External Email - Use Caution        

I tryed to run the elmo.2005 case in the administrator directory /usr/local with 23 GB free space, but the elaboration is stopped a little bit before the elaboration maded in a directory with 2 GB of free space.
So I think is not a problem of memory, maybe could be a problem with the download of Freesurfer V 6.0, could you sand me the check sum link please? I can't find it.


Anyway ....Thanks!!!!








----Messaggio originale----
Da: freesurfer-request@nmr.mgh.harvard.edu
Data: 13-set-2018 17.48
A: <freesurfer@nmr.mgh.harvard.edu>
Ogg: Freesurfer Digest, Vol 175, Issue 16

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When replying, please edit your Subject line so it is more specific
than "Re: Contents of Freesurfer digest..."


Today's Topics:

   1. Re: 6.0.1 automatic download (Chris Gorgolewski)
   2.  segmentation fault with mri_vol2vol or lta_convert (valabregue)
   3. Re: Midline errors (Bruce Fischl)
   4. Re: /mri/orig/001.mgz vs T1.mgz (Alexopoulos, Dimitrios)
   5. Re: ???  questions about trac-all -stat (Yendiki, Anastasia)
   6. Re: problem with trac-preproc just at the middle of Priors
      point (Yendiki, Anastasia)


----------------------------------------------------------------------

Message: 1
Date: Thu, 13 Sep 2018 07:38:19 -0400
From: Chris Gorgolewski <krzysztof.gorgolewski@gmail.com>
Subject: Re: [Freesurfer] 6.0.1 automatic download
To: "Hoopes, Andrew" <AHOOPES@mgh.harvard.edu>
Cc: freesurfer <freesurfer@nmr.mgh.harvard.edu>
Message-ID:
<CAAQzouPbjjqwEuTvVkgLzHQ5MMSoXrDXz4HEb7P5F9L04wAouQ@mail.gmail.com>
Content-Type: text/plain; charset="utf-8"

        External Email - Use Caution       

Thanks!

Best,
Chris

PS Apologies for brevity and potential typos. This message was composed on
a phone.

On Wed, Sep 12, 2018, 5:06 PM Hoopes, Andrew <AHOOPES@mgh.harvard.edu>
wrote:

> Hi Chris, that is the same version as before. Sorry, our pubftp disk went
> down a few days ago and we had to restore some things manually (I guess the
> original filename was copied). I renamed the tarball back to
> freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.1.tar.gz
>
>
>
> best,
>
> Andrew
>
>
>
>
>
> *From: *<freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Chris
> Gorgolewski <krzysztof.gorgolewski@gmail.com>
> *Reply-To: *FS Help <freesurfer@nmr.mgh.harvard.edu>
> *Date: *Wednesday, September 12, 2018 at 11:03 AM
> *To: *FS Help <freesurfer@nmr.mgh.harvard.edu>
> *Subject: *[Freesurfer] 6.0.1 automatic download
>
>
>
> *        External Email - Use Caution        *
>
> Hi,
>
>
>
> I noticed that
>
>
> https://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/6.0.1/freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.1.tar.gz
>
>
> is no longer available, but instead there is
>
>
> https://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/6.0.1/freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.1-f53a55a.tar.gz
>
>
>
> Is it the same thing or an updated version (if so why not 6.0.2)? Is this
> the right way to grab the same 6.0.1 version in a programmatic way?
>
>
> Best,
>
> Chris
>
> The information in this e-mail is intended only for the person to whom it
> is
> addressed. If you believe this e-mail was sent to you in error and the
> e-mail
> contains patient information, please contact the Partners Compliance
> HelpLine at
> http://www.partners.org/complianceline . If the e-mail was sent to you in
> error
> but does not contain patient information, please contact the sender and
> properly
> dispose of the e-mail.
>
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Message: 2
Date: Thu, 13 Sep 2018 14:13:26 +0200
From: valabregue <romain.valabregue@upmc.fr>
Subject: [Freesurfer]  segmentation fault with mri_vol2vol or
lta_convert
To: freesurfer@nmr.mgh.harvard.edu
Message-ID: <48f50b85-44b9-f7b9-e22e-25628625ee4c@upmc.fr>
Content-Type: text/plain; charset="utf-8"; format="flowed"

        External Email - Use Caution       

Hello

I notice a systematic segmentation fault with several function that use
a .lta file (lta_convert or mri_vol2vol)
This is due to a too long filename path in the .lta file :
If I manually edit the .lta file and change the file_path associate to
the line
filename = manudally eddited

then the command runs

when the filename is longer than 255 this cause a segmentation fault

it seems to me that this ' filename= '? line is not used since I can
change the value (for something wrong) and the reslice or convert
function works properly. is that rigth

Would it be possible to fix this issue ?


I have also an other strange issue, even after the modification of the
filename in the lta file I get an other segmentation fault with the
command : mri_vol2vol
this time I modify manually the .lta file to have a wrong but short filename

if I run :

mri_vol2vol --interp nearest --lta very_lon_path/reg.lta --mov
very_long_path/vol.nii.gz --tarf very_long_path/voltarg.nii.gz -o
very_long_path/vol_out.nii.gz

I get a segmentation fault

then If I change directory to be in the same dir as the lta file and
make the exact same command but with relative path name for the lta file
(ie :?? --lta reg.lta )? then it works.



?lta_convert --all-info
$Id: lta_convert.cpp,v 1.9.2.1 2016/08/09 02:33:22 zkaufman Exp $

ProgramName: lta_convert? ProgramArguments: --all-info ProgramVersion:
$Name:? $? TimeStamp: 2018/09/13-12:11:39-GMT BuildTimeStamp: Jan 18
2017 16:38:58? CVS: $Id: lta_convert.cpp,v 1.9.2.1 2016/08/09 02:33:22
zkaufman Exp $? User: romain.valabregue Machine: icm-cenir-le03?
Platform: Linux? PlatformVersion: 4.4.0-104-generic? CompilerName: GCC?
CompilerVersion: 40400


mri_vol2vol --all-info
ProgramName: mri_vol2vol.bin? ProgramArguments: --all-info
ProgramVersion: $Name:? $? TimeStamp: 2018/09/13-12:12:11-GMT
BuildTimeStamp: Jan 18 2017 16:38:58? CVS: $Id: mri_vol2vol.c,v 1.88.2.1
2016/08/12 16:54:44 zkaufman Exp $? User: romain.valabregue? Machine:
icm-cenir-le03? Platform: Linux PlatformVersion: 4.4.0-104-generic?
CompilerName: GCC CompilerVersion: 40400

Thanks for your help

Romain



------------------------------

Message: 3
Date: Thu, 13 Sep 2018 10:08:48 -0400 (EDT)
From: Bruce Fischl <fischl@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] Midline errors
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Message-ID:
<alpine.LRH.2.20.1809131008120.28975@gate.nmr.mgh.harvard.edu>
Content-Type: text/plain; charset="utf-8"

Hi Maxime

if you upload a gzipped tar file of the entire subject dir to our ftp
site we will take a look. Please include voxel coordinates of the spots
you think are inaccurate.

cheers
Bruce
On Thu, 13 Sep 2018, Maxime Perron wrote:

>        External Email - Use Caution
>
> Hi Freesurfer Experts,
>
> I tried to correct the midline with the information you provided me. Indeed, I tried to correct the aseg.presurf (Freesurfer v.6) using Freeview. Although parcelisation has changed, the midline has not changed. I launched several types of autorecon (-noaseg, -cp, -wm), but it didn't work. Do you have an idea?
>
> Best,
> Maxime
>
>> On Aug 10, 2018, at 5:09 PM, Bruce Fischl <fischl@nmr.mgh.harvard.edu> wrote:
>>
>> HI Maxime
>>
>> check the aseg labels and make sure they are correct (and fix them if not). Probably a couple of left/right ventricle voxels are mislabeled
>> Bruce
>> On Fri, 10 Aug 2018, Maxime Perron wrote:
>>
>>>         External Email - Use Caution
>>> Hello FreeSurfer Developers,
>>>
>>> I use Freesurfer 6 on macOS Sierra 10.12.6. In several subjects, I found midline cutting error, that
>>> is the midline does not go through exactly the center of the brain in coronal cut. For example, the
>>> midline is a little bit fuzzy and goes through an hemisphere than the other (see attachment). I've
>>> searched in the mail list and ?I don't find the way to fix it. Does anyone have any idea to fix it?
>>> Thank you,
>>> Maxime Perron
>> _______________________________________________
>> Freesurfer mailing list
>> Freesurfer@nmr.mgh.harvard.edu
>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>
>>
>> The information in this e-mail is intended only for the person to whom it is
>> addressed. If you believe this e-mail was sent to you in error and the e-mail
>> contains patient information, please contact the Partners Compliance HelpLine at
>> http://www.partners.org/complianceline . If the e-mail was sent to you in error
>> but does not contain patient information, please contact the sender and properly
>> dispose of the e-mail.
>
>
> _______________________________________________
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
>

------------------------------

Message: 4
Date: Thu, 13 Sep 2018 14:37:43 +0000
From: "Alexopoulos, Dimitrios" <dimitriosalexopoulos@wustl.edu>
Subject: Re: [Freesurfer] /mri/orig/001.mgz vs T1.mgz
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Message-ID:
<CY1PR0201MB1914BE3DC0F5769DBAE05A42D61A0@CY1PR0201MB1914.namprd02.prod.outlook.com>

Content-Type: text/plain; charset="iso-8859-1"

        External Email - Use Caution       

These images were both opened in freeview. Should they be aligned differently?

-----Original Message-----
From: freesurfer-bounces@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] On Behalf Of Douglas N. Greve
Sent: Wednesday, September 12, 2018 2:15 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] /mri/orig/001.mgz vs T1.mgz

depends a little bit on the viewer, but we resample into the scanner space, so it could look like it is tilted

On 09/12/2018 12:33 PM, Alexopoulos, Dimitrios wrote:
>
>         External Email - Use Caution
>
> I have a quick question as it relates to image outputs from freesurfer
> 6.0 (i.e. /mri/orig/001.mgz vs. nu/T1.mgz). Images below:
>
> Left - /mri/orig/001.mgz
>
> Right - T1.mgz
>
> The outputs (segmentations/surfaces) look good, but I noticed the
> output  volumes (nu.mgz, T1.mgz, brainmask.mgz) looked tilted
>
> compared to the input image (/mri/orig/001.mgz) . Is this
> expected/possible?
>
> Jim
>
> ----------------------------------------------------------------------
> --
>
> The materials in this message are private and may contain Protected
> Healthcare Information or other information of a sensitive nature. If
> you are not the intended recipient, be advised that any unauthorized
> use, disclosure, copying or the taking of any action in reliance on
> the contents of this information is strictly prohibited. If you have
> received this email in error, please immediately notify the sender via
> telephone or return mail.
>
>
>
> _______________________________________________
> 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
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The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.


________________________________
The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail.




------------------------------

Message: 5
Date: Thu, 13 Sep 2018 15:44:52 +0000
From: "Yendiki, Anastasia" <AYENDIKI@mgh.harvard.edu>
Subject: Re: [Freesurfer] ???  questions about trac-all -stat
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Message-ID: <D7BFFADB.266DC%ayendiki@mgh.harvard.edu>
Content-Type: text/plain; charset="utf-8"

Hi Qianwen,

(1) & (2): The native space coordinates along the path of all subjects (which are in their path stats files) are mapped to MNI space simply to identify a common midpoint for all subjects. This midpoint is mapped back to native space, and the FA/MD/etc. values for each subject are sampled along the path by stepping out by equally sized steps from the midpoint towards both ends. At each step, you get one row of the group table.

(3): Look for the paragraph "This text file contains various diffusion measures?? in the tutorial:
http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/TraculaStatistics
And slide ?Path stats (values along the path)? in the course slides:
http://surfer.nmr.mgh.harvard.edu/pub/docs/tracula,fs.ppt

Hope this helps,
a.y

From: <freesurfer-bounces@nmr.mgh.harvard.edu<mailto:freesurfer-bounces@nmr.mgh.harvard.edu>> on behalf of ??? <627611631@qq.com<mailto:627611631@qq.com>>
Reply-To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>>
Date: Wednesday, September 12, 2018 at 9:47 PM
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: [Freesurfer] ??? questions about trac-all -stat


        External Email - Use Caution

Hi Yendiki, Anastasia,
I am very sorry that I did not make myself clear. I mean I want to know how trac-all ?stat does it.

(1)how to determine the first position and last position of all subjects' pathways when converting all pathstats.byvoxel.txt files to a table for group analyses?
In the tabel , The first position and last position of all subjects' pathways are determined by the longest pathway.

(2)how to complete correspondence of  points between subjects?
In the course slides, it said"Correspondence of points between subjects based on Euclidean distance in MNI space".This sentence is so vague that I can't understand it.

(3)what is values in table for group analyses,diffusion measure of center or something else?

I am very sorry that my question is a bit more, but I still hope that you can answer my doubts. Thanks!

Qianwen


------------------ ???? ------------------
???: "Yendiki, Anastasia"<AYENDIKI@mgh.harvard.edu<mailto:AYENDIKI@mgh.harvard.edu>>;
????: 2018?9?12?(???) ??10:40
???: "Freesurfer support list"<freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>>;
??: Re: [Freesurfer] questions about trac-all -stat

Hi Qianwen ? You don?t have to do (1) and (2), trac-all ?stat does that for you. For a description of the measures, see the tutorial:
http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/TraculaStatistics
and the course slides:
http://surfer.nmr.mgh.harvard.edu/pub/docs/tracula,fs.ppt

Best,

a.y



From: <freesurfer-bounces@nmr.mgh.harvard.edu<mailto:freesurfer-bounces@nmr.mgh.harvard.edu>> on behalf of ??? <627611631@qq.com<mailto:627611631@qq.com>>
Reply-To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>>
Date: Wednesday, September 12, 2018 at 1:13 AM
To: freesurfer <freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: [Freesurfer] questions about trac-all -stat


        External Email - Use Caution

Dear experts,
I have some questions about along-path analysis:
(1)how to determine the first position and last position of all subjects' pathway when converting all pathstats.byvoxel.txt files to a table for group analyses?

(2)how to complete correspondence of  points between subjects?

(3)what is values in table for group analyses,diffusion measure of center or something else?

Thanks!
Qianwen

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------------------------------

Message: 6
Date: Thu, 13 Sep 2018 15:47:55 +0000
From: "Yendiki, Anastasia" <AYENDIKI@mgh.harvard.edu>
Subject: Re: [Freesurfer] problem with trac-preproc just at the middle
of Priors point
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Message-ID: <D7BFFE3F.26700%ayendiki@mgh.harvard.edu>
Content-Type: text/plain; charset="windows-1252"

Hi Marco ? This is strange and it?s not something that we can replicate locally. Because it looks like it dies when loading 31/33 of the training data, my first guess would be that it runs out of memory.

Best,
a.y

From: <freesurfer-bounces@nmr.mgh.harvard.edu<mailto:freesurfer-bounces@nmr.mgh.harvard.edu>> on behalf of "marco.muti@tin.it<mailto:marco.muti@tin.it>" <marco.muti@tin.it<mailto:marco.muti@tin.it>>
Reply-To: "marco.muti@outlook.com<mailto:marco.muti@outlook.com>" <marco.muti@outlook.com<mailto:marco.muti@outlook.com>>, Freesurfer support list <freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>>
Date: Thursday, September 13, 2018 at 7:35 AM
To: "freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>" <freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: [Freesurfer] problem with trac-preproc just at the middle of Priors point


        External Email - Use Caution


I'm trying to run the TRACULA software (fresurfer V 6.0)  in the VM for FSL . I'm using the only elmo.2005 images but the program stops just at the middle of priors point.
In the follow the log file.
Can someone help me please?


marco


///////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////

Mon Sep 10 14:39:14 BST 2018
/home/fsluser/usr_/local_/diffusion_recons
/usr/local/freesurfer/bin/trac-all
-prep -c /home/fsluser/usr_/local_/diffusion_tutorial/dmrirc.tutorial
Subject elmo.2005
SUBJECTS_DIR /home/fsluser/usr_/local_/diffusion_recons
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
fsluser
localhost.localdomain
Linux localhost.localdomain 3.10.0-514.16.1.el7.x86_64 #1 SMP Wed Apr 12 15:04:24 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      4096
maxlocks     unlimited
maxsignal    7172
maxmessage   819200
maxnice      0
maxrtprio    0
maxrttime    unlimited

              total        used        free      shared  buff/cache   available
Mem:        1867264      702820      805888       12064      358556      947408
Swap:       3145724      506716     2639008

########################################
Program versions:
$Id: trac-all,v 1.60.2.1 2016/12/20 17:04:05 zkaufman Exp $
mri_convert.bin --all-info
ProgramName: mri_convert.bin  ProgramArguments: --all-info  ProgramVersion: $Name: stable6 $  TimeStamp: 2018/09/10-13:39:14-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: fsluser  Machine: localhost.localdomain  Platform: Linux  PlatformVersion: 3.10.0-514.16.1.el7.x86_64  CompilerName: GCC  CompilerVersion: 40400
FLIRT version 6.0
$Id: bbregister,v 1.75 2016/05/10 20:02:28 greve Exp $
$Id: mri_cvs_register,v 1.48 2016/03/06 21:31:56 lzollei Exp $
ProgramName: dmri_motion  ProgramArguments: --all-info  ProgramVersion: $Name: stable6 $  TimeStamp: 2018/09/10-13:39:15-GMT  BuildTimeStamp: Jan 18 2017 16:38:58  CVS:   User: fsluser  Machine: localhost.localdomain  Platform: Linux  PlatformVersion: 3.10.0-514.16.1.el7.x86_64  CompilerName: GCC  CompilerVersion: 40400
ProgramName: dmri_train  ProgramArguments: --all-info  ProgramVersion: $Name: stable6 $  TimeStamp: 2018/09/10-13:39:15-GMT  BuildTimeStamp: Jan 18 2017 16:38:58  CVS:   User: fsluser  Machine: localhost.localdomain  Platform: Linux  PlatformVersion: 3.10.0-514.16.1.el7.x86_64  CompilerName: GCC  CompilerVersion: 40400
ProgramName: dmri_paths  ProgramArguments: --all-info  ProgramVersion: $Name:  $  TimeStamp: 2018/09/10-13:39:15-GMT  BuildTimeStamp: Jan 18 2017 16:38:58  CVS:   User: fsluser  Machine: localhost.localdomain  Platform: Linux  PlatformVersion: 3.10.0-514.16.1.el7.x86_64  CompilerName: GCC  CompilerVersion: 40400
ProgramName: dmri_pathstats  ProgramArguments: --all-info  ProgramVersion: $Name: stable6 $  TimeStamp: 2018/09/10-13:39:15-GMT  BuildTimeStamp: Jan 18 2017 16:38:58  CVS:   User: fsluser  Machine: localhost.localdomain  Platform: Linux  PlatformVersion: 3.10.0-514.16.1.el7.x86_64  CompilerName: GCC  CompilerVersion: 40400
ProgramName: dmri_mergepaths  ProgramArguments: --all-info  ProgramVersion: $Name: stable6 $  TimeStamp: 2018/09/10-13:39:15-GMT  BuildTimeStamp: Jan 18 2017 16:38:58  CVS:   User: fsluser  Machine: localhost.localdomain  Platform: Linux  PlatformVersion: 3.10.0-514.16.1.el7.x86_64  CompilerName: GCC  CompilerVersion: 40400
ProgramName: dmri_group  ProgramArguments: --all-info  ProgramVersion: $Name:  $  TimeStamp: 2018/09/10-13:39:15-GMT  BuildTimeStamp: Jan 18 2017 16:38:58  CVS:   User: fsluser  Machine: localhost.localdomain  Platform: Linux  PlatformVersion: 3.10.0-514.16.1.el7.x86_64  CompilerName: GCC  CompilerVersion: 40400


New invocation of trac-preproc


fsluser
localhost.localdomain
Linux localhost.localdomain 3.10.0-514.16.1.el7.x86_64 #1 SMP Wed Apr 12 15:04:24 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      4096
maxlocks     unlimited
maxsignal    7172
maxmessage   819200
maxnice      0
maxrtprio    0
maxrttime    unlimited

              total        used        free      shared  buff/cache   available
Mem:        1867264      703636      772376       12064      391252      946564
Swap:       3145724      506712     2639012

#-------------------------------------
/usr/local/freesurfer/bin/trac-preproc
#-------------------------------------
#@# Image corrections Mon Sep 10 14:39:15 BST 2018
mri_convert --bvec-voxel /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/orig/656000-11-1.dcm /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/dwi_orig.nii.gz
mri_convert.bin --bvec-voxel /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/orig/656000-11-1.dcm /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/dwi_orig.nii.gz
$Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $
reading from /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/orig/656000-11-1.dcm...
Getting Series No
INFO: Found 78 files in /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/orig
INFO: Scanning for Series Number 11
Scanning Directory
INFO: found 70 files in series
INFO: loading series header info.

RunNo = 10
WARNING: Run 1 appears to be truncated
  Files Found: 70, Files Expected (lRep+1): 120
FileName /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/orig/656000-11-1.dcm
Identification
NumarisVer        syngo MR 2004A 4VA25A
ScannerModel      Trio
PatientName       Trio_calib_002_run2
Date and time
StudyDate         20050905
StudyTime         100821.656000
SeriesTime        104226.748000
AcqTime           104209.522496
Acquisition parameters
PulseSeq          ep_b0#0
Protocol          DIFFUSION_HighRes
PhEncDir          COL
EchoNo            0
FlipAngle         90
EchoTime          100
InversionTime     -1
RepetitionTime    10100
PhEncFOV          256
ReadoutFOV        256
Image information
RunNo             10
SeriesNo          11
ImageNo           1
NImageRows        1024
NImageCols        1024
NFrames           70
SliceArraylSize   60
IsMosaic          1
ImgPos            1048.1801 1002.6923 -265.4914
VolRes              2.0000   2.0000   2.0000
VolDim            128      128       60
Vc                 -0.9997   0.0244   0.0005
Vr                 -0.0238  -0.9764   0.2147
Vs                  0.0057   0.2147   0.9767
VolCenter           0.0000   0.0000   0.0000
TransferSyntaxUID unknown
INFO: sorting.
INFO: (128 128  60), nframes = 70, ismosaic=1
sdfi->UseSliceScaleFactor 0
datatype = 4, short=4, float=3
Numaris Version: syngo MR 2004A 4VA25A  Maj = 4, Min=2, MinMin = 5
Repetition Time = 10100, TR = 10100 ms
PE Dir COL COL
AutoAlign matrix detected
AutoAlign Matrix ---------------------
0.99970   0.02376  -0.00570  -0.49480;
-0.02443   0.97638  -0.21466  -40.55519;
0.00047   0.21474   0.97667   12.50291;
0.00000   0.00000   0.00000   1.00000;

FileName /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/orig/656000-11-1.dcm
Identification
NumarisVer        syngo MR 2004A 4VA25A
ScannerModel      Trio
PatientName       Trio_calib_002_run2
Date and time
StudyDate         20050905
StudyTime         100821.656000
SeriesTime        104226.748000
AcqTime           104209.522496
Acquisition parameters
PulseSeq          ep_b0#0
Protocol          DIFFUSION_HighRes
PhEncDir          COL
EchoNo            0
FlipAngle         90
EchoTime          100
InversionTime     -1
RepetitionTime    10100
PhEncFOV          256
ReadoutFOV        256
Image information
RunNo             10
SeriesNo          11
ImageNo           1
NImageRows        1024
NImageCols        1024
NFrames           70
SliceArraylSize   60
IsMosaic          1
ImgPos            131.1612 149.7402 -72.6670
VolRes              2.0000   2.0000   2.0000
VolDim            128      128       60
Vc                 -0.9997   0.0244   0.0005
Vr                 -0.0238  -0.9764   0.2147
Vs                  0.0057   0.2147   0.9767
VolCenter           0.5005  40.7699  13.4796
TransferSyntaxUID unknown
UseSliceScaleFactor 0 (slice 0: 1)
IsDWI = 0
sagrev = 1, correv =1, trarev = 0
Vs = 0.0057 0.214665 0.976671
INFO: no Siemens slice order reversal detected (good!).
TR=10100.00, TE=100.00, TI=-1.00, flip angle=90.00
i_ras = (-0.999702, 0.0244268, 0.000465598)
j_ras = (-0.023757, -0.976382, 0.21474)
k_ras = (0.0057, 0.214665, 0.976671)
writing to /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/dwi_orig.nii.gz...
mri_probedicom --i /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/orig/656000-11-1.dcm > /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/dcminfo.dat
cp /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/orig/bvecs.txt /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/dwi_orig.bvecs
cp /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/orig/bvals.txt /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/dwi_orig.bvals
mv -f /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/bvecs.tmp /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/dwi_orig.bvecs
mv -f /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/bvals.tmp /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/dwi_orig.bvals
orientLAS /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/dwi_orig.nii.gz /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/dwi_orig_las.nii.gz
INFO: input image orientation is LPS
INFO: input image determinant is 8
mri_convert -oni 128 -onj 128 -onk 60 -oid -0.999701 0.0244268 0.000465598 -ojd 0.023757 0.976382 -0.21474 -okd 0.0057 0.214665 0.976671 -oc 0.548018 42.7227 13.0501 -rt nearest /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/dwi_orig.nii.gz /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/dwi_orig_las.nii.gz
mri_convert.bin -oni 128 -onj 128 -onk 60 -oid -0.999701 0.0244268 0.000465598 -ojd 0.023757 0.976382 -0.21474 -okd 0.0057 0.214665 0.976671 -oc 0.548018 42.7227 13.0501 -rt nearest /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/dwi_orig.nii.gz /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/dwi_orig_las.nii.gz
normalizing out_i_direction: (-0.999701, 0.0244268, 0.000465598) -> (-0.999702, 0.0244268, 0.000465598)
normalizing out_j_direction: (0.023757, 0.976382, -0.21474) -> (0.023757, 0.976382, -0.21474)
normalizing out_k_direction: (0.0057, 0.214665, 0.976671) -> (0.0057, 0.214665, 0.976671)
$Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $
reading from /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/dwi_orig.nii.gz...
TR=10100.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-0.999701, 0.0244268, 0.000465598)
j_ras = (-0.023757, -0.976382, 0.21474)
k_ras = (0.0057, 0.214665, 0.976671)
Reslicing using nearest
writing to /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/dwi_orig_las.nii.gz...
INFO: found /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/dwi_orig.bvals, copying
INFO: found /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/dwi_orig.bvecs, converting to LAS
mv -f /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/dwi_orig_las.bvecs /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/bvecs
mv -f /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/dwi_orig_las.bvals /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/bvals
eddy_correct /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/dwi_orig_las.nii.gz /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/dwi.nii.gz 0
processing /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/dwi_tmp0000
processing /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/dwi_tmp0001
processing /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/dwi_tmp0002
processing /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/dwi_tmp0003
processing /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/dwi_tmp0004
processing /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/dwi_tmp0005
processing /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/dwi_tmp0006
processing /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/dwi_tmp0007
processing /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/dwi_tmp0008
processing /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/dwi_tmp0009
processing /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/dwi_tmp0010
processing /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/dwi_tmp0011
processing /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/dwi_tmp0012
processing /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/dwi_tmp0013
processing /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/dwi_tmp0014
processing /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/dwi_tmp0015
processing /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/dwi_tmp0016
processing /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/dwi_tmp0017
processing /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/dwi_tmp0018
processing /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/dwi_tmp0019
processing /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/dwi_tmp0020
processing /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/dwi_tmp0021
processing /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/dwi_tmp0022
processing /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/dwi_tmp0023
processing /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/dwi_tmp0024
processing /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/dwi_tmp0025
processing /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/dwi_tmp0026
processing /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/dwi_tmp0027
processing /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/dwi_tmp0028
processing /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/dwi_tmp0029
processing /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/dwi_tmp0030
processing /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/dwi_tmp0031
processing /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/dwi_tmp0032
processing /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/dwi_tmp0033
processing /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/dwi_tmp0034
processing /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/dwi_tmp0035
processing /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/dwi_tmp0036
processing /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/dwi_tmp0037
processing /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/dwi_tmp0038
processing /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/dwi_tmp0039
processing /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/dwi_tmp0040
processing /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/dwi_tmp0041
processing /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/dwi_tmp0042
processing /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/dwi_tmp0043
processing /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/dwi_tmp0044
processing /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/dwi_tmp0045
processing /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/dwi_tmp0046
processing /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/dwi_tmp0047
processing /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/dwi_tmp0048
processing /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/dwi_tmp0049
processing /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/dwi_tmp0050
processing /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/dwi_tmp0051
processing /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/dwi_tmp0052
processing /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/dwi_tmp0053
processing /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/dwi_tmp0054
processing /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/dwi_tmp0055
processing /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/dwi_tmp0056
processing /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/dwi_tmp0057
processing /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/dwi_tmp0058
processing /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/dwi_tmp0059
processing /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/dwi_tmp0060
processing /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/dwi_tmp0061
processing /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/dwi_tmp0062
processing /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/dwi_tmp0063
processing /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/dwi_tmp0064
processing /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/dwi_tmp0065
processing /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/dwi_tmp0066
processing /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/dwi_tmp0067
processing /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/dwi_tmp0068
processing /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/dwi_tmp0069
mv -f /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/bvecs /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/bvecs.norot
xfmrot /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/dwi.ecclog /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/bvecs.norot /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/bvecs
ln -sf /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/dwi.nii.gz /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/data.nii.gz
mri_convert --frame 0 1 2 3 4 5 6 7 8 9 /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/dwi.nii.gz /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/lowb.nii.gz
mri_convert.bin --frame 0 1 2 3 4 5 6 7 8 9 /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/dwi.nii.gz /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/lowb.nii.gz
$Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $
reading from /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/dwi.nii.gz...
TR=1000.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-0.999701, 0.0244268, 0.000465598)
j_ras = (0.023757, 0.976382, -0.21474)
k_ras = (0.0057, 0.214665, 0.976671)
keeping frames 0 1 2 3 4 5 6 7 8 9
writing to /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/lowb.nii.gz...
mri_concat --i /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/lowb.nii.gz --mean --o /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/lowb.nii.gz
ninputs = 1
Checking inputs
nframestot = 10
Allocing output
Done allocing
nframes = 10
Computing mean across frames
Writing to /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/lowb.nii.gz
bet /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/lowb.nii.gz /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/lowb_brain.nii.gz -m -f 0.3
mv -f /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/lowb_brain_mask.nii.gz /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dlabel/diff
#-------------------------------------
#@# Image quality assessment Mon Sep 10 14:50:58 BST 2018
/usr/local/freesurfer/bin/dmri_motion --dwi /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/dwi_orig.nii.gz --mat /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/dwi.ecclog --bval /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/bvals --T 139.399994 --out /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/dwi_motion.txt


cwd /home/fsluser/usr_/local_/diffusion_recons
cmdline /usr/local/freesurfer/bin/dmri_motion --dwi /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/dwi_orig.nii.gz --mat /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/dwi.ecclog --bval /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/bvals --T 139.399994 --out /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/dwi_motion.txt
sysname  Linux
hostname localhost.localdomain
machine  x86_64
user     fsluser
Output motion measure file: /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/dwi_motion.txt
Input transform file: /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/dwi.ecclog
Input DWI file: /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/dwi_orig.nii.gz
Input b-value table: /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/bvals
Low-b image intensity threshold: 139.4
Nominal diffusivity: 0.001
Loading volume-to-baseline affine transformations
Computing between-volume head motion measures
INFO: Processed transforms for 70 volumes
Loading DWI volume series from /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/dwi_orig.nii.gz
Loading b-value table from /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/bvals
Computing within-volume head motion measures
Done in 4.418 sec.
dmri_motion done
#-------------------------------------
#@# Intra-subject registration Mon Sep 10 14:51:03 BST 2018
mri_convert /home/fsluser/usr_/local_/diffusion_recons/elmo.2005/mri/brain.mgz /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/brain_anat_orig.nii.gz
mri_convert.bin /home/fsluser/usr_/local_/diffusion_recons/elmo.2005/mri/brain.mgz /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/brain_anat_orig.nii.gz
$Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $
reading from /home/fsluser/usr_/local_/diffusion_recons/elmo.2005/mri/brain.mgz...
TR=2530.00, TE=3.45, TI=1100.00, flip angle=7.00
i_ras = (-1, 6.33299e-08, -2.04891e-08)
j_ras = (-9.31323e-09, 2.32831e-10, -1)
k_ras = (7.07805e-08, 1, 1.74623e-09)
writing to /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/brain_anat_orig.nii.gz...
orientLAS /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/brain_anat_orig.nii.gz /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/brain_anat.nii.gz
INFO: input image orientation is LIA
INFO: input image determinant is -1
mri_convert -oni 256 -onj 256 -onk 256 -oid -1 6.33299e-08 -2.04891e-08 -ojd 7.07805e-08 1 1.74623e-09 -okd 9.31323e-09 -2.32831e-10 1 -oc 3.70524 44.2681 16.0046 -rt nearest /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/brain_anat_orig.nii.gz /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/brain_anat.nii.gz
mri_convert.bin -oni 256 -onj 256 -onk 256 -oid -1 6.33299e-08 -2.04891e-08 -ojd 7.07805e-08 1 1.74623e-09 -okd 9.31323e-09 -2.32831e-10 1 -oc 3.70524 44.2681 16.0046 -rt nearest /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/brain_anat_orig.nii.gz /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/brain_anat.nii.gz
$Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $
reading from /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/brain_anat_orig.nii.gz...
TR=2530.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-1, 6.33299e-08, -2.04891e-08)
j_ras = (-9.31323e-09, 2.32831e-10, -1)
k_ras = (7.07805e-08, 1, 1.74623e-09)
Reslicing using nearest
writing to /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/brain_anat.nii.gz...
tkregister2 --mov /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/brain_anat_orig.nii.gz --targ /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/brain_anat.nii.gz --regheader --noedit --fslregout /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/xfms/anatorig2anat.mat --reg /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/xfms/anat2anatorig.dat
tkregister_tcl /usr/local/freesurfer/tktools/tkregister2.tcl
target  volume /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/brain_anat.nii.gz
movable volume /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/brain_anat_orig.nii.gz
reg file       /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/xfms/anat2anatorig.dat
LoadVol        0
ZeroCRAS       0
$Id: tkregister2.c,v 1.132.2.1 2016/08/02 21:17:29 greve Exp $
Diagnostic Level -1
INFO: loading target /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/brain_anat.nii.gz
INFO: target does not conform to COR format, so I'm going to
reslice to COR. This will not affect the final registration.
Ttarg: --------------------
-1.00000   0.00000   0.00000   128.00000;
0.00000   0.00000   1.00000  -128.00000;
0.00000  -1.00000   0.00000   128.00000;
0.00000   0.00000   0.00000   1.00000;
INFO: loading movable /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/brain_anat_orig.nii.gz
Tmov: --------------------
-1.00000   0.00000   0.00000   128.00000;
0.00000   0.00000   1.00000  -128.00000;
0.00000  -1.00000   0.00000   128.00000;
0.00000   0.00000   0.00000   1.00000;
mkheaderreg = 1, float2int = 0
Computing reg from header (and possibly input matrix)
---- Input registration matrix (computed) --------
1.00000  -0.00000  -0.00000  -0.00002;
0.00000   1.00000   0.00000   0.00004;
-0.00000  -0.00000   1.00000   0.99997;
0.00000   0.00000   0.00000   1.00000;
---------------------------------------
---- Input registration matrix --------
1.00000  -0.00000  -0.00000  -0.00002;
0.00000   1.00000   0.00000   0.00004;
-0.00000  -0.00000   1.00000   0.99997;
0.00000   0.00000   0.00000   1.00000;
Determinant 1
subject = subject-unknown
RegMat ---------------------------
1.00000   0.00000   0.00000  -0.00001;
0.00000  -0.00000  -1.00000   0.00004;
0.00000   1.00000  -0.00000   0.99997;
0.00000   0.00000   0.00000   1.00000;
FSLOUTPUTTYPE NIFTI_GZ
tkreg2FSL: mov det = -1, ref det = -1
convert_xfm -omat /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/xfms/anat2anatorig.mat -inverse /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/xfms/anatorig2anat.mat
tmp /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/xfms/tmp.bbregister.28041
Log file is /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/xfms/anatorig2diff.bbr.dat.log
Mon Sep 10 14:51:06 BST 2018

setenv SUBJECTS_DIR /home/fsluser/usr_/local_/diffusion_recons
cd /home/fsluser/usr_/local_/diffusion_recons
/usr/local/freesurfer/bin/bbregister --s elmo.2005 --init-fsl --dti --mov /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/dwi.nii.gz --reg /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/xfms/anatorig2diff.bbr.dat --fslmat /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/xfms/diff2anatorig.bbr.mat

$Id: bbregister,v 1.75 2016/05/10 20:02:28 greve Exp $
Linux localhost.localdomain 3.10.0-514.16.1.el7.x86_64 #1 SMP Wed Apr 12 15:04:24 UTC 2017 x86_64 x86_64 x86_64 GNU/Linux
FREESURFER_HOME /usr/local/freesurfer
mri_convert /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/dwi.nii.gz /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/xfms/tmp.bbregister.28041/template.nii
mri_convert.bin /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/dwi.nii.gz /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/xfms/tmp.bbregister.28041/template.nii
$Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $
reading from /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/dwi.nii.gz...
TR=1000.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-0.999701, 0.0244268, 0.000465598)
j_ras = (0.023757, 0.976382, -0.21474)
k_ras = (0.0057, 0.214665, 0.976671)
writing to /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/xfms/tmp.bbregister.28041/template.nii...
fslregister --s elmo.2005 --mov /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/xfms/tmp.bbregister.28041/template.nii --reg /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/xfms/tmp.bbregister.28041/reg.init.dat --niters 1 --maxangle 90 --tmp /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/xfms/tmp.bbregister.28041/fslregister --dof 6 --fsvol brainmask.mgz --nobetmov

Log file is /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/xfms/tmp.bbregister.28041/reg.init.dat.fslregister.log

Mon Sep 10 14:51:12 BST 2018
--s elmo.2005 --mov /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/xfms/tmp.bbregister.28041/template.nii --reg /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/xfms/tmp.bbregister.28041/reg.init.dat --niters 1 --maxangle 90 --tmp /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/xfms/tmp.bbregister.28041/fslregister --dof 6 --fsvol brainmask.mgz --nobetmov
$Id: fslregister,v 1.40 2016/02/12 21:43:15 zkaufman Exp $
localhost.localdomain
Linux localhost.localdomain 3.10.0-514.16.1.el7.x86_64 #1 SMP Wed Apr 12 15:04:24 UTC 2017 x86_64 x86_64 x86_64 GNU/Linux
nIters 1
--------------------------------------
/home/fsluser/usr_/local_/diffusion_recons
mri_convert /home/fsluser/usr_/local_/diffusion_recons/elmo.2005/mri/brainmask.mgz /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/xfms/tmp.bbregister.28041/fslregister/refvol.fslregister.nii
mri_convert.bin /home/fsluser/usr_/local_/diffusion_recons/elmo.2005/mri/brainmask.mgz /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/xfms/tmp.bbregister.28041/fslregister/refvol.fslregister.nii
$Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $
reading from /home/fsluser/usr_/local_/diffusion_recons/elmo.2005/mri/brainmask.mgz...
TR=2530.00, TE=3.45, TI=1100.00, flip angle=7.00
i_ras = (-1, 6.33299e-08, -2.04891e-08)
j_ras = (-9.31323e-09, 2.32831e-10, -1)
k_ras = (7.07805e-08, 1, 1.74623e-09)
writing to /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/xfms/tmp.bbregister.28041/fslregister/refvol.fslregister.nii...
--------------------------------------
/home/fsluser/usr_/local_/diffusion_recons
mri_convert /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/xfms/tmp.bbregister.28041/template.nii /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/xfms/tmp.bbregister.28041/fslregister/movvol.fslregister.nii --frame 0
mri_convert.bin /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/xfms/tmp.bbregister.28041/template.nii /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/xfms/tmp.bbregister.28041/fslregister/movvol.fslregister.nii --frame 0
$Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $
reading from /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/xfms/tmp.bbregister.28041/template.nii...
TR=1000.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-0.999701, 0.0244268, 0.000465598)
j_ras = (0.023757, 0.976382, -0.21474)
k_ras = (0.0057, 0.214665, 0.976671)
keeping frame 0
writing to /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/xfms/tmp.bbregister.28041/fslregister/movvol.fslregister.nii...
Mov determinant is -8
/home/fsluser/usr_/local_/diffusion_recons
tkregister2_cmdl --mov /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/xfms/tmp.bbregister.28041/fslregister/movvol.fslregister.nii --reg /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/xfms/tmp.bbregister.28041/fslregister/reg0.28082.dat --regheader --fslregout /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/xfms/tmp.bbregister.28041/reg.init.dat.fsl.mat0 --s elmo.2005 --noedit
tkregister_tcl /usr/local/freesurfer/tktools/tkregister2.tcl
INFO: no target volume specified, assuming FreeSurfer orig volume.
target  volume orig
movable volume /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/xfms/tmp.bbregister.28041/fslregister/movvol.fslregister.nii
reg file       /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/xfms/tmp.bbregister.28041/fslregister/reg0.28082.dat
LoadVol        0
ZeroCRAS       0
$Id: tkregister2.c,v 1.132.2.1 2016/08/02 21:17:29 greve Exp $
Diagnostic Level -1
INFO: loading target /home/fsluser/usr_/local_/diffusion_recons/elmo.2005/mri/orig.mgz
Ttarg: --------------------
-1.00000   0.00000   0.00000   128.00000;
0.00000   0.00000   1.00000  -128.00000;
0.00000  -1.00000   0.00000   128.00000;
0.00000   0.00000   0.00000   1.00000;
INFO: loading movable /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/xfms/tmp.bbregister.28041/fslregister/movvol.fslregister.nii
Tmov: --------------------
-2.00000   0.00000   0.00000   128.00000;
0.00000   0.00000   2.00000  -60.00000;
0.00000  -2.00000   0.00000   128.00000;
0.00000   0.00000   0.00000   1.00000;
mkheaderreg = 1, float2int = 0
Computing reg from header (and possibly input matrix)
---- Input registration matrix (computed) --------
0.99970  -0.02443  -0.00047   3.11760;
0.00570   0.21466   0.97667   2.25865;
-0.02376  -0.97638   0.21474  -1.16418;
0.00000   0.00000   0.00000   1.00000;
---------------------------------------
---- Input registration matrix --------
0.99970  -0.02443  -0.00047   3.11760;
0.00570   0.21466   0.97667   2.25865;
-0.02376  -0.97638   0.21474  -1.16418;
0.00000   0.00000   0.00000   1.00000;
Determinant 1
subject = elmo.2005
RegMat ---------------------------
0.99970  -0.02443  -0.00047   3.11760;
0.00570   0.21466   0.97667   2.25865;
-0.02376  -0.97638   0.21474  -1.16418;
0.00000   0.00000   0.00000   1.00000;
FSLOUTPUTTYPE NIFTI
tkreg2FSL: mov det = -8, ref det = -1
Mon Sep 10 14:51:17 BST 2018
/home/fsluser/usr_/local_/diffusion_recons
flirt.fsl -ref /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/xfms/tmp.bbregister.28041/fslregister/refvol.fslregister.nii -in /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/xfms/tmp.bbregister.28041/fslregister/movvol.fslregister.nii -bins 256 -cost corratio -dof 6 -searchrx -90 90 -searchry -90 90 -searchrz -90 90 -verbose 0 -omat /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/xfms/tmp.bbregister.28041/fslregister/fslmat0.trans.mat -schedule /usr/local/freesurfer/bin/fsl.5.0.2.xyztrans.sch -init /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/xfms/tmp.bbregister.28041/reg.init.dat.fsl.mat0
Mon Sep 10 14:51:23 BST 2018
/home/fsluser/usr_/local_/diffusion_recons
flirt.fsl -ref /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/xfms/tmp.bbregister.28041/fslregister/refvol.fslregister.nii -in /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/xfms/tmp.bbregister.28041/fslregister/movvol.fslregister.nii -bins 256 -cost corratio -dof 6 -searchrx -90 90 -searchry -90 90 -searchrz -90 90 -verbose 0 -omat /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/xfms/tmp.bbregister.28041/reg.init.dat.fsl.mat -init /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/xfms/tmp.bbregister.28041/fslregister/fslmat0.trans.mat -schedule /usr/local/freesurfer/bin/flirt.newdefault.20080811.sch
tkregister2_cmdl --s elmo.2005 --mov /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/xfms/tmp.bbregister.28041/template.nii --reg /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/xfms/tmp.bbregister.28041/reg.init.dat --fslreg /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/xfms/tmp.bbregister.28041/reg.init.dat.fsl.mat --noedit
tkregister_tcl /usr/local/freesurfer/tktools/tkregister2.tcl
---- FSL registration matrix --------
0.99918  -0.04042   0.00180   7.99378;
0.01127   0.23516  -0.97189   154.31700;
0.03886   0.97112   0.23542  -17.03460;
0.00000   0.00000   0.00000   1.00000;
---------------------------------------
INFO: no target volume specified, assuming FreeSurfer orig volume.
target  volume orig
movable volume /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/xfms/tmp.bbregister.28041/template.nii
reg file       /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/xfms/tmp.bbregister.28041/reg.init.dat
LoadVol        0
ZeroCRAS       0
$Id: tkregister2.c,v 1.132.2.1 2016/08/02 21:17:29 greve Exp $
Diagnostic Level -1
INFO: loading target /home/fsluser/usr_/local_/diffusion_recons/elmo.2005/mri/orig.mgz
Ttarg: --------------------
-1.00000   0.00000   0.00000   128.00000;
0.00000   0.00000   1.00000  -128.00000;
0.00000  -1.00000   0.00000   128.00000;
0.00000   0.00000   0.00000   1.00000;
INFO: loading movable /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/xfms/tmp.bbregister.28041/template.nii
Tmov: --------------------
-2.00000   0.00000   0.00000   128.00000;
0.00000   0.00000   2.00000  -60.00000;
0.00000  -2.00000   0.00000   128.00000;
0.00000   0.00000   0.00000   1.00000;
mkheaderreg = 0, float2int = 0
FSLOUTPUTTYPE NIFTI
fsl2TkReg: mov det = -8, ref det = -1
---- Input registration matrix (computed) --------
0.99918  -0.03886   0.01127   2.75252;
-0.00180   0.23542   0.97189  -0.06236;
-0.04042  -0.97112   0.23516  -1.80609;
0.00000   0.00000   0.00000   1.00000;
---------------------------------------
---- Input registration matrix --------
0.99918  -0.03886   0.01127   2.75252;
-0.00180   0.23542   0.97189  -0.06236;
-0.04042  -0.97112   0.23516  -1.80609;
0.00000   0.00000   0.00000   1.00000;
Determinant 0.999999
subject = elmo.2005
RegMat ---------------------------
0.99918  -0.03886   0.01127   2.75252;
-0.00180   0.23542   0.97189  -0.06236;
-0.04042  -0.97112   0.23516  -1.80609;
0.00000   0.00000   0.00000   1.00000;
(standard_in) 1: syntax error

Started at Mon Sep 10 14:51:12 BST 2018
Ended   at Mon Sep 10 14:51:41 BST 2018

fslregister Done

To check results, run:
tkregister2 --mov /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/xfms/tmp.bbregister.28041/template.nii --reg /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/xfms/tmp.bbregister.28041/reg.init.dat --surf orig

mri_segreg --mov /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/xfms/tmp.bbregister.28041/template.nii --init-reg /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/xfms/tmp.bbregister.28041/reg.init.dat --out-reg /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/xfms/tmp.bbregister.28041/bbr.pass1.dat --subsamp-brute 100 --subsamp 100 --tol 1e-4 --tol1d 1e-3 --brute -4 4 4 --surf white --gm-proj-frac 0.5 --gm-gt-wm 0.5
$Id: mri_segreg.c,v 1.113 2016/05/10 03:23:20 greve Exp $
setenv SUBJECTS_DIR /home/fsluser/usr_/local_/diffusion_recons
cd /home/fsluser/usr_/local_/diffusion_recons
mri_segreg --mov /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/xfms/tmp.bbregister.28041/template.nii --init-reg /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/xfms/tmp.bbregister.28041/reg.init.dat --out-reg /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/xfms/tmp.bbregister.28041/bbr.pass1.dat --subsamp-brute 100 --subsamp 100 --tol 1e-4 --tol1d 1e-3 --brute -4 4 4 --surf white --gm-proj-frac 0.5 --gm-gt-wm 0.5
sysname  Linux
hostname localhost.localdomain
machine  x86_64
user     fsluser
movvol /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/xfms/tmp.bbregister.28041/template.nii
regfile /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/xfms/tmp.bbregister.28041/reg.init.dat
subject elmo.2005
dof 6
outregfile /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/xfms/tmp.bbregister.28041/bbr.pass1.dat
UseMask 0
UseLH 1
UseRH 1
nsubsamp 100
PenaltySign  -1
PenaltySlope 0.500000
PenaltyCenter 0.000000
surfname white
GMProjFrac 0.500000
WMProjAbs 2.000000
lhcostfile (null)
rhcostfile (null)
interp  trilinear (1)
frame  0
TolPowell 0.000100
nMaxItersPowell 36
n1dmin  3
Profile   0
Gdiag_no  -1
AddNoise  0 (0)
SynthSeed 1537118316
TransRandMax 0.000000
RotRandMax 0.000000
Translations 0.000000 0.000000 0.000000
Rotations   0.000000 0.000000 0.000000
Input reg
0.99918  -0.03886   0.01127   2.75252;
-0.00180   0.23542   0.97189  -0.06236;
-0.04042  -0.97112   0.23516  -1.80609;
0.00000   0.00000   0.00000   1.00000;

Loading mov
Extracting frame 0
Projecting LH Surfs
Loading lh.white surf
Loading lh.thickness for GM
GM Proj: 1 0.500000 2.000000
WM Proj: 0 0.500000 2.000000
Projecting RH Surfs
Loading rh.white surf
Loading rh.thickness for GM
Projecting RH Surfs
Using lh.cortex.label
Using rh.cortex.label
Computing relative cost
0  -25.0 -25.0 -25.0   0.985304
1  -25.0 -25.0  25.0   1.003463
2  -25.0  25.0 -25.0   0.981149
3  -25.0  25.0  25.0   1.010608
4   25.0 -25.0 -25.0   0.997072
5   25.0 -25.0  25.0   1.010833
6   25.0  25.0 -25.0   0.981523
7   25.0  25.0  25.0   1.019362
REL:  8  0.481295    7.989313  0.998664 rel = 0.481938
Initial costs ----------------
Number of surface hits 2679
WM  Intensity   208.1729 +/- 115.2740
Ctx Intensity   275.5693 +/- 149.3314
Pct Contrast     23.8307 +/-  42.4267
Cost   0.4813
RelCost   0.4819

------------------------------------
Brute force preopt -4 4 4, n = 729
     0  -4.0000  -4.0000  -4.0000  -4.0000  -4.0000  -4.0000      0.9886   0.9886  0.0
     1  -4.0000  -4.0000  -4.0000  -4.0000  -4.0000   0.0000      0.9625   0.9625  0.0
     2  -4.0000  -4.0000  -4.0000  -4.0000  -4.0000   4.0000      0.9370   0.9370  0.0
     6  -4.0000  -4.0000  -4.0000  -4.0000   4.0000  -4.0000      0.9237   0.9237  0.0
     7  -4.0000  -4.0000  -4.0000  -4.0000   4.0000   0.0000      0.8538   0.8538  0.0
    97  -4.0000   0.0000  -4.0000   0.0000   4.0000   0.0000      0.8210   0.8210  0.0
   123  -4.0000   0.0000   0.0000   0.0000   4.0000  -4.0000      0.7789   0.7789  0.0
   124  -4.0000   0.0000   0.0000   0.0000   4.0000   0.0000      0.7606   0.7606  0.0
   363   0.0000   0.0000   0.0000   0.0000   0.0000  -4.0000      0.7168   0.7168  0.0
   364   0.0000   0.0000   0.0000   0.0000   0.0000   0.0000      0.4813   0.4813  0.0
Brute Force --------------------------
Min cost was 0.481295
Number of iterations   729
Search time 1.611000 sec
Parameters at best (transmm, rotdeg)
  0.000   0.000   0.000  0.000  0.000  0.000
--------------------------------------------

Starting Powell Minimization
Init Powel Params dof = 6
0 0
1 0
2 0
3 0
4 0
5 0
fs_powell::minimize
  nparams 6
  maxfev 36
  ftol   0.000100
  linmin_xtol_   0.001000
  powell nthiter 0: fret = 0.481295
   7  0.135  0.000  0.000  0.000  0.000  0.000   0.4779112049
  10  0.122  0.000  0.000  0.000  0.000  0.000   0.4778248409
  12  0.123  0.000  0.000  0.000  0.000  0.000   0.4778223804
  25  0.123 -0.044  0.000  0.000  0.000  0.000   0.4778011390
  29  0.123 -0.036  0.000  0.000  0.000  0.000   0.4777963222
  31  0.123 -0.039  0.000  0.000  0.000  0.000   0.4777931744
  35  0.123 -0.039  1.000  0.000  0.000  0.000   0.4654924758
  44  0.123 -0.039  1.033  0.000  0.000  0.000   0.4649766994
  45  0.123 -0.039  1.037  0.000  0.000  0.000   0.4649588157
  47  0.123 -0.039  1.039  0.000  0.000  0.000   0.4649545250
  54  0.123 -0.039  1.039 -0.618  0.000  0.000   0.4613594586
  56  0.123 -0.039  1.039 -0.356  0.000  0.000   0.4606742453
  57  0.123 -0.039  1.039 -0.432  0.000  0.000   0.4592808449
  58  0.123 -0.039  1.039 -0.476  0.000  0.000   0.4591395480
  59  0.123 -0.039  1.039 -0.466  0.000  0.000   0.4588285780
  60  0.123 -0.039  1.039 -0.455  0.000  0.000   0.4586162323
  62  0.123 -0.039  1.039 -0.452  0.000  0.000   0.4586004888
  63  0.123 -0.039  1.039 -0.451  0.000  0.000   0.4586003764
  75  0.123 -0.039  1.039 -0.451 -0.010  0.000   0.4585257072
  76  0.123 -0.039  1.039 -0.451 -0.014  0.000   0.4585225156
  77  0.123 -0.039  1.039 -0.451 -0.013  0.000   0.4585219959
  87  0.123 -0.039  1.039 -0.451 -0.013  0.032   0.4585072286
  88  0.123 -0.039  1.039 -0.451 -0.013  0.018   0.4584264964
  89  0.123 -0.039  1.039 -0.451 -0.013  0.016   0.4584253499
  90  0.123 -0.039  1.039 -0.451 -0.013  0.015   0.4584251210
  powell nthiter 1: fret = 0.458425
  99 -0.030 -0.039  1.039 -0.451 -0.013  0.015   0.4548510808
100 -0.071 -0.039  1.039 -0.451 -0.013  0.015   0.4543073001
104 -0.062 -0.039  1.039 -0.451 -0.013  0.015   0.4542563468
106 -0.063 -0.039  1.039 -0.451 -0.013  0.015   0.4542556740
113 -0.063 -0.657  1.039 -0.451 -0.013  0.015   0.4514610163
115 -0.063 -0.401  1.039 -0.451 -0.013  0.015   0.4419651219
116 -0.063 -0.368  1.039 -0.451 -0.013  0.015   0.4417822150
118 -0.063 -0.381  1.039 -0.451 -0.013  0.015   0.4415713539
129 -0.063 -0.381  0.949 -0.451 -0.013  0.015   0.4409935232
131 -0.063 -0.381  0.983 -0.451 -0.013  0.015   0.4399692941
132 -0.063 -0.381  0.989 -0.451 -0.013  0.015   0.4399364486
133 -0.063 -0.381  0.991 -0.451 -0.013  0.015   0.4399362054
144 -0.063 -0.381  0.991 -0.435 -0.013  0.015   0.4396884912
146 -0.063 -0.381  0.991 -0.436 -0.013  0.015   0.4396863031
159 -0.063 -0.381  0.991 -0.436 -0.012  0.015   0.4396857374
168 -0.063 -0.381  0.991 -0.436 -0.012  0.002   0.4396353849
169 -0.063 -0.381  0.991 -0.436 -0.012  0.001   0.4396340069
170 -0.063 -0.381  0.991 -0.436 -0.012 -0.002   0.4396327392
172 -0.063 -0.381  0.991 -0.436 -0.012 -0.001   0.4396322829
  powell nthiter 2: fret = 0.439632
184 -0.064 -0.381  0.991 -0.436 -0.012 -0.001   0.4396101542
185 -0.070 -0.381  0.991 -0.436 -0.012 -0.001   0.4395798553
208 -0.070 -0.381  0.977 -0.436 -0.012 -0.001   0.4394650593
210 -0.070 -0.381  0.979 -0.436 -0.012 -0.001   0.4394625826
222 -0.070 -0.381  0.979 -0.431 -0.012 -0.001   0.4394569675
223 -0.070 -0.381  0.979 -0.433 -0.012 -0.001   0.4394533231
234 -0.070 -0.381  0.979 -0.433 -0.004 -0.001   0.4394149746
235 -0.070 -0.381  0.979 -0.433 -0.006 -0.001   0.4394125073
  powell nthiter 3: fret = 0.439413
259 -0.069 -0.381  0.979 -0.433 -0.006 -0.001   0.4394122592
269 -0.069 -0.380  0.979 -0.433 -0.006 -0.001   0.4394115605
281 -0.069 -0.380  0.975 -0.433 -0.006 -0.001   0.4393971568
305 -0.069 -0.380  0.975 -0.433 -0.004 -0.001   0.4393957905
318 -0.069 -0.380  0.975 -0.433 -0.004 -0.003   0.4393945423
Powell done niters = 3
Computing relative cost
0  -25.0 -25.0 -25.0   0.981197
1  -25.0 -25.0  25.0   1.000288
2  -25.0  25.0 -25.0   0.994687
3  -25.0  25.0  25.0   1.000546
4   25.0 -25.0 -25.0   1.008915
5   25.0 -25.0  25.0   1.016643
6   25.0  25.0 -25.0   0.996728
7   25.0  25.0  25.0   1.026021
REL:  8  0.439395    8.025025  1.003128 rel = 0.438024
Number of iterations     3
Min cost was 0.439395
Number of FunctionCalls   320
TolPowell 0.000100
nMaxItersPowell 36
OptimizationTime 0.933000 sec
Parameters at optimum (transmm) -0.06893 -0.37986  0.97505
Parameters at optimum (rotdeg) -0.43286 -0.00427 -0.00320
Final costs ----------------
Number of surface hits 2680
WM  Intensity   204.6878 +/- 112.1423
Ctx Intensity   275.3361 +/- 147.5540
Pct Contrast     25.6014 +/-  41.7909
Cost   0.4394
RelCost   0.4819
Reg at min cost was
0.99918  -0.03878   0.01130   2.68372;
-0.00216   0.22808   0.97364  -0.45602;
-0.04033  -0.97287   0.22781  -0.83031;
0.00000   0.00000   0.00000   1.00000;

Writing optimal reg to /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/xfms/tmp.bbregister.28041/bbr.pass1.dat, type = 14
Original Reg
0.99918  -0.03886   0.01127   2.75252;
-0.00180   0.23542   0.97189  -0.06236;
-0.04042  -0.97112   0.23516  -1.80609;
0.00000   0.00000   0.00000   1.00000;

Original Reg - Optimal Reg
-0.00000  -0.00009  -0.00004   0.06880;
0.00036   0.00734  -0.00175   0.39366;
-0.00009   0.00175   0.00735  -0.97578;
0.00000   0.00000   0.00000   0.00000;

Computing change in lh position
LH rmsDiffMean 1.025998
Computing change in rh position
Surface-RMS-Diff-mm 1.020289 0.188730 1.405123
mri_segreg done
mri_segreg --mov /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/xfms/tmp.bbregister.28041/template.nii --init-reg /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/xfms/tmp.bbregister.28041/bbr.pass1.dat --out-reg /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/xfms/anatorig2diff.bbr.dat --interp trilinear --wm-proj-abs 2 --tol 1e-8 --tol1d 1e-3 --c0 0 --mincost /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/xfms/anatorig2diff.bbr.dat.mincost --dof 6 --nmax 36 --param /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/xfms/anatorig2diff.bbr.dat.param --surf white --brute -0.1 0.1 0.1 --cur-reg /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/xfms/tmp.bbregister.28041/reg.curopt.dat --gm-proj-frac 0.5 --nsub 1 --gm-gt-wm 0.5
$Id: mri_segreg.c,v 1.113 2016/05/10 03:23:20 greve Exp $
setenv SUBJECTS_DIR /home/fsluser/usr_/local_/diffusion_recons
cd /home/fsluser/usr_/local_/diffusion_recons
mri_segreg --mov /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/xfms/tmp.bbregister.28041/template.nii --init-reg /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/xfms/tmp.bbregister.28041/bbr.pass1.dat --out-reg /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/xfms/anatorig2diff.bbr.dat --interp trilinear --wm-proj-abs 2 --tol 1e-8 --tol1d 1e-3 --c0 0 --mincost /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/xfms/anatorig2diff.bbr.dat.mincost --dof 6 --nmax 36 --param /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/xfms/anatorig2diff.bbr.dat.param --surf white --brute -0.1 0.1 0.1 --cur-reg /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/xfms/tmp.bbregister.28041/reg.curopt.dat --gm-proj-frac 0.5 --nsub 1 --gm-gt-wm 0.5
sysname  Linux
hostname localhost.localdomain
machine  x86_64
user     fsluser
movvol /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/xfms/tmp.bbregister.28041/template.nii
regfile /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/xfms/tmp.bbregister.28041/bbr.pass1.dat
subject elmo.2005
dof 6
outregfile /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/xfms/anatorig2diff.bbr.dat
UseMask 0
UseLH 1
UseRH 1
nsubsamp 1
PenaltySign  -1
PenaltySlope 0.500000
PenaltyCenter 0.000000
surfname white
GMProjFrac 0.500000
WMProjAbs 2.000000
lhcostfile (null)
rhcostfile (null)
interp  trilinear (1)
frame  0
TolPowell 0.000000
nMaxItersPowell 36
n1dmin  3
Profile   0
Gdiag_no  -1
AddNoise  0 (0)
SynthSeed 1537544095
TransRandMax 0.000000
RotRandMax 0.000000
Translations 0.000000 0.000000 0.000000
Rotations   0.000000 0.000000 0.000000
Input reg
0.99918  -0.03878   0.01130   2.68372;
-0.00216   0.22808   0.97364  -0.45602;
-0.04033  -0.97287   0.22781  -0.83031;
0.00000   0.00000   0.00000   1.00000;

Loading mov
Extracting frame 0
Projecting LH Surfs
Loading lh.white surf
Loading lh.thickness for GM
GM Proj: 1 0.500000 2.000000
WM Proj: 0 0.500000 2.000000
Projecting RH Surfs
Loading rh.white surf
Loading rh.thickness for GM
Projecting RH Surfs
Using lh.cortex.label
Using rh.cortex.label
Computing relative cost
0  -25.0 -25.0 -25.0   0.994360
1  -25.0 -25.0  25.0   1.009170
2  -25.0  25.0 -25.0   1.028103
3  -25.0  25.0  25.0   0.993501
4   25.0 -25.0 -25.0   1.009256
5   25.0 -25.0  25.0   1.005871
6   25.0  25.0 -25.0   0.984198
7   25.0  25.0  25.0   1.020678
REL:  8  0.457378    8.045138  1.005642 rel = 0.454812
Initial costs ----------------
Number of surface hits 267146
WM  Intensity   206.3564 +/- 113.7131
Ctx Intensity   277.7282 +/- 152.7763
Pct Contrast     25.3732 +/-  42.7352
Cost   0.4574
RelCost   0.4548

------------------------------------
Brute force preopt -0.1 0.1 0.1, n = 729
     0  -0.1000  -0.1000  -0.1000  -0.1000  -0.1000  -0.1000      0.4515   0.4515  0.0
     3  -0.1000  -0.1000  -0.1000  -0.1000   0.0000  -0.1000      0.4497   0.4497  0.0
     6  -0.1000  -0.1000  -0.1000  -0.1000   0.1000  -0.1000      0.4462   0.4462  0.0
    12  -0.1000  -0.1000  -0.1000   0.0000   0.0000  -0.1000      0.4461   0.4461  0.0
    21  -0.1000  -0.1000  -0.1000   0.1000   0.0000  -0.1000      0.4457   0.4457  0.0
    24  -0.1000  -0.1000  -0.1000   0.1000   0.1000  -0.1000      0.4444   0.4444  0.0
    36  -0.1000  -0.1000   0.0000   0.0000  -0.1000  -0.1000      0.4435   0.4435  0.0
    54  -0.1000  -0.1000   0.1000  -0.1000  -0.1000  -0.1000      0.4427   0.4427  0.0
    63  -0.1000  -0.1000   0.1000   0.0000  -0.1000  -0.1000      0.4415   0.4415  0.0
   258   0.0000  -0.1000  -0.1000   0.0000   0.1000  -0.1000      0.4412   0.4412  0.0
   282   0.0000  -0.1000   0.0000   0.0000   0.0000  -0.1000      0.4404   0.4404  0.0
   364   0.0000   0.0000   0.0000   0.0000   0.0000   0.0000      0.4394   0.4394  0.0
Brute Force --------------------------
Min cost was 0.439395
Number of iterations   729
Search time 1.510000 sec
Parameters at best (transmm, rotdeg)
  0.000   0.000   0.000  0.000  0.000  0.000
--------------------------------------------

Starting Powell Minimization
Init Powel Params dof = 6
0 0
1 0
2 0
3 0
4 0
5 0
fs_powell::minimize
  nparams 6
  maxfev 36
  ftol   0.000000
  linmin_xtol_   0.001000
  powell nthiter 0: fret = 0.457378
   7  0.151  0.000  0.000  0.000  0.000  0.000   0.4567799639
   9  0.149  0.000  0.000  0.000  0.000  0.000   0.4567796745
  10  0.148  0.000  0.000  0.000  0.000  0.000   0.4567792997
  11  0.142  0.000  0.000  0.000  0.000  0.000   0.4567788014
  12  0.144  0.000  0.000  0.000  0.000  0.000   0.4567786136
  20  0.144 -0.113  0.000  0.000  0.000  0.000   0.4562133870
  21  0.144 -0.102  0.000  0.000  0.000  0.000   0.4562102480
  36  0.144 -0.102  0.005  0.000  0.000  0.000   0.4562068973
  40  0.144 -0.102  0.016  0.000  0.000  0.000   0.4562045472
  41  0.144 -0.102  0.015  0.000  0.000  0.000   0.4562045116
  42  0.144 -0.102  0.014  0.000  0.000  0.000   0.4562044856
  51  0.144 -0.102  0.014 -0.115  0.000  0.000   0.4555371966
  53  0.144 -0.102  0.014 -0.123  0.000  0.000   0.4555367143
  55  0.144 -0.102  0.014 -0.127  0.000  0.000   0.4555352434
  57  0.144 -0.102  0.014 -0.125  0.000  0.000   0.4555347108
  58  0.144 -0.102  0.014 -0.124  0.000  0.000   0.4555344977
  65  0.144 -0.102  0.014 -0.124 -0.030  0.000   0.4553394364
  67  0.144 -0.102  0.014 -0.124 -0.071  0.000   0.4552874340
  68  0.144 -0.102  0.014 -0.124 -0.079  0.000   0.4552792468
  69  0.144 -0.102  0.014 -0.124 -0.101  0.000   0.4552413108
  71  0.144 -0.102  0.014 -0.124 -0.102  0.000   0.4552404588
  72  0.144 -0.102  0.014 -0.124 -0.104  0.000   0.4552395026
  82  0.144 -0.102  0.014 -0.124 -0.104 -0.293   0.4522931503
  83  0.144 -0.102  0.014 -0.124 -0.104 -0.291   0.4522918016
  powell nthiter 1: fret = 0.452292
  95  0.133 -0.102  0.014 -0.124 -0.104 -0.291   0.4522544133
  96  0.090 -0.102  0.014 -0.124 -0.104 -0.291   0.4522221844
  98  0.105 -0.102  0.014 -0.124 -0.104 -0.291   0.4522023296
  99  0.106 -0.102  0.014 -0.124 -0.104 -0.291   0.4522022033
107  0.106 -0.174  0.014 -0.124 -0.104 -0.291   0.4516567107
109  0.106 -0.189  0.014 -0.124 -0.104 -0.291   0.4516347638
110  0.106 -0.190  0.014 -0.124 -0.104 -0.291   0.4516342016
111  0.106 -0.195  0.014 -0.124 -0.104 -0.291   0.4516309356
114  0.106 -0.194  0.014 -0.124 -0.104 -0.291   0.4516305236
122  0.106 -0.194  0.022 -0.124 -0.104 -0.291   0.4515978255
123  0.106 -0.194  0.075 -0.124 -0.104 -0.291   0.4515177696
125  0.106 -0.194  0.068 -0.124 -0.104 -0.291   0.4515073442
126  0.106 -0.194  0.060 -0.124 -0.104 -0.291   0.4515053860
127  0.106 -0.194  0.062 -0.124 -0.104 -0.291   0.4515048438
137  0.106 -0.194  0.062 -0.144 -0.104 -0.291   0.4514614868
138  0.106 -0.194  0.062 -0.149 -0.104 -0.291   0.4514588764
147  0.106 -0.194  0.062 -0.149 -0.008 -0.291   0.4511294521
148  0.106 -0.194  0.062 -0.149 -0.013 -0.291   0.4511263788
149  0.106 -0.194  0.062 -0.149 -0.018 -0.291   0.4511189418
150  0.106 -0.194  0.062 -0.149 -0.051 -0.291   0.4510869949
152  0.106 -0.194  0.062 -0.149 -0.038 -0.291   0.4510857743
153  0.106 -0.194  0.062 -0.149 -0.044 -0.291   0.4510847166
154  0.106 -0.194  0.062 -0.149 -0.043 -0.291   0.4510847161
164  0.106 -0.194  0.062 -0.149 -0.043 -0.296   0.4510831507
165  0.106 -0.194  0.062 -0.149 -0.043 -0.297   0.4510831286
  powell nthiter 2: fret = 0.451083
174  0.099 -0.194  0.062 -0.149 -0.043 -0.297   0.4510503240
176  0.077 -0.194  0.062 -0.149 -0.043 -0.297   0.4510213872
178  0.080 -0.194  0.062 -0.149 -0.043 -0.297   0.4510195676
180  0.083 -0.194  0.062 -0.149 -0.043 -0.297   0.4510186920
201  0.084 -0.194  0.073 -0.149 -0.043 -0.297   0.4510115521
203  0.084 -0.194  0.072 -0.149 -0.043 -0.297   0.4510115142
215  0.084 -0.194  0.072 -0.148 -0.043 -0.297   0.4510112026
223  0.084 -0.194  0.072 -0.148  0.005 -0.297   0.4509468373
226  0.084 -0.194  0.072 -0.148  0.006 -0.297   0.4509467632
236  0.084 -0.194  0.072 -0.148  0.007 -0.307   0.4509344989
242  0.062 -0.194  0.082 -0.147  0.057 -0.314   0.4509154629
  powell nthiter 3: fret = 0.450934
249  0.075 -0.194  0.072 -0.148  0.007 -0.306   0.4508891386
251  0.050 -0.194  0.072 -0.148  0.007 -0.306   0.4508574823
254  0.049 -0.194  0.072 -0.148  0.007 -0.306   0.4508574680
255  0.048 -0.194  0.072 -0.148  0.007 -0.306   0.4508572280
258  0.046 -0.194  0.072 -0.148  0.007 -0.306   0.4508570447
268  0.047 -0.189  0.072 -0.148  0.007 -0.306   0.4508534999
279  0.047 -0.189  0.063 -0.148  0.007 -0.306   0.4508490816
280  0.047 -0.189  0.061 -0.148  0.007 -0.306   0.4508484187
282  0.047 -0.189  0.057 -0.148  0.007 -0.306   0.4508481470
283  0.047 -0.189  0.058 -0.148  0.007 -0.306   0.4508481128
294  0.047 -0.189  0.058 -0.147  0.007 -0.306   0.4508480229
302  0.047 -0.189  0.058 -0.147  0.027 -0.306   0.4508401595
303  0.047 -0.189  0.058 -0.147  0.022 -0.306   0.4508368880
304  0.047 -0.189  0.058 -0.147  0.020 -0.306   0.4508368307
306  0.047 -0.189  0.058 -0.147  0.021 -0.306   0.4508366606
314  0.047 -0.189  0.058 -0.147  0.021 -0.330   0.4507887096
317  0.047 -0.189  0.058 -0.147  0.021 -0.331   0.4507886723
  powell nthiter 4: fret = 0.450789
327  0.040 -0.189  0.058 -0.147  0.021 -0.331   0.4507863478
338  0.040 -0.202  0.058 -0.147  0.021 -0.331   0.4507856198
339  0.040 -0.196  0.058 -0.147  0.021 -0.331   0.4507778523
340  0.040 -0.195  0.058 -0.147  0.021 -0.331   0.4507778168
350  0.040 -0.195  0.057 -0.147  0.021 -0.331   0.4507776939
359  0.040 -0.195  0.057 -0.140  0.021 -0.331   0.4507760945
360  0.040 -0.195  0.057 -0.141  0.021 -0.331   0.4507753773
368  0.040 -0.195  0.057 -0.141  0.034 -0.331   0.4507701303
379  0.040 -0.195  0.057 -0.141  0.034 -0.342   0.4507598537
381  0.040 -0.195  0.057 -0.141  0.034 -0.341   0.4507597243
  powell nthiter 5: fret = 0.450760
392  0.036 -0.195  0.057 -0.141  0.034 -0.341   0.4507576686
393  0.035 -0.195  0.057 -0.141  0.034 -0.341   0.4507573174
395  0.034 -0.195  0.057 -0.141  0.034 -0.341   0.4507572876
404  0.034 -0.194  0.057 -0.141  0.034 -0.341   0.4507572313
413  0.034 -0.194  0.052 -0.141  0.034 -0.341   0.4507558538
414  0.034 -0.194  0.050 -0.141  0.034 -0.341   0.4507554828
427  0.034 -0.194  0.050 -0.140  0.034 -0.341   0.4507551369
428  0.034 -0.194  0.050 -0.139  0.034 -0.341   0.4507551204
437  0.034 -0.194  0.050 -0.139  0.033 -0.341   0.4507549405
450  0.034 -0.194  0.050 -0.139  0.033 -0.343   0.4507547248
  powell nthiter 6: fret = 0.450755
480  0.035 -0.194  0.049 -0.139  0.033 -0.343   0.4507544467
481  0.035 -0.194  0.046 -0.139  0.033 -0.343   0.4507537921
483  0.035 -0.194  0.043 -0.139  0.033 -0.343   0.4507536567
484  0.035 -0.194  0.044 -0.139  0.033 -0.343   0.4507536554
493  0.035 -0.194  0.044 -0.138  0.033 -0.343   0.4507533174
494  0.035 -0.194  0.044 -0.137  0.033 -0.343   0.4507532305
503  0.035 -0.194  0.044 -0.137  0.032 -0.343   0.4507531155
514  0.035 -0.194  0.044 -0.137  0.032 -0.342   0.4507531014
516  0.036 -0.194  0.039 -0.135  0.031 -0.341   0.4507523120
530  0.036 -0.194  0.039 -0.135  0.031 -0.341   0.4507522623
  powell nthiter 7: fret = 0.450752
542  0.035 -0.194  0.039 -0.135  0.031 -0.341   0.4507520844
552  0.035 -0.195  0.039 -0.135  0.031 -0.341   0.4507516977
563  0.035 -0.195  0.039 -0.135  0.031 -0.342   0.4507516535
591  0.035 -0.195  0.037 -0.134  0.029 -0.341   0.4507515057
592  0.035 -0.195  0.036 -0.134  0.029 -0.341   0.4507514870
593  0.035 -0.195  0.035 -0.134  0.029 -0.341   0.4507513959
  powell nthiter 8: fret = 0.450751
612  0.034 -0.195  0.035 -0.134  0.029 -0.341   0.4507512254
622  0.034 -0.196  0.035 -0.134  0.029 -0.341   0.4507510902
  powell nthiter 9: fret = 0.450751
Powell done niters = 9
Computing relative cost
0  -25.0 -25.0 -25.0   0.993321
1  -25.0 -25.0  25.0   1.009943
2  -25.0  25.0 -25.0   1.031408
3  -25.0  25.0  25.0   0.987702
4   25.0 -25.0 -25.0   1.008434
5   25.0 -25.0  25.0   1.004908
6   25.0  25.0 -25.0   0.987196
7   25.0  25.0  25.0   1.021866
REL:  8  0.450751    8.044778  1.005597 rel = 0.448242
Number of iterations     9
Min cost was 0.450751
Number of FunctionCalls   741
TolPowell 0.000000
nMaxItersPowell 36
OptimizationTime 40.719000 sec
Parameters at optimum (transmm)  0.03411 -0.19584  0.03511
Parameters at optimum (rotdeg) -0.13370  0.02919 -0.34094
Final costs ----------------
Number of surface hits 267260
WM  Intensity   205.3026 +/- 114.1749
Ctx Intensity   276.2650 +/- 150.7064
Pct Contrast     25.5313 +/-  42.4962
Cost   0.4508
RelCost   0.4548
Reg at min cost was
0.99913  -0.03793   0.01722   2.71464;
-0.00820   0.22604   0.97408  -0.66975;
-0.04084  -0.97338   0.22553  -0.79550;
0.00000   0.00000   0.00000   1.00000;

Writing optimal reg to /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/xfms/anatorig2diff.bbr.dat, type = 14
Original Reg
0.99918  -0.03878   0.01130   2.68372;
-0.00216   0.22808   0.97364  -0.45602;
-0.04033  -0.97287   0.22781  -0.83031;
0.00000   0.00000   0.00000   1.00000;

Original Reg - Optimal Reg
0.00005  -0.00085  -0.00591  -0.03092;
0.00604   0.00204  -0.00044   0.21373;
0.00050   0.00051   0.00228  -0.03481;
0.00000   0.00000   0.00000   0.00000;

Computing change in lh position
LH rmsDiffMean 0.210903
Computing change in rh position
Surface-RMS-Diff-mm 0.304233 0.140570 0.625049
mri_segreg done
MinCost: 0.450751 205.302557 276.265001 25.531318
tkregister2_cmdl --mov /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/dwi.nii.gz --reg /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/xfms/anatorig2diff.bbr.dat --noedit --fslregout /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/xfms/diff2anatorig.bbr.mat
tkregister_tcl /usr/local/freesurfer/tktools/tkregister2.tcl
INFO: no target volume specified, assuming FreeSurfer orig volume.
target  volume orig
movable volume /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/dwi.nii.gz
reg file       /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/xfms/anatorig2diff.bbr.dat
LoadVol        0
ZeroCRAS       0
$Id: tkregister2.c,v 1.132.2.1 2016/08/02 21:17:29 greve Exp $
Diagnostic Level -1
---- Input registration matrix --------
0.99913  -0.03793   0.01722   2.71464;
-0.00820   0.22604   0.97408  -0.66975;
-0.04084  -0.97338   0.22553  -0.79550;
0.00000   0.00000   0.00000   1.00000;
float2int = 0
---------------------------------------
INFO: loading target /home/fsluser/usr_/local_/diffusion_recons/elmo.2005/mri/orig.mgz
Ttarg: --------------------
-1.00000   0.00000   0.00000   128.00000;
0.00000   0.00000   1.00000  -128.00000;
0.00000  -1.00000   0.00000   128.00000;
0.00000   0.00000   0.00000   1.00000;
INFO: loading movable /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/dwi.nii.gz
Tmov: --------------------
-2.00000   0.00000   0.00000   128.00000;
0.00000   0.00000   2.00000  -60.00000;
0.00000  -2.00000   0.00000   128.00000;
0.00000   0.00000   0.00000   1.00000;
mkheaderreg = 0, float2int = 0
---- Input registration matrix --------
0.99913  -0.03793   0.01722   2.71464;
-0.00820   0.22604   0.97408  -0.66975;
-0.04084  -0.97338   0.22553  -0.79550;
0.00000   0.00000   0.00000   1.00000;
Determinant 0.999999
subject = elmo.2005
RegMat ---------------------------
0.99913  -0.03793   0.01722   2.71464;
-0.00820   0.22604   0.97408  -0.66975;
-0.04084  -0.97338   0.22553  -0.79550;
0.00000   0.00000   0.00000   1.00000;
FSLOUTPUTTYPE NIFTI_GZ
tkreg2FSL: mov det = -8, ref det = -1
Cleaning up

Started at Mon Sep 10 14:51:06 BST 2018
Ended   at Mon Sep 10 14:52:47 BST 2018
BBR-Run-Time-Sec 101

bbregister Done
To check results, run:
tkregisterfv --mov /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/dwi.nii.gz --reg /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/xfms/anatorig2diff.bbr.dat --surfs

convert_xfm -omat /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/xfms/anatorig2diff.bbr.mat -inverse /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/xfms/diff2anatorig.bbr.mat
convert_xfm -omat /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/xfms/anat2diff.bbr.mat -concat /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/xfms/anatorig2diff.bbr.mat /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/xfms/anat2anatorig.mat
convert_xfm -omat /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/xfms/diff2anat.bbr.mat -inverse /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/xfms/anat2diff.bbr.mat
#-------------------------------------
#@# Inter-subject registration Mon Sep 10 14:52:47 BST 2018
flirt -in /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/brain_anat.nii.gz -ref /usr/local/fsl/data/standard/MNI152_T1_1mm_brain.nii.gz -out /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/brain_anat_mni.nii.gz -omat /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/xfms/anat2mni.mat -cost mutualinfo
convert_xfm -omat /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/xfms/mni2anat.mat -inverse /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/xfms/anat2mni.mat
convert_xfm -omat /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/xfms/diff2mni.bbr.mat -concat /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/xfms/anat2mni.mat /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/xfms/diff2anat.bbr.mat
convert_xfm -omat /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/xfms/mni2diff.bbr.mat -inverse /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/xfms/diff2mni.bbr.mat
convert_xfm -omat /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/xfms/anatorig2mni.mat -concat /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/xfms/anat2mni.mat /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/xfms/anatorig2anat.mat
convert_xfm -omat /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/xfms/mni2anatorig.mat -inverse /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/xfms/anatorig2mni.mat
#-------------------------------------
#@# Masks Mon Sep 10 14:54:35 BST 2018
mri_binarize --i /home/fsluser/usr_/local_/diffusion_recons/elmo.2005/mri/aparc+aseg.mgz --match 2 --match 7 --match 41 --match 46 --match 77 --o /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dlabel/anatorig/White-Matter.nii.gz

$Id: mri_binarize.c,v 1.43 2016/06/09 20:46:21 greve Exp $
cwd /home/fsluser/usr_/local_/diffusion_recons
cmdline mri_binarize.bin --i /home/fsluser/usr_/local_/diffusion_recons/elmo.2005/mri/aparc+aseg.mgz --match 2 --match 7 --match 41 --match 46 --match 77 --o /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dlabel/anatorig/White-Matter.nii.gz
sysname  Linux
hostname localhost.localdomain
machine  x86_64
user     fsluser

input      /home/fsluser/usr_/local_/diffusion_recons/elmo.2005/mri/aparc+aseg.mgz
frame      0
nErode3d   0
nErode2d   0
output     /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dlabel/anatorig/White-Matter.nii.gz
Binarizing based on matching values
nMatch 5
0     2
1     7
2    41
3    46
4    77
binval        1
binvalnot     0
fstart = 0, fend = 0, nframes = 1
Found 466816 values in range
Counting number of voxels in first frame
Found 466816 voxels in final mask
Count: 466816 466816.000000 16777216 2.782440
mri_binarize done
mri_binarize --i /home/fsluser/usr_/local_/diffusion_recons/elmo.2005/mri/aparc+aseg.mgz --match 2 --match 7 --match 41 --match 46 --match 77 --match 28 --match 60 --match 16 --o /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dlabel/anatorig/White-Matter++.nii.gz

$Id: mri_binarize.c,v 1.43 2016/06/09 20:46:21 greve Exp $
cwd /home/fsluser/usr_/local_/diffusion_recons
cmdline mri_binarize.bin --i /home/fsluser/usr_/local_/diffusion_recons/elmo.2005/mri/aparc+aseg.mgz --match 2 --match 7 --match 41 --match 46 --match 77 --match 28 --match 60 --match 16 --o /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dlabel/anatorig/White-Matter++.nii.gz
sysname  Linux
hostname localhost.localdomain
machine  x86_64
user     fsluser

input      /home/fsluser/usr_/local_/diffusion_recons/elmo.2005/mri/aparc+aseg.mgz
frame      0
nErode3d   0
nErode2d   0
output     /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dlabel/anatorig/White-Matter++.nii.gz
Binarizing based on matching values
nMatch 8
0     2
1     7
2    41
3    46
4    77
5    28
6    60
7    16
binval        1
binvalnot     0
fstart = 0, fend = 0, nframes = 1
Found 496933 values in range
Counting number of voxels in first frame
Found 496933 voxels in final mask
Count: 496933 496933.000000 16777216 2.961951
mri_binarize done
mri_binarize --i /home/fsluser/usr_/local_/diffusion_recons/elmo.2005/mri/aparc+aseg.mgz --match 4 --match 43 --binval 0 --binvalnot 1 --o /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dlabel/anatorig/notventricles.nii.gz

$Id: mri_binarize.c,v 1.43 2016/06/09 20:46:21 greve Exp $
cwd /home/fsluser/usr_/local_/diffusion_recons
cmdline mri_binarize.bin --i /home/fsluser/usr_/local_/diffusion_recons/elmo.2005/mri/aparc+aseg.mgz --match 4 --match 43 --binval 0 --binvalnot 1 --o /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dlabel/anatorig/notventricles.nii.gz
sysname  Linux
hostname localhost.localdomain
machine  x86_64
user     fsluser

input      /home/fsluser/usr_/local_/diffusion_recons/elmo.2005/mri/aparc+aseg.mgz
frame      0
nErode3d   0
nErode2d   0
output     /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dlabel/anatorig/notventricles.nii.gz
Binarizing based on matching values
nMatch 2
0     4
1    43
binval        0
binvalnot     1
fstart = 0, fend = 0, nframes = 1
Found 23114 values in range
Counting number of voxels in first frame
Found 23114 voxels in final mask
Count: 23114 23114.000000 16777216 0.137770
mri_binarize done
mri_aparc2aseg --s elmo.2005 --annot aparc --wmparc-dmax 2 --labelwm --hypo-as-wm --o /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dlabel/anatorig/aparc+aseg+2mm.nii.gz
SUBJECTS_DIR /home/fsluser/usr_/local_/diffusion_recons
subject elmo.2005
outvol /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dlabel/anatorig/aparc+aseg+2mm.nii.gz
useribbon 0
baseoffset 0
labeling wm
labeling hypo-intensities as wm
dmaxctx 2.000000
RipUnknown 0

Reading lh white surface
/home/fsluser/usr_/local_/diffusion_recons/elmo.2005/surf/lh.white

Reading lh pial surface
/home/fsluser/usr_/local_/diffusion_recons/elmo.2005/surf/lh.pial

Loading lh annotations from /home/fsluser/usr_/local_/diffusion_recons/elmo.2005/label/lh.aparc.annot
reading colortable from annotation file...
colortable with 36 entries read (originally /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt)

Reading rh white surface
/home/fsluser/usr_/local_/diffusion_recons/elmo.2005/surf/rh.white

Reading rh pial surface
/home/fsluser/usr_/local_/diffusion_recons/elmo.2005/surf/rh.pial

Loading rh annotations from /home/fsluser/usr_/local_/diffusion_recons/elmo.2005/label/rh.aparc.annot
reading colortable from annotation file...
colortable with 36 entries read (originally /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt)
Have color table for lh white annotation
Have color table for rh white annotation
Loading ribbon segmentation from /home/fsluser/usr_/local_/diffusion_recons/elmo.2005/mri/ribbon.mgz
Loading filled from /home/fsluser/usr_/local_/diffusion_recons/elmo.2005/mri/ribbon.mgz

Building hash of lh white

Building hash of lh pial

Building hash of rh white

Building hash of rh pial

Loading aseg from /home/fsluser/usr_/local_/diffusion_recons/elmo.2005/mri/aseg.mgz
ASeg Vox2RAS: -----------
-1.00000   0.00000   0.00000   128.00000;
0.00000   0.00000   1.00000  -128.00000;
0.00000  -1.00000   0.00000   128.00000;
0.00000   0.00000   0.00000   1.00000;
-------------------------

Labeling Slice
  0   1   2   3   4   5   6   7   8   9  10  11  12  13  14  15  16  17  18  19
20  21  22  23  24  25  26  27  28  29  30  31  32  33  34  35  36  37  38  39
40  41  42  43  44  45  46  47  48  49  50  51  52  53  54  55  56  57  58  59
60  61  62  63  64  65  66  67  68  69  70  71  72  73  74  75  76  77  78  79
80  81  82  83  84  85  86  87  88  89  90  91  92  93  94  95  96  97  98  99
100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119
120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139
140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159
160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179
180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199
200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218 219
220 221 222 223 224 225 226 227 228 229 230 231 232 233 234 235 236 237 238 239
240 241 242 243 244 245 246 247 248 249 250 251 252 253 254 255 nctx = 1019533
Used brute-force search on 0 voxels
Fixing Parahip LH WM
  Found 1 clusters
     0 k 889.000000
Fixing Parahip RH WM
  Found 1 clusters
     0 k 714.000000
Writing output aseg to /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dlabel/anatorig/aparc+aseg+2mm.nii.gz
mri_binarize --i /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dlabel/anatorig/aparc+aseg+2mm.nii.gz --min 1000 --max 2999 --o /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dlabel/anatorig/cortex.nii.gz

$Id: mri_binarize.c,v 1.43 2016/06/09 20:46:21 greve Exp $
cwd /home/fsluser/usr_/local_/diffusion_recons
cmdline mri_binarize.bin --i /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dlabel/anatorig/aparc+aseg+2mm.nii.gz --min 1000 --max 2999 --o /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dlabel/anatorig/cortex.nii.gz
sysname  Linux
hostname localhost.localdomain
machine  x86_64
user     fsluser

input      /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dlabel/anatorig/aparc+aseg+2mm.nii.gz
frame      0
nErode3d   0
nErode2d   0
output     /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dlabel/anatorig/cortex.nii.gz
Binarizing based on threshold
min        1000
max        2999
binval        1
binvalnot     0
fstart = 0, fend = 0, nframes = 1
Found 577605 values in range
Counting number of voxels in first frame
Found 577605 voxels in final mask
Count: 577605 577605.000000 16777216 3.442794
mri_binarize done
mri_binarize --i /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dlabel/anatorig/aparc+aseg+2mm.nii.gz --min 1000 --max 4999 --o /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dlabel/anatorig/cortex+2mm.nii.gz

$Id: mri_binarize.c,v 1.43 2016/06/09 20:46:21 greve Exp $
cwd /home/fsluser/usr_/local_/diffusion_recons
cmdline mri_binarize.bin --i /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dlabel/anatorig/aparc+aseg+2mm.nii.gz --min 1000 --max 4999 --o /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dlabel/anatorig/cortex+2mm.nii.gz
sysname  Linux
hostname localhost.localdomain
machine  x86_64
user     fsluser

input      /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dlabel/anatorig/aparc+aseg+2mm.nii.gz
frame      0
nErode3d   0
nErode2d   0
output     /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dlabel/anatorig/cortex+2mm.nii.gz
Binarizing based on threshold
min        1000
max        4999
binval        1
binvalnot     0
fstart = 0, fend = 0, nframes = 1
Found 848289 values in range
Counting number of voxels in first frame
Found 848289 voxels in final mask
Count: 848289 848289.000000 16777216 5.056196
mri_binarize done
mri_binarize --i /home/fsluser/usr_/local_/diffusion_recons/elmo.2005/mri/aparc+aseg.mgz --match 16 --o /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dlabel/anatorig/Brain-Stem.nii.gz

$Id: mri_binarize.c,v 1.43 2016/06/09 20:46:21 greve Exp $
cwd /home/fsluser/usr_/local_/diffusion_recons
cmdline mri_binarize.bin --i /home/fsluser/usr_/local_/diffusion_recons/elmo.2005/mri/aparc+aseg.mgz --match 16 --o /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dlabel/anatorig/Brain-Stem.nii.gz
sysname  Linux
hostname localhost.localdomain
machine  x86_64
user     fsluser

input      /home/fsluser/usr_/local_/diffusion_recons/elmo.2005/mri/aparc+aseg.mgz
frame      0
nErode3d   0
nErode2d   0
output     /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dlabel/anatorig/Brain-Stem.nii.gz
Binarizing based on matching values
nMatch 1
0    16
binval        1
binvalnot     0
fstart = 0, fend = 0, nframes = 1
Found 21835 values in range
Counting number of voxels in first frame
Found 21835 voxels in final mask
Count: 21835 21835.000000 16777216 0.130147
mri_binarize done
fslmaths /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dlabel/anatorig/cortex+2mm.nii.gz -add /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dlabel/anatorig/Brain-Stem.nii.gz /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dlabel/anatorig/cortex+2mm+bs.nii.gz
mri_convert /home/fsluser/usr_/local_/diffusion_recons/elmo.2005/mri/brainmask.mgz /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dlabel/anatorig/anat_brain_mask.nii.gz
mri_convert.bin /home/fsluser/usr_/local_/diffusion_recons/elmo.2005/mri/brainmask.mgz /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dlabel/anatorig/anat_brain_mask.nii.gz
$Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $
reading from /home/fsluser/usr_/local_/diffusion_recons/elmo.2005/mri/brainmask.mgz...
TR=2530.00, TE=3.45, TI=1100.00, flip angle=7.00
i_ras = (-1, 6.33299e-08, -2.04891e-08)
j_ras = (-9.31323e-09, 2.32831e-10, -1)
k_ras = (7.07805e-08, 1, 1.74623e-09)
writing to /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dlabel/anatorig/anat_brain_mask.nii.gz...
fslmaths /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dlabel/anatorig/anat_brain_mask.nii.gz -mul /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dlabel/anatorig/notventricles.nii.gz /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dlabel/anatorig/anat_brain_mask-vent.nii.gz
mri_convert /home/fsluser/usr_/local_/diffusion_recons/elmo.2005/mri/aparc+aseg.mgz /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dlabel/anatorig/aparc+aseg.nii.gz
mri_convert.bin /home/fsluser/usr_/local_/diffusion_recons/elmo.2005/mri/aparc+aseg.mgz /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dlabel/anatorig/aparc+aseg.nii.gz
$Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $
reading from /home/fsluser/usr_/local_/diffusion_recons/elmo.2005/mri/aparc+aseg.mgz...
TR=2530.00, TE=3.45, TI=1100.00, flip angle=7.00
i_ras = (-1, 6.33299e-08, -2.04891e-08)
j_ras = (-9.31323e-09, 2.32831e-10, -1)
k_ras = (7.07805e-08, 1, 1.74623e-09)
writing to /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dlabel/anatorig/aparc+aseg.nii.gz...
fslmaths /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dlabel/anatorig/aparc+aseg.nii.gz -dilM -bin /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dlabel/anatorig/aparc+aseg_mask.nii.gz
orientLAS /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dlabel/anatorig/White-Matter.nii.gz /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dlabel/anat/White-Matter.nii.gz
INFO: input image orientation is LIA
INFO: input image determinant is -1
mri_convert -oni 256 -onj 256 -onk 256 -oid -1 6.33299e-08 -2.04891e-08 -ojd 7.07805e-08 1 1.74623e-09 -okd 9.31323e-09 -2.32831e-10 1 -oc 3.70524 44.2681 16.0046 -rt nearest /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dlabel/anatorig/White-Matter.nii.gz /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dlabel/anat/White-Matter.nii.gz
mri_convert.bin -oni 256 -onj 256 -onk 256 -oid -1 6.33299e-08 -2.04891e-08 -ojd 7.07805e-08 1 1.74623e-09 -okd 9.31323e-09 -2.32831e-10 1 -oc 3.70524 44.2681 16.0046 -rt nearest /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dlabel/anatorig/White-Matter.nii.gz /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dlabel/anat/White-Matter.nii.gz
$Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $
reading from /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dlabel/anatorig/White-Matter.nii.gz...
TR=2530.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-1, 6.33299e-08, -2.04891e-08)
j_ras = (-9.31323e-09, 2.32831e-10, -1)
k_ras = (7.07805e-08, 1, 1.74623e-09)
Reslicing using nearest
writing to /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dlabel/anat/White-Matter.nii.gz...
flirt -in /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dlabel/anat/White-Matter.nii.gz -ref /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/lowb.nii.gz -out /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dlabel/diff/White-Matter.bbr.nii.gz -applyxfm -init /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/xfms/anat2diff.bbr.mat -interp nearestneighbour
flirt -in /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dlabel/anat/White-Matter.nii.gz -ref /usr/local/fsl/data/standard/MNI152_T1_1mm_brain.nii.gz -out /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dlabel/mni/White-Matter.nii.gz -applyxfm -init /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/xfms/anat2mni.mat -interp nearestneighbour
orientLAS /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dlabel/anatorig/White-Matter++.nii.gz /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dlabel/anat/White-Matter++.nii.gz
INFO: input image orientation is LIA
INFO: input image determinant is -1
mri_convert -oni 256 -onj 256 -onk 256 -oid -1 6.33299e-08 -2.04891e-08 -ojd 7.07805e-08 1 1.74623e-09 -okd 9.31323e-09 -2.32831e-10 1 -oc 3.70524 44.2681 16.0046 -rt nearest /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dlabel/anatorig/White-Matter++.nii.gz /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dlabel/anat/White-Matter++.nii.gz
mri_convert.bin -oni 256 -onj 256 -onk 256 -oid -1 6.33299e-08 -2.04891e-08 -ojd 7.07805e-08 1 1.74623e-09 -okd 9.31323e-09 -2.32831e-10 1 -oc 3.70524 44.2681 16.0046 -rt nearest /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dlabel/anatorig/White-Matter++.nii.gz /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dlabel/anat/White-Matter++.nii.gz
$Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $
reading from /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dlabel/anatorig/White-Matter++.nii.gz...
TR=2530.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-1, 6.33299e-08, -2.04891e-08)
j_ras = (-9.31323e-09, 2.32831e-10, -1)
k_ras = (7.07805e-08, 1, 1.74623e-09)
Reslicing using nearest
writing to /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dlabel/anat/White-Matter++.nii.gz...
flirt -in /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dlabel/anat/White-Matter++.nii.gz -ref /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/lowb.nii.gz -out /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dlabel/diff/White-Matter++.bbr.nii.gz -applyxfm -init /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/xfms/anat2diff.bbr.mat -interp nearestneighbour
flirt -in /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dlabel/anat/White-Matter++.nii.gz -ref /usr/local/fsl/data/standard/MNI152_T1_1mm_brain.nii.gz -out /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dlabel/mni/White-Matter++.nii.gz -applyxfm -init /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/xfms/anat2mni.mat -interp nearestneighbour
orientLAS /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dlabel/anatorig/notventricles.nii.gz /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dlabel/anat/notventricles.nii.gz
INFO: input image orientation is LIA
INFO: input image determinant is -1
mri_convert -oni 256 -onj 256 -onk 256 -oid -1 6.33299e-08 -2.04891e-08 -ojd 7.07805e-08 1 1.74623e-09 -okd 9.31323e-09 -2.32831e-10 1 -oc 3.70524 44.2681 16.0046 -rt nearest /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dlabel/anatorig/notventricles.nii.gz /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dlabel/anat/notventricles.nii.gz
mri_convert.bin -oni 256 -onj 256 -onk 256 -oid -1 6.33299e-08 -2.04891e-08 -ojd 7.07805e-08 1 1.74623e-09 -okd 9.31323e-09 -2.32831e-10 1 -oc 3.70524 44.2681 16.0046 -rt nearest /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dlabel/anatorig/notventricles.nii.gz /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dlabel/anat/notventricles.nii.gz
$Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $
reading from /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dlabel/anatorig/notventricles.nii.gz...
TR=2530.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-1, 6.33299e-08, -2.04891e-08)
j_ras = (-9.31323e-09, 2.32831e-10, -1)
k_ras = (7.07805e-08, 1, 1.74623e-09)
Reslicing using nearest
writing to /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dlabel/anat/notventricles.nii.gz...
flirt -in /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dlabel/anat/notventricles.nii.gz -ref /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/lowb.nii.gz -out /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dlabel/diff/notventricles.bbr.nii.gz -applyxfm -init /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/xfms/anat2diff.bbr.mat -interp nearestneighbour
flirt -in /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dlabel/anat/notventricles.nii.gz -ref /usr/local/fsl/data/standard/MNI152_T1_1mm_brain.nii.gz -out /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dlabel/mni/notventricles.nii.gz -applyxfm -init /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/xfms/anat2mni.mat -interp nearestneighbour
orientLAS /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dlabel/anatorig/cortex.nii.gz /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dlabel/anat/cortex.nii.gz
INFO: input image orientation is LIA
INFO: input image determinant is -1
mri_convert -oni 256 -onj 256 -onk 256 -oid -1 6.33299e-08 -2.04891e-08 -ojd 7.07805e-08 1 1.74623e-09 -okd 9.31323e-09 -2.32831e-10 1 -oc 3.70524 44.2681 16.0046 -rt nearest /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dlabel/anatorig/cortex.nii.gz /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dlabel/anat/cortex.nii.gz
mri_convert.bin -oni 256 -onj 256 -onk 256 -oid -1 6.33299e-08 -2.04891e-08 -ojd 7.07805e-08 1 1.74623e-09 -okd 9.31323e-09 -2.32831e-10 1 -oc 3.70524 44.2681 16.0046 -rt nearest /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dlabel/anatorig/cortex.nii.gz /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dlabel/anat/cortex.nii.gz
$Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $
reading from /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dlabel/anatorig/cortex.nii.gz...
TR=2530.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-1, 6.33299e-08, -2.04891e-08)
j_ras = (-9.31323e-09, 2.32831e-10, -1)
k_ras = (7.07805e-08, 1, 1.74623e-09)
Reslicing using nearest
writing to /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dlabel/anat/cortex.nii.gz...
flirt -in /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dlabel/anat/cortex.nii.gz -ref /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/lowb.nii.gz -out /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dlabel/diff/cortex.bbr.nii.gz -applyxfm -init /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/xfms/anat2diff.bbr.mat -interp nearestneighbour
flirt -in /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dlabel/anat/cortex.nii.gz -ref /usr/local/fsl/data/standard/MNI152_T1_1mm_brain.nii.gz -out /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dlabel/mni/cortex.nii.gz -applyxfm -init /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/xfms/anat2mni.mat -interp nearestneighbour
orientLAS /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dlabel/anatorig/cortex+2mm.nii.gz /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dlabel/anat/cortex+2mm.nii.gz
INFO: input image orientation is LIA
INFO: input image determinant is -1
mri_convert -oni 256 -onj 256 -onk 256 -oid -1 6.33299e-08 -2.04891e-08 -ojd 7.07805e-08 1 1.74623e-09 -okd 9.31323e-09 -2.32831e-10 1 -oc 3.70524 44.2681 16.0046 -rt nearest /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dlabel/anatorig/cortex+2mm.nii.gz /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dlabel/anat/cortex+2mm.nii.gz
mri_convert.bin -oni 256 -onj 256 -onk 256 -oid -1 6.33299e-08 -2.04891e-08 -ojd 7.07805e-08 1 1.74623e-09 -okd 9.31323e-09 -2.32831e-10 1 -oc 3.70524 44.2681 16.0046 -rt nearest /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dlabel/anatorig/cortex+2mm.nii.gz /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dlabel/anat/cortex+2mm.nii.gz
$Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $
reading from /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dlabel/anatorig/cortex+2mm.nii.gz...
TR=2530.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-1, 6.33299e-08, -2.04891e-08)
j_ras = (-9.31323e-09, 2.32831e-10, -1)
k_ras = (7.07805e-08, 1, 1.74623e-09)
Reslicing using nearest
writing to /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dlabel/anat/cortex+2mm.nii.gz...
flirt -in /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dlabel/anat/cortex+2mm.nii.gz -ref /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/lowb.nii.gz -out /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dlabel/diff/cortex+2mm.bbr.nii.gz -applyxfm -init /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/xfms/anat2diff.bbr.mat -interp nearestneighbour
flirt -in /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dlabel/anat/cortex+2mm.nii.gz -ref /usr/local/fsl/data/standard/MNI152_T1_1mm_brain.nii.gz -out /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dlabel/mni/cortex+2mm.nii.gz -applyxfm -init /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/xfms/anat2mni.mat -interp nearestneighbour
orientLAS /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dlabel/anatorig/cortex+2mm+bs.nii.gz /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dlabel/anat/cortex+2mm+bs.nii.gz
INFO: input image orientation is LIA
INFO: input image determinant is -1
mri_convert -oni 256 -onj 256 -onk 256 -oid -1 6.33299e-08 -2.04891e-08 -ojd 7.07805e-08 1 1.74623e-09 -okd 9.31323e-09 -2.32831e-10 1 -oc 3.70524 44.2681 16.0046 -rt nearest /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dlabel/anatorig/cortex+2mm+bs.nii.gz /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dlabel/anat/cortex+2mm+bs.nii.gz
mri_convert.bin -oni 256 -onj 256 -onk 256 -oid -1 6.33299e-08 -2.04891e-08 -ojd 7.07805e-08 1 1.74623e-09 -okd 9.31323e-09 -2.32831e-10 1 -oc 3.70524 44.2681 16.0046 -rt nearest /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dlabel/anatorig/cortex+2mm+bs.nii.gz /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dlabel/anat/cortex+2mm+bs.nii.gz
$Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $
reading from /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dlabel/anatorig/cortex+2mm+bs.nii.gz...
TR=2530.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-1, 6.33299e-08, -2.04891e-08)
j_ras = (-9.31323e-09, 2.32831e-10, -1)
k_ras = (7.07805e-08, 1, 1.74623e-09)
Reslicing using nearest
writing to /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dlabel/anat/cortex+2mm+bs.nii.gz...
flirt -in /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dlabel/anat/cortex+2mm+bs.nii.gz -ref /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/lowb.nii.gz -out /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dlabel/diff/cortex+2mm+bs.bbr.nii.gz -applyxfm -init /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/xfms/anat2diff.bbr.mat -interp nearestneighbour
flirt -in /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dlabel/anat/cortex+2mm+bs.nii.gz -ref /usr/local/fsl/data/standard/MNI152_T1_1mm_brain.nii.gz -out /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dlabel/mni/cortex+2mm+bs.nii.gz -applyxfm -init /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/xfms/anat2mni.mat -interp nearestneighbour
orientLAS /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dlabel/anatorig/aparc+aseg.nii.gz /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dlabel/anat/aparc+aseg.nii.gz
INFO: input image orientation is LIA
INFO: input image determinant is -1
mri_convert -oni 256 -onj 256 -onk 256 -oid -1 6.33299e-08 -2.04891e-08 -ojd 7.07805e-08 1 1.74623e-09 -okd 9.31323e-09 -2.32831e-10 1 -oc 3.70524 44.2681 16.0046 -rt nearest /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dlabel/anatorig/aparc+aseg.nii.gz /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dlabel/anat/aparc+aseg.nii.gz
mri_convert.bin -oni 256 -onj 256 -onk 256 -oid -1 6.33299e-08 -2.04891e-08 -ojd 7.07805e-08 1 1.74623e-09 -okd 9.31323e-09 -2.32831e-10 1 -oc 3.70524 44.2681 16.0046 -rt nearest /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dlabel/anatorig/aparc+aseg.nii.gz /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dlabel/anat/aparc+aseg.nii.gz
$Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $
reading from /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dlabel/anatorig/aparc+aseg.nii.gz...
TR=2530.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-1, 6.33299e-08, -2.04891e-08)
j_ras = (-9.31323e-09, 2.32831e-10, -1)
k_ras = (7.07805e-08, 1, 1.74623e-09)
Reslicing using nearest
writing to /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dlabel/anat/aparc+aseg.nii.gz...
flirt -in /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dlabel/anat/aparc+aseg.nii.gz -ref /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/lowb.nii.gz -out /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dlabel/diff/aparc+aseg.bbr.nii.gz -applyxfm -init /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/xfms/anat2diff.bbr.mat -interp nearestneighbour
flirt -in /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dlabel/anat/aparc+aseg.nii.gz -ref /usr/local/fsl/data/standard/MNI152_T1_1mm_brain.nii.gz -out /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dlabel/mni/aparc+aseg.nii.gz -applyxfm -init /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/xfms/anat2mni.mat -interp nearestneighbour
orientLAS /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dlabel/anatorig/aparc+aseg+2mm.nii.gz /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dlabel/anat/aparc+aseg+2mm.nii.gz
INFO: input image orientation is LIA
INFO: input image determinant is -1
mri_convert -oni 256 -onj 256 -onk 256 -oid -1 6.33299e-08 -2.04891e-08 -ojd 7.07805e-08 1 1.74623e-09 -okd 9.31323e-09 -2.32831e-10 1 -oc 3.70524 44.2681 16.0046 -rt nearest /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dlabel/anatorig/aparc+aseg+2mm.nii.gz /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dlabel/anat/aparc+aseg+2mm.nii.gz
mri_convert.bin -oni 256 -onj 256 -onk 256 -oid -1 6.33299e-08 -2.04891e-08 -ojd 7.07805e-08 1 1.74623e-09 -okd 9.31323e-09 -2.32831e-10 1 -oc 3.70524 44.2681 16.0046 -rt nearest /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dlabel/anatorig/aparc+aseg+2mm.nii.gz /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dlabel/anat/aparc+aseg+2mm.nii.gz
$Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $
reading from /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dlabel/anatorig/aparc+aseg+2mm.nii.gz...
TR=2530.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-1, 6.33299e-08, -2.04891e-08)
j_ras = (-9.31323e-09, 2.32831e-10, -1)
k_ras = (7.07805e-08, 1, 1.74623e-09)
Reslicing using nearest
writing to /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dlabel/anat/aparc+aseg+2mm.nii.gz...
flirt -in /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dlabel/anat/aparc+aseg+2mm.nii.gz -ref /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/lowb.nii.gz -out /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dlabel/diff/aparc+aseg+2mm.bbr.nii.gz -applyxfm -init /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/xfms/anat2diff.bbr.mat -interp nearestneighbour
flirt -in /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dlabel/anat/aparc+aseg+2mm.nii.gz -ref /usr/local/fsl/data/standard/MNI152_T1_1mm_brain.nii.gz -out /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dlabel/mni/aparc+aseg+2mm.nii.gz -applyxfm -init /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/xfms/anat2mni.mat -interp nearestneighbour
orientLAS /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dlabel/anatorig/aparc+aseg_mask.nii.gz /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dlabel/anat/aparc+aseg_mask.nii.gz
INFO: input image orientation is LIA
INFO: input image determinant is -1
mri_convert -oni 256 -onj 256 -onk 256 -oid -1 6.33299e-08 -2.04891e-08 -ojd 7.07805e-08 1 1.74623e-09 -okd 9.31323e-09 -2.32831e-10 1 -oc 3.70524 44.2681 16.0046 -rt nearest /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dlabel/anatorig/aparc+aseg_mask.nii.gz /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dlabel/anat/aparc+aseg_mask.nii.gz
mri_convert.bin -oni 256 -onj 256 -onk 256 -oid -1 6.33299e-08 -2.04891e-08 -ojd 7.07805e-08 1 1.74623e-09 -okd 9.31323e-09 -2.32831e-10 1 -oc 3.70524 44.2681 16.0046 -rt nearest /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dlabel/anatorig/aparc+aseg_mask.nii.gz /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dlabel/anat/aparc+aseg_mask.nii.gz
$Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $
reading from /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dlabel/anatorig/aparc+aseg_mask.nii.gz...
TR=2530.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-1, 6.33299e-08, -2.04891e-08)
j_ras = (-9.31323e-09, 2.32831e-10, -1)
k_ras = (7.07805e-08, 1, 1.74623e-09)
Reslicing using nearest
writing to /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dlabel/anat/aparc+aseg_mask.nii.gz...
flirt -in /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dlabel/anat/aparc+aseg_mask.nii.gz -ref /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/lowb.nii.gz -out /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dlabel/diff/aparc+aseg_mask.bbr.nii.gz -applyxfm -init /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/xfms/anat2diff.bbr.mat -interp nearestneighbour
flirt -in /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dlabel/anat/aparc+aseg_mask.nii.gz -ref /usr/local/fsl/data/standard/MNI152_T1_1mm_brain.nii.gz -out /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dlabel/mni/aparc+aseg_mask.nii.gz -applyxfm -init /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/xfms/anat2mni.mat -interp nearestneighbour
orientLAS /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dlabel/anatorig/anat_brain_mask.nii.gz /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dlabel/anat/anat_brain_mask.nii.gz
INFO: input image orientation is LIA
INFO: input image determinant is -1
mri_convert -oni 256 -onj 256 -onk 256 -oid -1 6.33299e-08 -2.04891e-08 -ojd 7.07805e-08 1 1.74623e-09 -okd 9.31323e-09 -2.32831e-10 1 -oc 3.70524 44.2681 16.0046 -rt nearest /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dlabel/anatorig/anat_brain_mask.nii.gz /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dlabel/anat/anat_brain_mask.nii.gz
mri_convert.bin -oni 256 -onj 256 -onk 256 -oid -1 6.33299e-08 -2.04891e-08 -ojd 7.07805e-08 1 1.74623e-09 -okd 9.31323e-09 -2.32831e-10 1 -oc 3.70524 44.2681 16.0046 -rt nearest /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dlabel/anatorig/anat_brain_mask.nii.gz /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dlabel/anat/anat_brain_mask.nii.gz
$Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $
reading from /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dlabel/anatorig/anat_brain_mask.nii.gz...
TR=2530.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-1, 6.33299e-08, -2.04891e-08)
j_ras = (-9.31323e-09, 2.32831e-10, -1)
k_ras = (7.07805e-08, 1, 1.74623e-09)
Reslicing using nearest
writing to /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dlabel/anat/anat_brain_mask.nii.gz...
flirt -in /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dlabel/anat/anat_brain_mask.nii.gz -ref /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/lowb.nii.gz -out /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dlabel/diff/anat_brain_mask.bbr.nii.gz -applyxfm -init /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/xfms/anat2diff.bbr.mat -interp nearestneighbour
flirt -in /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dlabel/anat/anat_brain_mask.nii.gz -ref /usr/local/fsl/data/standard/MNI152_T1_1mm_brain.nii.gz -out /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dlabel/mni/anat_brain_mask.nii.gz -applyxfm -init /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/xfms/anat2mni.mat -interp nearestneighbour
orientLAS /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dlabel/anatorig/anat_brain_mask-vent.nii.gz /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dlabel/anat/anat_brain_mask-vent.nii.gz
INFO: input image orientation is LIA
INFO: input image determinant is -1
mri_convert -oni 256 -onj 256 -onk 256 -oid -1 6.33299e-08 -2.04891e-08 -ojd 7.07805e-08 1 1.74623e-09 -okd 9.31323e-09 -2.32831e-10 1 -oc 3.70524 44.2681 16.0046 -rt nearest /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dlabel/anatorig/anat_brain_mask-vent.nii.gz /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dlabel/anat/anat_brain_mask-vent.nii.gz
mri_convert.bin -oni 256 -onj 256 -onk 256 -oid -1 6.33299e-08 -2.04891e-08 -ojd 7.07805e-08 1 1.74623e-09 -okd 9.31323e-09 -2.32831e-10 1 -oc 3.70524 44.2681 16.0046 -rt nearest /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dlabel/anatorig/anat_brain_mask-vent.nii.gz /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dlabel/anat/anat_brain_mask-vent.nii.gz
$Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $
reading from /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dlabel/anatorig/anat_brain_mask-vent.nii.gz...
TR=2530.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-1, 6.33299e-08, -2.04891e-08)
j_ras = (-9.31323e-09, 2.32831e-10, -1)
k_ras = (7.07805e-08, 1, 1.74623e-09)
Reslicing using nearest
writing to /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dlabel/anat/anat_brain_mask-vent.nii.gz...
flirt -in /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dlabel/anat/anat_brain_mask-vent.nii.gz -ref /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/lowb.nii.gz -out /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dlabel/diff/anat_brain_mask-vent.bbr.nii.gz -applyxfm -init /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/xfms/anat2diff.bbr.mat -interp nearestneighbour
flirt -in /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dlabel/anat/anat_brain_mask-vent.nii.gz -ref /usr/local/fsl/data/standard/MNI152_T1_1mm_brain.nii.gz -out /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dlabel/mni/anat_brain_mask-vent.nii.gz -applyxfm -init /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/xfms/anat2mni.mat -interp nearestneighbour
fslstats -t /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/dwi.nii.gz -k /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dlabel/diff/White-Matter++.bbr.nii.gz -m -s | awk '{print $1/$2}' > /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/dwi_snr.txt
flirt -in /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dlabel/diff/lowb_brain_mask.nii.gz -ref /usr/local/fsl/data/standard/MNI152_T1_1mm_brain.nii.gz -out /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dlabel/mni/lowb_brain_mask.bbr.nii.gz -applyxfm -init /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/xfms/diff2mni.bbr.mat -interp nearestneighbour
flirt -in /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dlabel/diff/lowb_brain_mask.nii.gz -ref /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/brain_anat_orig.nii.gz -out /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dlabel/anatorig/lowb_brain_mask.bbr.nii.gz -applyxfm -init /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/xfms/diff2anatorig.bbr.mat -interp nearestneighbour
ln -sf /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dlabel/diff/aparc+aseg_mask.bbr.nii.gz /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/nodif_brain_mask.nii.gz
#-------------------------------------
#@# Tensor fit Mon Sep 10 15:00:40 BST 2018
dtifit -k /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/dwi.nii.gz -m /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dlabel/diff/aparc+aseg_mask.bbr.nii.gz -r /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/bvecs -b /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/bvals -o /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/dtifit
0 128 0 128 0 60
0 slices processed
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flirt -in /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/dtifit_FA.nii.gz -ref /usr/local/fsl/data/standard/MNI152_T1_1mm_brain.nii.gz -out /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/mni/dtifit_FA.bbr.nii.gz -applyxfm -init /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/xfms/diff2mni.bbr.mat
flirt -in /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/dtifit_L1.nii.gz -ref /usr/local/fsl/data/standard/MNI152_T1_1mm_brain.nii.gz -out /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/mni/dtifit_L1.bbr.nii.gz -applyxfm -init /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/xfms/diff2mni.bbr.mat
flirt -in /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/dtifit_L2.nii.gz -ref /usr/local/fsl/data/standard/MNI152_T1_1mm_brain.nii.gz -out /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/mni/dtifit_L2.bbr.nii.gz -applyxfm -init /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/xfms/diff2mni.bbr.mat
flirt -in /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/dtifit_L3.nii.gz -ref /usr/local/fsl/data/standard/MNI152_T1_1mm_brain.nii.gz -out /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/mni/dtifit_L3.bbr.nii.gz -applyxfm -init /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/xfms/diff2mni.bbr.mat
flirt -in /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/dtifit_MD.nii.gz -ref /usr/local/fsl/data/standard/MNI152_T1_1mm_brain.nii.gz -out /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/mni/dtifit_MD.bbr.nii.gz -applyxfm -init /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/xfms/diff2mni.bbr.mat
flirt -in /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/dtifit_MO.nii.gz -ref /usr/local/fsl/data/standard/MNI152_T1_1mm_brain.nii.gz -out /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/mni/dtifit_MO.bbr.nii.gz -applyxfm -init /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/xfms/diff2mni.bbr.mat
flirt -in /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/dtifit_S0.nii.gz -ref /usr/local/fsl/data/standard/MNI152_T1_1mm_brain.nii.gz -out /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/mni/dtifit_S0.bbr.nii.gz -applyxfm -init /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/xfms/diff2mni.bbr.mat
#-------------------------------------
#@# Priors Mon Sep 10 15:00:50 BST 2018
/usr/local/freesurfer/bin/dmri_train --outdir /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dlabel/mni --out lh.cst_AS_avg33_mni_bbr rh.cst_AS_avg33_mni_bbr lh.ilf_AS_avg33_mni_bbr rh.ilf_AS_avg33_mni_bbr lh.unc_AS_avg33_mni_bbr rh.unc_AS_avg33_mni_bbr fmajor_PP_avg33_mni_bbr fminor_PP_avg33_mni_bbr lh.atr_PP_avg33_mni_bbr rh.atr_PP_avg33_mni_bbr lh.cab_PP_avg33_mni_bbr rh.cab_PP_avg33_mni_bbr lh.ccg_PP_avg33_mni_bbr rh.ccg_PP_avg33_mni_bbr lh.slfp_PP_avg33_mni_bbr rh.slfp_PP_avg33_mni_bbr lh.slft_PP_avg33_mni_bbr rh.slft_PP_avg33_mni_bbr --slist /tmp/subj33.elmo.2005.26311.txt --trk dlabel/mni/lh.cst_AS.bbr.trk dlabel/mni/rh.cst_AS.bbr.trk dlabel/mni/lh.ilf_AS.bbr.trk dlabel/mni/rh.ilf_AS.bbr.trk dlabel/mni/lh.unc_AS.bbr.trk dlabel/mni/rh.unc_AS.bbr.trk dlabel/mni/fmajor_PP.bbr.trk dlabel/mni/fminor_PP.bbr.trk dlabel/mni/lh.atr_PP.bbr.trk dlabel/mni/rh.atr_PP.bbr.trk dlabel/mni/lh.cab_PP.bbr.trk dlabel/mni/rh.cab_PP.bbr.trk dlabel/mni/lh.ccg_PP.bbr.trk dlabel/mni/rh.ccg_PP.
bbr.trk dlabel/mni/lh.slfp_PP.bbr.trk dlabel/mni/rh.slfp_PP.bbr.trk dlabel/mni/lh.slft_PP.bbr.trk dlabel/mni/rh.slft_PP.bbr.trk --seg dlabel/mni/aparc+aseg.nii.gz --cmask dlabel/mni/cortex+2mm.nii.gz --lmask 16 16 0 0 0 0 0 0 10 49 0 0 0 0 0 0 0 0 --rois dlabel/mni/lh.cst_AS_roi1.bbr.nii.gz dlabel/mni/lh.cst_AS_roi2.bbr.nii.gz dlabel/mni/rh.cst_AS_roi1.bbr.nii.gz dlabel/mni/rh.cst_AS_roi2.bbr.nii.gz dlabel/mni/lh.ilf_AS_roi1.bbr.nii.gz dlabel/mni/lh.ilf_AS_roi2.bbr.nii.gz dlabel/mni/rh.ilf_AS_roi1.bbr.nii.gz dlabel/mni/rh.ilf_AS_roi2.bbr.nii.gz dlabel/mni/lh.unc_AS_roi1.bbr.nii.gz dlabel/mni/lh.unc_AS_roi2.bbr.nii.gz dlabel/mni/rh.unc_AS_roi1.bbr.nii.gz dlabel/mni/rh.unc_AS_roi2.bbr.nii.gz dlabel/mni/fmajor_PP_roi1.bbr.nii.gz dlabel/mni/fmajor_PP_roi2.bbr.nii.gz dlabel/mni/fminor_PP_roi1.bbr.nii.gz dlabel/mni/fminor_PP_roi2.bbr.nii.gz dlabel/mni/lh.atr_PP_roi1.bbr.nii.gz dlabel/mni/lh.atr_PP_roi2.bbr.nii.gz dlabel/mni/rh.atr_PP_roi1.bbr.nii.gz dlabel/mni/rh.atr_PP_roi2.bbr.nii.gz dla
bel/mni/lh.cab_PP_roi1.bbr.nii.gz dlabel/mn!
i/lh.cab
_PP_roi2.bbr.nii.gz dlabel/mni/rh.cab_PP_roi1.bbr.nii.gz dlabel/mni/rh.cab_PP_roi2.bbr.nii.gz dlabel/mni/lh.ccg_PP_roi1.bbr.nii.gz dlabel/mni/lh.ccg_PP_roi2.bbr.nii.gz dlabel/mni/rh.ccg_PP_roi1.bbr.nii.gz dlabel/mni/rh.ccg_PP_roi2.bbr.nii.gz dlabel/mni/lh.slfp_PP_roi1.bbr.nii.gz dlabel/mni/lh.slfp_PP_roi2.bbr.nii.gz dlabel/mni/rh.slfp_PP_roi1.bbr.nii.gz dlabel/mni/rh.slfp_PP_roi2.bbr.nii.gz dlabel/mni/lh.slft_PP_roi1.bbr.nii.gz dlabel/mni/lh.slft_PP_roi2.bbr.nii.gz dlabel/mni/rh.slft_PP_roi1.bbr.nii.gz dlabel/mni/rh.slft_PP_roi2.bbr.nii.gz --bmask /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dlabel/mni/aparc+aseg_mask.nii.gz --fa /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/dtifit_FA.nii.gz --cptdir /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dlabel/diff --reg /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/xfms/mni2diff.bbr.mat --ncpts 6 6 5 5 5 5 7 5 5 5 5 5 4 4 5 5 5 5 --trunc


cwd /home/fsluser/usr_/local_/diffusion_recons
cmdline /usr/local/freesurfer/bin/dmri_train --outdir /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dlabel/mni --out lh.cst_AS_avg33_mni_bbr rh.cst_AS_avg33_mni_bbr lh.ilf_AS_avg33_mni_bbr rh.ilf_AS_avg33_mni_bbr lh.unc_AS_avg33_mni_bbr rh.unc_AS_avg33_mni_bbr fmajor_PP_avg33_mni_bbr fminor_PP_avg33_mni_bbr lh.atr_PP_avg33_mni_bbr rh.atr_PP_avg33_mni_bbr lh.cab_PP_avg33_mni_bbr rh.cab_PP_avg33_mni_bbr lh.ccg_PP_avg33_mni_bbr rh.ccg_PP_avg33_mni_bbr lh.slfp_PP_avg33_mni_bbr rh.slfp_PP_avg33_mni_bbr lh.slft_PP_avg33_mni_bbr rh.slft_PP_avg33_mni_bbr --slist /tmp/subj33.elmo.2005.26311.txt --trk dlabel/mni/lh.cst_AS.bbr.trk dlabel/mni/rh.cst_AS.bbr.trk dlabel/mni/lh.ilf_AS.bbr.trk dlabel/mni/rh.ilf_AS.bbr.trk dlabel/mni/lh.unc_AS.bbr.trk dlabel/mni/rh.unc_AS.bbr.trk dlabel/mni/fmajor_PP.bbr.trk dlabel/mni/fminor_PP.bbr.trk dlabel/mni/lh.atr_PP.bbr.trk dlabel/mni/rh.atr_PP.bbr.trk dlabel/mni/lh.cab_PP.bbr.trk dlabel/mni/rh.cab_PP.bbr.trk dlabel/mni/lh.ccg_PP.bbr.trk dlabel/mni/rh
.ccg_PP.bbr.trk dlabel/mni/lh.slfp_PP.bbr.trk dlabel/mni/rh.slfp_PP.bbr.trk dlabel/mni/lh.slft_PP.bbr.trk dlabel/mni/rh.slft_PP.bbr.trk --seg dlabel/mni/aparc+aseg.nii.gz --cmask dlabel/mni/cortex+2mm.nii.gz --lmask 16 16 0 0 0 0 0 0 10 49 0 0 0 0 0 0 0 0 --rois dlabel/mni/lh.cst_AS_roi1.bbr.nii.gz dlabel/mni/lh.cst_AS_roi2.bbr.nii.gz dlabel/mni/rh.cst_AS_roi1.bbr.nii.gz dlabel/mni/rh.cst_AS_roi2.bbr.nii.gz dlabel/mni/lh.ilf_AS_roi1.bbr.nii.gz dlabel/mni/lh.ilf_AS_roi2.bbr.nii.gz dlabel/mni/rh.ilf_AS_roi1.bbr.nii.gz dlabel/mni/rh.ilf_AS_roi2.bbr.nii.gz dlabel/mni/lh.unc_AS_roi1.bbr.nii.gz dlabel/mni/lh.unc_AS_roi2.bbr.nii.gz dlabel/mni/rh.unc_AS_roi1.bbr.nii.gz dlabel/mni/rh.unc_AS_roi2.bbr.nii.gz dlabel/mni/fmajor_PP_roi1.bbr.nii.gz dlabel/mni/fmajor_PP_roi2.bbr.nii.gz dlabel/mni/fminor_PP_roi1.bbr.nii.gz dlabel/mni/fminor_PP_roi2.bbr.nii.gz dlabel/mni/lh.atr_PP_roi1.bbr.nii.gz dlabel/mni/lh.atr_PP_roi2.bbr.nii.gz dlabel/mni/rh.atr_PP_roi1.bbr.nii.gz dlabel/mni/rh.atr_PP_roi2.bbr.n
i
i.gz dlabel/mni/lh.cab_PP_roi1.bbr.nii.gz d!
label/mn
i/lh.cab_PP_roi2.bbr.nii.gz dlabel/mni/rh.cab_PP_roi1.bbr.nii.gz dlabel/mni/rh.cab_PP_roi2.bbr.nii.gz dlabel/mni/lh.ccg_PP_roi1.bbr.nii.gz dlabel/mni/lh.ccg_PP_roi2.bbr.nii.gz dlabel/mni/rh.ccg_PP_roi1.bbr.nii.gz dlabel/mni/rh.ccg_PP_roi2.bbr.nii.gz dlabel/mni/lh.slfp_PP_roi1.bbr.nii.gz dlabel/mni/lh.slfp_PP_roi2.bbr.nii.gz dlabel/mni/rh.slfp_PP_roi1.bbr.nii.gz dlabel/mni/rh.slfp_PP_roi2.bbr.nii.gz dlabel/mni/lh.slft_PP_roi1.bbr.nii.gz dlabel/mni/lh.slft_PP_roi2.bbr.nii.gz dlabel/mni/rh.slft_PP_roi1.bbr.nii.gz dlabel/mni/rh.slft_PP_roi2.bbr.nii.gz --bmask /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dlabel/mni/aparc+aseg_mask.nii.gz --fa /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/dtifit_FA.nii.gz --cptdir /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dlabel/diff --reg /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/xfms/mni2diff.bbr.mat --ncpts 6 6 5 5 5 5 7 5 5 5 5 5 4 4 5 5 5 5 --trunc
sysname  Linux
hostname localhost.localdomain
machine  x86_64
user     fsluser
Output directory: /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dlabel/mni
Output directory in test subject's space: /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dlabel/diff
Output base: lh.cst_AS_avg33_mni_bbr rh.cst_AS_avg33_mni_bbr lh.ilf_AS_avg33_mni_bbr rh.ilf_AS_avg33_mni_bbr lh.unc_AS_avg33_mni_bbr rh.unc_AS_avg33_mni_bbr fmajor_PP_avg33_mni_bbr fminor_PP_avg33_mni_bbr lh.atr_PP_avg33_mni_bbr rh.atr_PP_avg33_mni_bbr lh.cab_PP_avg33_mni_bbr rh.cab_PP_avg33_mni_bbr lh.ccg_PP_avg33_mni_bbr rh.ccg_PP_avg33_mni_bbr lh.slfp_PP_avg33_mni_bbr rh.slfp_PP_avg33_mni_bbr lh.slft_PP_avg33_mni_bbr rh.slft_PP_avg33_mni_bbr
Training subject directory list: /tmp/subj33.elmo.2005.26311.txt
Location of streamline files relative to base: dlabel/mni/lh.cst_AS.bbr.trk dlabel/mni/rh.cst_AS.bbr.trk dlabel/mni/lh.ilf_AS.bbr.trk dlabel/mni/rh.ilf_AS.bbr.trk dlabel/mni/lh.unc_AS.bbr.trk dlabel/mni/rh.unc_AS.bbr.trk dlabel/mni/fmajor_PP.bbr.trk dlabel/mni/fminor_PP.bbr.trk dlabel/mni/lh.atr_PP.bbr.trk dlabel/mni/rh.atr_PP.bbr.trk dlabel/mni/lh.cab_PP.bbr.trk dlabel/mni/rh.cab_PP.bbr.trk dlabel/mni/lh.ccg_PP.bbr.trk dlabel/mni/rh.ccg_PP.bbr.trk dlabel/mni/lh.slfp_PP.bbr.trk dlabel/mni/rh.slfp_PP.bbr.trk dlabel/mni/lh.slft_PP.bbr.trk dlabel/mni/rh.slft_PP.bbr.trk
Location of start ROI files relative to base: dlabel/mni/lh.cst_AS_roi1.bbr.nii.gz dlabel/mni/rh.cst_AS_roi1.bbr.nii.gz dlabel/mni/lh.ilf_AS_roi1.bbr.nii.gz dlabel/mni/rh.ilf_AS_roi1.bbr.nii.gz dlabel/mni/lh.unc_AS_roi1.bbr.nii.gz dlabel/mni/rh.unc_AS_roi1.bbr.nii.gz dlabel/mni/fmajor_PP_roi1.bbr.nii.gz dlabel/mni/fminor_PP_roi1.bbr.nii.gz dlabel/mni/lh.atr_PP_roi1.bbr.nii.gz dlabel/mni/rh.atr_PP_roi1.bbr.nii.gz dlabel/mni/lh.cab_PP_roi1.bbr.nii.gz dlabel/mni/rh.cab_PP_roi1.bbr.nii.gz dlabel/mni/lh.ccg_PP_roi1.bbr.nii.gz dlabel/mni/rh.ccg_PP_roi1.bbr.nii.gz dlabel/mni/lh.slfp_PP_roi1.bbr.nii.gz dlabel/mni/rh.slfp_PP_roi1.bbr.nii.gz dlabel/mni/lh.slft_PP_roi1.bbr.nii.gz dlabel/mni/rh.slft_PP_roi1.bbr.nii.gz
Location of end ROI files relative to base: dlabel/mni/lh.cst_AS_roi2.bbr.nii.gz dlabel/mni/rh.cst_AS_roi2.bbr.nii.gz dlabel/mni/lh.ilf_AS_roi2.bbr.nii.gz dlabel/mni/rh.ilf_AS_roi2.bbr.nii.gz dlabel/mni/lh.unc_AS_roi2.bbr.nii.gz dlabel/mni/rh.unc_AS_roi2.bbr.nii.gz dlabel/mni/fmajor_PP_roi2.bbr.nii.gz dlabel/mni/fminor_PP_roi2.bbr.nii.gz dlabel/mni/lh.atr_PP_roi2.bbr.nii.gz dlabel/mni/rh.atr_PP_roi2.bbr.nii.gz dlabel/mni/lh.cab_PP_roi2.bbr.nii.gz dlabel/mni/rh.cab_PP_roi2.bbr.nii.gz dlabel/mni/lh.ccg_PP_roi2.bbr.nii.gz dlabel/mni/rh.ccg_PP_roi2.bbr.nii.gz dlabel/mni/lh.slfp_PP_roi2.bbr.nii.gz dlabel/mni/rh.slfp_PP_roi2.bbr.nii.gz dlabel/mni/lh.slft_PP_roi2.bbr.nii.gz dlabel/mni/rh.slft_PP_roi2.bbr.nii.gz
Location of cortex masks relative to base: dlabel/mni/cortex+2mm.nii.gz
Label ID's from aparc+aseg to add to cortex mask: 16 16 0 0 0 0 0 0 10 49 0 0 0 0 0 0 0 0
Location of aparc+aseg's relative to base: dlabel/mni/aparc+aseg.nii.gz
Brain mask for output subject: /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dlabel/mni/aparc+aseg_mask.nii.gz
FA map for output subject: /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/dtifit_FA.nii.gz
Affine registration from atlas to base for output subject: /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/xfms/mni2diff.bbr.mat
Number of control points for initial spline: 6 6 5 5 5 5 7 5 5 5 5 5 4 4 5 5 5 5
Exclude previously chosen center streamlines: 0
Use truncated streamlines: 1
Loading brain mask of output subject from /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dlabel/mni/aparc+aseg_mask.nii.gz
Loading FA map of output subject from /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/dtifit_FA.nii.gz
Loading affine registration from /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/xfms/mni2diff.bbr.mat
Loading streamline start ROI from /usr/local/freesurfer/trctrain/trc001/dlabel/mni/lh.cst_AS_roi1.bbr.nii.gz
Loading streamline end ROI from /usr/local/freesurfer/trctrain/trc001/dlabel/mni/lh.cst_AS_roi2.bbr.nii.gz
Loading streamlines from /usr/local/freesurfer/trctrain/trc001/dlabel/mni/lh.cst_AS.bbr.trk
Loading streamline start ROI from /usr/local/freesurfer/trctrain/trc002/dlabel/mni/lh.cst_AS_roi1.bbr.nii.gz
Loading streamline end ROI from /usr/local/freesurfer/trctrain/trc002/dlabel/mni/lh.cst_AS_roi2.bbr.nii.gz
Loading streamlines from /usr/local/freesurfer/trctrain/trc002/dlabel/mni/lh.cst_AS.bbr.trk
Loading streamline start ROI from /usr/local/freesurfer/trctrain/trc003/dlabel/mni/lh.cst_AS_roi1.bbr.nii.gz
Loading streamline end ROI from /usr/local/freesurfer/trctrain/trc003/dlabel/mni/lh.cst_AS_roi2.bbr.nii.gz
Loading streamlines from /usr/local/freesurfer/trctrain/trc003/dlabel/mni/lh.cst_AS.bbr.trk
Loading streamline start ROI from /usr/local/freesurfer/trctrain/trc004/dlabel/mni/lh.cst_AS_roi1.bbr.nii.gz
Loading streamline end ROI from /usr/local/freesurfer/trctrain/trc004/dlabel/mni/lh.cst_AS_roi2.bbr.nii.gz
Loading streamlines from /usr/local/freesurfer/trctrain/trc004/dlabel/mni/lh.cst_AS.bbr.trk
Loading streamline start ROI from /usr/local/freesurfer/trctrain/trc005/dlabel/mni/lh.cst_AS_roi1.bbr.nii.gz
Loading streamline end ROI from /usr/local/freesurfer/trctrain/trc005/dlabel/mni/lh.cst_AS_roi2.bbr.nii.gz
Loading streamlines from /usr/local/freesurfer/trctrain/trc005/dlabel/mni/lh.cst_AS.bbr.trk
Loading streamline start ROI from /usr/local/freesurfer/trctrain/trc006/dlabel/mni/lh.cst_AS_roi1.bbr.nii.gz
Loading streamline end ROI from /usr/local/freesurfer/trctrain/trc006/dlabel/mni/lh.cst_AS_roi2.bbr.nii.gz
Loading streamlines from /usr/local/freesurfer/trctrain/trc006/dlabel/mni/lh.cst_AS.bbr.trk
Loading streamline start ROI from /usr/local/freesurfer/trctrain/trc007/dlabel/mni/lh.cst_AS_roi1.bbr.nii.gz
Loading streamline end ROI from /usr/local/freesurfer/trctrain/trc007/dlabel/mni/lh.cst_AS_roi2.bbr.nii.gz
Loading streamlines from /usr/local/freesurfer/trctrain/trc007/dlabel/mni/lh.cst_AS.bbr.trk
Loading streamline start ROI from /usr/local/freesurfer/trctrain/trc008/dlabel/mni/lh.cst_AS_roi1.bbr.nii.gz
Loading streamline end ROI from /usr/local/freesurfer/trctrain/trc008/dlabel/mni/lh.cst_AS_roi2.bbr.nii.gz
Loading streamlines from /usr/local/freesurfer/trctrain/trc008/dlabel/mni/lh.cst_AS.bbr.trk
Loading streamline start ROI from /usr/local/freesurfer/trctrain/trc009/dlabel/mni/lh.cst_AS_roi1.bbr.nii.gz
Loading streamline end ROI from /usr/local/freesurfer/trctrain/trc009/dlabel/mni/lh.cst_AS_roi2.bbr.nii.gz
Loading streamlines from /usr/local/freesurfer/trctrain/trc009/dlabel/mni/lh.cst_AS.bbr.trk
Loading streamline start ROI from /usr/local/freesurfer/trctrain/trc010/dlabel/mni/lh.cst_AS_roi1.bbr.nii.gz
Loading streamline end ROI from /usr/local/freesurfer/trctrain/trc010/dlabel/mni/lh.cst_AS_roi2.bbr.nii.gz
Loading streamlines from /usr/local/freesurfer/trctrain/trc010/dlabel/mni/lh.cst_AS.bbr.trk
Loading streamline start ROI from /usr/local/freesurfer/trctrain/trc011/dlabel/mni/lh.cst_AS_roi1.bbr.nii.gz
Loading streamline end ROI from /usr/local/freesurfer/trctrain/trc011/dlabel/mni/lh.cst_AS_roi2.bbr.nii.gz
Loading streamlines from /usr/local/freesurfer/trctrain/trc011/dlabel/mni/lh.cst_AS.bbr.trk
Loading streamline start ROI from /usr/local/freesurfer/trctrain/trc012/dlabel/mni/lh.cst_AS_roi1.bbr.nii.gz
Loading streamline end ROI from /usr/local/freesurfer/trctrain/trc012/dlabel/mni/lh.cst_AS_roi2.bbr.nii.gz
Loading streamlines from /usr/local/freesurfer/trctrain/trc012/dlabel/mni/lh.cst_AS.bbr.trk
Loading streamline start ROI from /usr/local/freesurfer/trctrain/trc013/dlabel/mni/lh.cst_AS_roi1.bbr.nii.gz
Loading streamline end ROI from /usr/local/freesurfer/trctrain/trc013/dlabel/mni/lh.cst_AS_roi2.bbr.nii.gz
Loading streamlines from /usr/local/freesurfer/trctrain/trc013/dlabel/mni/lh.cst_AS.bbr.trk
Loading streamline start ROI from /usr/local/freesurfer/trctrain/trc014/dlabel/mni/lh.cst_AS_roi1.bbr.nii.gz
Loading streamline end ROI from /usr/local/freesurfer/trctrain/trc014/dlabel/mni/lh.cst_AS_roi2.bbr.nii.gz
Loading streamlines from /usr/local/freesurfer/trctrain/trc014/dlabel/mni/lh.cst_AS.bbr.trk
Loading streamline start ROI from /usr/local/freesurfer/trctrain/trc015/dlabel/mni/lh.cst_AS_roi1.bbr.nii.gz
Loading streamline end ROI from /usr/local/freesurfer/trctrain/trc015/dlabel/mni/lh.cst_AS_roi2.bbr.nii.gz
Loading streamlines from /usr/local/freesurfer/trctrain/trc015/dlabel/mni/lh.cst_AS.bbr.trk
Loading streamline start ROI from /usr/local/freesurfer/trctrain/trc016/dlabel/mni/lh.cst_AS_roi1.bbr.nii.gz
Loading streamline end ROI from /usr/local/freesurfer/trctrain/trc016/dlabel/mni/lh.cst_AS_roi2.bbr.nii.gz
Loading streamlines from /usr/local/freesurfer/trctrain/trc016/dlabel/mni/lh.cst_AS.bbr.trk
Loading streamline start ROI from /usr/local/freesurfer/trctrain/trc017/dlabel/mni/lh.cst_AS_roi1.bbr.nii.gz
Loading streamline end ROI from /usr/local/freesurfer/trctrain/trc017/dlabel/mni/lh.cst_AS_roi2.bbr.nii.gz
Loading streamlines from /usr/local/freesurfer/trctrain/trc017/dlabel/mni/lh.cst_AS.bbr.trk
Loading streamline start ROI from /usr/local/freesurfer/trctrain/trc018/dlabel/mni/lh.cst_AS_roi1.bbr.nii.gz
Loading streamline end ROI from /usr/local/freesurfer/trctrain/trc018/dlabel/mni/lh.cst_AS_roi2.bbr.nii.gz
Loading streamlines from /usr/local/freesurfer/trctrain/trc018/dlabel/mni/lh.cst_AS.bbr.trk
Loading streamline start ROI from /usr/local/freesurfer/trctrain/trc019/dlabel/mni/lh.cst_AS_roi1.bbr.nii.gz
Loading streamline end ROI from /usr/local/freesurfer/trctrain/trc019/dlabel/mni/lh.cst_AS_roi2.bbr.nii.gz
Loading streamlines from /usr/local/freesurfer/trctrain/trc019/dlabel/mni/lh.cst_AS.bbr.trk
Loading streamline start ROI from /usr/local/freesurfer/trctrain/trc020/dlabel/mni/lh.cst_AS_roi1.bbr.nii.gz
Loading streamline end ROI from /usr/local/freesurfer/trctrain/trc020/dlabel/mni/lh.cst_AS_roi2.bbr.nii.gz
Loading streamlines from /usr/local/freesurfer/trctrain/trc020/dlabel/mni/lh.cst_AS.bbr.trk
Loading streamline start ROI from /usr/local/freesurfer/trctrain/trc021/dlabel/mni/lh.cst_AS_roi1.bbr.nii.gz
Loading streamline end ROI from /usr/local/freesurfer/trctrain/trc021/dlabel/mni/lh.cst_AS_roi2.bbr.nii.gz
Loading streamlines from /usr/local/freesurfer/trctrain/trc021/dlabel/mni/lh.cst_AS.bbr.trk
Loading streamline start ROI from /usr/local/freesurfer/trctrain/trc022/dlabel/mni/lh.cst_AS_roi1.bbr.nii.gz
Loading streamline end ROI from /usr/local/freesurfer/trctrain/trc022/dlabel/mni/lh.cst_AS_roi2.bbr.nii.gz
Loading streamlines from /usr/local/freesurfer/trctrain/trc022/dlabel/mni/lh.cst_AS.bbr.trk
Loading streamline start ROI from /usr/local/freesurfer/trctrain/trc023/dlabel/mni/lh.cst_AS_roi1.bbr.nii.gz
Loading streamline end ROI from /usr/local/freesurfer/trctrain/trc023/dlabel/mni/lh.cst_AS_roi2.bbr.nii.gz
Loading streamlines from /usr/local/freesurfer/trctrain/trc023/dlabel/mni/lh.cst_AS.bbr.trk
Loading streamline start ROI from /usr/local/freesurfer/trctrain/trc024/dlabel/mni/lh.cst_AS_roi1.bbr.nii.gz
Loading streamline end ROI from /usr/local/freesurfer/trctrain/trc024/dlabel/mni/lh.cst_AS_roi2.bbr.nii.gz
Loading streamlines from /usr/local/freesurfer/trctrain/trc024/dlabel/mni/lh.cst_AS.bbr.trk
Loading streamline start ROI from /usr/local/freesurfer/trctrain/trc025/dlabel/mni/lh.cst_AS_roi1.bbr.nii.gz
Loading streamline end ROI from /usr/local/freesurfer/trctrain/trc025/dlabel/mni/lh.cst_AS_roi2.bbr.nii.gz
Loading streamlines from /usr/local/freesurfer/trctrain/trc025/dlabel/mni/lh.cst_AS.bbr.trk
Loading streamline start ROI from /usr/local/freesurfer/trctrain/trc026/dlabel/mni/lh.cst_AS_roi1.bbr.nii.gz
Loading streamline end ROI from /usr/local/freesurfer/trctrain/trc026/dlabel/mni/lh.cst_AS_roi2.bbr.nii.gz
Loading streamlines from /usr/local/freesurfer/trctrain/trc026/dlabel/mni/lh.cst_AS.bbr.trk
Loading streamline start ROI from /usr/local/freesurfer/trctrain/trc027/dlabel/mni/lh.cst_AS_roi1.bbr.nii.gz
Loading streamline end ROI from /usr/local/freesurfer/trctrain/trc027/dlabel/mni/lh.cst_AS_roi2.bbr.nii.gz
Loading streamlines from /usr/local/freesurfer/trctrain/trc027/dlabel/mni/lh.cst_AS.bbr.trk
Loading streamline start ROI from /usr/local/freesurfer/trctrain/trc028/dlabel/mni/lh.cst_AS_roi1.bbr.nii.gz
Loading streamline end ROI from /usr/local/freesurfer/trctrain/trc028/dlabel/mni/lh.cst_AS_roi2.bbr.nii.gz
Loading streamlines from /usr/local/freesurfer/trctrain/trc028/dlabel/mni/lh.cst_AS.bbr.trk
Loading streamline start ROI from /usr/local/freesurfer/trctrain/trc029/dlabel/mni/lh.cst_AS_roi1.bbr.nii.gz
Loading streamline end ROI from /usr/local/freesurfer/trctrain/trc029/dlabel/mni/lh.cst_AS_roi2.bbr.nii.gz
Loading streamlines from /usr/local/freesurfer/trctrain/trc029/dlabel/mni/lh.cst_AS.bbr.trk
Loading streamline start ROI from /usr/local/freesurfer/trctrain/trc030/dlabel/mni/lh.cst_AS_roi1.bbr.nii.gz
Loading streamline end ROI from /usr/local/freesurfer/trctrain/trc030/dlabel/mni/lh.cst_AS_roi2.bbr.nii.gz
Loading streamlines from /usr/local/freesurfer/trctrain/trc030/dlabel/mni/lh.cst_AS.bbr.trk
Loading streamline start ROI from /usr/local/freesurfer/trctrain/trc031/dlabel/mni/lh.cst_AS_roi1.bbr.nii.gz
Loading streamline end ROI from /usr/local/freesurfer/trctrain/trc031/dlabel/mni/lh.cst_AS_roi2.bbr.nii.gz
Loading streamlines from /usr/local/freesurfer/trctrain/trc031/dlabel/mni/lh.cst_AS.bbr.trk
Loading streamline start ROI from /usr/local/freesurfer/trctrain/trc032/dlabel/mni/lh.cst_AS_roi1.bbr.nii.gz
Loading streamline end ROI from /usr/local/freesurfer/trctrain/trc032/dlabel/mni/lh.cst_AS_roi2.bbr.nii.gz
Loading streamlines from /usr/local/freesurfer/trctrain/trc032/dlabel/mni/lh.cst_AS.bbr.trk
Loading streamline start ROI from /usr/local/freesurfer/trctrain/trc033/dlabel/mni/lh.cst_AS_roi1.bbr.nii.gz
Loading streamline end ROI from /usr/local/freesurfer/trctrain/trc033/dlabel/mni/lh.cst_AS_roi2.bbr.nii.gz
Loading streamlines from /usr/local/freesurfer/trctrain/trc033/dlabel/mni/lh.cst_AS.bbr.trk
INFO: Rejected 1094 streamlines for straying off mask
INFO: Rejected 73 streamlines for reversing direction
INFO: Rejected 17 streamlines as length outliers
INFO: Have 7248 total streamlines (min/mean/max length: 59/99/139)
Loading segmentation from /usr/local/freesurfer/trctrain/trc001/dlabel/mni/aparc+aseg.nii.gz
Loading cortex mask from /usr/local/freesurfer/trctrain/trc001/dlabel/mni/cortex+2mm.nii.gz
Loading segmentation from /usr/local/freesurfer/trctrain/trc002/dlabel/mni/aparc+aseg.nii.gz
Loading cortex mask from /usr/local/freesurfer/trctrain/trc002/dlabel/mni/cortex+2mm.nii.gz
Loading segmentation from /usr/local/freesurfer/trctrain/trc003/dlabel/mni/aparc+aseg.nii.gz
Loading cortex mask from /usr/local/freesurfer/trctrain/trc003/dlabel/mni/cortex+2mm.nii.gz
Loading segmentation from /usr/local/freesurfer/trctrain/trc004/dlabel/mni/aparc+aseg.nii.gz
Loading cortex mask from /usr/local/freesurfer/trctrain/trc004/dlabel/mni/cortex+2mm.nii.gz
Loading segmentation from /usr/local/freesurfer/trctrain/trc005/dlabel/mni/aparc+aseg.nii.gz
Loading cortex mask from /usr/local/freesurfer/trctrain/trc005/dlabel/mni/cortex+2mm.nii.gz
Loading segmentation from /usr/local/freesurfer/trctrain/trc006/dlabel/mni/aparc+aseg.nii.gz
Loading cortex mask from /usr/local/freesurfer/trctrain/trc006/dlabel/mni/cortex+2mm.nii.gz
Loading segmentation from /usr/local/freesurfer/trctrain/trc007/dlabel/mni/aparc+aseg.nii.gz
Loading cortex mask from /usr/local/freesurfer/trctrain/trc007/dlabel/mni/cortex+2mm.nii.gz
Loading segmentation from /usr/local/freesurfer/trctrain/trc008/dlabel/mni/aparc+aseg.nii.gz
Loading cortex mask from /usr/local/freesurfer/trctrain/trc008/dlabel/mni/cortex+2mm.nii.gz
Loading segmentation from /usr/local/freesurfer/trctrain/trc009/dlabel/mni/aparc+aseg.nii.gz
Loading cortex mask from /usr/local/freesurfer/trctrain/trc009/dlabel/mni/cortex+2mm.nii.gz
Loading segmentation from /usr/local/freesurfer/trctrain/trc010/dlabel/mni/aparc+aseg.nii.gz
Loading cortex mask from /usr/local/freesurfer/trctrain/trc010/dlabel/mni/cortex+2mm.nii.gz
Loading segmentation from /usr/local/freesurfer/trctrain/trc011/dlabel/mni/aparc+aseg.nii.gz
Loading cortex mask from /usr/local/freesurfer/trctrain/trc011/dlabel/mni/cortex+2mm.nii.gz
Loading segmentation from /usr/local/freesurfer/trctrain/trc012/dlabel/mni/aparc+aseg.nii.gz
Loading cortex mask from /usr/local/freesurfer/trctrain/trc012/dlabel/mni/cortex+2mm.nii.gz
Loading segmentation from /usr/local/freesurfer/trctrain/trc013/dlabel/mni/aparc+aseg.nii.gz
Loading cortex mask from /usr/local/freesurfer/trctrain/trc013/dlabel/mni/cortex+2mm.nii.gz
Loading segmentation from /usr/local/freesurfer/trctrain/trc014/dlabel/mni/aparc+aseg.nii.gz
Loading cortex mask from /usr/local/freesurfer/trctrain/trc014/dlabel/mni/cortex+2mm.nii.gz
Loading segmentation from /usr/local/freesurfer/trctrain/trc015/dlabel/mni/aparc+aseg.nii.gz
Loading cortex mask from /usr/local/freesurfer/trctrain/trc015/dlabel/mni/cortex+2mm.nii.gz
Loading segmentation from /usr/local/freesurfer/trctrain/trc016/dlabel/mni/aparc+aseg.nii.gz
Loading cortex mask from /usr/local/freesurfer/trctrain/trc016/dlabel/mni/cortex+2mm.nii.gz
Loading segmentation from /usr/local/freesurfer/trctrain/trc017/dlabel/mni/aparc+aseg.nii.gz
Loading cortex mask from /usr/local/freesurfer/trctrain/trc017/dlabel/mni/cortex+2mm.nii.gz
Loading segmentation from /usr/local/freesurfer/trctrain/trc018/dlabel/mni/aparc+aseg.nii.gz
Loading cortex mask from /usr/local/freesurfer/trctrain/trc018/dlabel/mni/cortex+2mm.nii.gz
Loading segmentation from /usr/local/freesurfer/trctrain/trc019/dlabel/mni/aparc+aseg.nii.gz
Loading cortex mask from /usr/local/freesurfer/trctrain/trc019/dlabel/mni/cortex+2mm.nii.gz
Loading segmentation from /usr/local/freesurfer/trctrain/trc020/dlabel/mni/aparc+aseg.nii.gz
Loading cortex mask from /usr/local/freesurfer/trctrain/trc020/dlabel/mni/cortex+2mm.nii.gz
Loading segmentation from /usr/local/freesurfer/trctrain/trc021/dlabel/mni/aparc+aseg.nii.gz
Loading cortex mask from /usr/local/freesurfer/trctrain/trc021/dlabel/mni/cortex+2mm.nii.gz
Loading segmentation from /usr/local/freesurfer/trctrain/trc022/dlabel/mni/aparc+aseg.nii.gz
Loading cortex mask from /usr/local/freesurfer/trctrain/trc022/dlabel/mni/cortex+2mm.nii.gz
Loading segmentation from /usr/local/freesurfer/trctrain/trc023/dlabel/mni/aparc+aseg.nii.gz
Loading cortex mask from /usr/local/freesurfer/trctrain/trc023/dlabel/mni/cortex+2mm.nii.gz
Loading segmentation from /usr/local/freesurfer/trctrain/trc024/dlabel/mni/aparc+aseg.nii.gz
Loading cortex mask from /usr/local/freesurfer/trctrain/trc024/dlabel/mni/cortex+2mm.nii.gz
Loading segmentation from /usr/local/freesurfer/trctrain/trc025/dlabel/mni/aparc+aseg.nii.gz
Loading cortex mask from /usr/local/freesurfer/trctrain/trc025/dlabel/mni/cortex+2mm.nii.gz
Loading segmentation from /usr/local/freesurfer/trctrain/trc026/dlabel/mni/aparc+aseg.nii.gz
Loading cortex mask from /usr/local/freesurfer/trctrain/trc026/dlabel/mni/cortex+2mm.nii.gz
Loading segmentation from /usr/local/freesurfer/trctrain/trc027/dlabel/mni/aparc+aseg.nii.gz
Loading cortex mask from /usr/local/freesurfer/trctrain/trc027/dlabel/mni/cortex+2mm.nii.gz
Loading segmentation from /usr/local/freesurfer/trctrain/trc028/dlabel/mni/aparc+aseg.nii.gz
Loading cortex mask from /usr/local/freesurfer/trctrain/trc028/dlabel/mni/cortex+2mm.nii.gz
Loading segmentation from /usr/local/freesurfer/trctrain/trc029/dlabel/mni/aparc+aseg.nii.gz
Loading cortex mask from /usr/local/freesurfer/trctrain/trc029/dlabel/mni/cortex+2mm.nii.gz
Loading segmentation from /usr/local/freesurfer/trctrain/trc030/dlabel/mni/aparc+aseg.nii.gz
Loading cortex mask from /usr/local/freesurfer/trctrain/trc030/dlabel/mni/cortex+2mm.nii.gz
Loading segmentation from /usr/local/freesurfer/trctrain/trc031/dlabel/mni/aparc+aseg.nii.gz
Loading cortex mask from /usr/local/freesurfer/trctrain/trc031/dlabel/mni/cortex+2mm.nii.gz
Linux localhost.localdomain 3.10.0-514.16.1.el7.x86_64 #1 SMP Wed Apr 12 15:04:24 UTC 2017 x86_64 x86_64 x86_64 GNU/Linux

trac-preproc exited with ERRORS at Mon Sep 10 15:07:07 BST 2018




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