJnF7G7lphKNy… . We look forward to your submissions and your presence at the workshop. Best regards, MLCN Organizing Committee

1 0

Re: [Freesurfer] Uncaught exceptions when processing some images with MiDeFace
by fsbuild 24 May '23

24 May '23

External Email - Use Caution If I understand your previous emails correctly, the failure cannot be reproduced on a stand alone machine running a standard version of linux or Mac OS.   Given that circumstance, even if we had your data to run the command with, we can’t reproduce the cluster run time environment.  I also don’t see you mentioning a core dump file which could help trace back an issue. Depending upon the version of samseg called in the script, there are comments reporting it can require 14G RAM (or maybe more)..   I would consult with the cluster admins to see if they can run your job with some kind of memory/resource profiling to incrementally log resource usage happening in real-time as the job progresses.  Then at the point (timestamp) of failure there might be some useful information from that and/or the system logs that can show if something is going on with memory and/or other resources. - R. On May 24, 2023, at 09:46, Patrick Sadil <psadil1(a)jh.edu> wrote:        External Email - Use Caution        I am definitely confused -- especially since the failures depend on the image (as I said at the start, about half of the images can be processed with MiDeFace just fine).I don't see how this could be an issue with compilers. One of the platforms that I tried was the official freesurfer container run on the HPC setup (MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to behttps://hub.docker.com/r/freesurfer/freesurfer; tag: 7.3.2). That HPC system is CentOS (yes, this is the Frontera system at TACC)$ lsb_release -aLSB Version: :core-4.1-amd64:core-4.1-noarch:cxx-4.1-amd64:cxx-4.1-noarch:desktop-4.1-amd64:desktop-4.1-noarch:languages-4.1-amd64:languages-4.1-noarch:printing-4.1-amd64:printing-4.1-noarchDistributor ID: CentOSDescription: CentOS Linux release 7.9.2009 (Core)Release: 7.9.2009Codename: CoreJust to be explicit, MiDeFace was run with$ apptainer exec -e -B $(pwd):$(pwd) --env "FS_LICENSE=$(pwd)/license" --env "FS_TIME_ALLOW=0" docker://freesurfer/freesurfer:7.3.2 mideface --i volume.nii.gz --o defaced.nii.gzand ended with[...]MiDeface::SegFace()===============================================Label 5 /usr/local/freesurfer/average/mideface-atlas/average.face.ear.right.dec44.us7.remesh3.label 2 3MiDeface::DistanceBounds() DeltaDist=0.333333Raw DistIn = 3, DistOut = 5.33333PostMinCheck DistIn = 3, DistOut = 5.33333MiDeface::SegFace()double free or corruption (!prev)AbortERROR:Patrick Sadil, PhD (he/him/his)Research Associatepsadil.github.io/psadilFrom: fsbuild <fsbuild@contbay.com>Sent: Thursday, May 18, 2023 9:22 PMTo: freesurfer@nmr.mgh.harvard.edu <freesurfer@nmr.mgh.harvard.edu>Cc: Patrick Sadil <psadil1@jh.edu>Subject: Re: [Freesurfer] Uncaught exceptions when processing some images with MiDeFace It does not make sense that it runs fine on a stand alone machine with no virtualization/container and not on the cluster.A reliable way to setup freesurfer on a linux system is to use the .rpm or .deb package installers.  Since that requires sudo, some users host a VM for this since it contains a built in X-server allowing freeview to work out of the box.   A linux VM with freesurfer installed runs on any machine with an Intel processor where the host OS is Windows, MacOS, or Linux.  Similarly it works to install Freesurfer with sudo privs in a docker CentOS7, 8, Ubuntu 18, 20, 22 container (e.g., hosted from a linux server) and run the entire recon-all pipeline in the container.   We don't support running freesurfer Intel MacOS binaries on Apple silicon hardware thru a container/virtualization.Clusters may use modules or a tool like spack to setup the run time environment and system library dependenices for a given application.  I tested running a recon-all a while back on the XSEDE cluster under CentOS8 using an older freesurfer 7.X release and it worked fine.  But if the runtime dependencies are not correct, then maybe you could get a segfault.   Freesurfer is compiled with gcc on linux, so it might not work if the cluster runtime environment somehow included libraries specific to the install of the icc compilers/toolschain instead of the gcc environment.- R.On 5/18/23 15:38, Bennet Fauber (bennet(a)umich.edu) wrote: External Email - Use Caution Patrick, I notice that you are running this on Frontera at TACC. I believe that TACC uses the Intel compilers as their default. I would guess that FreeSurfer is compiled with GCC, not Intel. You might try unloading the Intel compilers and loading the GCC compiler module instead. You might also want to send something to the mailing list for support at TACC (used to be XSEDE, but its name changed last year, I think). For a segfault like this, the system administrators are probably best positioned to answer. If you can give them instructions for running it themselves, that is the best situation. I hope this make sense and is of some help. On Thu, May 18, 2023 at 3:26 PM Patrick Sadil <psadil1(a)jh.edu> wrote: External Email - Use Caution Thanks for the responses! Yes -- the same input volume will sometimes succeed and sometimes fail depending upon the platform. Here is an example of the mri_info for one such volume $ mri_info volume.nii.gz niiRead(): detected input as 64 bit double, reading in as 32 bit float Volume information for volume.nii.gz type: nii dimensions: 193 x 229 x 193 voxel sizes: 1.000000, 1.000000, 1.000000 type: FLOAT (3) fov: 193.000 dof: 1 xstart: -96.5, xend: 96.5 ystart: -114.5, yend: 114.5 zstart: -96.5, zend: 96.5 TR: 0.00 msec, TE: 0.00 msec, TI: 0.00 msec, flip angle: 0.00 degrees nframes: 1 PhEncDir: UNKNOWN FieldStrength: 0.000000 ras xform present xform info: x_r = -1.0000, y_r = 0.0000, z_r = 0.0000, c_r = -0.5000 : x_a = 0.0000, y_a = -1.0000, z_a = 0.0000, c_a = -18.5000 : x_s = 0.0000, y_s = 0.0000, z_s = 1.0000, c_s = 18.5000 Orientation : LPS Primary Slice Direction: axial voxel to ras transform: -1.0000 0.0000 0.0000 96.0000 0.0000 -1.0000 0.0000 96.0000 0.0000 0.0000 1.0000 -78.0000 0.0000 0.0000 0.0000 1.0000 voxel-to-ras determinant 1 ras to voxel transform: -1.0000 0.0000 0.0000 96.0000 0.0000 -1.0000 0.0000 96.0000 0.0000 0.0000 1.0000 78.0000 0.0000 0.0000 0.0000 1.0000 Thanks for the information about memory swapping. Here's a log of the memory usage as reported by `free` every 5 seconds during a failing run on the HPC (FS 7.3.2, no containers) date time total used free shared buff/cache available 2023-05-17 17:32:04 191515 4753 186381 10 379 184648 2023-05-17 17:32:09 191515 4760 186369 10 385 184638 2023-05-17 17:32:14 191515 4774 186346 10 393 184620 2023-05-17 17:32:19 191515 4779 186334 10 401 184612 2023-05-17 17:32:24 191515 4792 186311 10 411 184593 2023-05-17 17:32:29 191515 5251 185817 10 446 184117 2023-05-17 17:32:34 191515 5250 185817 10 447 184117 2023-05-17 17:32:39 191515 5253 185814 10 447 184114 2023-05-17 17:32:44 191515 5254 185813 10 447 184113 2023-05-17 17:32:50 191515 5180 185887 10 447 184188 2023-05-17 17:32:55 191515 5179 185888 10 447 184189 2023-05-17 17:33:00 191515 5178 185889 10 447 184189 2023-05-17 17:33:05 191515 5180 185887 10 447 184188 2023-05-17 17:33:10 191515 5180 185887 10 447 184187 2023-05-17 17:33:15 191515 5181 185886 10 447 184187 2023-05-17 17:33:20 191515 5180 185887 10 447 184188 2023-05-17 17:33:25 191515 5179 185888 10 447 184188 2023-05-17 17:33:30 191515 5180 185886 10 447 184187 2023-05-17 17:33:35 191515 5181 185886 10 447 184187 2023-05-17 17:33:40 191515 5180 185887 10 447 184187 2023-05-17 17:33:45 191515 5181 185886 10 447 184186 2023-05-17 17:33:50 191515 5181 185886 10 447 184186 2023-05-17 17:33:55 191515 5181 185886 10 447 184186 2023-05-17 17:34:00 191515 5136 185925 10 453 184229 2023-05-17 17:34:05 191515 5157 185875 10 482 184193 2023-05-17 17:34:10 191515 5411 185621 10 482 183939 2023-05-17 17:34:15 191515 5344 185676 10 494 184001 2023-05-17 17:34:20 191515 5348 185667 10 498 183994 I think this indicates that the system should has plenty of memory. FWIW, here is the terminal output produced during the logged run (error is always at the same place) $ mideface --i volume.nii.gz --o defaced.nii.gz Wed May 17 17:31:59 CDT 2023 setenv SUBJECTS_DIR /work2/08266/psadil/freesurfer/subjects cd /[...redacted...]/jobs/release /work2/08266/psadil/freesurfer/bin/mideface --i volume.nii.gz --o defaced.nii.gz -rwx------ 1 psadil G-821866 27366 Aug 3 2022 /work2/08266/psadil/freesurfer/bin/mideface freesurfer-linux-centos7_x86_64-7.3.2-20220804-6354275 $Id$ Linux c103-211.frontera.tacc.utexas.edu 3.10.0-1160.45.1.el7.x86_64 #1 SMP Wed Oct 13 17:20:51 UTC 2021 x86_64 x86_64 x86_64 GNU/Linux pid 205539 UseXvfb 1 samseg --i /[...redacted...]/jobs/release/volume.nii.gz --o /[...redacted.....]/jobs/release/tmpdir.midefacer.205539/samseg --threads 1 --block-coordinate-descent --options /work2/08266/psadil/freesurfer/average/mideface-atlas/samseg-options.json /[...redacted...]/jobs/release/tmpdir.midefacer.205539/samseg /[...redacted.....]/jobs/release /[...redacted...]/jobs/release Wed May 17 17:32:00 CDT 2023 setenv SUBJECTS_DIR /work2/08266/psadil/freesurfer/subjects cd /[...redacted...]/jobs/release /work2/08266/psadil/freesurfer/bin/samseg --i /[...redacted...]/jobs/release/volume.nii.gz --o /[...redacted...]/jobs/release/tmpdir.midefacer.205539/samseg --threads 1 --block-coordinate-descent --options /work2/08266/psadil/freesurfer/average/mideface-atlas/samseg-options.json freesurfer-linux-centos7_x86_64-7.3.2-20220804-6354275 samseg 7.3.2 Linux c103-211.frontera.tacc.utexas.edu 3.10.0-1160.45.1.el7.x86_64 #1 SMP Wed Oct 13 17:20:51 UTC 2021 x86_64 x86_64 x86_64 GNU/Linux Using Block Coordinate Descent fs_time run_samseg -o /[...redacted...]/jobs/release/tmpdir.midefacer.205539/samseg --threads 1 --save-warp --options /work2/08266/psadil/freesurfer/average/mideface-atlas/samseg-options.json -i /[...redacted...]/jobs/release/volume.nii.gz Constructing image-to-world transform from header information (/[...redacted...]/jobs/release/volume.nii.gz) Read image: /[...redacted...]/jobs/release/volume.nii.gz Constructing image-to-world transform from header information (/work2/08266/psadil/freesurfer/average/samseg/20Subjects_smoothing2_down2_smoothingForAffine2/template.nii) Read image: /work2/08266/psadil/freesurfer/average/samseg/20Subjects_smoothing2_down2_smoothingForAffine2/template.nii Read mesh collection: /work2/08266/psadil/freesurfer/average/samseg/20Subjects_smoothing2_down2_smoothingForAffine2/atlasForAffineRegistration.txt.gz Transforming points Transforming points AFFINE min: -48.627 max: 1250.65 robustMin: -1.51633 robustMax: 1096.98 histogram[ 0 ]: 1 histogram[ 1 ]: 0 histogram[ 2 ]: 0 histogram[ 3997 ]: 0 histogram[ 3998 ]: 0 histogram[ 3999 ]: 1 cumulativeHistogram[ 0 ]: 3.07385e-06 cumulativeHistogram[ 1 ]: 3.07385e-06 cumulativeHistogram[ 2 ]: 3.07385e-06 cumulativeHistogram[ 3997 ]: 0.999997 cumulativeHistogram[ 3998 ]: 0.999997 cumulativeHistogram[ 3999 ]: 1 AFFINE min: -48.627 max: 1250.65 robustMin: -1.51633 robustMax: 1096.98 histogram[ 0 ]: 1 histogram[ 1 ]: 0 histogram[ 2 ]: 0 histogram[ 3997 ]: 0 histogram[ 3998 ]: 0 histogram[ 3999 ]: 1 cumulativeHistogram[ 0 ]: 3.07385e-06 cumulativeHistogram[ 1 ]: 3.07385e-06 cumulativeHistogram[ 2 ]: 3.07385e-06 cumulativeHistogram[ 3997 ]: 0.999997 cumulativeHistogram[ 3998 ]: 0.999997 cumulativeHistogram[ 3999 ]: 1 Read mesh collection: /work2/08266/psadil/freesurfer/average/samseg/20Subjects_smoothing2_down2_smoothingForAffine2/atlasForAffineRegistration.txt.gz Transforming points Transforming points AFFINE L-BFGS BFGS-MaximumMemoryLength: 12 LineSearchMaximalDeformationIntervalStopCriterion: 0.005 MaximalDeformationStopCriterion: 0.005 Verbose: 0 min: -48.627 max: 1250.65 robustMin: -1.51633 robustMax: 1096.98 histogram[ 0 ]: 1 histogram[ 1 ]: 0 histogram[ 2 ]: 0 histogram[ 3997 ]: 0 histogram[ 3998 ]: 0 histogram[ 3999 ]: 1 cumulativeHistogram[ 0 ]: 3.07385e-06 cumulativeHistogram[ 1 ]: 3.07385e-06 cumulativeHistogram[ 2 ]: 3.07385e-06 cumulativeHistogram[ 3997 ]: 0.999997 cumulativeHistogram[ 3998 ]: 0.999997 cumulativeHistogram[ 3999 ]: 1 Read mesh collection: /work2/08266/psadil/freesurfer/average/samseg/20Subjects_smoothing2_down2_smoothingForAffine2/atlasForAffineRegistration.txt.gz Transforming points Transforming points AFFINE L-BFGS BFGS-MaximumMemoryLength: 12 LineSearchMaximalDeformationIntervalStopCriterion: 0.005 MaximalDeformationStopCriterion: 0.005 Verbose: 0 min: -48.627 max: 1250.65 robustMin: -1.51633 robustMax: 1096.98 histogram[ 0 ]: 1 histogram[ 1 ]: 0 histogram[ 2 ]: 0 histogram[ 3997 ]: 0 histogram[ 3998 ]: 0 histogram[ 3999 ]: 1 cumulativeHistogram[ 0 ]: 3.07385e-06 cumulativeHistogram[ 1 ]: 3.07385e-06 cumulativeHistogram[ 2 ]: 3.07385e-06 cumulativeHistogram[ 3997 ]: 0.999997 cumulativeHistogram[ 3998 ]: 0.999997 cumulativeHistogram[ 3999 ]: 1 Read mesh collection: /work2/08266/psadil/freesurfer/average/samseg/20Subjects_smoothing2_down2_smoothingForAffine2/atlasForAffineRegistration.txt.gz Transforming points Transforming points AFFINE L-BFGS BFGS-MaximumMemoryLength: 12 LineSearchMaximalDeformationIntervalStopCriterion: 0.005 MaximalDeformationStopCriterion: 0.005 Verbose: 0 min: -48.627 max: 1250.65 robustMin: -1.51633 robustMax: 1096.98 histogram[ 0 ]: 1 histogram[ 1 ]: 0 histogram[ 2 ]: 0 histogram[ 3997 ]: 0 histogram[ 3998 ]: 0 histogram[ 3999 ]: 1 cumulativeHistogram[ 0 ]: 3.07385e-06 cumulativeHistogram[ 1 ]: 3.07385e-06 cumulativeHistogram[ 2 ]: 3.07385e-06 cumulativeHistogram[ 3997 ]: 0.999997 cumulativeHistogram[ 3998 ]: 0.999997 cumulativeHistogram[ 3999 ]: 1 Constructing image-to-world transform from header information (/[...redacted...]/jobs/release/volume.nii.gz) Read image: /[...redacted...]/jobs/release/volume.nii.gz Read mesh collection: /work2/08266/psadil/freesurfer/average/samseg/20Subjects_smoothing2_down2_smoothingForAffine2/atlas_level2.txt.gz Transforming points Transforming points ##---------------------------------------------- Samsegment Options ##---------------------------------------------- output directory: /[...redacted...]/jobs/release/tmpdir.midefacer.205539/samseg input images: /[...redacted...]/jobs/release/volume.nii.gz modelSpecifications: {'FreeSurferLabels': [0, 165, 258, 16, 24, 8, 47, 15, 259, 3, 42, 7, 46, 41, 2, 63, 54, 18, 53, 44, 17, 31, 5, 85, 60, 28, 14, 26, 12, 51, 62, 58, 77, 4, 30, 43, 52, 11, 49, 13, 50, 10, 80, 72], 'atlasFileName': '/work2/08266/psadil/freesurfer/average/samseg/20Subjects_smoothing2_down2_smoothingForAffine2/atlas_level2.txt.gz', 'names': ['Unknown', 'Skull', 'Soft_Nonbrain_Tissue', 'Brain-Stem', 'CSF', 'Left-Cerebellum-Cortex', 'Right-Cerebellum-Cortex', '4th-Ventricle', 'Fluid_Inside_Eyes', 'Left-Cerebral-Cortex', 'Right-Cerebral-Cortex', 'Left-Cerebellum-White-Matter', 'Right-Cerebellum-White-Matter', 'Right-Cerebral-White-Matter', 'Left-Cerebral-White-Matter', 'Right-choroid-plexus', 'Right-Amygdala', 'Left-Amygdala', 'Right-Hippocampus', 'Right-Inf-Lat-Vent', 'Left-Hippocampus', 'Left-choroid-plexus', 'Left-Inf-Lat-Vent', 'Optic-Chiasm', 'Right-VentralDC', 'Left-VentralDC', '3rd-Ventricle', 'Left-Accumbens-area', 'Left-Putamen', 'Right-Putamen', 'Right-vessel', 'Right-Accumbens-area', 'WM-hypointensities', 'Left-Lateral-Ventricle', 'Left-vessel', 'Right-Lateral-Ventricle', 'Right-Pallidum', 'Left-Caudate', 'Right-Thalamus', 'Left-Pallidum', 'Right-Caudate', 'Left-Thalamus', 'non-WM-hypointensities', '5th-Ventricle'], 'colors': [[0, 0, 0, 0], [255, 165, 0, 255], [128, 128, 128, 255], [119, 159, 176, 255], [60, 60, 60, 255], [230, 148, 34, 255], [230, 148, 34, 255], [42, 204, 164, 255], [128, 0, 128, 255], [205, 62, 78, 255], [205, 62, 78, 255], [220, 248, 164, 255], [220, 248, 164, 255], [0, 225, 0, 255], [245, 245, 245, 255], [0, 200, 221, 255], [103, 255, 255, 255], [103, 255, 255, 255], [220, 216, 20, 255], [196, 58, 250, 255], [220, 216, 20, 255], [0, 200, 200, 255], [196, 58, 250, 255], [234, 169, 30, 255], [165, 42, 42, 255], [165, 42, 42, 255], [204, 182, 142, 255], [255, 165, 0, 255], [236, 13, 176, 255], [236, 13, 176, 255], [160, 32, 240, 255], [255, 165, 0, 255], [200, 70, 255, 255], [120, 18, 134, 255], [160, 32, 240, 255], [120, 18, 134, 255], [13, 48, 255, 255], [122, 186, 22 0, 255], [0, 118, 14, 255], [12, 48, 255, 255], [122, 186, 220, 255], [0, 118, 14, 255], [164, 108, 226, 255], [120, 190, 150, 255]], 'sharedGMMParameters': [GMMparameter(mergedName='Unknown', numberOfComponents=1, searchStrings=['Unknown', 'Skull']), GMMparameter(mergedName='GlobalWM', numberOfComponents=1, searchStrings=['White', 'Brain-Stem', 'VentralDC', 'Optic-Chiasm', 'Thalamus', 'Pallidum']), GMMparameter(mergedName='GlobalGM', numberOfComponents=1, searchStrings=['Cortex', 'Caudate', 'Hippocampus', 'Amygdala', 'Accumbens', 'hypointensities', 'Thalamus']), GMMparameter(mergedName='GlobalCSF_messy', numberOfComponents=1, searchStrings=['CSF', 'vessel', 'choroid-plexus', 'Fluid']), GMMparameter(mergedName='GlobalCSF_clean', numberOfComponents=1, searchStrings=['Ventricle', 'Inf-Lat-Vent', 'Fluid']), GMMparameter(mergedName='Putamen', numberOfComponents=1, searchStrings=['Putamen']), GMMparameter(mergedName='Soft', numberOfComponents=3, searchStrings=['Soft'])], 'useDiagonalCovarianceMatrices': True, 'maskingProbabilityThreshold': 0.5, 'maskingDistance': 10.0, 'K': 0.1, 'biasFieldSmoothingKernelSize': 50, 'whiteMatterAndCortexSmoothingSigma': 0} optimizationOptions: {'maximumNumberOfDeformationIterations': 1, 'absoluteCostPerVoxelDecreaseStopCriterion': 0.01, 'verbose': False, 'maximalDeformationStopCriterion': 0.01, 'lineSearchMaximalDeformationIntervalStopCriterion': 0.01, 'maximalDeformationAppliedStopCriterion': 0.0, 'BFGSMaximumMemoryLength': 12, 'multiResolutionSpecification': [{'atlasFileName': '/work2/08266/psadil/freesurfer/average/samseg/20Subjects_smoothing2_down2_smoothingForAffine2/atlas_level1.txt.gz', 'targetDownsampledVoxelSpacing': 2.0, 'maximumNumberOfIterations': 50, 'estimateBiasField': True}, {'atlasFileName': '/work2/08266/psadil/freesurfer/average/samseg/20Subjects_smoothing2_down2_smoothingForAffine2/atlas_level2.txt.gz', 'targetDownsampledVoxelSpacing': 1.0, 'maximumNumberOfIterations': 2, 'estimateBiasField': True}]} performing affine atlas registration image: /[...redacted...]/jobs/release/volume.nii.gz template: /work2/08266/psadil/freesurfer/average/samseg/20Subjects_smoothing2_down2_smoothingForAffine2/template.nii maximalDeformation=1.0000 minLogLikelihood=-0.7440 maximalDeformation=1.0371 minLogLikelihood=-0.7600 maximalDeformation=0.8439 minLogLikelihood=-0.7668 maximalDeformation=8.9885 minLogLikelihood=-0.8230 maximalDeformation=2.1805 minLogLikelihood=-0.8250 maximalDeformation=1.8946 minLogLikelihood=-0.8368 maximalDeformation=3.3974 minLogLikelihood=-0.8455 maximalDeformation=0.0787 minLogLikelihood=-0.8459 maximalDeformation=0.0193 minLogLikelihood=-0.8459 maximalDeformation=0.0000 minLogLikelihood=-0.8459 appliedScaling: 1.0158 maximalDeformation=1.0000 minLogLikelihood=-0.8630 maximalDeformation=0.2734 minLogLikelihood=-0.8636 maximalDeformation=0.2836 minLogLikelihood=-0.8638 maximalDeformation=0.1536 minLogLikelihood=-0.8640 maximalDeformation=0.5760 minLogLikelihood=-0.8641 maximalDeformation=0.3851 minLogLikelihood=-0.8642 maximalDeformation=0.0000 minLogLikelihood=-0.8642 appliedScaling: 1.0047 maximalDeformation=1.0000 minLogLikelihood=-0.8699 maximalDeformation=0.0000 minLogLikelihood=-0.8699 appliedScaling: 1.0017 writing template transform to /[...redacted...]/jobs/release/tmpdir.midefacer.205539/samseg/template.lta writing talairach transform to /[...redacted...]/jobs/release/tmpdir.midefacer.205539/samseg/samseg.talairach.lta atlas registration complete: 0:01:34.254165 [1. 1. 1.] Unknown Unknown (100%) Skull (100%) GlobalWM Brain-Stem (100%) Left-Cerebellum-White-Matter (100%) Right-Cerebellum-White-Matter (100%) Right-Cerebral-White-Matter (100%) Left-Cerebral-White-Matter (100%) Optic-Chiasm (100%) Right-VentralDC (100%) Left-VentralDC (100%) Right-Pallidum (100%) Right-Thalamus (50%) Left-Pallidum (100%) Left-Thalamus (50%) GlobalGM Left-Cerebellum-Cortex (100%) Right-Cerebellum-Cortex (100%) Left-Cerebral-Cortex (100%) Right-Cerebral-Cortex (100%) Right-Amygdala (100%) Left-Amygdala (100%) Right-Hippocampus (100%) Left-Hippocampus (100%) Left-Accumbens-area (100%) Right-Accumbens-area (100%) WM-hypointensities (100%) Left-Caudate (100%) Right-Thalamus (50%) Right-Caudate (100%) Left-Thalamus (50%) non-WM-hypointensities (100%) GlobalCSF_messy CSF (100%) Fluid_Inside_Eyes (50%) Right-choroid-plexus (100%) Left-choroid-plexus (100%) Right-vessel (100%) Left-vessel (100%) GlobalCSF_clean 4th-Ventricle (100%) Fluid_Inside_Eyes (50%) Right-Inf-Lat-Vent (100%) Left-Inf-Lat-Vent (100%) 3rd-Ventricle (100%) Left-Lateral-Ventricle (100%) Right-Lateral-Ventricle (100%) 5th-Ventricle (100%) Putamen Left-Putamen (100%) Right-Putamen (100%) Soft Soft_Nonbrain_Tissue (100%) ==================== Read mesh collection: /work2/08266/psadil/freesurfer/average/samseg/20Subjects_smoothing2_down2_smoothingForAffine2/atlas_level1.txt.gz Transforming points Transforming points 1 0.398942 SLIDING L-BFGS BFGS-MaximumMemoryLength: 12 LineSearchMaximalDeformationIntervalStopCriterion: 0.01 MaximalDeformationStopCriterion: 0.01 MaximumNumberOfIterations: 1 Verbose: 0 L-BFGS BFGS-MaximumMemoryLength: 12 LineSearchMaximalDeformationIntervalStopCriterion: 0.01 MaximalDeformationStopCriterion: 0.01 MaximumNumberOfIterations: 1 Verbose: 0 L-BFGS BFGS-MaximumMemoryLength: 12 LineSearchMaximalDeformationIntervalStopCriterion: 0.01 MaximalDeformationStopCriterion: 0.01 MaximumNumberOfIterations: 1 Verbose: 0 L-BFGS BFGS-MaximumMemoryLength: 12 LineSearchMaximalDeformationIntervalStopCriterion: 0.01 MaximalDeformationStopCriterion: 0.01 MaximumNumberOfIterations: 1 Verbose: 0 L-BFGS BFGS-MaximumMemoryLength: 12 LineSearchMaximalDeformationIntervalStopCriterion: 0.01 MaximalDeformationStopCriterion: 0.01 MaximumNumberOfIterations: 1 Verbose: 0 L-BFGS BFGS-MaximumMemoryLength: 12 LineSearchMaximalDeformationIntervalStopCriterion: 0.01 MaximalDeformationStopCriterion: 0.01 MaximumNumberOfIterations: 1 Verbose: 0 1 0.398942 SLIDING 1 0.398942 SLIDING Read mesh collection: /work2/08266/psadil/freesurfer/average/samseg/20Subjects_smoothing2_down2_smoothingForAffine2/atlas_level2.txt.gz Transforming points Transforming points Read mesh collection: /work2/08266/psadil/freesurfer/average/samseg/20Subjects_smoothing2_down2_smoothingForAffine2/atlas_level1.txt.gz Read mesh collection: /work2/08266/psadil/freesurfer/average/samseg/20Subjects_smoothing2_down2_smoothingForAffine2/atlas_level2.txt.gz SLIDING L-BFGS BFGS-MaximumMemoryLength: 12 LineSearchMaximalDeformationIntervalStopCriterion: 0.005 MaximalDeformationStopCriterion: 0.005 Verbose: 1 [BRACKETING] Hit a really bad solution -- ready for zooming: 1 [ZOOMING] Zooming with low=0 and high=1 bisected: 0.5 bisected: 0.25 bisected: 0.125 interpolated: 1.2403e-11 Too small for current range [0 0.125]; using something forcibly bigger instead: 0.0125 interpolated: 1.22363e-11 Too small for current range [0 0.0125]; using something forcibly bigger instead: 0.00125 [ZOOMING] Zooming interval size too low; returning best: 0 ----------------------- Optimizer: maximalDeformation is too small; stopping 1 0.398942 SLIDING L-BFGS BFGS-MaximumMemoryLength: 12 LineSearchMaximalDeformationIntervalStopCriterion: 0.01 MaximalDeformationStopCriterion: 0.01 MaximumNumberOfIterations: 1 Verbose: 0 L-BFGS BFGS-MaximumMemoryLength: 12 LineSearchMaximalDeformationIntervalStopCriterion: 0.01 MaximalDeformationStopCriterion: 0.01 MaximumNumberOfIterations: 1 Verbose: 0 L-BFGS BFGS-MaximumMemoryLength: 12 LineSearchMaximalDeformationIntervalStopCriterion: 0.01 MaximalDeformationStopCriterion: 0.01 MaximumNumberOfIterations: 1 Verbose: 0 L-BFGS BFGS-MaximumMemoryLength: 12 LineSearchMaximalDeformationIntervalStopCriterion: 0.01 MaximalDeformationStopCriterion: 0.01 MaximumNumberOfIterations: 1 Verbose: 0 L-BFGS BFGS-MaximumMemoryLength: 12 LineSearchMaximalDeformationIntervalStopCriterion: 0.01 MaximalDeformationStopCriterion: 0.01 MaximumNumberOfIterations: 1 Verbose: 0 L-BFGS BFGS-MaximumMemoryLength: 12 LineSearchMaximalDeformationIntervalStopCriterion: 0.01 MaximalDeformationStopCriterion: 0.01 MaximumNumberOfIterations: 1 Verbose: 0 1 0.398942 SLIDING Read mesh collection: /work2/08266/psadil/freesurfer/average/samseg/20Subjects_smoothing2_down2_smoothingForAffine2/atlas_level2.txt.gz Transforming points Transforming points Read mesh collection: /work2/08266/psadil/freesurfer/average/samseg/20Subjects_smoothing2_down2_smoothingForAffine2/atlas_level2.txt.gz Read mesh collection: /work2/08266/psadil/freesurfer/average/samseg/20Subjects_smoothing2_down2_smoothingForAffine2/atlas_level2.txt.gz Constructing image-to-world transform from header information (/[...redacted...]/jobs/release/volume.nii.gz) Read image: /[...redacted...]/jobs/release/volume.nii.gz Read mesh collection: /work2/08266/psadil/freesurfer/average/samseg/20Subjects_smoothing2_down2_smoothingForAffine2/atlas_level2.txt.gz Transforming points Transforming points Read mesh collection: /work2/08266/psadil/freesurfer/average/samseg/20Subjects_smoothing2_down2_smoothingForAffine2/atlas_level2.txt.gz Read mesh collection: /work2/08266/psadil/freesurfer/average/samseg/20Subjects_smoothing2_down2_smoothingForAffine2/atlas_level2.txt.gz niiRead(): detected input as 64 bit double, reading in as 32 bit float Read mesh collection: /work2/08266/psadil/freesurfer/average/samseg/20Subjects_smoothing2_down2_smoothingForAffine2/atlas_level2.txt.gz { depth: 1 maximumNumberOfDeformationIterations: 1 absoluteCostPerVoxelDecreaseStopCriterion: 0.01 verbose: False maximalDeformationStopCriterion: 0.01 lineSearchMaximalDeformationIntervalStopCriterion: 0.01 maximalDeformationAppliedStopCriterion: 0.0 BFGSMaximumMemoryLength: 12 multiResolutionSpecification: { depth: 2 atlasFileName: /work2/08266/psadil/freesurfer/average/samseg/20Subjects_smoothing2_down2_smoothingForAffine2/atlas_level1.txt.gz targetDownsampledVoxelSpacing: 2.0 maximumNumberOfIterations: 50 estimateBiasField: True }, { depth: 2 atlasFileName: /work2/08266/psadil/freesurfer/average/samseg/20Subjects_smoothing2_down2_smoothingForAffine2/atlas_level2.txt.gz targetDownsampledVoxelSpacing: 1.0 maximumNumberOfIterations: 2 estimateBiasField: True } } ==================== iterationNumber: 0 EM converged! blockNumber 0 efficiency: 127.8986 % relative size: 19.7796 % setup time: 0.6695 sec blockNumber 1 efficiency: 129.5280 % relative size: 20.8106 % setup time: 0.4791 sec blockNumber 2 efficiency: 124.7648 % relative size: 23.2798 % setup time: 0.4969 sec blockNumber 3 efficiency: 127.9526 % relative size: 20.9638 % setup time: 0.4770 sec blockNumber 4 efficiency: 124.4211 % relative size: 23.4852 % setup time: 0.4918 sec blockNumber 5 efficiency: 127.3941 % relative size: 18.5357 % setup time: 0.4698 sec Total time spent: 0.0033 sec maximalDeformation=0.0000 maximalDeformationApplied: 0.0000 ======================================================= iterationNumber: 1 EM converged! ProbabilisticAtlas reusing warm optimizers!! Total time spent: 0.0034 sec maximalDeformation=0.0000 maximalDeformationApplied: 0.0000 ======================================================= iterationNumber: 2 EM converged! ProbabilisticAtlas reusing warm optimizers!! Total time spent: 0.0034 sec maximalDeformation=0.0000 maximalDeformationApplied: 0.0000 ======================================================= iterationNumber: 0 EM converged! blockNumber 0 efficiency: 118.7363 % relative size: 20.8927 % setup time: 1.6169 sec blockNumber 1 efficiency: 121.0767 % relative size: 20.8433 % setup time: 1.0427 sec blockNumber 2 efficiency: 123.9971 % relative size: 18.9659 % setup time: 1.0240 sec blockNumber 3 efficiency: 118.9662 % relative size: 20.6564 % setup time: 1.0509 sec blockNumber 4 efficiency: 117.7030 % relative size: 19.9348 % setup time: 1.0399 sec blockNumber 5 efficiency: 122.6568 % relative size: 19.1271 % setup time: 1.0273 sec Total time spent: 0.0124 sec maximalDeformation=0.0000 maximalDeformationApplied: 0.0000 ======================================================= iterationNumber: 1 EM converged! ProbabilisticAtlas reusing warm optimizers!! Total time spent: 0.0089 sec maximalDeformation=0.0000 maximalDeformationApplied: 0.0000 ======================================================= using default intracranial structures to compute sbtiv measure Saving the template warp run_samseg complete: 0:04:08.072359 GCAMwrite @#@FSTIME 2023:05:17:17:32:00 run_samseg N 9 e 276.60 S 6.87 U 226.42 P 84% M 5448744 F 4116 R 1612330 W 0 c 42 w 14636 I 267688 O 323136 L 0.01 1.32 2.98 @#@FSLOADPOST 2023:05:17:17:36:36 run_samseg N 9 0.96 1.06 2.44 run_samseg complete Wed May 17 17:36:36 CDT 2023 lta_convert --inlta /[...redacted...]/jobs/release/tmpdir.midefacer.205539/samseg/samseg.talairach.lta --outmni /[...redacted...]/jobs/release/tmpdir.midefacer.205539/samseg/samseg.talairach.xfm 7.3.2 --inlta: /[...redacted...]/jobs/release/tmpdir.midefacer.205539/samseg/samseg.talairach.lta input LTA transform. --outmni: /[...redacted...]/jobs/release/tmpdir.midefacer.205539/samseg/samseg.talairach.xfm output MNI/XFM matrix. LTA read, type : 1 1.02236 0.01245 0.12949 0.58992; -0.00437 1.08080 -0.00870 2.62878; -0.15613 0.06510 1.14175 12.21557; 0.00000 0.00000 0.00000 1.00000; lta_convert successful. mri_segstats --ctab-default --seg /[...redacted...]/jobs/release/tmpdir.midefacer.205539/samseg/seg.mgz --sum /[...redacted...]/jobs/release/tmpdir.midefacer.205539/samseg/seg.stats Using defalt ctab /work2/08266/psadil/freesurfer/FreeSurferColorLUT.txt 7.3.2 cwd cmdline mri_segstats --ctab-default --seg /[...redacted...]/jobs/release/tmpdir.midefacer.205539/samseg/seg.mgz --sum /[...redacted...]/jobs/release/tmpdir.midefacer.205539/samseg/seg.stats sysname Linux hostname c103-211.frontera.tacc.utexas.edu machine x86_64 user psadil whitesurfname white UseRobust 0 Loading /[...redacted...]/jobs/release/tmpdir.midefacer.205539/samseg/seg.mgz Voxel Volume is 1 mm^3 Generating list of segmentation ids Found 1436 segmentations Computing statistics for each segmentation Reporting on 44 segmentations Using PrintSegStat mri_segstats done Started at Wed May 17 17:31:59 CDT 2023 Ended at Wed May 17 17:36:40 CDT 2023 Samseg-Run-Time-Min 4.68 Samseg-Run-Time-Hours 0.08 samseg Done @#@FSTIME 2023:05:17:17:31:59 samseg N 9 e 280.79 S 6.97 U 230.29 P 84% M 5448744 F 4122 R 1647009 W 0 c 108 w 15165 I 283968 O 323472 L 0.01 1.32 2.98 @#@FSLOADPOST 2023:05:17:17:36:40 samseg N 9 0.96 1.06 2.43 mri_binarize --i /[...redacted...]/jobs/release/tmpdir.midefacer.205539/samseg/seg.mgz --match 2 3 7 8 16 24 41 42 46 47 165 259 4 5 10 11 12 13 17 18 26 28 30 31 14 15 16 77 85 43 44 49 50 51 52 53 54 58 60 62 63 --o /[...redacted...]/jobs/release/tmpdir.midefacer.205539/seg.bin.dil.mgz --dilate 1 7.3.2 cwd /[...redacted...]/jobs/release cmdline mri_binarize --i /[...redacted...]/jobs/release/tmpdir.midefacer.205539/samseg/seg.mgz --match 2 3 7 8 16 24 41 42 46 47 165 259 4 5 10 11 12 13 17 18 26 28 30 31 14 15 16 77 85 43 44 49 50 51 52 53 54 58 60 62 63 --o /[...redacted...]/jobs/release/tmpdir.midefacer.205539/seg.bin.dil.mgz --dilate 1 sysname Linux hostname c103-211.frontera.tacc.utexas.edu machine x86_64 user psadil input /[...redacted...]/jobs/release/tmpdir.midefacer.205539/samseg/seg.mgz frame 0 nErode3d 0 nErode2d 0 output /[...redacted...]/jobs/release/tmpdir.midefacer.205539/seg.bin.dil.mgz Binarizing based on matching values nMatch 41 0 2 1 3 2 7 3 8 4 16 5 24 6 41 7 42 8 46 9 47 10 165 11 259 12 4 13 5 14 10 15 11 16 12 17 13 18 17 19 18 20 26 21 28 22 30 23 31 24 14 25 15 26 16 27 77 28 85 29 43 30 44 31 49 32 50 33 51 34 52 35 53 36 54 37 58 38 60 39 62 40 63 binval 1 binvalnot 0 fstart = 0, fend = 0, nframes = 1 Starting parallel 1 Found 1843081 values in range Dilating 1 voxels in 3d Counting number of voxels in first frame Found 2059752 voxels in final mask Writing output to /[...redacted...]/jobs/release/tmpdir.midefacer.205539/seg.bin.dil.mgz Count: 2059752 2059752.000000 8530021 24.147092 mri_binarize done mri_concatenate_lta /work2/08266/psadil/freesurfer/average/mideface-atlas/reg.samseg-default.lta /[...redacted...]/jobs/release/tmpdir.midefacer.205539/samseg/template.lta /[...redacted...]/jobs/release/tmpdir.midefacer.205539/atlas2input.lta Read individual LTAs Combining the two LTAs to get a RAS-to-RAS from src of LTA1 to dst of LTA2..... Writing combined LTA to file /[...redacted...]/jobs/release/tmpdir.midefacer.205539/atlas2input.lta... mri_concatenate_lta successful. lta_convert --subject defacing-atlas --invert --inlta /[...redacted...]/jobs/release/tmpdir.midefacer.205539/atlas2input.lta --outlta /[...redacted...]/jobs/release/tmpdir.midefacer.205539/input2atlas.lta 7.3.2 --s: defacing-atlas subject name --invert: will invert transform. --inlta: /[...redacted...]/jobs/release/tmpdir.midefacer.205539/atlas2input...lta input LTA transform. --outlta: /[...redacted...]/jobs/release/tmpdir.midefacer.205539/input2atlas.lta output LTA. LTA read, type : 1 0.92032 0.00244 -0.09021 -0.96096; 0.00139 0.90319 0.03621 -3.20219; 0.11587 -0.08143 0.79401 -4.69215; -0.00000 -0.00000 -0.00000 1.00000; setting subject to defacing-atlas Writing LTA to file /[...redacted...]/jobs/release/tmpdir.midefacer.205539/input2atlas.lta... lta_convert successful. mris_apply_reg --lta /work2/08266/psadil/freesurfer/average/mideface-atlas/average.head.dec44.us7.remesh3.ripple.surf /[...redacted...]/jobs/release/tmpdir.midefacer.205539/atlas2input.lta /[...redacted...]/jobs/release/tmpdir.midefacer.205539/template.surf Reading in /work2/08266/psadil/freesurfer/average/mideface-atlas/average.head.dec44.us7.remesh3.ripple.surf Reading in /[...redacted...]/jobs/release/tmpdir.midefacer.205539/atlas2input.lta Changing type to REGISTER_DAT MRISltaMultiply(): applying matrix 0.92032 -0.09021 -0.00244 1.39829; 0.11587 0.79401 0.08143 -47.35222; 0.00139 0.03621 -0.90319 7.85163; -0.00000 -0.00000 0.00000 1.00000; ----------------------------------- Determinant of linear transform is negative, so reversing face order Writing surf to /[...redacted...]/jobs/release/tmpdir.midefacer.205539/template.surf mris_apply_reg done mkheadsurf -i /[...redacted...]/jobs/release/volume.nii.gz -o /[...redacted.....]/jobs/release/tmpdir.midefacer.205539/head.mgz -surf /[...redacted...]/jobs/release/tmpdir.midefacer.205539/head.surf -rescale -no-inflate -fill-holes-islands -mc -no-curv INFO: log file is /[...redacted...]/jobs/release/tmpdir.midefacer.205539/mkheadsurf.log -------------------------------- Wed May 17 17:36:46 CDT 2023 /[...redacted...]/jobs/release mri_seghead --invol /[...redacted...]/jobs/release/volume.nii.gz --outvol /[...redacted...]/jobs/release/tmpdir.midefacer.205539/head.mgz --fill 1 --thresh1 20 --thresh2 20 --nhitsmin 2 --rescale --fill-holes-islands -------------------------------- input volume: /[...redacted...]/jobs/release/volume.nii.gz output volume: /[...redacted...]/jobs/release/tmpdir.midefacer.205539/head.mgz threshold1: 20 threshold2: 20 nhitsmin: 2 fill value: 1 Loading input volume niiRead(): detected input as 64 bit double, reading in as 32 bit float Changing type, rescale = 1 MRIchangeType: Building histogram -68.7235 1307.2 1000, flo=0, fhi=255, dest_type=0 Filling Columns Filling Rows Filling Slices Merging nhits = 2945860 Removing islands MRIremoveVolumeIslands() thresh=0.5, nKeep=1, nclusters = 687 Removing Volume Holes MRIremoveVolumeHoles() thresh=0.5, nKeep=1 MRIremoveVolumeIslands() thresh=0.5, nKeep=1, nclusters = 1 Filling axial Slice Holes ostr LPS slicedir 6 slicediruse 3 slicedim 193 229 1 MRIremoveSliceHodes() removed 16112 voxels Filling sag Slice Holes ostr LPS slicedir 4 slicediruse 1 slicedim 1 229 193 MRIremoveSliceHodes() removed 2775 voxels Filling cor Slice Holes slicedir 2 slicediruse 2 slicedim 193 1 193 MRIremoveSliceHodes() removed 822 voxels Counting N Head Voxels = 2964151 N Back Voxels = 5565870 Avg. Back Intensity = 13.248070 Max. Back Intensity = 1151.476440 Writing output Done -------------------------------- Wed May 17 17:36:58 CDT 2023 /[...redacted...]/jobs/release mri_mc /[...redacted...]/jobs/release/tmpdir.midefacer.205539/head.mgz 1 /[.....redacted...]/jobs/release/tmpdir.midefacer.205539/head.surf -------------------------------- preprocessing...done starting generation of surface... slice nb 10... slice nb 20... slice nb 30... slice nb 40... slice nb 50... slice nb 60... slice nb 70... slice nb 80... slice nb 90... slice nb 100... slice nb 110... slice nb 120... slice nb 130... slice nb 140... slice nb 150... slice nb 160... constructing final surface... (surface with 354632 faces and 177302 vertices)...done computing the maximum edge length...1.414214 mm reversing orientation of faces... checking orientation of surface... 0.000 % of the vertices (0 vertices) exhibit an orientation change counting number of connected components... 177302 voxel in cpt #1: X=-14 [v=177302,e=531948,f=354632] located at (2.291599, -29.413504, -3.787194) For the whole surface: X=-14 [v=177302,e=531948,f=354632] One single component has been found nothing to do writing out surface...done -------------------------------- Wed May 17 17:37:01 CDT 2023 /[...redacted...]/jobs/release mris_smooth -n 10 -nw /[...redacted...]/jobs/release/tmpdir.midefacer.205539/head.surf /[...redacted...]/jobs/release/tmpdir.midefacer.205539/head.surf -------------------------------- smoothing for 10 iterations smoothing surface tessellation for 10 iterations... smoothing complete - recomputing first and second fundamental forms... Started at: Wed May 17 17:36:46 CDT 2023 Ended at: Wed May 17 17:37:05 CDT 2023 mkheadsurf done @#@FSTIME 2023:05:17:17:36:46 mkheadsurf N 11 e 18.35 S 0.59 U 17.37 P 97% M 434560 F 3 R 278026 W 0 c 49 w 584 I 21736 O 25328 L 0.97 1.06 2.42 @#@FSLOADPOST 2023:05:17:17:37:05 mkheadsurf N 11 0.97 1.05 2.39 mri_defacer --i /[...redacted...]/jobs/release/volume.nii.gz --ts /[...redacted...]/jobs/release/tmpdir.midefacer.205539/template.surf --min /[...redacted...]/jobs/release/tmpdir.midefacer.205539/min.surf --max /[...redacted.....]/jobs/release/tmpdir.midefacer.205539/max.surf --m /[...redacted...]/jobs/release/tmpdir.midefacer.205539/face.mask.mgz --o /[...redacted...]/jobs/release/defaced.nii.gz --hm /[...redacted...]/jobs/release/tmpdir.midefacer..205539/head.mgz --distdat /[...redacted...]/jobs/release/tmpdir.midefacer.205539/dist.samples --stats /[...redacted...]/jobs/release/tmpdir.midefacer..205539/stats.dat --w /work2/08266/psadil/freesurfer/average/mideface-atlas/mideface.watermark.dec44.us7.remesh3.label 5 --l /work2/08266/psadil/freesurfer/average/mideface-atlas/average.face.lower.dec44.us7.remesh3.label --l /work2/08266/psadil/freesurfer/average/mideface-atlas/average.face.upper.no-eyes.no-nose.dec44.us7.remesh3.label --l /work2/08266/psadil/freesurfer/average/mideface-atlas/average.face.nose.dec44.us7.remesh3.label --l /work2/08266/psadil/freesurfer/average/mideface-atlas/average.face.eyes.dec44.us7.remesh3.label --l /work2/08266/psadil/freesurfer/average/mideface-atlas/average.face.ear.left.dec44.us7.remesh3.label 2 3 --l /work2/08266/psadil/freesurfer/average/mideface-atlas/average.face.ear.right.dec44.us7.remesh3.label 2 3 --xmask /[...redacted...]/jobs/release/tmpdir.midefacer.205539/seg..bin.dil.mgz 7.3.2 cd /[...redacted...]/jobs/release mri_defacer --i /[...redacted...]/jobs/release/volume.nii.gz --ts /[...redacted...]/jobs/release/tmpdir.midefacer.205539/template.surf --min /[...redacted...]/jobs/release/tmpdir.midefacer.205539/min.surf --max /[...redacted.....]/jobs/release/tmpdir.midefacer.205539/max.surf --m /[...redacted...]/jobs/release/tmpdir.midefacer.205539/face.mask.mgz --o /[...redacted...]/jobs/release/defaced.nii.gz --hm /[...redacted...]/jobs/release/tmpdir.midefacer..205539/head.mgz --distdat /[...redacted...]/jobs/release/tmpdir.midefacer.205539/dist.samples --stats /[...redacted...]/jobs/release/tmpdir.midefacer..205539/stats.dat --w /work2/08266/psadil/freesurfer/average/mideface-atlas/mideface.watermark.dec44.us7.remesh3.label 5 --l /work2/08266/psadil/freesurfer/average/mideface-atlas/average.face.lower.dec44.us7.remesh3.label --l /work2/08266/psadil/freesurfer/average/mideface-atlas/average.face.upper.no-eyes.no-nose.dec44.us7.remesh3.label --l /work2/08266/psadil/freesurfer/average/mideface-atlas/average.face.nose.dec44.us7.remesh3.label --l /work2/08266/psadil/freesurfer/average/mideface-atlas/average.face.eyes.dec44.us7.remesh3.label --l /work2/08266/psadil/freesurfer/average/mideface-atlas/average.face.ear.left.dec44.us7.remesh3.label 2 3 --l /work2/08266/psadil/freesurfer/average/mideface-atlas/average.face.ear.right.dec44.us7.remesh3.label 2 3 --xmask /[...redacted...]/jobs/release/tmpdir.midefacer.205539/seg..bin.dil.mgz sysname Linux hostname c103-211.frontera.tacc.utexas.edu machine x86_64 user psadil niiRead(): detected input as 64 bit double, reading in as 32 bit float Applying watermark d=5 Applying watermark 2207 DeltaDist = 0.333333, dL = 0.111111 DistInMin 2 DistInMax 100 DistInFrac 0.9 DistOutMin 2 DistOutMax 100 DistOutFrac 1 DeltaDist 0.333333 dL 0.111111 Pad 5 5 5 FillType 1 FillConstIn 0 FillConstOut 0 DoRipple 0 =============================================== Label 0 /work2/08266/psadil/freesurfer/average/mideface-atlas/average.face.lower.dec44.us7.remesh3.label 2 20 MiDeface::DistanceBounds() DeltaDist=0.333333 Raw DistIn = 0, DistOut = 0 DistIn=0 < DistInMin=2, resetting DistOut=0 < DistOutMin=2, resetting PostMinCheck DistIn = 2, DistOut = 2 MiDeface::SegFace() =============================================== Label 1 /work2/08266/psadil/freesurfer/average/mideface-atlas/average.face.upper.no-eyes.no-nose.dec44.us7.remesh3.label 2 20 MiDeface::DistanceBounds() DeltaDist=0.333333 Raw DistIn = 1, DistOut = 9.33333 DistIn=1 < DistInMin=2, resetting PostMinCheck DistIn = 2, DistOut = 9.33333 MiDeface::SegFace() =============================================== Label 2 /work2/08266/psadil/freesurfer/average/mideface-atlas/average.face.nose.dec44.us7.remesh3.label 2 20 MiDeface::DistanceBounds() DeltaDist=0.333333 Raw DistIn = 2.66667, DistOut = 2.66667 PostMinCheck DistIn = 2.66667, DistOut = 2.66667 MiDeface::SegFace() =============================================== Label 3 /work2/08266/psadil/freesurfer/average/mideface-atlas/average.face.eyes.dec44.us7.remesh3.label 2 20 MiDeface::DistanceBounds() DeltaDist=0.333333 Raw DistIn = 7, DistOut = 6.66667 PostMinCheck DistIn = 7, DistOut = 6.66667 MiDeface::SegFace() =============================================== Label 4 /work2/08266/psadil/freesurfer/average/mideface-atlas/average.face.ear.left.dec44.us7.remesh3.label 2 3 MiDeface::DistanceBounds() DeltaDist=0.333333 Raw DistIn = 3, DistOut = 2 PostMinCheck DistIn = 3, DistOut = 2 MiDeface::SegFace() =============================================== Label 5 /work2/08266/psadil/freesurfer/average/mideface-atlas/average.face.ear.right.dec44.us7.remesh3.label 2 3 MiDeface::DistanceBounds() DeltaDist=0.333333 Raw DistIn = 3, DistOut = 5.33333 PostMinCheck DistIn = 3, DistOut = 5.33333 MiDeface::SegFace() *** Error in `mri_defacer': double free or corruption (!prev): 0x000000000f9e1090 *** ======= Backtrace: ========= /lib64/libc.so.6(+0x81329)[0x2b0d12670329] mri_defacer[0x4aaa0e] mri_defacer[0x423bd5] mri_defacer[0x4163d8] /lib64/libc.so.6(__libc_start_main+0xf5)[0x2b0d12611555] mri_defacer[0x419327] ======= Memory map: ======== 00400000-006f7000 r-xp 00000000 3d8:ad14e 144121710017324715 /work2/08266/psadil/freesurfer/bin/mri_defacer 008f6000-008fe000 r--p 002f6000 3d8:ad14e 144121710017324715 /work2/08266/psadil/freesurfer/bin/mri_defacer 008fe000-00928000 rw-p 002fe000 3d8:ad14e 144121710017324715 /work2/08266/psadil/freesurfer/bin/mri_defacer 00928000-011c1000 rw-p 00000000 00:00 0 026c1000-13727000 rw-p 00000000 00:00 0 [heap] 2b0d11411000-2b0d11433000 r-xp 00000000 fd:00 402880897 /usr/lib64/ld-2.17.so 2b0d11433000-2b0d11437000 rw-p 00000000 00:00 0 2b0d11454000-2b0d11456000 rw-p 00000000 00:00 0 2b0d11456000-2b0d1145e000 r--p 00000000 fd:00 278039021 /opt/apps/gcc/8.3.0/lib64/libgomp.so.1.0.0 2b0d1145e000-2b0d1147c000 r-xp 00008000 fd:00 278039021 /opt/apps/gcc/8.3.0/lib64/libgomp.so.1.0.0 2b0d1147c000-2b0d11484000 r--p 00026000 fd:00 278039021 /opt/apps/gcc/8.3.0/lib64/libgomp.so.1.0.0 2b0d11484000-2b0d11485000 r--p 0002d000 fd:00 278039021 /opt/apps/gcc/8.3.0/lib64/libgomp.so.1.0.0 2b0d11485000-2b0d11486000 rw-p 0002e000 fd:00 278039021 /opt/apps/gcc/8.3.0/lib64/libgomp.so.1.0.0 2b0d11486000-2b0d11487000 rw-p 00000000 00:00 0 2b0d11487000-2b0d11518000 r--p 00000000 fd:00 278039063 /opt/apps/gcc/8.3.0/lib64/libstdc++.so.6.0.25 2b0d11518000-2b0d115c4000 r-xp 00091000 fd:00 278039063 /opt/apps/gcc/8.3.0/lib64/libstdc++.so.6.0.25 2b0d115c4000-2b0d11602000 r--p 0013d000 fd:00 278039063 /opt/apps/gcc/8.3.0/lib64/libstdc++.so.6.0.25 2b0d11602000-2b0d11603000 ---p 0017b000 fd:00 278039063 /opt/apps/gcc/8.3.0/lib64/libstdc++.so.6.0.25 2b0d11603000-2b0d1160d000 r--p 0017b000 fd:00 278039063 /opt/apps/gcc/8.3.0/lib64/libstdc++.so.6.0.25 2b0d1160d000-2b0d1160f000 rw-p 00185000 fd:00 278039063 /opt/apps/gcc/8.3.0/lib64/libstdc++.so.6.0.25 2b0d1160f000-2b0d11613000 rw-p 00000000 00:00 0 2b0d11613000-2b0d11616000 r--p 00000000 fd:00 278039010 /opt/apps/gcc/8.3.0/lib64/libgcc_s.so.1 2b0d11616000-2b0d11627000 r-xp 00003000 fd:00 278039010 /opt/apps/gcc/8.3.0/lib64/libgcc_s.so.1 2b0d11627000-2b0d1162a000 r--p 00014000 fd:00 278039010 /opt/apps/gcc/8.3.0/lib64/libgcc_s.so.1 2b0d1162a000-2b0d1162b000 ---p 00017000 fd:00 278039010 /opt/apps/gcc/8.3.0/lib64/libgcc_s.so.1 2b0d1162b000-2b0d1162c000 r--p 00017000 fd:00 278039010 /opt/apps/gcc/8.3.0/lib64/libgcc_s.so.1 2b0d1162c000-2b0d1162d000 rw-p 00018000 fd:00 278039010 /opt/apps/gcc/8.3.0/lib64/libgcc_s.so.1 2b0d1162d000-2b0d11632000 rw-p 00000000 00:00 0 2b0d11632000-2b0d11633000 r--p 00021000 fd:00 402880897 /usr/lib64/ld-2.17.so 2b0d11633000-2b0d11634000 rw-p 00022000 fd:00 402880897 /usr/lib64/ld-2.17.so 2b0d11634000-2b0d11635000 rw-p 00000000 00:00 0 2b0d11635000-2b0d11675000 r-xp 00000000 fd:00 269642820 /opt/apps/xalt/2.10.34/lib64/libxalt_init.so 2b0d11675000-2b0d11875000 ---p 00040000 fd:00 269642820 /opt/apps/xalt/2.10.34/lib64/libxalt_init.so 2b0d11875000-2b0d11876000 r--p 00040000 fd:00 269642820 /opt/apps/xalt/2.10.34/lib64/libxalt_init.so 2b0d11876000-2b0d11877000 rw-p 00041000 fd:00 269642820 /opt/apps/xalt/2.10.34/lib64/libxalt_init.so 2b0d11877000-2b0d11878000 rw-p 00000000 00:00 0 2b0d11878000-2b0d1188d000 r-xp 00000000 fd:00 404656596 /usr/lib64/libz.so.1.2.7 2b0d1188d000-2b0d11a8c000 ---p 00015000 fd:00 404656596 /usr/lib64/libz.so.1.2.7 2b0d11a8c000-2b0d11a8d000 r--p 00014000 fd:00 404656596 /usr/lib64/libz.so.1.2.7 2b0d11a8d000-2b0d11a8e000 rw-p 00015000 fd:00 404656596 /usr/lib64/libz.so.1.2.7 2b0d11a8e000-2b0d11aa5000 r-xp 00000000 fd:00 402965799 /usr/lib64/libpthread-2.17.so 2b0d11aa5000-2b0d11ca4000 ---p 00017000 fd:00 402965799 /usr/lib64/libpthread-2.17.so 2b0d11ca4000-2b0d11ca5000 r--p 00016000 fd:00 402965799 /usr/lib64/libpthread-2.17.so 2b0d11ca5000-2b0d11ca6000 rw-p 00017000 fd:00 402965799 /usr/lib64/libpthread-2.17.so 2b0d11ca6000-2b0d11caa000 rw-p 00000000 00:00 0 2b0d11caa000-2b0d11cac000 r-xp 00000000 fd:00 402880903 /usr/lib64/libdl-2.17.so 2b0d11cac000-2b0d11eac000 ---p 00002000 fd:00 402880903 /usr/lib64/libdl-2.17.so 2b0d11eac000-2b0d11ead000 r--p 00002000 fd:00 402880903 /usr/lib64/libdl-2.17.so 2b0d11ead000-2b0d11eae000 rw-p 00003000 fd:00 402880903 /usr/lib64/libdl-2.17.so 2b0d11eae000-2b0d11faf000 r-xp 00000000 fd:00 402880909 /usr/lib64/libm-2.17.so 2b0d11faf000-2b0d121ae000 ---p 00101000 fd:00 402880909 /usr/lib64/libm-2.17.so 2b0d121ae000-2b0d121af000 r--p 00100000 fd:00 402880909 /usr/lib64/libm-2.17.so 2b0d121af000-2b0d121b0000 rw-p 00101000 fd:00 402880909 /usr/lib64/libm-2.17.so 2b0d121b0000-2b0d121b8000 r-xp 00000000 fd:00 402704011 /usr/lib64/libcrypt-2.17.so 2b0d121b8000-2b0d123b7000 ---p 00008000 fd:00 402704011 /usr/lib64/libcrypt-2.17.so 2b0d123b7000-2b0d123b8000 r--p 00007000 fd:00 402704011 /usr/lib64/libcrypt-2.17.so 2b0d123b8000-2b0d123b9000 rw-p 00008000 fd:00 402704011 /usr/lib64/libcrypt-2.17.so 2b0d123b9000-2b0d123e7000 rw-p 00000000 00:00 0 2b0d123e7000-2b0d123ee000 r-xp 00000000 fd:00 403139684 /usr/lib64/librt-2.17.so 2b0d123ee000-2b0d125ed000 ---p 00007000 fd:00 403139684 /usr/lib64/librt-2.17.so 2b0d125ed000-2b0d125ee000 r--p 00006000 fd:00 403139684 /usr/lib64/librt-2.17.so 2b0d125ee000-2b0d125ef000 rw-p 00007000 fd:00 403139684 /usr/lib64/librt-2.17.so 2b0d125ef000-2b0d127b3000 r-xp 00000000 fd:00 402704007 /usr/lib64/libc-2.17.so 2b0d127b3000-2b0d129b2000 ---p 001c4000 fd:00 402704007 /usr/lib64/libc-2.17.so 2b0d129b2000-2b0d129b6000 r--p 001c3000 fd:00 402704007 /usr/lib64/libc-2.17.so=============================================== MiDeface::FaceIntensityStats() Mode2 12 12 4352 @#@FSTIME 2023:05:17:17:37:05 mri_defacer N 39 e 12.40 S 0.44 U 11.68 P 97% M 801792 F 1 R 283367 W 0 c 2 w 129 I 10144 O 1392 L 0.97 1.05 2.39 @#@FSLOADPOST 2023:05:17:17:37:17 mri_defacer N 39 0.98 1.05 2.38 ERROR: Patrick Sadil, PhD (he/him/his) Research Associate psadil.github.io/psadil _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://secure-web.cisco.com/1zAGHDjLv0cEFFcHUwZV0UwFrJRbZndb6D7V-kbbDSW6rz… 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://secure-web.cisco.com/1Ik2XgIi9JI6jyIG7mtSp6lJHT-sodGM6CBmxlMEEzOG4e… <https://secure-web.cisco.com/1Ik2XgIi9JI6jyIG7mtSp6lJHT-sodGM6CBmxlMEEzOG4eUhqaf_vcQqr8RiwfPo5hg4-545zbjpmzL3ii1BHuZu66f75-h5URCdmjFLbUueG18kNVbRsnOYKTwQ12r_hvyl0swhI2qaDadned13wZ79YXcHx8Oaeo33crNWxVokahWNyJyur5Q83kCFEZ7NPO3VoWotP9YCr_q5agVy3w5ezyLOgKymeTnG9TxRBvZbuvhKa3sOitLzggi6bvCN2dnp04QmuBzlipm-Ma8qZZpaUXJ3kv2TJy7yYc6Z5VPpUecdzB9jZxaHyauuOu-cocIIbACPr7lmFazKU44rn0SGObNQvneOXYx59N6Nqbog/https%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline> . 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. _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://secure-web.cisco.com/1gQXhm7Q1kGgbFmbJPSRBspvX1-Vgo0ERoYdMms-4H52WH… 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://secure-web.cisco.com/1bbK74dX_iKOZzxluqUv-7U2YWmCL1mdwhItD1akR5CRAy… <https://secure-web.cisco.com/1oEh-TESgy3As50PoOa5_xTnsa0-WDUusxTkC8oNrY0izo_nDLhfxztmLO7CPw5TYJ9tNix3VPvp3av93GmHEHjHOftYKySep9YUgLiSBSKlF4wEnQYcnqgbPcySMDwp-0nlgypGodQh9-R2CZ7a7icXog70zyK458x4aP5u1x0UD_bryVyL4P8OLIOr7NyTQKt3K4WRfwYs1NwAbMX92GFaNHYCRPJUCJ4Cl_zRY0IoU2_d0EQOJYi93DcK2DEFeraStbKDLyOX_fmNvj9xiasFY1h9P6Kh9c_s3TMw83KLwE0WjPbc3J-Ake_LSiKJBKqLqDbEMX6k8AjaAA2Sg5w/https%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline%26gt; . 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. _______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

1 0

FW: Inquiry about mris_euler_number command
by Yun, Jenna 24 May '23

24 May '23

External Email - Use Caution Dear all, I hope this email finds you well. I was trying to run mris_euler_number command for QC of the recent Freesurfer segmentation. It seems as though there is no information about the command available in your wiki page. I can see recent literature reviewing the reliability of the command, which indicates the command is still available. Could you provide me details on different arguments available for the command? Kind Regards, Jenna -- Juyoung (Jenna) Yun CID: 01718249 MSc Translational Neuroscience Imperial College London

2 1

fMRIPrep: anatomical part
by Michelle Diniz 24 May '23

24 May '23

External Email - Use Caution Can I use fmriprep to analyze only the anatomical part? -- Michelle Diniz Lopes

2 1

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