External Email - Use Caution
Yes, you are right. I saw the error.
I have been running one of the participants and here it is the report.log.
Also, because these kind of participants are special, I used some bet
parameters to run the skull-stripping. This is the main reason why I did
not run recon all -all. I would like to replace the skull stripped image by
my betted one. Is this right?
Thanks,
Rosalia
On Thu, Oct 18, 2018 at 7:47 PM Bruce Fischl <fis...@nmr.mgh.harvard.edu>
wrote:
> Hi Rosalia
>
> -i must point to a file that you want to import, usually a single dicom
> file in the correct (e.g. mprage) series.
> cheers
> Bruce
> On Thu, 18 Oct 2018, Rosalia
> Dacosta Aguayo wrote:
>
> >
> > External Email - Use Caution
> >
> > Hi Bruce,
> >
> > There is not recon-all.log.
> >
> > The full command line is:
> > rosalia@rosalia-Lenovo-Y520-15IKBN ~/Desktop/MS_STUDY/subjects $
> recon-all -sd
> > ~/Desktop/MS_STUDY/subjects -s 001 -i
> /home/rosalia/Desktop/MS_STUDY/subjects/MS001/mri -autorecon1
> > ERROR: You cannot give recon-all a folder as input. It must be an image
> file.
> > If you have multiple files, you need multiple -i flags.
> > Linux rosalia-Lenovo-Y520-15IKBN 4.10.0-40-generic #44~16.04.1-Ubuntu
> SMP Thu Nov 9 15:37:44 UTC
> > 2017 x86_64 x86_64 x86_64 GNU/Linux
> >
> > recon-all -s 001 exited with ERRORS at Thu 18 Oct 19:13:35 CEST 2018
> >
> > For more details, see the log file
> > To report a problem, see
> http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
> >
> > rosalia@rosalia-Lenovo-Y520-15IKBN ~/Desktop/MS_STUDY/subjects $
> >
> >
> >
> > On Thu, Oct 18, 2018 at 7:11 PM Bruce Fischl <fis...@nmr.mgh.harvard.edu>
> wrote:
> > Hi Rosalia
> >
> > can you send us the full command line, screen output and
> recon-all.log?
> > In the arrangement you show below it would be:
> >
> > recon-all -sd ~/Desktop/MS_STUDY/subjects -s 001 -i <path to dicom
> file> -all
> >
> > cheers
> > Bruce
> > On Thu, 18 Oct 2018, Rosalia
> > Dacosta Aguayo wrote:
> >
> > >
> > > External Email - Use Caution
> > >
> > > Hi Bruce,
> > >
> > > Thank you very much for answering my questions.
> > > This is how I have organized my subject_dir for one subject so
> you can see better. It
> > is still not
> > > working.
> > > rosalia@rosalia-Lenovo-Y520-15IKBN ~/Desktop/MS_STUDY/subjects
> $ ls
> > > FOLDERS S_011.nii.gz S_020.nii.gz S_028.nii.gz
> S_041.nii.gz
> > > MS001 S_012.nii.gz S_021.nii.gz S_029.nii.gz
> S_042.nii.gz
> > > S_004.nii.gz S_013.nii.gz S_022.nii.gz S_030.nii.gz
> S_043.nii.gz
> > > S_005.nii.gz S_014.nii.gz S_023.nii.gz S_031.nii.gz
> S_044.nii.gz
> > > S_006.nii.gz S_015.nii.gz S_024.nii.gz S_032.nii.gz
> S_045.nii.gz
> > > S_008.nii.gz S_016.nii.gz S_025.nii.gz S_033.nii.gz
> S_046.nii.gz
> > > S_009.nii.gz S_017.nii.gz S_026.nii.gz S_034.nii.gz
> S_047.nii.gz
> > > S_010.nii.gz S_018.nii.gz S_027.nii.gz S_040.nii.gz SCRIPTS
> > > rosalia@rosalia-Lenovo-Y520-15IKBN ~/Desktop/MS_STUDY/subjects
> $ cd MS001/
> > > rosalia@rosalia-Lenovo-Y520-15IKBN
> ~/Desktop/MS_STUDY/subjects/MS001 $ ls
> > > mri orig
> > > rosalia@rosalia-Lenovo-Y520-15IKBN
> ~/Desktop/MS_STUDY/subjects/MS001 $ cd mri/
> > > rosalia@rosalia-Lenovo-Y520-15IKBN
> ~/Desktop/MS_STUDY/subjects/MS001/mri $ ls
> > > 001.nii.gz
> > > rosalia@rosalia-Lenovo-Y520-15IKBN
> ~/Desktop/MS_STUDY/subjects/MS001/mri $ cd
> > > ..rosalia@rosalia-Lenovo-Y520-15IKBN
> ~/Desktop/MS_STUDY/subjects/MS001 $ cd orig
> > > rosalia@rosalia-Lenovo-Y520-15IKBN
> ~/Desktop/MS_STUDY/subjects/MS001/orig $ ls
> > > 001.nii.gz
> > > rosalia@rosalia-Lenovo-Y520-15IKBN
> ~/Desktop/MS_STUDY/subjects/MS001/orig $
> > >
> > > Regards,
> > > Rosalia
> > >
> > > On Thu, Oct 18, 2018 at 6:55 PM Bruce Fischl <
> fis...@nmr.mgh.harvard.edu> wrote:
> > > Hi Rosalia
> > >
> > > you either need to give recon-all an input file (or more
> than one) with the
> > > -i switch, or create the subject directory tree under
> SUBJECTS_DIR for that
> > > subject, and put a file named 001.mgz in the mri/orig
> subdir. Note you can
> > > also specify SUBJECTS_DIR explicitly on the recon-all
> command line with -sd
> > <dir>
> > > if you don't want to put it in the environment.
> > >
> > > That is, try this:
> > >
> > > recon-all -s 001 -autorecon1 -sd ~/Desktop/subjects
> > >
> > > cheers
> > > Bruce
> > >
> > > On Thu, 18 Oct 2018, Rosalia Dacosta Aguayo wrote:
> > >
> > > >
> > > > External Email - Use Caution
> > > >
> > > > Dear Free Surfer team,
> > > >
> > > > Surely this is a basic question but I am having a
> trouble setting the
> > subjects_dir in
> > > my terminal
> > > > and, as a result, any of the commands work.
> > > >
> > > > This is how I have my Free Surfer configurated in my
> computer:
> > > >
> > > > --------
> freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c --------
> > > > Setting up environment for FreeSurfer/FS-FAST (and FSL)
> > > > FREESURFER_HOME /usr/local/freesurfer
> > > > FSFAST_HOME /usr/local/freesurfer/fsfast
> > > > FSF_OUTPUT_FORMAT nii.gz
> > > > SUBJECTS_DIR /usr/local/freesurfer/subjects
> > > > MNI_DIR /usr/local/freesurfer/mni
> > > > FSL_DIR /usr/share/fsl/5.0
> > >
>
> >-------------------------------------------------------------------------------------------------
> > --
> > >
> > > > -----
> > > >
> > > > As it is, I cannot work in the SUBJECTS_DIR, as it is
> protected.
> > > > I tried to set a new subjects_dir:
> > > > export SUBJECTS_DIR=/home/rosalia/Desktop
> > > >
> > > > Then I try to run the first step (autorecon1) with one
> subject, and it appears
> > the
> > > following error:
> > > > rosalia@rosalia-Lenovo-Y520-15IKBN ~/Desktop/subjects $
> recon-all -s 001
> > -autorecon1
> > > > ERROR: cannot find /usr/local/freesurfer/subjects/001
> > > > rosalia@rosalia-Lenovo-Y520-15IKBN ~/Desktop/subjects $
> > > >
> > > > I have even changed my .bashrc file...but it seems I am
> doing something wrong
> > as my
> > > terminal keeps
> > > > pointing to the same subject_dir.
> > > > I have tried to use sudo so in order to move my folder
> and subfolders to the
> > > subjects_dir set by
> > > > default, and I am experiencing problems as well.
> > > >
> > > > I would much appreciate any help with this basic
> question.
> > > > Kind regards,
> > > > Rosalia
> > > >
> > > >
> > > >
> > > >
> > > >
> > > >_______________________________________________
> > > Freesurfer mailing list
> > > Freesurfer@nmr.mgh.harvard.edu
> > >
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> > >
> > >
> > >_______________________________________________
> > Freesurfer mailing list
> > Freesurfer@nmr.mgh.harvard.edu
> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> >
> >
> >_______________________________________________
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Thu 18 Oct 19:24:44 CEST 2018
/home/rosalia/Desktop/MS_STUDY/subjects/001
/usr/local/freesurfer/bin/recon-all
-sd /home/rosalia/Desktop/MS_STUDY/subjects -s 001 -i /home/rosalia/Desktop/MS_STUDY/subjects/MS001/mri/001.nii.gz -autorecon1
subjid 001
setenv SUBJECTS_DIR /home/rosalia/Desktop/MS_STUDY/subjects
FREESURFER_HOME /usr/local/freesurfer
Actual FREESURFER_HOME /usr/local/freesurfer
build-stamp.txt: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c
Linux rosalia-Lenovo-Y520-15IKBN 4.10.0-40-generic #44~16.04.1-Ubuntu SMP Thu Nov 9 15:37:44 UTC 2017 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 128010
maxlocks unlimited
maxsignal 128010
maxmessage 819200
maxnice 0
maxrtprio 0
maxrttime unlimited
total used free shared buff/cache available
Mem: 32817868 2543052 25213944 545576 5060872 29185684
Swap: 31250428 0 31250428
########################################
program versions used
$Id: recon-all,v 1.580.2.16 2017/01/18 14:11:24 zkaufman Exp $
$Id: mri_motion_correct.fsl,v 1.15 2016/02/16 17:17:20 zkaufman Exp $
mri_convert.bin -all-info
ProgramName: mri_convert.bin ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/10/18-17:24:44-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ User: rosalia Machine: rosalia-Lenovo-Y520-15IKBN Platform: Linux PlatformVersion: 4.10.0-40-generic CompilerName: GCC CompilerVersion: 40400
FLIRT version 5.5
$Id: talairach_avi,v 1.13 2015/12/23 04:25:17 greve Exp $
mri_convert.bin --version
stable6
ProgramName: tkregister2_cmdl ProgramArguments: --all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/10/18-17:24:44-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: tkregister2.c,v 1.132.2.1 2016/08/02 21:17:29 greve Exp $ User: rosalia Machine: rosalia-Lenovo-Y520-15IKBN Platform: Linux PlatformVersion: 4.10.0-40-generic CompilerName: GCC CompilerVersion: 40400
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
ProgramName: mri_make_uchar ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/10/18-17:24:44-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_make_uchar.c,v 1.4 2011/03/02 00:04:14 nicks Exp $ User: rosalia Machine: rosalia-Lenovo-Y520-15IKBN Platform: Linux PlatformVersion: 4.10.0-40-generic CompilerName: GCC CompilerVersion: 40400
ProgramName: mri_normalize ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2018/10/18-17:24:45-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_normalize.c,v 1.88.2.3 2016/12/27 16:47:13 zkaufman Exp $ User: rosalia Machine: rosalia-Lenovo-Y520-15IKBN Platform: Linux PlatformVersion: 4.10.0-40-generic CompilerName: GCC CompilerVersion: 40400
ProgramName: mri_watershed ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/10/18-17:24:45-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_watershed.cpp,v 1.103 2016/06/17 18:00:49 zkaufman Exp $ User: rosalia Machine: rosalia-Lenovo-Y520-15IKBN Platform: Linux PlatformVersion: 4.10.0-40-generic CompilerName: GCC CompilerVersion: 40400
ProgramName: mri_gcut ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/10/18-17:24:45-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_gcut.cpp,v 1.14 2011/03/02 00:04:16 nicks Exp $ User: rosalia Machine: rosalia-Lenovo-Y520-15IKBN Platform: Linux PlatformVersion: 4.10.0-40-generic CompilerName: GCC CompilerVersion: 40400
ProgramName: mri_segment ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2018/10/18-17:24:45-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_segment.c,v 1.43.2.1 2016/10/27 22:24:52 zkaufman Exp $ User: rosalia Machine: rosalia-Lenovo-Y520-15IKBN Platform: Linux PlatformVersion: 4.10.0-40-generic CompilerName: GCC CompilerVersion: 40400
ProgramName: mri_label2label.bin ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2018/10/18-17:24:45-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_label2label.c,v 1.48.2.2 2016/12/12 14:15:26 zkaufman Exp $ User: rosalia Machine: rosalia-Lenovo-Y520-15IKBN Platform: Linux PlatformVersion: 4.10.0-40-generic CompilerName: GCC CompilerVersion: 40400
ProgramName: mri_em_register ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2018/10/18-17:24:45-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_em_register.c,v 1.105.2.1 2016/10/27 22:25:10 zkaufman Exp $ User: rosalia Machine: rosalia-Lenovo-Y520-15IKBN Platform: Linux PlatformVersion: 4.10.0-40-generic CompilerName: GCC CompilerVersion: 40400
ProgramName: mri_ca_normalize ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2018/10/18-17:24:45-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_ca_normalize.c,v 1.67.2.2 2016/10/27 22:25:09 zkaufman Exp $ User: rosalia Machine: rosalia-Lenovo-Y520-15IKBN Platform: Linux PlatformVersion: 4.10.0-40-generic CompilerName: GCC CompilerVersion: 40400
ProgramName: mri_ca_register ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2018/10/18-17:24:45-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_ca_register.c,v 1.96.2.3 2016/10/27 22:25:10 zkaufman Exp $ User: rosalia Machine: rosalia-Lenovo-Y520-15IKBN Platform: Linux PlatformVersion: 4.10.0-40-generic CompilerName: GCC CompilerVersion: 40400
ProgramName: mri_ca_label ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2018/10/18-17:24:45-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_ca_label.c,v 1.113.2.2 2016/10/27 22:25:10 zkaufman Exp $ User: rosalia Machine: rosalia-Lenovo-Y520-15IKBN Platform: Linux PlatformVersion: 4.10.0-40-generic CompilerName: GCC CompilerVersion: 40400
ProgramName: mri_pretess ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/10/18-17:24:45-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_pretess.c,v 1.22 2013/08/30 18:12:25 mreuter Exp $ User: rosalia Machine: rosalia-Lenovo-Y520-15IKBN Platform: Linux PlatformVersion: 4.10.0-40-generic CompilerName: GCC CompilerVersion: 40400
ProgramName: mri_fill ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/10/18-17:24:45-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_fill.c,v 1.119 2011/10/25 14:09:58 fischl Exp $ User: rosalia Machine: rosalia-Lenovo-Y520-15IKBN Platform: Linux PlatformVersion: 4.10.0-40-generic CompilerName: GCC CompilerVersion: 40400
ProgramName: mri_tessellate ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2018/10/18-17:24:45-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_tessellate.c,v 1.38.2.1 2016/07/26 18:46:38 zkaufman Exp $ User: rosalia Machine: rosalia-Lenovo-Y520-15IKBN Platform: Linux PlatformVersion: 4.10.0-40-generic CompilerName: GCC CompilerVersion: 40400
ProgramName: mri_concatenate_lta.bin ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/10/18-17:24:45-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_concatenate_lta.c,v 1.16 2015/11/21 00:06:20 greve Exp $ User: rosalia Machine: rosalia-Lenovo-Y520-15IKBN Platform: Linux PlatformVersion: 4.10.0-40-generic CompilerName: GCC CompilerVersion: 40400
ProgramName: mri_normalize_tp2 ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/10/18-17:24:45-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_normalize_tp2.c,v 1.8 2011/03/02 00:04:23 nicks Exp $ User: rosalia Machine: rosalia-Lenovo-Y520-15IKBN Platform: Linux PlatformVersion: 4.10.0-40-generic CompilerName: GCC CompilerVersion: 40400
ProgramName: mris_smooth ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/10/18-17:24:45-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_smooth.c,v 1.30 2014/01/21 18:48:21 fischl Exp $ User: rosalia Machine: rosalia-Lenovo-Y520-15IKBN Platform: Linux PlatformVersion: 4.10.0-40-generic CompilerName: GCC CompilerVersion: 40400
ProgramName: mris_inflate ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/10/18-17:24:45-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_inflate.c,v 1.45 2016/01/20 23:42:15 greve Exp $ User: rosalia Machine: rosalia-Lenovo-Y520-15IKBN Platform: Linux PlatformVersion: 4.10.0-40-generic CompilerName: GCC CompilerVersion: 40400
ProgramName: mris_curvature ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/10/18-17:24:45-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_curvature.c,v 1.31 2011/03/02 00:04:30 nicks Exp $ User: rosalia Machine: rosalia-Lenovo-Y520-15IKBN Platform: Linux PlatformVersion: 4.10.0-40-generic CompilerName: GCC CompilerVersion: 40400
ProgramName: mris_sphere ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/10/18-17:24:45-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_sphere.c,v 1.61 2016/01/20 23:42:15 greve Exp $ User: rosalia Machine: rosalia-Lenovo-Y520-15IKBN Platform: Linux PlatformVersion: 4.10.0-40-generic CompilerName: GCC CompilerVersion: 40400
ProgramName: mris_fix_topology ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2018/10/18-17:24:45-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_fix_topology.c,v 1.50.2.1 2016/10/27 22:25:58 zkaufman Exp $ User: rosalia Machine: rosalia-Lenovo-Y520-15IKBN Platform: Linux PlatformVersion: 4.10.0-40-generic CompilerName: GCC CompilerVersion: 40400
ProgramName: mris_topo_fixer ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/10/18-17:24:45-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_topo_fixer.cpp,v 1.29 2011/03/02 00:04:34 nicks Exp $ User: rosalia Machine: rosalia-Lenovo-Y520-15IKBN Platform: Linux PlatformVersion: 4.10.0-40-generic CompilerName: GCC CompilerVersion: 40400
ProgramName: mris_ca_label ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/10/18-17:24:45-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_ca_label.c,v 1.37 2014/02/04 17:46:42 fischl Exp $ User: rosalia Machine: rosalia-Lenovo-Y520-15IKBN Platform: Linux PlatformVersion: 4.10.0-40-generic CompilerName: GCC CompilerVersion: 40400
ProgramName: mris_euler_number ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/10/18-17:24:45-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_euler_number.c,v 1.10 2013/01/14 22:39:14 greve Exp $ User: rosalia Machine: rosalia-Lenovo-Y520-15IKBN Platform: Linux PlatformVersion: 4.10.0-40-generic CompilerName: GCC CompilerVersion: 40400
ProgramName: mris_make_surfaces ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2018/10/18-17:24:45-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_make_surfaces.c,v 1.164.2.4 2016/12/13 22:26:32 zkaufman Exp $ User: rosalia Machine: rosalia-Lenovo-Y520-15IKBN Platform: Linux PlatformVersion: 4.10.0-40-generic CompilerName: GCC CompilerVersion: 40400
ProgramName: mris_register ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/10/18-17:24:45-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_register.c,v 1.63 2016/01/20 23:43:04 greve Exp $ User: rosalia Machine: rosalia-Lenovo-Y520-15IKBN Platform: Linux PlatformVersion: 4.10.0-40-generic CompilerName: GCC CompilerVersion: 40400
ProgramName: mris_volmask ProgramArguments: --all-info ProgramVersion: $Name: $ TimeStamp: 2018/10/18-17:24:45-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_volmask.cpp,v 1.26.2.2 2016/11/18 20:05:18 zkaufman Exp $ User: rosalia Machine: rosalia-Lenovo-Y520-15IKBN Platform: Linux PlatformVersion: 4.10.0-40-generic CompilerName: GCC CompilerVersion: 40400
ProgramName: mris_anatomical_stats ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/10/18-17:24:45-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_anatomical_stats.c,v 1.79 2016/03/14 15:15:34 greve Exp $ User: rosalia Machine: rosalia-Lenovo-Y520-15IKBN Platform: Linux PlatformVersion: 4.10.0-40-generic CompilerName: GCC CompilerVersion: 40400
ProgramName: mrisp_paint ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/10/18-17:24:45-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mrisp_paint.c,v 1.12 2016/03/22 14:47:57 fischl Exp $ User: rosalia Machine: rosalia-Lenovo-Y520-15IKBN Platform: Linux PlatformVersion: 4.10.0-40-generic CompilerName: GCC CompilerVersion: 40400
ProgramName: mris_curvature_stats ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/10/18-17:24:45-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_curvature_stats.c,v 1.65 2015/06/04 20:50:51 nicks Exp $ User: rosalia Machine: rosalia-Lenovo-Y520-15IKBN Platform: Linux PlatformVersion: 4.10.0-40-generic CompilerName: GCC CompilerVersion: 40400
ProgramName: mris_calc ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/10/18-17:24:45-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_calc.c,v 1.54.2.1 2016/09/27 18:51:28 greve Exp $ User: rosalia Machine: rosalia-Lenovo-Y520-15IKBN Platform: Linux PlatformVersion: 4.10.0-40-generic CompilerName: GCC CompilerVersion: 40400
$Id: mri_robust_register.cpp,v 1.77 2016/01/20 23:36:17 greve Exp $
ProgramName: mri_robust_register.bin ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/10/18-17:24:45-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_robust_register.cpp,v 1.77 2016/01/20 23:36:17 greve Exp $ User: rosalia Machine: rosalia-Lenovo-Y520-15IKBN Platform: Linux PlatformVersion: 4.10.0-40-generic CompilerName: GCC CompilerVersion: 40400
$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: stable6 $ TimeStamp: 2018/10/18-17:24:45-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_robust_template.cpp,v 1.54 2016/05/05 21:17:08 mreuter Exp $ User: rosalia Machine: rosalia-Lenovo-Y520-15IKBN Platform: Linux PlatformVersion: 4.10.0-40-generic CompilerName: GCC CompilerVersion: 40400
ProgramName: mri_and ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/10/18-17:24:45-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_and.c,v 1.4 2011/03/02 00:04:13 nicks Exp $ User: rosalia Machine: rosalia-Lenovo-Y520-15IKBN Platform: Linux PlatformVersion: 4.10.0-40-generic CompilerName: GCC CompilerVersion: 40400
ProgramName: mri_or ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/10/18-17:24:45-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_or.c,v 1.5 2013/03/20 15:03:29 lzollei Exp $ User: rosalia Machine: rosalia-Lenovo-Y520-15IKBN Platform: Linux PlatformVersion: 4.10.0-40-generic CompilerName: GCC CompilerVersion: 40400
ProgramName: mri_fuse_segmentations ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/10/18-17:24:45-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_fuse_segmentations.c,v 1.8 2011/03/02 00:04:15 nicks Exp $ User: rosalia Machine: rosalia-Lenovo-Y520-15IKBN Platform: Linux PlatformVersion: 4.10.0-40-generic CompilerName: GCC CompilerVersion: 40400
ProgramName: mri_segstats ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/10/18-17:24:45-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_segstats.c,v 1.121 2016/05/31 17:27:11 greve Exp $ User: rosalia Machine: rosalia-Lenovo-Y520-15IKBN Platform: Linux PlatformVersion: 4.10.0-40-generic CompilerName: GCC CompilerVersion: 40400
ProgramName: mri_relabel_hypointensities ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/10/18-17:24:45-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_relabel_hypointensities.c,v 1.13 2015/05/15 18:44:10 nicks Exp $ User: rosalia Machine: rosalia-Lenovo-Y520-15IKBN Platform: Linux PlatformVersion: 4.10.0-40-generic CompilerName: GCC CompilerVersion: 40400
#######################################
GCADIR /usr/local/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 /usr/local/freesurfer/average
GCS DKaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs
#######################################
/home/rosalia/Desktop/MS_STUDY/subjects/001
mri_convert /home/rosalia/Desktop/MS_STUDY/subjects/MS001/mri/001.nii.gz /home/rosalia/Desktop/MS_STUDY/subjects/001/mri/orig/001.mgz
mri_convert.bin /home/rosalia/Desktop/MS_STUDY/subjects/MS001/mri/001.nii.gz /home/rosalia/Desktop/MS_STUDY/subjects/001/mri/orig/001.mgz
$Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $
reading from /home/rosalia/Desktop/MS_STUDY/subjects/MS001/mri/001.nii.gz...
TR=1000.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-0.999084, 0.0425307, 0.00465376)
j_ras = (0.0422088, 0.997577, -0.0553119)
k_ras = (0.00699493, 0.0550648, 0.998458)
writing to /home/rosalia/Desktop/MS_STUDY/subjects/001/mri/orig/001.mgz...
#--------------------------------------------
#@# MotionCor Thu 18 Oct 19:24:49 CEST 2018
Found 1 runs
/home/rosalia/Desktop/MS_STUDY/subjects/001/mri/orig/001.mgz
Checking for (invalid) multi-frame inputs...
WARNING: only one run found. This is OK, but motion
correction cannot be performed on one run, so I'll
copy the run to rawavg and continue.
cp /home/rosalia/Desktop/MS_STUDY/subjects/001/mri/orig/001.mgz /home/rosalia/Desktop/MS_STUDY/subjects/001/mri/rawavg.mgz
/home/rosalia/Desktop/MS_STUDY/subjects/001
mri_convert /home/rosalia/Desktop/MS_STUDY/subjects/001/mri/rawavg.mgz /home/rosalia/Desktop/MS_STUDY/subjects/001/mri/orig.mgz --conform
mri_convert.bin /home/rosalia/Desktop/MS_STUDY/subjects/001/mri/rawavg.mgz /home/rosalia/Desktop/MS_STUDY/subjects/001/mri/orig.mgz --conform
$Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $
reading from /home/rosalia/Desktop/MS_STUDY/subjects/001/mri/rawavg.mgz...
TR=1000.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-0.999084, 0.0425307, 0.00465376)
j_ras = (0.0422088, 0.997577, -0.0553119)
k_ras = (0.00699493, 0.0550648, 0.998458)
changing data type from float to uchar (noscale = 0)...
MRIchangeType: Building histogram
Reslicing using trilinear interpolation
writing to /home/rosalia/Desktop/MS_STUDY/subjects/001/mri/orig.mgz...
mri_add_xform_to_header -c /home/rosalia/Desktop/MS_STUDY/subjects/001/mri/transforms/talairach.xfm /home/rosalia/Desktop/MS_STUDY/subjects/001/mri/orig.mgz /home/rosalia/Desktop/MS_STUDY/subjects/001/mri/orig.mgz
INFO: extension is mgz
#--------------------------------------------
#@# Talairach Thu 18 Oct 19:24:57 CEST 2018
/home/rosalia/Desktop/MS_STUDY/subjects/001/mri
mri_nu_correct.mni --no-rescale --i orig.mgz --o orig_nu.mgz --n 1 --proto-iters 1000 --distance 50
/home/rosalia/Desktop/MS_STUDY/subjects/001/mri
/usr/local/freesurfer/bin/mri_nu_correct.mni
--no-rescale --i orig.mgz --o orig_nu.mgz --n 1 --proto-iters 1000 --distance 50
nIters 1
$Id: mri_nu_correct.mni,v 1.27 2016/02/26 16:19:49 mreuter Exp $
Linux rosalia-Lenovo-Y520-15IKBN 4.10.0-40-generic #44~16.04.1-Ubuntu SMP Thu Nov 9 15:37:44 UTC 2017 x86_64 x86_64 x86_64 GNU/Linux
Thu 18 Oct 19:24:57 CEST 2018
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
/usr/bin/bc
tmpdir is ./tmp.mri_nu_correct.mni.15758
/home/rosalia/Desktop/MS_STUDY/subjects/001/mri
mri_convert orig.mgz ./tmp.mri_nu_correct.mni.15758/nu0.mnc -odt float
mri_convert.bin orig.mgz ./tmp.mri_nu_correct.mni.15758/nu0.mnc -odt float
$Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $
reading from orig.mgz...
TR=1000.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-1, 1.60071e-09, -4.65661e-10)
j_ras = (-4.65661e-10, -3.72529e-09, -1)
k_ras = (2.06637e-09, 1, 0)
changing data type from uchar to float (noscale = 0)...
writing to ./tmp.mri_nu_correct.mni.15758/nu0.mnc...
--------------------------------------------------------
Iteration 1 Thu 18 Oct 19:24:58 CEST 2018
nu_correct -clobber ./tmp.mri_nu_correct.mni.15758/nu0.mnc ./tmp.mri_nu_correct.mni.15758/nu1.mnc -tmpdir ./tmp.mri_nu_correct.mni.15758/0/ -iterations 1000 -distance 50
[rosalia@rosalia-Lenovo-Y520-15IKBN:/home/rosalia/Desktop/MS_STUDY/subjects/001/mri/] [2018-10-18 19:24:58] running:
/usr/local/freesurfer/mni/bin/nu_estimate_np_and_em -parzen -log -sharpen 0.15 0.01 -iterations 1000 -stop 0.001 -shrink 4 -auto_mask -nonotify -b_spline 1.0e-7 -distance 50 -quiet -execute -clobber -nokeeptmp -tmpdir ./tmp.mri_nu_correct.mni.15758/0/ ./tmp.mri_nu_correct.mni.15758/nu0.mnc ./tmp.mri_nu_correct.mni.15758/nu1.imp
Processing:.................................................................Done
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Processing:.................................................................Done
Number of iterations: 26
CV of field change: 0.000987642
mri_convert ./tmp.mri_nu_correct.mni.15758/nu1.mnc orig_nu.mgz --like orig.mgz --conform
mri_convert.bin ./tmp.mri_nu_correct.mni.15758/nu1.mnc orig_nu.mgz --like orig.mgz --conform
$Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $
reading from ./tmp.mri_nu_correct.mni.15758/nu1.mnc...
TR=0.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-1, 1.60071e-09, -4.65661e-10)
j_ras = (-4.65661e-10, -3.72529e-09, -1)
k_ras = (2.06637e-09, 1, 0)
INFO: transform src into the like-volume: orig.mgz
changing data type from float to uchar (noscale = 0)...
MRIchangeType: Building histogram
writing to orig_nu.mgz...
Thu 18 Oct 19:25:32 CEST 2018
mri_nu_correct.mni done
talairach_avi --i orig_nu.mgz --xfm transforms/talairach.auto.xfm
talairach_avi log file is transforms/talairach_avi.log...
Started at Thu 18 Oct 19:25:32 CEST 2018
Ended at Thu 18 Oct 19:25:59 CEST 2018
talairach_avi done
cp transforms/talairach.auto.xfm transforms/talairach.xfm
#--------------------------------------------
#@# Talairach Failure Detection Thu 18 Oct 19:26:01 CEST 2018
/home/rosalia/Desktop/MS_STUDY/subjects/001/mri
talairach_afd -T 0.005 -xfm transforms/talairach.xfm
talairach_afd: Talairach Transform: transforms/talairach.xfm OK (p=0.7269, pval=0.6675 >= threshold=0.0050)
awk -f /usr/local/freesurfer/bin/extract_talairach_avi_QA.awk /home/rosalia/Desktop/MS_STUDY/subjects/001/mri/transforms/talairach_avi.log
tal_QC_AZS /home/rosalia/Desktop/MS_STUDY/subjects/001/mri/transforms/talairach_avi.log
TalAviQA: 0.96891
z-score: -2
#--------------------------------------------
#@# Nu Intensity Correction Thu 18 Oct 19:26:01 CEST 2018
mri_nu_correct.mni --i orig.mgz --o nu.mgz --uchar transforms/talairach.xfm --n 2
/home/rosalia/Desktop/MS_STUDY/subjects/001/mri
/usr/local/freesurfer/bin/mri_nu_correct.mni
--i orig.mgz --o nu.mgz --uchar transforms/talairach.xfm --n 2
nIters 2
$Id: mri_nu_correct.mni,v 1.27 2016/02/26 16:19:49 mreuter Exp $
Linux rosalia-Lenovo-Y520-15IKBN 4.10.0-40-generic #44~16.04.1-Ubuntu SMP Thu Nov 9 15:37:44 UTC 2017 x86_64 x86_64 x86_64 GNU/Linux
Thu 18 Oct 19:26:01 CEST 2018
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
/usr/bin/bc
tmpdir is ./tmp.mri_nu_correct.mni.16329
/home/rosalia/Desktop/MS_STUDY/subjects/001/mri
mri_convert orig.mgz ./tmp.mri_nu_correct.mni.16329/nu0.mnc -odt float
mri_convert.bin orig.mgz ./tmp.mri_nu_correct.mni.16329/nu0.mnc -odt float
$Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $
reading from orig.mgz...
TR=1000.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-1, 1.60071e-09, -4.65661e-10)
j_ras = (-4.65661e-10, -3.72529e-09, -1)
k_ras = (2.06637e-09, 1, 0)
changing data type from uchar to float (noscale = 0)...
writing to ./tmp.mri_nu_correct.mni.16329/nu0.mnc...
--------------------------------------------------------
Iteration 1 Thu 18 Oct 19:26:03 CEST 2018
nu_correct -clobber ./tmp.mri_nu_correct.mni.16329/nu0.mnc ./tmp.mri_nu_correct.mni.16329/nu1.mnc -tmpdir ./tmp.mri_nu_correct.mni.16329/0/
[rosalia@rosalia-Lenovo-Y520-15IKBN:/home/rosalia/Desktop/MS_STUDY/subjects/001/mri/] [2018-10-18 19:26:03] running:
/usr/local/freesurfer/mni/bin/nu_estimate_np_and_em -parzen -log -sharpen 0.15 0.01 -iterations 50 -stop 0.001 -shrink 4 -auto_mask -nonotify -b_spline 1.0e-7 -distance 200 -quiet -execute -clobber -nokeeptmp -tmpdir ./tmp.mri_nu_correct.mni.16329/0/ ./tmp.mri_nu_correct.mni.16329/nu0.mnc ./tmp.mri_nu_correct.mni.16329/nu1.imp
Processing:.................................................................Done
Processing:.................................................................Done
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Processing:.................................................................Done
Processing:.................................................................Done
Number of iterations: 21
CV of field change: 0.000988972
--------------------------------------------------------
Iteration 2 Thu 18 Oct 19:26:30 CEST 2018
nu_correct -clobber ./tmp.mri_nu_correct.mni.16329/nu1.mnc ./tmp.mri_nu_correct.mni.16329/nu2.mnc -tmpdir ./tmp.mri_nu_correct.mni.16329/1/
[rosalia@rosalia-Lenovo-Y520-15IKBN:/home/rosalia/Desktop/MS_STUDY/subjects/001/mri/] [2018-10-18 19:26:30] running:
/usr/local/freesurfer/mni/bin/nu_estimate_np_and_em -parzen -log -sharpen 0.15 0.01 -iterations 50 -stop 0.001 -shrink 4 -auto_mask -nonotify -b_spline 1.0e-7 -distance 200 -quiet -execute -clobber -nokeeptmp -tmpdir ./tmp.mri_nu_correct.mni.16329/1/ ./tmp.mri_nu_correct.mni.16329/nu1.mnc ./tmp.mri_nu_correct.mni.16329/nu2.imp
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
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Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
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Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Number of iterations: 20
CV of field change: 0.000967307
mri_binarize --i ./tmp.mri_nu_correct.mni.16329/nu2.mnc --min -1 --o ./tmp.mri_nu_correct.mni.16329/ones.mgz
$Id: mri_binarize.c,v 1.43 2016/06/09 20:46:21 greve Exp $
cwd /home/rosalia/Desktop/MS_STUDY/subjects/001/mri
cmdline mri_binarize.bin --i ./tmp.mri_nu_correct.mni.16329/nu2.mnc --min -1 --o ./tmp.mri_nu_correct.mni.16329/ones.mgz
sysname Linux
hostname rosalia-Lenovo-Y520-15IKBN
machine x86_64
user rosalia
input ./tmp.mri_nu_correct.mni.16329/nu2.mnc
frame 0
nErode3d 0
nErode2d 0
output ./tmp.mri_nu_correct.mni.16329/ones.mgz
Binarizing based on threshold
min -1
max +infinity
binval 1
binvalnot 0
fstart = 0, fend = 0, nframes = 1
Found 16777216 values in range
Counting number of voxels in first frame
Found 16777216 voxels in final mask
Count: 16777216 16777216.000000 16777216 100.000000
mri_binarize done
mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.16329/ones.mgz --i orig.mgz --sum ./tmp.mri_nu_correct.mni.16329/sum.junk --avgwf ./tmp.mri_nu_correct.mni.16329/input.mean.dat
$Id: mri_segstats.c,v 1.121 2016/05/31 17:27:11 greve Exp $
cwd
cmdline mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.16329/ones.mgz --i orig.mgz --sum ./tmp.mri_nu_correct.mni.16329/sum.junk --avgwf ./tmp.mri_nu_correct.mni.16329/input.mean.dat
sysname Linux
hostname rosalia-Lenovo-Y520-15IKBN
machine x86_64
user rosalia
UseRobust 0
Loading ./tmp.mri_nu_correct.mni.16329/ones.mgz
Loading orig.mgz
Voxel Volume is 1 mm^3
Generating list of segmentation ids
Found 1 segmentations
Computing statistics for each segmentation
Reporting on 1 segmentations
Using PrintSegStat
Computing spatial average of each frame
0
Writing to ./tmp.mri_nu_correct.mni.16329/input.mean.dat
mri_segstats done
mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.16329/ones.mgz --i ./tmp.mri_nu_correct.mni.16329/nu2.mnc --sum ./tmp.mri_nu_correct.mni.16329/sum.junk --avgwf ./tmp.mri_nu_correct.mni.16329/output.mean.dat
$Id: mri_segstats.c,v 1.121 2016/05/31 17:27:11 greve Exp $
cwd
cmdline mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.16329/ones.mgz --i ./tmp.mri_nu_correct.mni.16329/nu2.mnc --sum ./tmp.mri_nu_correct.mni.16329/sum.junk --avgwf ./tmp.mri_nu_correct.mni.16329/output.mean.dat
sysname Linux
hostname rosalia-Lenovo-Y520-15IKBN
machine x86_64
user rosalia
UseRobust 0
Loading ./tmp.mri_nu_correct.mni.16329/ones.mgz
Loading ./tmp.mri_nu_correct.mni.16329/nu2.mnc
Voxel Volume is 1 mm^3
Generating list of segmentation ids
Found 1 segmentations
Computing statistics for each segmentation
Reporting on 1 segmentations
Using PrintSegStat
Computing spatial average of each frame
0
Writing to ./tmp.mri_nu_correct.mni.16329/output.mean.dat
mri_segstats done
mris_calc -o ./tmp.mri_nu_correct.mni.16329/nu2.mnc ./tmp.mri_nu_correct.mni.16329/nu2.mnc mul 1.03856207600868913147
Saving result to './tmp.mri_nu_correct.mni.16329/nu2.mnc' (type = MINC ) [ ok ]
mri_convert ./tmp.mri_nu_correct.mni.16329/nu2.mnc nu.mgz --like orig.mgz
mri_convert.bin ./tmp.mri_nu_correct.mni.16329/nu2.mnc nu.mgz --like orig.mgz
$Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $
reading from ./tmp.mri_nu_correct.mni.16329/nu2.mnc...
TR=0.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-1, 1.60071e-09, -4.65661e-10)
j_ras = (-4.65661e-10, -3.72529e-09, -1)
k_ras = (2.06637e-09, 1, 0)
INFO: transform src into the like-volume: orig.mgz
writing to nu.mgz...
mri_make_uchar nu.mgz transforms/talairach.xfm nu.mgz
type change took 0 minutes and 5 seconds.
mapping ( 5, 167) to ( 3, 110)
Thu 18 Oct 19:27:18 CEST 2018
mri_nu_correct.mni done
mri_add_xform_to_header -c /home/rosalia/Desktop/MS_STUDY/subjects/001/mri/transforms/talairach.xfm nu.mgz nu.mgz
INFO: extension is mgz
#--------------------------------------------
#@# Intensity Normalization Thu 18 Oct 19:27:19 CEST 2018
/home/rosalia/Desktop/MS_STUDY/subjects/001/mri
mri_normalize -g 1 -mprage nu.mgz T1.mgz
using max gradient = 1.000
assuming input volume is MGH (Van der Kouwe) MP-RAGE
reading from nu.mgz...
normalizing image...
talairach transform
1.06054 0.00204 0.02524 0.33235;
0.05102 1.05315 0.37685 3.42719;
0.01099 -0.22669 1.10181 -3.75677;
0.00000 0.00000 0.00000 1.00000;
processing without aseg, no1d=0
MRInormInit():
INFO: Modifying talairach volume c_(r,a,s) based on average_305
MRInormalize():
MRIsplineNormalize(): npeaks = 16
Starting OpenSpline(): npoints = 16
building Voronoi diagram...
performing soap bubble smoothing, sigma = 8...
Iterating 2 times
---------------------------------
3d normalization pass 1 of 2
white matter peak found at 110
white matter peak found at 109
gm peak at 67 (67), valley at 52 (52)
csf peak at 35, setting threshold to 56
building Voronoi diagram...
performing soap bubble smoothing, sigma = 8...
---------------------------------
3d normalization pass 2 of 2
white matter peak found at 110
white matter peak found at 110
gm peak at 67 (67), valley at 52 (52)
csf peak at 35, setting threshold to 56
building Voronoi diagram...
performing soap bubble smoothing, sigma = 8...
Done iterating ---------------------------------
writing output to T1.mgz
3D bias adjustment took 1 minutes and 25 seconds.
#--------------------------------------------
#@# Skull Stripping Thu 18 Oct 19:28:44 CEST 2018
/home/rosalia/Desktop/MS_STUDY/subjects/001/mri
mri_em_register -rusage /home/rosalia/Desktop/MS_STUDY/subjects/001/touch/rusage.mri_em_register.skull.dat -skull nu.mgz /usr/local/freesurfer/average/RB_all_withskull_2016-05-10.vc700.gca transforms/talairach_with_skull.lta
aligning to atlas containing skull, setting unknown_nbr_spacing = 5
== Number of threads available to mri_em_register for OpenMP = 1 ==
reading 1 input volumes...
logging results to talairach_with_skull.log
reading '/usr/local/freesurfer/average/RB_all_withskull_2016-05-10.vc700.gca'...
average std = 22.9 using min determinant for regularization = 52.6
0 singular and 9002 ill-conditioned covariance matrices regularized
reading 'nu.mgz'...
freeing gibbs priors...done.
accounting for voxel sizes in initial transform
bounding unknown intensity as < 8.7 or > 569.1
total sample mean = 77.6 (1399 zeros)
************************************************
spacing=8, using 3243 sample points, tol=1.00e-05...
************************************************
register_mri: find_optimal_transform
find_optimal_transform: nsamples 3243, passno 0, spacing 8
resetting wm mean[0]: 100 --> 108
resetting gm mean[0]: 61 --> 61
input volume #1 is the most T1-like
using real data threshold=8.0
skull bounding box = (44, 27, 13) --> (212, 177, 212)
using (100, 77, 113) as brain centroid...
mean wm in atlas = 108, using box (79,59,88) --> (120, 95,137) to find MRI wm
before smoothing, mri peak at 106
robust fit to distribution - 107 +- 5.0
after smoothing, mri peak at 107, scaling input intensities by 1.009
scaling channel 0 by 1.00935
initial log_p = -4.448
************************************************
First Search limited to translation only.
************************************************
max log p = -4.438350 @ (-9.091, 9.091, -9.091)
max log p = -4.224692 @ (4.545, 4.545, 4.545)
max log p = -4.162993 @ (2.273, 2.273, 2.273)
max log p = -4.132318 @ (1.136, 1.136, -3.409)
max log p = -4.110374 @ (-0.568, 0.568, 0.568)
max log p = -4.110374 @ (0.000, 0.000, 0.000)
Found translation: (-1.7, 17.6, -5.1): log p = -4.110
****************************************
Nine parameter search. iteration 0 nscales = 0 ...
****************************************
Result so far: scale 1.000: max_log_p=-3.897, old_max_log_p =-4.110 (thresh=-4.1)
1.00000 0.00000 0.00000 -1.70455;
0.00000 1.19413 0.31997 -36.19451;
0.00000 -0.27823 1.03837 25.09055;
0.00000 0.00000 0.00000 1.00000;
****************************************
Nine parameter search. iteration 1 nscales = 0 ...
****************************************
Result so far: scale 1.000: max_log_p=-3.878, old_max_log_p =-3.897 (thresh=-3.9)
1.00000 0.00000 0.00000 -1.70455;
0.00000 1.10457 0.29597 -22.81687;
0.00000 -0.29910 1.11625 26.15309;
0.00000 0.00000 0.00000 1.00000;
****************************************
Nine parameter search. iteration 2 nscales = 0 ...
****************************************
Result so far: scale 1.000: max_log_p=-3.872, old_max_log_p =-3.878 (thresh=-3.9)
1.00000 0.00000 0.00000 -1.70455;
0.00000 1.18741 0.31817 -35.19120;
0.00000 -0.29910 1.11625 26.15309;
0.00000 0.00000 0.00000 1.00000;
****************************************
Nine parameter search. iteration 3 nscales = 0 ...
****************************************
Result so far: scale 1.000: max_log_p=-3.872, old_max_log_p =-3.872 (thresh=-3.9)
1.00000 0.00000 0.00000 -1.70455;
0.00000 1.18741 0.31817 -35.19120;
0.00000 -0.29910 1.11625 26.15309;
0.00000 0.00000 0.00000 1.00000;
reducing scale to 0.2500
****************************************
Nine parameter search. iteration 4 nscales = 1 ...
****************************************
Result so far: scale 0.250: max_log_p=-3.803, old_max_log_p =-3.872 (thresh=-3.9)
1.01820 0.03922 0.01186 -10.00909;
-0.03333 1.19794 0.36234 -35.01948;
0.00000 -0.31762 1.04432 34.36309;
0.00000 0.00000 0.00000 1.00000;
****************************************
Nine parameter search. iteration 5 nscales = 1 ...
****************************************
Result so far: scale 0.250: max_log_p=-3.803, old_max_log_p =-3.803 (thresh=-3.8)
1.01820 0.03922 0.01186 -10.00909;
-0.03333 1.19794 0.36234 -35.01948;
0.00000 -0.31762 1.04432 34.36309;
0.00000 0.00000 0.00000 1.00000;
reducing scale to 0.0625
****************************************
Nine parameter search. iteration 6 nscales = 2 ...
****************************************
Result so far: scale 0.062: max_log_p=-3.789, old_max_log_p =-3.803 (thresh=-3.8)
1.01926 0.03407 0.02894 -10.94709;
-0.03341 1.20073 0.36327 -35.89384;
-0.01664 -0.31701 1.04034 35.89679;
0.00000 0.00000 0.00000 1.00000;
****************************************
Nine parameter search. iteration 7 nscales = 2 ...
****************************************
Result so far: scale 0.062: max_log_p=-3.780, old_max_log_p =-3.789 (thresh=-3.8)
1.02048 0.00878 0.03930 -10.18563;
-0.01749 1.18426 0.40528 -41.06069;
-0.03219 -0.36761 1.02762 44.32310;
0.00000 0.00000 0.00000 1.00000;
****************************************
Nine parameter search. iteration 8 nscales = 2 ...
****************************************
Result so far: scale 0.062: max_log_p=-3.780, old_max_log_p =-3.780 (thresh=-3.8)
1.02048 0.00878 0.03930 -10.18563;
-0.01749 1.18426 0.40528 -41.06069;
-0.03219 -0.36761 1.02762 44.32310;
0.00000 0.00000 0.00000 1.00000;
min search scale 0.025000 reached
***********************************************
Computing MAP estimate using 3243 samples...
***********************************************
dt = 5.00e-06, momentum=0.80, tol=1.00e-05
l_intensity = 1.0000
Aligning input volume to GCA...
Transform matrix
1.02048 0.00878 0.03930 -10.18563;
-0.01749 1.18426 0.40528 -41.06069;
-0.03219 -0.36761 1.02762 44.32310;
0.00000 0.00000 0.00000 1.00000;
nsamples 3243
Quasinewton: input matrix
1.02048 0.00878 0.03930 -10.18563;
-0.01749 1.18426 0.40528 -41.06069;
-0.03219 -0.36761 1.02762 44.32310;
0.00000 0.00000 0.00000 1.00000;
outof QuasiNewtonEMA: 011: -log(p) = -0.0 tol 0.000010
Resulting transform:
1.02048 0.00878 0.03930 -10.18563;
-0.01749 1.18426 0.40528 -41.06069;
-0.03219 -0.36761 1.02762 44.32310;
0.00000 0.00000 0.00000 1.00000;
pass 1, spacing 8: log(p) = -3.780 (old=-4.448)
transform before final EM align:
1.02048 0.00878 0.03930 -10.18563;
-0.01749 1.18426 0.40528 -41.06069;
-0.03219 -0.36761 1.02762 44.32310;
0.00000 0.00000 0.00000 1.00000;
**************************************************
EM alignment process ...
Computing final MAP estimate using 364799 samples.
**************************************************
dt = 5.00e-06, momentum=0.80, tol=1.00e-07
l_intensity = 1.0000
Aligning input volume to GCA...
Transform matrix
1.02048 0.00878 0.03930 -10.18563;
-0.01749 1.18426 0.40528 -41.06069;
-0.03219 -0.36761 1.02762 44.32310;
0.00000 0.00000 0.00000 1.00000;
nsamples 364799
Quasinewton: input matrix
1.02048 0.00878 0.03930 -10.18563;
-0.01749 1.18426 0.40528 -41.06069;
-0.03219 -0.36761 1.02762 44.32310;
0.00000 0.00000 0.00000 1.00000;
outof QuasiNewtonEMA: 013: -log(p) = 4.2 tol 0.000000
final transform:
1.02048 0.00878 0.03930 -10.18563;
-0.01749 1.18426 0.40528 -41.06069;
-0.03219 -0.36761 1.02762 44.32310;
0.00000 0.00000 0.00000 1.00000;
writing output transformation to transforms/talairach_with_skull.lta...
mri_em_register utimesec 1059.768000
mri_em_register stimesec 0.724000
mri_em_register ru_maxrss 614032
mri_em_register ru_ixrss 0
mri_em_register ru_idrss 0
mri_em_register ru_isrss 0
mri_em_register ru_minflt 156152
mri_em_register ru_majflt 6
mri_em_register ru_nswap 0
mri_em_register ru_inblock 150296
mri_em_register ru_oublock 16
mri_em_register ru_msgsnd 0
mri_em_register ru_msgrcv 0
mri_em_register ru_nsignals 0
mri_em_register ru_nvcsw 30
mri_em_register ru_nivcsw 2571
registration took 17 minutes and 41 seconds.
mri_watershed -rusage /home/rosalia/Desktop/MS_STUDY/subjects/001/touch/rusage.mri_watershed.dat -T1 -brain_atlas /usr/local/freesurfer/average/RB_all_withskull_2016-05-10.vc700.gca transforms/talairach_with_skull.lta T1.mgz brainmask.auto.mgz
Mode: T1 normalized volume
Mode: Use the information of atlas (default parms, --help for details)
*********************************************************
The input file is T1.mgz
The output file is brainmask.auto.mgz
Weighting the input with atlas information before watershed
*************************WATERSHED**************************
Sorting...
first estimation of the COG coord: x=128 y=98 z=107 r=72
first estimation of the main basin volume: 1564584 voxels
Looking for seedpoints
2 found in the cerebellum
16 found in the rest of the brain
global maximum in x=150, y=76, z=83, Imax=255
CSF=14, WM_intensity=110, WM_VARIANCE=5
WM_MIN=110, WM_HALF_MIN=110, WM_HALF_MAX=110, WM_MAX=110
preflooding height equal to 10 percent
done.
Analyze...
main basin size=669374246 voxels, voxel volume =1.000
= 669374246 mmm3 = 669374.272 cm3
done.
PostAnalyze...Basin Prior
5 basins merged thanks to atlas
***** 0 basin(s) merged in 1 iteration(s)
***** 0 voxel(s) added to the main basin
done.
Weighting the input with prior template
****************TEMPLATE DEFORMATION****************
second estimation of the COG coord: x=127,y=105, z=102, r=9859 iterations
^^^^^^^^ couldn't find WM with original limits - expanding ^^^^^^
GLOBAL CSF_MIN=0, CSF_intensity=9, CSF_MAX=32 , nb = 44920
RIGHT_CER CSF_MIN=1, CSF_intensity=2, CSF_MAX=28 , nb = -1031234735
LEFT_CER CSF_MIN=1, CSF_intensity=2, CSF_MAX=26 , nb = -1043561981
RIGHT_BRAIN CSF_MIN=0, CSF_intensity=9, CSF_MAX=31 , nb = -1079762686
LEFT_BRAIN CSF_MIN=0, CSF_intensity=9, CSF_MAX=29 , nb = 1076900980
OTHER CSF_MIN=1, CSF_intensity=2, CSF_MAX=4 , nb = 1076957134
Problem with the least square interpolation in GM_MIN calculation.
Problem with the least square interpolation in GM_MIN calculation.
(2) Problem with the least square interpolation in GM_MIN calculation.
CSF_MAX TRANSITION GM_MIN GM
GLOBAL
before analyzing : 32, 26, 15, 64
after analyzing : 20, 26, 26, 35
RIGHT_CER
before analyzing : 28, 23, 12, 70
after analyzing : 23, 24, 25, 35
LEFT_CER
before analyzing : 26, 25, 25, 71
after analyzing : 18, 25, 25, 36
RIGHT_BRAIN
before analyzing : 31, 26, 16, 65
after analyzing : 20, 26, 26, 35
LEFT_BRAIN
before analyzing : 29, 24, 15, 64
after analyzing : 19, 24, 25, 34
OTHER
before analyzing : 4, 3, 0, 9
after analyzing : 3, 17, 25, 19
mri_strip_skull: done peeling brain
highly tesselated surface with 10242 vertices
matching...61 iterations
*********************VALIDATION*********************
curvature mean = -0.013, std = 0.009
curvature mean = 70.851, std = 6.312
No Rigid alignment: -atlas Mode Off (basic atlas / no registration)
before rotation: sse = 3.43, sigma = 5.31
after rotation: sse = 3.43, sigma = 5.31
Localization of inacurate regions: Erosion-Dilation steps
the sse mean is 3.75, its var is 4.93
before Erosion-Dilatation 1.13% of inacurate vertices
after Erosion-Dilatation 0.00% of inacurate vertices
Validation of the shape of the surface done.
Scaling of atlas fields onto current surface fields
********FINAL ITERATIVE TEMPLATE DEFORMATION********
Compute Local values csf/gray
Fine Segmentation...34 iterations
mri_strip_skull: done peeling brain
Brain Size = 1647626 voxels, voxel volume = 1.000 mm3
= 1647626 mmm3 = 1647.626 cm3
******************************
Saving brainmask.auto.mgz
done
mri_watershed utimesec 24.832000
mri_watershed stimesec 0.228000
mri_watershed ru_maxrss 829320
mri_watershed ru_ixrss 0
mri_watershed ru_idrss 0
mri_watershed ru_isrss 0
mri_watershed ru_minflt 210765
mri_watershed ru_majflt 9
mri_watershed ru_nswap 0
mri_watershed ru_inblock 9680
mri_watershed ru_oublock 2704
mri_watershed ru_msgsnd 0
mri_watershed ru_msgrcv 0
mri_watershed ru_nsignals 0
mri_watershed ru_nvcsw 49
mri_watershed ru_nivcsw 588
mri_watershed done
cp brainmask.auto.mgz brainmask.mgz
Started at Thu 18 Oct 19:24:44 CEST 2018
Ended at Thu 18 Oct 19:46:51 CEST 2018
#@#%# recon-all-run-time-hours 0.369
recon-all -s 001 finished without error at Thu 18 Oct 19:46:51 CEST 2018
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