Freesurfer

freesurfer@nmr.mgh.harvard.edu

11 participants
30080 discussions

Re: [Freesurfer] Longitudinal Stream Error
by Douglas N. Greve 17 Feb '22

17 Feb '22

Does that file exist? ps. Please remember to post to the list. Thanks! On 2/15/2022 5:06 PM, Willett, Andrew Sunday wrote: > > Dr. Greve, > > I hope this email finds you well. Thank you for your response to my > listed question on Freesurfer’s mailing list on Sunday! I wanted to > reach out to followup re: longitudinal stream error. > > The main error I receive with the base code is as follows: > > SUBJECTS_DIR /PHShome/asw39/subjects > FREESURFER_HOME /PHShome/asw39/freesurfer > Loading source label. > Invalid argument > ERROR reading /PHShome/asw39/subjects/fsaverage/label/lh.BA1_exvivo.label > Linux rgs10.research.partners.org 2.6.32-696.28.1.el6.x86_64 #1 SMP > Thu Apr 26 04:27:41 EDT 2018 x86_64 x86_64 x86_64 GNU/Linux > > recon-all -s MSA12 exited with ERRORS at Tue Nov 30 20:43:37 EST 2021 > We got this error after we used Freesurfer v6.0 to process the data > cross-sectionally and then run the base template. Do you know whether > it is possible for v7.0 cross-sectional output to be run through v6.0 > longitudinal stream (as v6.0 is the most recent longitudinal stream > version)? > > Thanks, > > /Andee Sunday Willett, M.S./ > > / > > //_Pronouns_: they/them// > > / > // > > / > / > > /Research Assistant II/ > > /Department of Neurology, Division of Movement Disorders > / > > /Brigham and Women’s Hospital/ > // > > // > > //// > > /awillett(a)bwh.harvard.edu <mailto:jkim@bwh.harvard.edu>* > *brighamandwomens.org <http://www.brighamandwomens.org/>/ > > / > /

2 2

SAMSEG mesh format and content
by Martin Kavec 17 Feb '22

17 Feb '22

External Email - Use Caution Hi all, previous question from Florent triggered my interest in SAMSEG and I am running now couple of cases to see what it gives. I would like to ask - SAMSEG can also output a mesh. How is the mesh stored in file? - how can it be visualized (Paraview?) - what does the mesh represent. Individual structures? Thanks, Martin

2 1

Re: [Freesurfer] FW: Problems with recon for manually fixed Talairach
by Douglas N. Greve 17 Feb '22

17 Feb '22

I'm a bit puzzled by this. Are you saving the xfm file to talairach.xfm? In the log file, it clearly says: INFO: transforms/talairach.xfm already exists! The new transforms/talairach.auto.xfm will not be copied to transforms/talairach.xfm This is done to retain any edits made to transforms/talairach.xfm Add the -clean-tal flag to recon-all to overwrite transforms/talairach.xfm and there is no command in the log that indicates that it was overwritten, and I cannot replicate this behavior here On 1/31/2022 10:33 AM, Goeckner, Bryna wrote: > External Email - Use Caution > > Sorry - Sending these directly since I tried to send these earlier, but they were blocked by the list-serve. > > Bryna Goeckner (she/her) > Graduate Student > Medical College of Wisconsin > Neuroscience Doctoral Program > > -----Original Message----- > From: Goeckner, Bryna > Sent: Friday, January 28, 2022 11:36 AM > To: freesurfer(a)nmr.mgh.harvard.edu > Subject: Re: [Freesurfer] Problems with recon for manually fixed Talairach > > I'm attaching the two recon-all.logs. Both were generated for same subject using the same corrected talairach.xfm file, one with -notal-check and the other with -notalairach. Please let me know if you have any other questions. Thanks! > > Bryna Goeckner (she/her) > Graduate Student > Medical College of Wisconsin > Neuroscience Doctoral Program > > Subject: Re: [Freesurfer] Problems with recon for manually fixed > To: freesurfer(a)nmr.mgh.harvard.edu > Message-ID: <95652ab6-b36a-c708-edd7-b8734c1c7402(a)mgh.harvard.edu> > Content-Type: text/plain; charset=UTF-8; format=flowed > > Can you send the recon-all.log? > > On 1/27/2022 9:34 AM, Goeckner, Bryna wrote: >> External Email - Use Caution >> >> We are using FS 7.2 >> >> Bryna Goeckner (she/her) >> Graduate Student >> Medical College of Wisconsin >> Neuroscience Doctoral Program >> >> Date: Wed, 26 Jan 2022 16:43:44 -0500 >> From: "Douglas N. Greve" <dgreve(a)mgh.harvard.edu> >> Subject: Re: [Freesurfer] Problems with recon for manually fixed >> Talairach >> To: freesurfer(a)nmr.mgh.harvard.edu >> Message-ID: <8e0752c5-13fa-755e-c416-4253ce5043b3(a)mgh.harvard.edu> >> Content-Type: text/plain; charset="utf-8" >> >> what version of FS are you using? >> >> On 1/21/2022 2:21 PM, Goeckner, Bryna wrote: >>> ????????External Email - Use Caution >>> >>> Hi, >>> >>> I am trying to decide how to proceed after manually updating a >>> talairach since various ways I?ve tried the recon process give me >>> different results. >>> >>> Our group used Freesurfer 7.2 for processing data with the T2 and 3T >>> flags as follows: >>> >>> recon-all -subject $1 -i $2/rawT1.ORIG.nii.gz -T2 >>> $2/rawT2.ORIG.nii.gz -T2pial -parallel -openmp 12 -3T -all >>> >>> After visual inspection, I made adjustments to the talairach using >>> tkregister2 and then used the code below to rerun the recon: >>> >>> recon-all -subject $1 -T2 $2/rawT2.ORIG.nii.gz -T2pial -parallel >>> -openmp 12 -3T? -all >>> >>> When this was done, the talairach.xfm file was restored to the >>> talairach from the original recon, while the talairach.xfm~ was still >>> the fixed version. At no point in this entire process did the >>> talairach (fixed or original) generate an error. >>> >>> To avoid the overwriting of the talairach.xfm file, I tried using >>> (separately) the -notalairach and -notal-check flags. For both, the >>> talairach.xfm file stayed as the fixed talairach, but I got different >>> aseg and aparc results. >>> >>> I?d like to know more about how these to flags differ and if you have >>> a recommendation on which process is best.? The plan is to eventually >>> use this data in TRACULA. >>> >>> Thanks for your help, >>> >>> *Bryna Goeckner*?(she/her) >>> >>> Graduate Student >>> >>> Medical College of Wisconsin >>> >>> Neuroscience Doctoral Program

2 4

Re: [Freesurfer] Freesurfer Virtual Box VM (ubuntu 18) - developer account
by fsbuild 17 Feb '22

17 Feb '22

External Email - Use Caution Sending the into to your email shortly. - R. On Feb 17, 2022, at 16:50, Haniya Saleh <hsaleh(a)uoguelph.ca> wrote:        External Email - Use Caution        Hi Freesurfer team, We are trying to setup Freesurfer on an Ubuntu 18 Virtual Box VM. We are at the step in the setup guide to get into the developer user account. Could you please provide the password for this? Thanks!<image.png>Warm Regards,Haniya Saleh________________________________________________Haniya Saleh | OVC IT Technician - Client ProductivityOntario Veterinary College (OVC) | University of GuelphMacNabb House rm. 103 | 2 College Avenue West | Guelph, ON | N1G 2W1519-824-4120 x54691 | hsaleh@uoguelph.ca_______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

1 0

Freesurfer Virtual Box VM (ubuntu 18) - developer account
by Haniya Saleh 17 Feb '22

17 Feb '22

External Email - Use Caution Hi Freesurfer team, We are trying to setup Freesurfer on an Ubuntu 18 Virtual Box VM. We are at the step in the setup guide to get into the developer user account. Could you please provide the password for this? Thanks! [cid:ba8ad87a-d323-482d-9b3a-2eaa57e2f62d] Warm Regards, Haniya Saleh ________________________________________________ Haniya Saleh | OVC IT Technician - Client Productivity Ontario Veterinary College (OVC) | University of Guelph MacNabb House rm. 103 | 2 College Avenue West | Guelph, ON | N1G 2W1 519-824-4120 x54691 | hsaleh(a)uoguelph.ca

1 0

Re: [Freesurfer] Virtual Machine (VM_67) password request
by fsbuild 17 Feb '22

17 Feb '22

External Email - Use Caution Sending the info to your email shortly. - R. From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of daedalus39@aol.com<daedalus39@aol.com>Sent: Thursday, February 17, 2022 12:41 PMTo: freesurfer@nmr.mgh.harvard.edu <freesurfer@nmr.mgh.harvard.edu>Subject: [Freesurfer] Virtual Machine (VM_67) password request         External Email - Use Caution        Dear Admins, I have installed the VirtualBox software and I am following the steps outlined in Vbox_load_image.pdf.  I’m at the point where I’ll need a password for “developer”.  Could you please send the pw? Thanks in advance, -Randy_______________________________________________Freesurfer mailing listFreesurfer(a)nmr.mgh.harvard.eduMailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://secure-web.cisco.com/1u4GUfIxBmpaEoU1law9EzIidad-q8iGMCeri3… mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

1 0

Virtual Machine (VM_67) password request
by daedalus39＠aol.com 17 Feb '22

17 Feb '22

External Email - Use Caution Dear Admins, I have installed the VirtualBox software and I am followingthe steps outlined in Vbox_load_image.pdf. I’m at the point where I’llneed a password for “developer”. Could you please send the pw? Thanks in advance, -Randy

2 2

Question glm analysis g4v0
by Laura Willers de Souza 17 Feb '22

17 Feb '22

External Email - Use Caution Hello FreeSurfer Developers, I am performing a GLM analysis to assess cortical thickness between 4 groups, without any covariates. I followed exactly what is on the wiki https://secure-web.cisco.com/1VuhMA49mKmIDKH_rGPy4c67MdbjL6bNv2i_WwNDwvMA5-… In a previous analysis (https://secure-web.cisco.com/1qw-8Oc7vg0Tc3_ilXhnADw1_lWmUuUCQVr-MNNAiNRRR1…) Dr Douglas had told me that before any analysis I should test whether the interaction is significant or not. I would like to know if this also applies to this case, the interaction being tested by contrast number 7 of the wiki. Thanks in advance! Best, Laura Willers de Souza Master Student in Biochemistry Zimmer Lab - Federal University of Rio Grande do Sul - Porto Alegre/RS - Brazil

1 0

-cw256 flag
by Harriet Dempsey-Jones 16 Feb '22

16 Feb '22

External Email - Use Caution Hi, sorry, this just bounced back due to an issue with my subscription which is now fixed. Please see below From: Harriet Dempsey-Jones <h.dempseyjones(a)uq.edu.au> Date: Thursday, 17 February 2022 at 11:56 am To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] -cw256 flag Hi there, Thanks for getting back to me I tried using the -cw256 flag and I still got an error (and freesurfer stopped recon-all). The error was asking me to use the flag, though I had already put the flag in. Could you look at my code (below) to see if I have implemented it incorrectly? Thank you, Harriet ---------------------------- MY CODE #!bin/tcsh # Freesurfer start-up module load freesurfer # Set up vars set subj = P00_FG set recon_use = (-all) set anat = /scratch/inode/uqhdemp1/Fingertip_maps/{$subj}/{$subj}.results/{$subj_init}_uniden_avg_wholebrain_unpad_warped_3dQ.nii set base_dir = /scratch/inode/uqhdemp1 set expert_file = 1b_FS_expertfile ## 1. Freesurfer recon all recon-all {$recon_use} -cw256 -s {$subj}_3dD_cw_try2 -hires -i $anat -sd $base_dir/Surfaces -openmp 12 -expert $base_dir/Parent_scripts/Surfaces/$expert_file SAMPLE OF ERROR IN COMMAND WINDOW #-------------------------------------------- #@# MotionCor Thu Feb 17 11:44:30 AEST 2022 Found 1 runs /scratch/inode/uqhdemp1/Surfaces/P00_FG_3dD_cw_try2/mri/orig/001.mgz Checking for (invalid) multi-frame inputs... Only one run found so motion correction will not be performed. I'll copy the run to rawavg and continue. cp /scratch/inode/uqhdemp1/Surfaces/P00_FG_3dD_cw_try2/mri/orig/001.mgz /scratch/inode/uqhdemp1/Surfaces/P00_FG_3dD_cw_try2/mri/rawavg.mgz /scratch/inode/uqhdemp1/Surfaces/P00_FG_3dD_cw_try2 mri_convert /scratch/inode/uqhdemp1/Surfaces/P00_FG_3dD_cw_try2/mri/rawavg.mgz /scratch/inode/uqhdemp1/Surfaces/P00_FG_3dD_cw_try2/mri/orig.mgz --conform_min mri_convert /scratch/inode/uqhdemp1/Surfaces/P00_FG_3dD_cw_try2/mri/rawavg.mgz /scratch/inode/uqhdemp1/Surfaces/P00_FG_3dD_cw_try2/mri/orig.mgz --conform_min $Id: mri_convert.c,v 1.227 2017/02/16 19:15:42 greve Exp $ reading from /scratch/inode/uqhdemp1/Surfaces/P00_FG_3dD_cw_try2/mri/rawavg.mgz... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-0, -1, 0) j_ras = (-0, -0, -1) k_ras = (1, -0, 0) changing data type from float to uchar (noscale = 0)... MRIchangeType: Building histogram 0 4078 1000, flo=0, fhi=0.999, dest_type=0 Reslicing using trilinear interpolation writing to /scratch/inode/uqhdemp1/Surfaces/P00_FG_3dD_cw_try2/mri/orig.mgz... **************************************** ERROR! FOV=273.000 > 256 Include the flag -cw256 with recon-all! Inspect orig.mgz to ensure the head is fully visible. **************************************** Linux inode2.hpc.dc.uq.edu.au 3.10.0-1160.36.2.el7.x86_64 #1 SMP Wed Jul 21 11:57:15 UTC 2021 x86_64 x86_64 x86_64 GNU/Linux recon-all -s P00_FG_3dD_cw_try2 exited with ERRORS at Thu Feb 17 11:45:38 AEST 2022 For more details, see the log file /scratch/inode/uqhdemp1/Surfaces/P00_FG_3dD_cw_try2/scripts/recon-all.log To report a problem, see http://secure-web.cisco.com/1EazoIQDEQ5C0xk6kgC_HrVs1qLbDRhir6_Z00m8PdXgaaA… Recon-all-status.log status file for recon-all Thu Feb 17 11:44:10 AEST 2022 #@# MotionCor Thu Feb 17 11:44:30 AEST 2022 Linux inode2.hpc.dc.uq.edu.au 3.10.0-1160.36.2.el7.x86_64 #1 SMP Wed Jul 21 11:57:15 UTC 2021 x86_64 x86_64 x86_64 GNU/Linux recon-all -s P00_FG_3dD_cw_try2 exited with ERRORS at Thu Feb 17 11:45:38 AEST 2022 Recon-all.error ------------------------------ SUBJECT P00_FG_3dD_cw_try2 DATE Thu Feb 17 11:45:38 AEST 2022 USER uqhdemp1 HOST inode2.hpc.dc.uq.edu.au PROCESSOR x86_64 OS Linux Linux inode2.hpc.dc.uq.edu.au 3.10.0-1160.36.2.el7.x86_64 #1 SMP Wed Jul 21 11:57:15 UTC 2021 x86_64 x86_64 x86_64 GNU/Linux $Id: recon-all,v 1.601 2017/02/08 21:17:33 greve Exp $ /opt/ohpc/pub/apps/freesurfer/bin/recon-all PWD /scratch/inode/uqhdemp1/Surfaces/P00_FG_3dD_cw_try2 CMD mri_convert /scratch/inode/uqhdemp1/Surfaces/P00_FG_3dD_cw_try2/mri/rawavg.mgz /scratch/inode/uqhdemp1/Surfaces/P00_FG_3dD_cw_try2/mri/orig.mgz --conform_min Recon-all.log Thu Feb 17 11:44:09 AEST 2022 /scratch/inode/uqhdemp1/Surfaces/P00_FG_3dD_cw_try2 /opt/ohpc/pub/apps/freesurfer/bin/recon-all -all -cw256 -s P00_FG_3dD_cw_try2 -hires -i /scratch/inode/uqhdemp1/Fingertip_maps/P00_FG/P00_FG.results/FG_uniden_avg_wholebrain_unpad_warped_3dQ.nii -sd /scratch/inode/uqhdemp1/Surfaces -openmp 12 -expert /scratch/inode/uqhdemp1/Parent_scripts/Surfaces/1b_FS_expertfile subjid P00_FG_3dD_cw_try2 setenv SUBJECTS_DIR /scratch/inode/uqhdemp1/Surfaces FREESURFER_HOME /opt/ohpc/pub/apps/freesurfer Actual FREESURFER_HOME /opt/ohpc/pub/apps/freesurfer build-stamp.txt: freesurfer-linux-centos7_x86_64-dev-20181029-665a1b6 Linux inode2.hpc.dc.uq.edu.au 3.10.0-1160.36.2.el7.x86_64 #1 SMP Wed Jul 21 11:57:15 UTC 2021 x86_64 x86_64 x86_64 GNU/Linux cputime unlimited filesize unlimited datasize unlimited stacksize 8192 kbytes coredumpsize 0 kbytes memoryuse unlimited vmemoryuse unlimited descriptors 1024 memorylocked 64 kbytes maxproc 4096 maxlocks unlimited maxsignal 2059413 maxmessage 819200 maxnice 0 maxrtprio 0 maxrttime unlimited total used free shared buff/cache available Mem: 527413880 142260852 261204056 4462024 123948972 379278760 Swap: 4192252 2147228 2045024 ######################################## program versions used $Id: recon-all,v 1.601 2017/02/08 21:17:33 greve Exp $ $Id: lta_convert.cpp,v 1.10 2016/08/09 02:11:11 zkaufman Exp $ ProgramName: lta_convert ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2022/02/17-01:44:09-GMT BuildTimeStamp: Oct 29 2018 00:06:18 Id: $Id: lta_convert.cpp,v 1.10 2016/08/09 02:11:11 zkaufman Exp $ User: uqhdemp1 Machine: inode2.hpc.dc.uq.edu.au Platform: Linux PlatformVersion: 3.10.0-1160.36.2.el7.x86_64 CompilerName: GCC CompilerVersion: 40800 ProgramName: mri_and ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2022/02/17-01:44:09-GMT BuildTimeStamp: Oct 29 2018 00:06:18 Id: $Id: mri_and.c,v 1.4 2011/03/02 00:04:13 nicks Exp $ User: uqhdemp1 Machine: inode2.hpc.dc.uq.edu.au Platform: Linux PlatformVersion: 3.10.0-1160.36.2.el7.x86_64 CompilerName: GCC CompilerVersion: 40800 ProgramName: mri_annotation2label ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2022/02/17-01:44:09-GMT BuildTimeStamp: Oct 29 2018 00:06:18 Id: $Id: mri_annotation2label.c,v 1.32 2016/08/02 21:20:27 nicks Exp $ User: uqhdemp1 Machine: inode2.hpc.dc.uq.edu.au Platform: Linux PlatformVersion: 3.10.0-1160.36.2.el7.x86_64 CompilerName: GCC CompilerVersion: 40800 ProgramName: mri_aparc2aseg ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2022/02/17-01:44:09-GMT BuildTimeStamp: Oct 29 2018 00:06:18 Id: $Id: mri_aparc2aseg.c,v 1.54 2016/12/26 15:29:30 fischl Exp $ User: uqhdemp1 Machine: inode2.hpc.dc.uq.edu.au Platform: Linux PlatformVersion: 3.10.0-1160.36.2.el7.x86_64 CompilerName: GCC CompilerVersion: 40800 ProgramName: mri_aparc2wmseg ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2022/02/17-01:44:09-GMT BuildTimeStamp: Oct 29 2018 00:06:18 Id: $Id: mri_aparc2wmseg.c,v 1.6 2011/03/02 00:04:13 nicks Exp $ User: uqhdemp1 Machine: inode2.hpc.dc.uq.edu.au Platform: Linux PlatformVersion: 3.10.0-1160.36.2.el7.x86_64 CompilerName: GCC CompilerVersion: 40800 ProgramName: mri_binarize ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2022/02/17-01:44:09-GMT BuildTimeStamp: Oct 29 2018 00:06:18 Id: $Id: mri_binarize.c,v 1.43 2016/06/09 20:46:21 greve Exp $ User: uqhdemp1 Machine: inode2.hpc.dc.uq.edu.au Platform: Linux PlatformVersion: 3.10.0-1160.36.2.el7.x86_64 CompilerName: GCC CompilerVersion: 40800 ProgramName: mri_ca_label ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2022/02/17-01:44:09-GMT BuildTimeStamp: Oct 29 2018 00:06:18 Id: $Id: mri_ca_label.c,v 1.115 2016/10/22 17:31:36 fischl Exp $ User: uqhdemp1 Machine: inode2.hpc.dc.uq.edu.au Platform: Linux PlatformVersion: 3.10.0-1160.36.2.el7.x86_64 CompilerName: GCC CompilerVersion: 40800 ProgramName: mri_ca_normalize ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2022/02/17-01:44:09-GMT BuildTimeStamp: Oct 29 2018 00:06:18 Id: $Id: mri_ca_normalize.c,v 1.69 2016/10/22 17:30:57 fischl Exp $ User: uqhdemp1 Machine: inode2.hpc.dc.uq.edu.au Platform: Linux PlatformVersion: 3.10.0-1160.36.2.el7.x86_64 CompilerName: GCC CompilerVersion: 40800 ProgramName: mri_ca_register ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2022/02/17-01:44:09-GMT BuildTimeStamp: Oct 29 2018 00:06:18 Id: $Id: mri_ca_register.c,v 1.99 2016/10/22 17:31:24 fischl Exp $ User: uqhdemp1 Machine: inode2.hpc.dc.uq.edu.au Platform: Linux PlatformVersion: 3.10.0-1160.36.2.el7.x86_64 CompilerName: GCC CompilerVersion: 40800 ProgramName: mri_cc ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2022/02/17-01:44:09-GMT BuildTimeStamp: Oct 29 2018 00:06:18 Id: $Id: mri_cc.c,v 1.39 2015/12/04 13:59:56 fischl Exp $ User: uqhdemp1 Machine: inode2.hpc.dc.uq.edu.au Platform: Linux PlatformVersion: 3.10.0-1160.36.2.el7.x86_64 CompilerName: GCC CompilerVersion: 40800 ProgramName: mri_compute_overlap ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2022/02/17-01:44:09-GMT BuildTimeStamp: Oct 29 2018 00:06:18 Id: $Id: mri_compute_overlap.c,v 1.19 2015/10/20 20:07:19 fischl Exp $ User: uqhdemp1 Machine: inode2.hpc.dc.uq.edu.au Platform: Linux PlatformVersion: 3.10.0-1160.36.2.el7.x86_64 CompilerName: GCC CompilerVersion: 40800 ProgramName: mri_compute_seg_overlap ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2022/02/17-01:44:09-GMT BuildTimeStamp: Oct 29 2018 00:06:18 Id: $Id: mri_compute_seg_overlap.c,v 1.18 2015/08/28 18:05:30 greve Exp $ User: uqhdemp1 Machine: inode2.hpc.dc.uq.edu.au Platform: Linux PlatformVersion: 3.10.0-1160.36.2.el7.x86_64 CompilerName: GCC CompilerVersion: 40800 ProgramName: mri_concat ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2022/02/17-01:44:09-GMT BuildTimeStamp: Oct 29 2018 00:06:18 Id: $Id: mri_concat.c,v 1.67 2017/02/16 19:49:35 greve Exp $ User: uqhdemp1 Machine: inode2.hpc.dc.uq.edu.au Platform: Linux PlatformVersion: 3.10.0-1160.36.2.el7.x86_64 CompilerName: GCC CompilerVersion: 40800 ProgramName: mri_concatenate_lta ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2022/02/17-01:44:09-GMT BuildTimeStamp: Oct 29 2018 00:06:18 Id: $Id: mri_concatenate_lta.c,v 1.16 2015/11/21 00:06:20 greve Exp $ User: uqhdemp1 Machine: inode2.hpc.dc.uq.edu.au Platform: Linux PlatformVersion: 3.10.0-1160.36.2.el7.x86_64 CompilerName: GCC CompilerVersion: 40800 mri_convert -all-info ProgramName: mri_convert ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2022/02/17-01:44:09-GMT BuildTimeStamp: Oct 29 2018 00:06:18 Id: $Id: mri_convert.c,v 1.227 2017/02/16 19:15:42 greve Exp $ User: uqhdemp1 Machine: inode2.hpc.dc.uq.edu.au Platform: Linux PlatformVersion: 3.10.0-1160.36.2.el7.x86_64 CompilerName: GCC CompilerVersion: 40800 ProgramName: mri_diff ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2022/02/17-01:44:09-GMT BuildTimeStamp: Oct 29 2018 00:06:18 Id: $Id: mri_diff.c,v 1.37 2017/01/11 18:15:33 greve Exp $ User: uqhdemp1 Machine: inode2.hpc.dc.uq.edu.au Platform: Linux PlatformVersion: 3.10.0-1160.36.2.el7.x86_64 CompilerName: GCC CompilerVersion: 40800 ProgramName: mri_edit_wm_with_aseg ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2022/02/17-01:44:09-GMT BuildTimeStamp: Oct 29 2018 00:06:18 Id: $Id: mri_edit_wm_with_aseg.c,v 1.25 2012/03/29 13:17:38 fischl Exp $ User: uqhdemp1 Machine: inode2.hpc.dc.uq.edu.au Platform: Linux PlatformVersion: 3.10.0-1160.36.2.el7.x86_64 CompilerName: GCC CompilerVersion: 40800 ProgramName: mri_em_register ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2022/02/17-01:44:09-GMT BuildTimeStamp: Oct 29 2018 00:06:18 Id: $Id: mri_em_register.c,v 1.106 2016/10/22 17:31:12 fischl Exp $ User: uqhdemp1 Machine: inode2.hpc.dc.uq.edu.au Platform: Linux PlatformVersion: 3.10.0-1160.36.2.el7.x86_64 CompilerName: GCC CompilerVersion: 40800 ProgramName: mri_fill ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2022/02/17-01:44:09-GMT BuildTimeStamp: Oct 29 2018 00:06:18 Id: $Id: mri_fill.c,v 1.119 2011/10/25 14:09:58 fischl Exp $ User: uqhdemp1 Machine: inode2.hpc.dc.uq.edu.au Platform: Linux PlatformVersion: 3.10.0-1160.36.2.el7.x86_64 CompilerName: GCC CompilerVersion: 40800 ProgramName: mri_fuse_segmentations ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2022/02/17-01:44:09-GMT BuildTimeStamp: Oct 29 2018 00:06:18 Id: $Id: mri_fuse_segmentations.cpp,v 1.8 2011/03/02 00:04:15 nicks Exp $ User: uqhdemp1 Machine: inode2.hpc.dc.uq.edu.au Platform: Linux PlatformVersion: 3.10.0-1160.36.2.el7.x86_64 CompilerName: GCC CompilerVersion: 40800 ProgramName: mri_fwhm ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2022/02/17-01:44:09-GMT BuildTimeStamp: Oct 29 2018 00:06:18 Id: $Id: mri_fwhm.c,v 1.35 2016/11/01 20:25:24 greve Exp $ User: uqhdemp1 Machine: inode2.hpc.dc.uq.edu.au Platform: Linux PlatformVersion: 3.10.0-1160.36.2.el7.x86_64 CompilerName: GCC CompilerVersion: 40800 ProgramName: mri_gcut ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2022/02/17-01:44:09-GMT BuildTimeStamp: Oct 29 2018 00:06:18 Id: $Id: mri_gcut.cpp,v 1.14 2011/03/02 00:04:16 nicks Exp $ User: uqhdemp1 Machine: inode2.hpc.dc.uq.edu.au Platform: Linux PlatformVersion: 3.10.0-1160.36.2.el7.x86_64 CompilerName: GCC CompilerVersion: 40800 ProgramName: mri_info ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2022/02/17-01:44:09-GMT BuildTimeStamp: Oct 29 2018 00:06:18 Id: $Id: mri_info.c,v 1.87 2014/11/20 23:46:54 greve Exp $ User: uqhdemp1 Machine: inode2.hpc.dc.uq.edu.au Platform: Linux PlatformVersion: 3.10.0-1160.36.2.el7.x86_64 CompilerName: GCC CompilerVersion: 40800 ProgramName: mri_label2label ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2022/02/17-01:44:09-GMT BuildTimeStamp: Oct 29 2018 00:06:18 Id: $Id: mri_label2label.c,v 1.50 2016/12/10 22:57:43 fischl Exp $ User: uqhdemp1 Machine: inode2.hpc.dc.uq.edu.au Platform: Linux PlatformVersion: 3.10.0-1160.36.2.el7.x86_64 CompilerName: GCC CompilerVersion: 40800 ProgramName: mri_label2vol ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2022/02/17-01:44:09-GMT BuildTimeStamp: Oct 29 2018 00:06:18 Id: $Id: mri_label2vol.c,v 1.46 2014/12/08 21:11:54 greve Exp $ User: uqhdemp1 Machine: inode2.hpc.dc.uq.edu.au Platform: Linux PlatformVersion: 3.10.0-1160.36.2.el7.x86_64 CompilerName: GCC CompilerVersion: 40800 ProgramName: mri_log_likelihood ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2022/02/17-01:44:09-GMT BuildTimeStamp: Oct 29 2018 00:06:18 Id: $Id: mri_log_likelihood.c,v 1.4 2011/03/02 00:04:22 nicks Exp $ User: uqhdemp1 Machine: inode2.hpc.dc.uq.edu.au Platform: Linux PlatformVersion: 3.10.0-1160.36.2.el7.x86_64 CompilerName: GCC CompilerVersion: 40800 ProgramName: mri_mask ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2022/02/17-01:44:09-GMT BuildTimeStamp: Oct 29 2018 00:06:18 Id: $Id: mri_mask.c,v 1.24 2016/11/28 20:30:57 fischl Exp $ User: uqhdemp1 Machine: inode2.hpc.dc.uq.edu.au Platform: Linux PlatformVersion: 3.10.0-1160.36.2.el7.x86_64 CompilerName: GCC CompilerVersion: 40800 ProgramName: mri_matrix_multiply ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2022/02/17-01:44:09-GMT BuildTimeStamp: Oct 29 2018 00:06:18 Id: $Id: mri_matrix_multiply.c,v 1.13 2011/03/02 00:04:23 nicks Exp $ User: uqhdemp1 Machine: inode2.hpc.dc.uq.edu.au Platform: Linux PlatformVersion: 3.10.0-1160.36.2.el7.x86_64 CompilerName: GCC CompilerVersion: 40800 ProgramName: mri_normalize ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2022/02/17-01:44:09-GMT BuildTimeStamp: Oct 29 2018 00:06:18 Id: $Id: mri_normalize.c,v 1.92 2017/01/27 22:31:34 ah221 Exp $ User: uqhdemp1 Machine: inode2.hpc.dc.uq.edu.au Platform: Linux PlatformVersion: 3.10.0-1160.36.2.el7.x86_64 CompilerName: GCC CompilerVersion: 40800 ProgramName: mri_normalize_tp2 ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2022/02/17-01:44:09-GMT BuildTimeStamp: Oct 29 2018 00:06:18 Id: $Id: mri_normalize_tp2.c,v 1.8 2011/03/02 00:04:23 nicks Exp $ User: uqhdemp1 Machine: inode2.hpc.dc.uq.edu.au Platform: Linux PlatformVersion: 3.10.0-1160.36.2.el7.x86_64 CompilerName: GCC CompilerVersion: 40800 ProgramName: mri_or ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2022/02/17-01:44:09-GMT BuildTimeStamp: Oct 29 2018 00:06:18 Id: $Id: mri_or.c,v 1.5 2013/03/20 15:03:29 lzollei Exp $ User: uqhdemp1 Machine: inode2.hpc.dc.uq.edu.au Platform: Linux PlatformVersion: 3.10.0-1160.36.2.el7.x86_64 CompilerName: GCC CompilerVersion: 40800 ProgramName: mri_relabel_hypointensities ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2022/02/17-01:44:09-GMT BuildTimeStamp: Oct 29 2018 00:06:18 Id: $Id: mri_relabel_hypointensities.c,v 1.13 2015/05/15 18:44:10 nicks Exp $ User: uqhdemp1 Machine: inode2.hpc.dc.uq.edu.au Platform: Linux PlatformVersion: 3.10.0-1160.36.2.el7.x86_64 CompilerName: GCC CompilerVersion: 40800 ProgramName: mri_relabel_nonwm_hypos ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2022/02/17-01:44:09-GMT BuildTimeStamp: Oct 29 2018 00:06:18 Id: $Id: mri_relabel_nonwm_hypos.c,v 1.2 2014/04/17 18:03:22 greve Exp $ User: uqhdemp1 Machine: inode2.hpc.dc.uq.edu.au Platform: Linux PlatformVersion: 3.10.0-1160.36.2.el7.x86_64 CompilerName: GCC CompilerVersion: 40800 ProgramName: mri_remove_neck ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2022/02/17-01:44:09-GMT BuildTimeStamp: Oct 29 2018 00:06:18 Id: $Id: mri_remove_neck.c,v 1.10 2011/03/02 00:04:24 nicks Exp $ User: uqhdemp1 Machine: inode2.hpc.dc.uq.edu.au Platform: Linux PlatformVersion: 3.10.0-1160.36.2.el7.x86_64 CompilerName: GCC CompilerVersion: 40800 $Id: mri_robust_register.cpp,v 1.77 2016/01/20 23:36:17 greve Exp $ ProgramName: mri_robust_register ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2022/02/17-01:44:09-GMT BuildTimeStamp: Oct 29 2018 00:06:18 Id: $Id: mri_robust_register.cpp,v 1.77 2016/01/20 23:36:17 greve Exp $ User: uqhdemp1 Machine: inode2.hpc.dc.uq.edu.au Platform: Linux PlatformVersion: 3.10.0-1160.36.2.el7.x86_64 CompilerName: GCC CompilerVersion: 40800 $Id: mri_robust_template.cpp,v 1.54 2016/05/05 21:17:08 mreuter Exp $ ProgramName: mri_robust_template ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2022/02/17-01:44:09-GMT BuildTimeStamp: Oct 29 2018 00:06:18 Id: $Id: mri_robust_template.cpp,v 1.54 2016/05/05 21:17:08 mreuter Exp $ User: uqhdemp1 Machine: inode2.hpc.dc.uq.edu.au Platform: Linux PlatformVersion: 3.10.0-1160.36.2.el7.x86_64 CompilerName: GCC CompilerVersion: 40800 ProgramName: mris_anatomical_stats ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2022/02/17-01:44:09-GMT BuildTimeStamp: Oct 29 2018 00:06:18 Id: $Id: mris_anatomical_stats.c,v 1.79 2016/03/14 15:15:34 greve Exp $ User: uqhdemp1 Machine: inode2.hpc.dc.uq.edu.au Platform: Linux PlatformVersion: 3.10.0-1160.36.2.el7.x86_64 CompilerName: GCC CompilerVersion: 40800 ProgramName: mris_ca_label ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2022/02/17-01:44:09-GMT BuildTimeStamp: Oct 29 2018 00:06:18 Id: $Id: mris_ca_label.c,v 1.37 2014/02/04 17:46:42 fischl Exp $ User: uqhdemp1 Machine: inode2.hpc.dc.uq.edu.au Platform: Linux PlatformVersion: 3.10.0-1160.36.2.el7.x86_64 CompilerName: GCC CompilerVersion: 40800 ProgramName: mris_calc ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2022/02/17-01:44:09-GMT BuildTimeStamp: Oct 29 2018 00:06:18 Id: $Id: mris_calc.c,v 1.55 2016/09/27 18:50:16 greve Exp $ User: uqhdemp1 Machine: inode2.hpc.dc.uq.edu.au Platform: Linux PlatformVersion: 3.10.0-1160.36.2.el7.x86_64 CompilerName: GCC CompilerVersion: 40800 ProgramName: mris_convert ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2022/02/17-01:44:09-GMT BuildTimeStamp: Oct 29 2018 00:06:18 Id: $Id$ User: uqhdemp1 Machine: inode2.hpc.dc.uq.edu.au Platform: Linux PlatformVersion: 3.10.0-1160.36.2.el7.x86_64 CompilerName: GCC CompilerVersion: 40800 ProgramName: mris_curvature ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2022/02/17-01:44:09-GMT BuildTimeStamp: Oct 29 2018 00:06:18 Id: $Id: mris_curvature.c,v 1.31 2011/03/02 00:04:30 nicks Exp $ User: uqhdemp1 Machine: inode2.hpc.dc.uq.edu.au Platform: Linux PlatformVersion: 3.10.0-1160.36.2.el7.x86_64 CompilerName: GCC CompilerVersion: 40800 ProgramName: mris_curvature_stats ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2022/02/17-01:44:09-GMT BuildTimeStamp: Oct 29 2018 00:06:18 Id: $Id: mris_curvature_stats.c,v 1.65 2015/06/04 20:50:51 nicks Exp $ User: uqhdemp1 Machine: inode2.hpc.dc.uq.edu.au Platform: Linux PlatformVersion: 3.10.0-1160.36.2.el7.x86_64 CompilerName: GCC CompilerVersion: 40800 ProgramName: mris_diff ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2022/02/17-01:44:09-GMT BuildTimeStamp: Oct 29 2018 00:06:18 Id: $Id: mris_diff.c,v 1.20 2014/03/21 23:57:48 greve Exp $ User: uqhdemp1 Machine: inode2.hpc.dc.uq.edu.au Platform: Linux PlatformVersion: 3.10.0-1160.36.2.el7.x86_64 CompilerName: GCC CompilerVersion: 40800 ProgramName: mris_divide_parcellation ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2022/02/17-01:44:09-GMT BuildTimeStamp: Oct 29 2018 00:06:18 Id: $Id: mris_divide_parcellation.c,v 1.12 2012/10/24 19:50:06 maritza Exp $ User: uqhdemp1 Machine: inode2.hpc.dc.uq.edu.au Platform: Linux PlatformVersion: 3.10.0-1160.36.2.el7.x86_64 CompilerName: GCC CompilerVersion: 40800 ProgramName: mri_segment ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2022/02/17-01:44:09-GMT BuildTimeStamp: Oct 29 2018 00:06:18 Id: $Id: mri_segment.c,v 1.44 2016/10/22 17:29:37 fischl Exp $ User: uqhdemp1 Machine: inode2.hpc.dc.uq.edu.au Platform: Linux PlatformVersion: 3.10.0-1160.36.2.el7.x86_64 CompilerName: GCC CompilerVersion: 40800 ProgramName: mri_segstats ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2022/02/17-01:44:09-GMT BuildTimeStamp: Oct 29 2018 00:06:18 Id: $Id: mri_segstats.c,v 1.122 2017/01/23 18:23:14 greve Exp $ User: uqhdemp1 Machine: inode2.hpc.dc.uq.edu.au Platform: Linux PlatformVersion: 3.10.0-1160.36.2.el7.x86_64 CompilerName: GCC CompilerVersion: 40800 ProgramName: mris_euler_number ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2022/02/17-01:44:09-GMT BuildTimeStamp: Oct 29 2018 00:06:18 Id: $Id: mris_euler_number.c,v 1.10 2013/01/14 22:39:14 greve Exp $ User: uqhdemp1 Machine: inode2.hpc.dc.uq.edu.au Platform: Linux PlatformVersion: 3.10.0-1160.36.2.el7.x86_64 CompilerName: GCC CompilerVersion: 40800 ProgramName: mris_fix_topology ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2022/02/17-01:44:09-GMT BuildTimeStamp: Oct 29 2018 00:06:18 Id: $Id: mris_fix_topology.c,v 1.51 2016/10/27 19:43:58 fischl Exp $ User: uqhdemp1 Machine: inode2.hpc.dc.uq.edu.au Platform: Linux PlatformVersion: 3.10.0-1160.36.2.el7.x86_64 CompilerName: GCC CompilerVersion: 40800 ProgramName: mris_topo_fixer ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2022/02/17-01:44:09-GMT BuildTimeStamp: Oct 29 2018 00:06:18 Id: $Id: mris_topo_fixer.cpp,v 1.29 2011/03/02 00:04:34 nicks Exp $ User: uqhdemp1 Machine: inode2.hpc.dc.uq.edu.au Platform: Linux PlatformVersion: 3.10.0-1160.36.2.el7.x86_64 CompilerName: GCC CompilerVersion: 40800 ProgramName: mris_jacobian ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2022/02/17-01:44:09-GMT BuildTimeStamp: Oct 29 2018 00:06:18 Id: $Id: mris_jacobian.c,v 1.11 2015/02/05 23:34:40 zkaufman Exp $ User: uqhdemp1 Machine: inode2.hpc.dc.uq.edu.au Platform: Linux PlatformVersion: 3.10.0-1160.36.2.el7.x86_64 CompilerName: GCC CompilerVersion: 40800 ProgramName: mris_label2annot ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2022/02/17-01:44:09-GMT BuildTimeStamp: Oct 29 2018 00:06:18 Id: $Id: mris_label2annot.c,v 1.20 2016/01/07 23:28:11 greve Exp $ User: uqhdemp1 Machine: inode2.hpc.dc.uq.edu.au Platform: Linux PlatformVersion: 3.10.0-1160.36.2.el7.x86_64 CompilerName: GCC CompilerVersion: 40800 ProgramName: mris_left_right_register ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2022/02/17-01:44:09-GMT BuildTimeStamp: Oct 29 2018 00:06:18 Id: $Id: mris_left_right_register.c,v 1.2 2011/12/16 20:49:37 greve Exp $ User: uqhdemp1 Machine: inode2.hpc.dc.uq.edu.au Platform: Linux PlatformVersion: 3.10.0-1160.36.2.el7.x86_64 CompilerName: GCC CompilerVersion: 40800 ProgramName: mris_make_surfaces ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2022/02/17-01:44:09-GMT BuildTimeStamp: Oct 29 2018 00:06:18 Id: $Id: mris_make_surfaces.c,v 1.172 2017/02/16 19:42:36 fischl Exp $ User: uqhdemp1 Machine: inode2.hpc.dc.uq.edu.au Platform: Linux PlatformVersion: 3.10.0-1160.36.2.el7.x86_64 CompilerName: GCC CompilerVersion: 40800 ProgramName: mrisp_paint ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2022/02/17-01:44:09-GMT BuildTimeStamp: Oct 29 2018 00:06:18 Id: $Id: mrisp_paint.c,v 1.12 2016/03/22 14:47:57 fischl Exp $ User: uqhdemp1 Machine: inode2.hpc.dc.uq.edu.au Platform: Linux PlatformVersion: 3.10.0-1160.36.2.el7.x86_64 CompilerName: GCC CompilerVersion: 40800 ProgramName: mris_register ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2022/02/17-01:44:09-GMT BuildTimeStamp: Oct 29 2018 00:06:18 Id: $Id: mris_register.c,v 1.64 2017/02/07 19:04:44 fischl Exp $ User: uqhdemp1 Machine: inode2.hpc.dc.uq.edu.au Platform: Linux PlatformVersion: 3.10.0-1160.36.2.el7.x86_64 CompilerName: GCC CompilerVersion: 40800 ProgramName: mris_smooth ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2022/02/17-01:44:09-GMT BuildTimeStamp: Oct 29 2018 00:06:18 Id: $Id: mris_smooth.c,v 1.30 2014/01/21 18:48:21 fischl Exp $ User: uqhdemp1 Machine: inode2.hpc.dc.uq.edu.au Platform: Linux PlatformVersion: 3.10.0-1160.36.2.el7.x86_64 CompilerName: GCC CompilerVersion: 40800 ProgramName: mris_sphere ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2022/02/17-01:44:09-GMT BuildTimeStamp: Oct 29 2018 00:06:18 Id: $Id: mris_sphere.c,v 1.62 2017/02/07 19:04:37 fischl Exp $ User: uqhdemp1 Machine: inode2.hpc.dc.uq.edu.au Platform: Linux PlatformVersion: 3.10.0-1160.36.2.el7.x86_64 CompilerName: GCC CompilerVersion: 40800 ProgramName: mris_surface_stats ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2022/02/17-01:44:09-GMT BuildTimeStamp: Oct 29 2018 00:06:18 Id: $Id: mris_surface_stats.c,v 1.10 2011/03/02 00:04:34 nicks Exp $ User: uqhdemp1 Machine: inode2.hpc.dc.uq.edu.au Platform: Linux PlatformVersion: 3.10.0-1160.36.2.el7.x86_64 CompilerName: GCC CompilerVersion: 40800 ProgramName: mri_stats2seg ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2022/02/17-01:44:09-GMT BuildTimeStamp: Oct 29 2018 00:06:18 Id: $Id: mri_stats2seg.c,v 1.9 2011/03/02 00:04:24 nicks Exp $ User: uqhdemp1 Machine: inode2.hpc.dc.uq.edu.au Platform: Linux PlatformVersion: 3.10.0-1160.36.2.el7.x86_64 CompilerName: GCC CompilerVersion: 40800 ProgramName: mris_thickness ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2022/02/17-01:44:09-GMT BuildTimeStamp: Oct 29 2018 00:06:18 Id: $Id: mris_thickness.c,v 1.28 2012/11/27 17:41:26 fischl Exp $ User: uqhdemp1 Machine: inode2.hpc.dc.uq.edu.au Platform: Linux PlatformVersion: 3.10.0-1160.36.2.el7.x86_64 CompilerName: GCC CompilerVersion: 40800 ProgramName: mris_thickness_diff ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2022/02/17-01:44:09-GMT BuildTimeStamp: Oct 29 2018 00:06:18 Id: $Id: mris_thickness_diff.c,v 1.16 2011/03/02 00:04:34 nicks Exp $ User: uqhdemp1 Machine: inode2.hpc.dc.uq.edu.au Platform: Linux PlatformVersion: 3.10.0-1160.36.2.el7.x86_64 CompilerName: GCC CompilerVersion: 40800 ProgramName: mris_topo_fixer ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2022/02/17-01:44:09-GMT BuildTimeStamp: Oct 29 2018 00:06:18 Id: $Id: mris_topo_fixer.cpp,v 1.29 2011/03/02 00:04:34 nicks Exp $ User: uqhdemp1 Machine: inode2.hpc.dc.uq.edu.au Platform: Linux PlatformVersion: 3.10.0-1160.36.2.el7.x86_64 CompilerName: GCC CompilerVersion: 40800 ProgramName: mri_surf2surf ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2022/02/17-01:44:09-GMT BuildTimeStamp: Oct 29 2018 00:06:18 Id: $Id: mri_surf2surf.c,v 1.103 2015/11/05 22:07:33 greve Exp $ User: uqhdemp1 Machine: inode2.hpc.dc.uq.edu.au Platform: Linux PlatformVersion: 3.10.0-1160.36.2.el7.x86_64 CompilerName: GCC CompilerVersion: 40800 ProgramName: mri_surf2vol ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2022/02/17-01:44:09-GMT BuildTimeStamp: Oct 29 2018 00:06:18 Id: $Id: mri_surf2vol.c,v 1.28 2014/12/08 19:49:02 greve Exp $ User: uqhdemp1 Machine: inode2.hpc.dc.uq.edu.au Platform: Linux PlatformVersion: 3.10.0-1160.36.2.el7.x86_64 CompilerName: GCC CompilerVersion: 40800 ProgramName: mri_surfcluster ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2022/02/17-01:44:09-GMT BuildTimeStamp: Oct 29 2018 00:06:18 Id: $Id: mri_surfcluster.c,v 1.60 2016/11/01 19:49:22 greve Exp $ User: uqhdemp1 Machine: inode2.hpc.dc.uq.edu.au Platform: Linux PlatformVersion: 3.10.0-1160.36.2.el7.x86_64 CompilerName: GCC CompilerVersion: 40800 ProgramName: mris_volmask ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2022/02/17-01:44:09-GMT BuildTimeStamp: Oct 29 2018 00:06:18 Id: $Id: mris_volmask.cpp,v 1.28 2016/11/18 19:19:29 fischl Exp $ User: uqhdemp1 Machine: inode2.hpc.dc.uq.edu.au Platform: Linux PlatformVersion: 3.10.0-1160.36.2.el7.x86_64 CompilerName: GCC CompilerVersion: 40800 ProgramName: mri_tessellate ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2022/02/17-01:44:09-GMT BuildTimeStamp: Oct 29 2018 00:06:18 Id: $Id: mri_tessellate.c,v 1.39 2016/07/20 21:05:04 zkaufman Exp $ User: uqhdemp1 Machine: inode2.hpc.dc.uq.edu.au Platform: Linux PlatformVersion: 3.10.0-1160.36.2.el7.x86_64 CompilerName: GCC CompilerVersion: 40800 ProgramName: mri_vol2surf ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2022/02/17-01:44:09-GMT BuildTimeStamp: Oct 29 2018 00:06:18 Id: $Id: mri_vol2surf.c,v 1.68 2014/05/30 20:58:47 greve Exp $ User: uqhdemp1 Machine: inode2.hpc.dc.uq.edu.au Platform: Linux PlatformVersion: 3.10.0-1160.36.2.el7.x86_64 CompilerName: GCC CompilerVersion: 40800 ProgramName: mri_vol2vol ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2022/02/17-01:44:09-GMT BuildTimeStamp: Oct 29 2018 00:06:18 Id: $Id: mri_vol2vol.c,v 1.89 2016/06/22 22:33:40 fischl Exp $ User: uqhdemp1 Machine: inode2.hpc.dc.uq.edu.au Platform: Linux PlatformVersion: 3.10.0-1160.36.2.el7.x86_64 CompilerName: GCC CompilerVersion: 40800 ProgramName: mri_voldiff ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2022/02/17-01:44:09-GMT BuildTimeStamp: Oct 29 2018 00:06:18 Id: $Id: mri_voldiff.c,v 1.6 2011/03/02 00:04:25 nicks Exp $ User: uqhdemp1 Machine: inode2.hpc.dc.uq.edu.au Platform: Linux PlatformVersion: 3.10.0-1160.36.2.el7.x86_64 CompilerName: GCC CompilerVersion: 40800 ProgramName: mri_watershed ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2022/02/17-01:44:09-GMT BuildTimeStamp: Oct 29 2018 00:06:18 Id: $Id: mri_watershed.cpp,v 1.103 2016/06/17 18:00:49 zkaufman Exp $ User: uqhdemp1 Machine: inode2.hpc.dc.uq.edu.au Platform: Linux PlatformVersion: 3.10.0-1160.36.2.el7.x86_64 CompilerName: GCC CompilerVersion: 40800 ProgramName: tkregister2_cmdl ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2022/02/17-01:44:09-GMT BuildTimeStamp: Oct 29 2018 00:06:18 Id: $Id: tkregister2.c,v 1.133 2016/08/02 21:17:11 greve Exp $ User: uqhdemp1 Machine: inode2.hpc.dc.uq.edu.au Platform: Linux PlatformVersion: 3.10.0-1160.36.2.el7.x86_64 CompilerName: GCC CompilerVersion: 40800 $Id: mri_motion_correct.fsl,v 1.15 2016/02/16 17:17:20 zkaufman Exp $ mri_convert -all-info ProgramName: mri_convert ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2022/02/17-01:44:10-GMT BuildTimeStamp: Oct 29 2018 00:06:18 Id: $Id: mri_convert.c,v 1.227 2017/02/16 19:15:42 greve Exp $ User: uqhdemp1 Machine: inode2.hpc.dc.uq.edu.au Platform: Linux PlatformVersion: 3.10.0-1160.36.2.el7.x86_64 CompilerName: GCC CompilerVersion: 40800 FLIRT version 6.0 Program nu_correct, built from: Package MNI N3, version 1.12.0, compiled by nicks@terrier (x86_64-unknown-linux-gnu) on 2015-06-19 at 01:25:34 ####################################### GCADIR /opt/ohpc/pub/apps/freesurfer/average GCA RB_all_2016-05-10.vc700.gca GCASkull RB_all_withskull_2016-05-10.vc700.gca AvgCurvTif folding.atlas.acfb40.noaparc.i12.2016-08-02.tif GCSDIR /opt/ohpc/pub/apps/freesurfer/average GCS DKaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs ####################################### -cw256 option is now persistent (remove with -clean-cw256) /scratch/inode/uqhdemp1/Surfaces/P00_FG_3dD_cw_try2 mri_convert /scratch/inode/uqhdemp1/Fingertip_maps/P00_FG/P00_FG.results/FG_uniden_avg_wholebrain_unpad_warped_3dQ.nii /scratch/inode/uqhdemp1/Surfaces/P00_FG_3dD_cw_try2/mri/orig/001.mgz mri_convert /scratch/inode/uqhdemp1/Fingertip_maps/P00_FG/P00_FG.results/FG_uniden_avg_wholebrain_unpad_warped_3dQ.nii /scratch/inode/uqhdemp1/Surfaces/P00_FG_3dD_cw_try2/mri/orig/001.mgz $Id: mri_convert.c,v 1.227 2017/02/16 19:15:42 greve Exp $ reading from /scratch/inode/uqhdemp1/Fingertip_maps/P00_FG/P00_FG.results/FG_uniden_avg_wholebrain_unpad_warped_3dQ.nii... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-0, -1, 0) j_ras = (-0, -0, -1) k_ras = (1, -0, 0) writing to /scratch/inode/uqhdemp1/Surfaces/P00_FG_3dD_cw_try2/mri/orig/001.mgz... #-------------------------------------------- #@# MotionCor Thu Feb 17 11:44:30 AEST 2022 Found 1 runs /scratch/inode/uqhdemp1/Surfaces/P00_FG_3dD_cw_try2/mri/orig/001.mgz Checking for (invalid) multi-frame inputs... Only one run found so motion correction will not be performed. I'll copy the run to rawavg and continue. cp /scratch/inode/uqhdemp1/Surfaces/P00_FG_3dD_cw_try2/mri/orig/001.mgz /scratch/inode/uqhdemp1/Surfaces/P00_FG_3dD_cw_try2/mri/rawavg.mgz /scratch/inode/uqhdemp1/Surfaces/P00_FG_3dD_cw_try2 mri_convert /scratch/inode/uqhdemp1/Surfaces/P00_FG_3dD_cw_try2/mri/rawavg.mgz /scratch/inode/uqhdemp1/Surfaces/P00_FG_3dD_cw_try2/mri/orig.mgz --conform_min mri_convert /scratch/inode/uqhdemp1/Surfaces/P00_FG_3dD_cw_try2/mri/rawavg.mgz /scratch/inode/uqhdemp1/Surfaces/P00_FG_3dD_cw_try2/mri/orig.mgz --conform_min $Id: mri_convert.c,v 1.227 2017/02/16 19:15:42 greve Exp $ reading from /scratch/inode/uqhdemp1/Surfaces/P00_FG_3dD_cw_try2/mri/rawavg.mgz... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-0, -1, 0) j_ras = (-0, -0, -1) k_ras = (1, -0, 0) changing data type from float to uchar (noscale = 0)... MRIchangeType: Building histogram 0 4078 1000, flo=0, fhi=0.999, dest_type=0 Reslicing using trilinear interpolation writing to /scratch/inode/uqhdemp1/Surfaces/P00_FG_3dD_cw_try2/mri/orig.mgz... **************************************** ERROR! FOV=273.000 > 256 Include the flag -cw256 with recon-all! Inspect orig.mgz to ensure the head is fully visible. **************************************** Linux inode2.hpc.dc.uq.edu.au 3.10.0-1160.36.2.el7.x86_64 #1 SMP Wed Jul 21 11:57:15 UTC 2021 x86_64 x86_64 x86_64 GNU/Linux recon-all -s P00_FG_3dD_cw_try2 exited with ERRORS at Thu Feb 17 11:45:38 AEST 2022 To report a problem, see http://secure-web.cisco.com/1EazoIQDEQ5C0xk6kgC_HrVs1qLbDRhir6_Z00m8PdXgaaA… From: freesurfer-bounces(a)nmr.mgh.harvard.edu <freesurfer-bounces(a)nmr.mgh.harvard.edu> on behalf of Douglas N. Greve <dgreve(a)MGH.HARVARD.EDU> Date: Monday, 14 February 2022 at 8:35 am To: freesurfer(a)nmr.mgh.harvard.edu <freesurfer(a)nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] -cw256 flag Yes, this is ok. This was a bit of a hack that someone introduced into recon-all a number of years ago, and we have not gotten around to fixing it. On 2/8/2022 7:25 PM, Harriet Dempsey-Jones wrote: External Email - Use Caution Hi there, I am using AFNI to process some epi data. As part of this analysis, I am creating anatomical surfaces on which to project my data using recon-all in Freesurfer. My pre-processing in AFNI indicated that best alignment of my epi to anatomical image is achieved using a combination of affine and non-linear warping (3dQwarp in AFNI). So I was hoping to use this warped anatomical image from my experimental data to create a surface from with recon-all. I just tried to set this to run, and it errored and failed (see bottom of email) The gist appears to be that when it was completing the mri_convert stage it errored because the anatomical nifti image I had fed it, was not 256 FOV. It appears to be larger because I had to add some space to the image to rotate it during alignment. The error suggests using the flag -cw256 with recon-all, but I cannot find any documentation about how this works or what it does. I searched the forum archives as well, which came up with 60k hits, but none of them seemed to contain -cw256 when I control+f looking for it. Could someone let me know a bit more about this flag and whether it is ok to use for my purposes? I have included my recon-all code too for reference purposes. Please also let me know if there is anything glaringly wrong there, I am very new to fMRI analysis. Thank you for any help you might be able to give me! ERROR -------------------- mri_convert /scratch/inode/uqhdemp1/Surfaces/P00_FG/mri/rawavg.mgz /scratch/inode/uqhdemp1/Surfaces/P00_FG/mri/orig.mgz --conform_min $Id: mri_convert.c,v 1.227 2017/02/16 19:15:42 greve Exp $ reading from /scratch/inode/uqhdemp1/Surfaces/P00_FG/mri/rawavg.mgz... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-0, -1, 0) j_ras = (-0, -0, -1) k_ras = (1, -0, 0) changing data type from float to uchar (noscale = 0)... MRIchangeType: Building histogram 0 4078 1000, flo=0, fhi=0.999, dest_type=0 Reslicing using trilinear interpolation writing to /scratch/inode/uqhdemp1/Surfaces/P00_FG/mri/orig.mgz... **************************************** ERROR! FOV=273.000 > 256 Include the flag -cw256 with recon-all! Inspect orig.mgz to ensure the head is fully visible. **************************************** Linux inode2.hpc.dc.uq.edu.au 3.10.0-1160.36.2.el7.x86_64 #1 SMP Wed Jul 21 11:57:15 UTC 2021 x86_64 x86_64 x86_64 GNU/Linux recon-all -s P00_FG exited with ERRORS at Tue Feb 8 22:13:53 AEST 2022 MY CODE -------------------------- #!bin/tcsh # Freesurfer start-up module load freesurfer # Set up vars set subj_init = FG set subj_num = P00 set subj = {$subj_num}_{$subj_init} set recon_use = (-all) # set recon_use = (-autorecon1) set anat = /scratch/inode/uqhdemp1/Fingertip_maps/{$subj}/{$subj}.results/{$subj_init}_uniden_avg_wholebrain_unpad_warped_3dQ.nii set base_dir = /scratch/inode/ set subj = {$subj_num}_{$subj_init} set expert_file = 1b_FS_expertfile ## 1. Freesurfer recon all recon-all $recon_use -s $subj -hires -i $anat -sd $base_dir/Surfaces -openmp 12 -expert $base_dir/Parent_scripts/Surfaces/$expert_file [cid:part1.ftNxeNKN.hsfFhubR@mgh.harvard.edu] _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu> https://secure-web.cisco.com/1IMQWa_W4wyvJiMeYdk5Wm4RkRuM-ROCNyZy_2dYYZpvEx…

1 0

Re: [Freesurfer] Get the password by sending an email request to the freesurfer help list. - Freesurfer VirtualBox Image
by fsbuild 16 Feb '22

16 Feb '22

External Email - Use Caution Sending the info to your email shortly. - R. On Feb 16, 2022, at 10:02, Cristina Pereira Priego <cristinapereira_31(a)hotmail.com> wrote:        External Email - Use Caution        Hi,My name is Cristina and I'm a PhD Student from Clinical Neurosciences Group in IRB LLEIDA. I downloaded " Freesurfer VirtualBox Image" and I need the paswword to login as the user "developer" in the login menu. I'm waiting for your answer,Best regards,Cristina _______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

1 0

Jump to page:

2026

2025

2024

2023

2022

2021

2020

2019

2018

2017

2016

2015

2014

2013

2012

2011

2010

2009

2008

2007

2006

2005

2004

Freesurfer