subject:"\[Freesurfer\] TRACULA problems"

[Freesurfer] TRACULA problems

2016-07-01 Thread Koubiyr, Ismail


Hi everyone,

It’s been two weeks that I’ve been facing some issues with Tracula. I hope you 
could help me with that.

I run trac-all -prep -c on some DICOM files but I had the following error :
WARNING: file 
/Users/ismailkoubiyr/Documents/PFE/Tracula/dti/SER_5/MR.1.2.826.0.1.3680043.6.8878.22551.20150806120704.648.1017
 does not contain a Siemens ASCII header
has this file been anonymized?
ERROR: cannot unpack mosiacs without ASCII header
I also tried to de-mosiac the DICOMs, it gave me the same error.

Then I converted the DICOMs into NIFTI, which allowed me not to get this error 
but something else weird happened. Now I get :
ERROR: fMRIframe: frame >= nframes
I checked the bvecs and bvals files, they seem normal, no additional space, but 
when the new bvecs  and bvals are created, they seem messed up. I will attach 
you all the bvecs and bvals I used and the ones I get too.

Ideally, the DICOMs should work fine but I have no idea why I get these errors.
The bvecs and bvals are obtained from dcm2nii and then corrected to avoid any 
additional space.

Thank you in advance for your help.

Best,

Ismail

P.S : 3T2_bvecs.txt and 3T2_bvals.txt are the original files used.





bvals
Description: bvals


bvecs
Description: bvecs


bvecs.norot
Description: bvecs.norot


dwi_orig.mghdti.bvecs
Description: dwi_orig.mghdti.bvecs


dwi_orig.mghdti.bvals
Description: dwi_orig.mghdti.bvals
0
1000
1000
1000
1000
1000
1000
1000
1000
1000
1000
1000
1000
1000
1000
1000
1000
1000
1000
1000
1000
1000
1000
1000
1000
1000
1000
1000
1000
1000
1000
0
1000
1000
1000
1000
1000
1000
1000
1000
1000
1000
1000
1000
1000
1000
1000
1000
1000
1000
1000
1000
1000
1000
1000
1000
1000
1000
1000
1000
1000
1000
0
00 0 0
-0.203086 0.51882 -0.83041
0.19699 0.519109 -0.831697
0.400451 0.175928 -0.899271
-0.402681 0.730255 -0.551883
-0.201801 0.940841 -0.272204
-0.852534 0.518969 -0.0621066
-0.729693 0.519789 -0.444259
-0.406 0.176399 -0.896687
-0.730687 0.176545 -0.659491
-0.650821 0.731986 0.201565
-0.321998 0.941721 0.0973547
-0.325885 0.523495 0.787243
-0.652464 0.522204 0.549176
-0.979115 0.177805 0.0985869
-0.857087 0.178312 0.48333
0.00074441 0.735199 0.677851
0.00317198 0.943882 0.330266
0.656176 0.522342 0.544602
0.331016 0.523908 0.784824
0.197021 -0.176144 -0.964446
0.20548 0.177881 0.96236
0.651496 0.731864 0.199821
0.324279 0.941458 0.0921958
0.200221 0.939774 -0.277014
0.402681 0.730255 -0.551883
0.730024 0.176561 -0.66022
0.726896 0.519093 -0.449628
0.851743 0.519522 -0.0680449
0.859934 0.178306 0.478247
0.979641 0.177715 0.0933861
0 0 0
-0.203086 0.51882 -0.83041
0.19699 0.519109 -0.831697
0.400451 0.175928 -0.899271
-0.402681 0.730255 -0.551883
-0.201801 0.940841 -0.272204
-0.852534 0.518969 -0.0621066
-0.729693 0.519789 -0.444259
-0.406 0.176399 -0.896687
-0.730687 0.176545 -0.659491
-0.650821 0.731986 0.201565
-0.321998 0.941721 0.0973547
-0.325885 0.523495 0.787243
-0.652464 0.522204 0.549176
-0.979115 0.177805 0.0985869
-0.857087 0.178312 0.48333
0.00074441 0.735199 0.677851
0.00317198 0.943882 0.330266
0.656176 0.522342 0.544602
0.331016 0.523908 0.784824
0.197021 -0.176144 -0.964446
0.20548 0.177881 0.96236
0.651496 0.731864 0.199821
0.324279 0.941458 0.0921958
0.200221 0.939774 -0.277014
0.402681 0.730255 -0.551883
0.730024 0.176561 -0.66022
0.726896 0.519093 -0.449628
0.851743 0.519522 -0.0680449
0.859934 0.178306 0.478247
0.979641 0.177715 0.0933861
0 0 0
0 0 0___
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Re: [Freesurfer] Tracula problems (creating symbolic link)

2016-04-05 Thread Anastasia Yendiki



Hi Efrat - You could just use cp instead of ln -s. This will duplicate the 
file, instead of creating a link to it.


a.y

On Tue, 5 Apr 2016, Efrat Kliper wrote:



Dear Anastasia,

 

Thank you for the fast replay.

I have tried both suggestions, however it still reports:  Operation not 
supported

Also, I have used the links that you have sent me but non work. This time 
(after changing according to the
links), I got the message: operation denied


I don’t know how to resolve the issue of virtual machine, as not much is 
written about that and the links are
not helping with that issue.


Do you have other suggestions regarding how to change the script, so it will 
create the data.nii without the
symbolic link (there are plenty "ln" commands uses in the script)?


Many thanks,

Efrat


On Wed, Mar 30, 2016 at 12:39 AM, Anastasia Yendiki 
 wrote:

  Hi Efrat - This appears to be a virtual machine problem:

  https://communities.vmware.com/thread/312591?tstart=0

  There are some solutions suggested in that thread. I'm wondering if using 
a relative instead of an
  absolute path for the symlink works, i.e.,

  ln -sf dwi.nii.gz /mnt/hgfs/linux_share/subjects/TB_480/dmri/data.nii.gz

  instead of:

  ln -sf /mnt/hgfs/linux_share/subjects/TB_480/dmri/dwi.nii.gz
  /mnt/hgfs/linux_share/subjects/TB_480/dmri/data.nii.gz

  Can you please try it both ways and let me know if the former works on a 
computer where the latter
  doesn't?

  And yes, if you fix error #1 it'll fix error #2 as well.

  Thanks,
  a.y


  On Tue, 29 Mar 2016, Efrat Kliper wrote:


Dear Freesurfer experts,


I upgraded to Freesurfer 5.3 from Freesurfer 5.1 (all of the 
preprocessing has already
been completed in Freesurfer 5.1) in order to run some new functions
of Tracula (I have also installed the latest Tracula update
(tracula.update.centos4_x86_64.5.3.2014_05_26).


I am using:

FREESURFER_HOME: /usr/local/freesurfer

Build stamp: freesurfer-Linux-centos4_x86_64-stable-pub-v5.3.0

RedHat release: CentOS release 5.3 (Final)

Kernel info: Linux 2.6.18-128.1.6.el5 x86_64

 

 I encountered two problems:


1.  When I run the initial code of Tracula: trac-all –prep code:

/home/fsl/

usr/local/freesurfer/bin/trac-all -prep -c
/mnt/hgfs/linux_share/Scripts/FreeSurfersScript/config_2.txt

Subject TB_480

SUBJECTS_DIR /mnt/hgfs/linux_share/subjects

FREESURFER_HOME /usr/local/freesurfer

Actual FREESURFER_HOME /usr/local/freesurfer

build-stamp.txt: freesurfer-Linux-centos4_x86_64-stable-pub-v5.3.0

fsl

localhost.localdomain

Linux localhost.localdomain 2.6.18-128.1.6.el5 #1 SMP Wed Apr 1 
09:10:25 EDT 2009 x86_64
x86_64 x86_64 GNU/Linux

 

I am getting the following message: ln -sf
/mnt/hgfs/linux_share/subjects/TB_480/dmri/dwi.nii.gz
/mnt/hgfs/linux_share/subjects/TB_480/dmri/data.nii.gz

 

ln: creating symbolic link 
`/mnt/hgfs/linux_share/subjects/TB_480/dmri/data.nii.gz' to
`/mnt/hgfs/linux_share/subjects/TB_480/dmri/dwi.nii.gz': Operation 
not
supported

 

2.  If I run the trac-all –bedp command of Tracula (on already 
trac-all data which
was preproc on Freesurfer version 5.1. /home/fsl

/usr/local/freesurfer/bin/trac-all

-bedp -c /home/fsl/Desktop/xxx.txt

Subject TB_201

SUBJECTS_DIR /mnt/hgfs/linux_share/subjects

FREESURFER_HOME /usr/local/freesurfer

Actual FREESURFER_HOME /usr/local/freesurfer

build-stamp.txt: freesurfer-Linux-centos4_x86_64-stable-pub-v5.3.0

fsl

localhost.localdomain

Linux localhost.localdomain 2.6.18-128.1.6.el5 #1 SMP Wed Apr 1 
09:10:25 EDT 2009 x86_64
x86_64 x86_64 GNU/Linux

 

I am getting the following message:

Program versions:

$Id: trac-all,v 1.56 2014/05/26 08:28:32 ayendiki Exp $

mri_convert --all-info

ProgramName: mri_convert  ProgramArguments: --all-info  
ProgramVersion: $Name:  $ 
TimeStamp: 2016/03/29-13:00:54-GMT  BuildTimeStamp: Aug 16 2014 
05:13:24 
CVS: $Id: mri_convert.c,v 1.213 2014/07/29 19:22:31 fischl Exp $  
User: fsl  Machine:
localhost.localdomain  Platform: Linux  PlatformVersion:
2.6.18-128.1.6.el5  CompilerName: GCC  CompilerVersion: 30400

FLIRT version 6.0

$Id: bbregister,v 1.49.2.3 2013/03/25 18:04:53 greve Exp $

$Id: mri_cvs_register,v 1.15.2.12 2013/02/09

Re: [Freesurfer] Tracula problems (creating symbolic link)

2016-04-05 Thread Efrat Kliper

Dear Anastasia,



Thank you for the fast replay.

I have tried both suggestions, however it still reports:  Operation not
supported

Also, I have used the links that you have sent me but non work. This time
(after changing according to the links), I got the message: operation denied


I don’t know how to resolve the issue of virtual machine, as not much is
written about that and the links are not helping with that issue.


Do you have other suggestions regarding how to change the script, so it
will create the data.nii without the symbolic link (there are plenty "ln"
commands uses in the script)?


Many thanks,

Efrat

On Wed, Mar 30, 2016 at 12:39 AM, Anastasia Yendiki <
ayend...@nmr.mgh.harvard.edu> wrote:

>
> Hi Efrat - This appears to be a virtual machine problem:
>
> https://communities.vmware.com/thread/312591?tstart=0
>
> There are some solutions suggested in that thread. I'm wondering if using
> a relative instead of an absolute path for the symlink works, i.e.,
>
> ln -sf dwi.nii.gz /mnt/hgfs/linux_share/subjects/TB_480/dmri/data.nii.gz
>
> instead of:
>
> ln -sf /mnt/hgfs/linux_share/subjects/TB_480/dmri/dwi.nii.gz
> /mnt/hgfs/linux_share/subjects/TB_480/dmri/data.nii.gz
>
> Can you please try it both ways and let me know if the former works on a
> computer where the latter doesn't?
>
> And yes, if you fix error #1 it'll fix error #2 as well.
>
> Thanks,
> a.y
>
>
>
> On Tue, 29 Mar 2016, Efrat Kliper wrote:
>
>
>> Dear Freesurfer experts,
>>
>>
>> I upgraded to Freesurfer 5.3 from Freesurfer 5.1 (all of the
>> preprocessing has already been completed in Freesurfer 5.1) in order to run
>> some new functions
>> of Tracula (I have also installed the latest Tracula update
>> (tracula.update.centos4_x86_64.5.3.2014_05_26).
>>
>>
>> I am using:
>>
>> FREESURFER_HOME: /usr/local/freesurfer
>>
>> Build stamp: freesurfer-Linux-centos4_x86_64-stable-pub-v5.3.0
>>
>> RedHat release: CentOS release 5.3 (Final)
>>
>> Kernel info: Linux 2.6.18-128.1.6.el5 x86_64
>>
>>
>>
>>  I encountered two problems:
>>
>>
>> 1.  When I run the initial code of Tracula: trac-all –prep code:
>>
>> /home/fsl/
>>
>> usr/local/freesurfer/bin/trac-all -prep -c
>> /mnt/hgfs/linux_share/Scripts/FreeSurfersScript/config_2.txt
>>
>> Subject TB_480
>>
>> SUBJECTS_DIR /mnt/hgfs/linux_share/subjects
>>
>> FREESURFER_HOME /usr/local/freesurfer
>>
>> Actual FREESURFER_HOME /usr/local/freesurfer
>>
>> build-stamp.txt: freesurfer-Linux-centos4_x86_64-stable-pub-v5.3.0
>>
>> fsl
>>
>> localhost.localdomain
>>
>> Linux localhost.localdomain 2.6.18-128.1.6.el5 #1 SMP Wed Apr 1 09:10:25
>> EDT 2009 x86_64 x86_64 x86_64 GNU/Linux
>>
>>
>>
>> I am getting the following message: ln -sf
>> /mnt/hgfs/linux_share/subjects/TB_480/dmri/dwi.nii.gz
>> /mnt/hgfs/linux_share/subjects/TB_480/dmri/data.nii.gz
>>
>>
>>
>> ln: creating symbolic link
>> `/mnt/hgfs/linux_share/subjects/TB_480/dmri/data.nii.gz' to
>> `/mnt/hgfs/linux_share/subjects/TB_480/dmri/dwi.nii.gz': Operation not
>> supported
>>
>>
>>
>> 2.  If I run the trac-all –bedp command of Tracula (on already
>> trac-all data which was preproc on Freesurfer version 5.1. /home/fsl
>>
>> /usr/local/freesurfer/bin/trac-all
>>
>> -bedp -c /home/fsl/Desktop/xxx.txt
>>
>> Subject TB_201
>>
>> SUBJECTS_DIR /mnt/hgfs/linux_share/subjects
>>
>> FREESURFER_HOME /usr/local/freesurfer
>>
>> Actual FREESURFER_HOME /usr/local/freesurfer
>>
>> build-stamp.txt: freesurfer-Linux-centos4_x86_64-stable-pub-v5.3.0
>>
>> fsl
>>
>> localhost.localdomain
>>
>> Linux localhost.localdomain 2.6.18-128.1.6.el5 #1 SMP Wed Apr 1 09:10:25
>> EDT 2009 x86_64 x86_64 x86_64 GNU/Linux
>>
>>
>>
>> I am getting the following message:
>>
>> Program versions:
>>
>> $Id: trac-all,v 1.56 2014/05/26 08:28:32 ayendiki Exp $
>>
>> mri_convert --all-info
>>
>> ProgramName: mri_convert  ProgramArguments: --all-info  ProgramVersion:
>> $Name:  $  TimeStamp: 2016/03/29-13:00:54-GMT  BuildTimeStamp: Aug 16 2014
>> 05:13:24
>> CVS: $Id: mri_convert.c,v 1.213 2014/07/29 19:22:31 fischl Exp $  User:
>> fsl  Machine: localhost.localdomain  Platform: Linux  PlatformVersion:
>> 2.6.18-128.1.6.el5  CompilerName: GCC  CompilerVersion: 30400
>>
>> FLIRT version 6.0
>>
>> $Id: bbregister,v 1.49.2.3 2013/03/25 18:04:53 greve Exp $
>>
>> $Id: mri_cvs_register,v 1.15.2.12 2013/02/09 00:37:37 nicks Exp $
>>
>> ProgramName: dmri_motion  ProgramArguments: --all-info  ProgramVersion:
>> $Name:  $  TimeStamp: 2016/03/29-13:00:54-GMT  BuildTimeStamp: Feb  2 2013
>> 22:46:06
>> CVS:   User: fsl  Machine: localhost.localdomain  Platform: Linux
>> PlatformVersion: 2.6.18-128.1.6.el5  CompilerName: GCC  CompilerVersion:
>> 30400
>>
>> ProgramName: dmri_train  ProgramArguments: --all-info  ProgramVersion:
>> $Name:  $  TimeStamp: 2016/03/29-13:00:54-GMT  BuildTimeStamp: May 23 2014
>> 05:15:35
>> CVS:   User: fsl  Machine: localhost.localdomain  Platform: Linux
>> PlatformVersion: 2.6.18-128.1.6.el5  CompilerName: GCC  CompilerVersion:
>> 30400
>>
>>

Re: [Freesurfer] Tracula problems (creating symbolic link)

2016-03-29 Thread Anastasia Yendiki



Hi Efrat - This appears to be a virtual machine problem:

https://communities.vmware.com/thread/312591?tstart=0

There are some solutions suggested in that thread. I'm wondering if using 
a relative instead of an absolute path for the symlink works, i.e.,


ln -sf dwi.nii.gz /mnt/hgfs/linux_share/subjects/TB_480/dmri/data.nii.gz

instead of:

ln -sf /mnt/hgfs/linux_share/subjects/TB_480/dmri/dwi.nii.gz 
/mnt/hgfs/linux_share/subjects/TB_480/dmri/data.nii.gz

Can you please try it both ways and let me know if the former works on a 
computer where the latter doesn't?


And yes, if you fix error #1 it'll fix error #2 as well.

Thanks,
a.y


On Tue, 29 Mar 2016, Efrat Kliper wrote:



Dear Freesurfer experts,


I upgraded to Freesurfer 5.3 from Freesurfer 5.1 (all of the preprocessing has 
already been completed in Freesurfer 5.1) in order to run some new functions
of Tracula (I have also installed the latest Tracula update 
(tracula.update.centos4_x86_64.5.3.2014_05_26).


I am using:

FREESURFER_HOME: /usr/local/freesurfer

Build stamp: freesurfer-Linux-centos4_x86_64-stable-pub-v5.3.0

RedHat release: CentOS release 5.3 (Final)

Kernel info: Linux 2.6.18-128.1.6.el5 x86_64

 

 I encountered two problems:


1.  When I run the initial code of Tracula: trac-all –prep code:

/home/fsl/

usr/local/freesurfer/bin/trac-all -prep -c 
/mnt/hgfs/linux_share/Scripts/FreeSurfersScript/config_2.txt

Subject TB_480

SUBJECTS_DIR /mnt/hgfs/linux_share/subjects

FREESURFER_HOME /usr/local/freesurfer

Actual FREESURFER_HOME /usr/local/freesurfer

build-stamp.txt: freesurfer-Linux-centos4_x86_64-stable-pub-v5.3.0

fsl

localhost.localdomain

Linux localhost.localdomain 2.6.18-128.1.6.el5 #1 SMP Wed Apr 1 09:10:25 EDT 
2009 x86_64 x86_64 x86_64 GNU/Linux

 

I am getting the following message: ln -sf 
/mnt/hgfs/linux_share/subjects/TB_480/dmri/dwi.nii.gz 
/mnt/hgfs/linux_share/subjects/TB_480/dmri/data.nii.gz

 

ln: creating symbolic link 
`/mnt/hgfs/linux_share/subjects/TB_480/dmri/data.nii.gz' to 
`/mnt/hgfs/linux_share/subjects/TB_480/dmri/dwi.nii.gz': Operation not
supported

 

2.  If I run the trac-all –bedp command of Tracula (on already trac-all 
data which was preproc on Freesurfer version 5.1. /home/fsl

/usr/local/freesurfer/bin/trac-all

-bedp -c /home/fsl/Desktop/xxx.txt

Subject TB_201

SUBJECTS_DIR /mnt/hgfs/linux_share/subjects

FREESURFER_HOME /usr/local/freesurfer

Actual FREESURFER_HOME /usr/local/freesurfer

build-stamp.txt: freesurfer-Linux-centos4_x86_64-stable-pub-v5.3.0

fsl

localhost.localdomain

Linux localhost.localdomain 2.6.18-128.1.6.el5 #1 SMP Wed Apr 1 09:10:25 EDT 
2009 x86_64 x86_64 x86_64 GNU/Linux

 

I am getting the following message:

Program versions:

$Id: trac-all,v 1.56 2014/05/26 08:28:32 ayendiki Exp $

mri_convert --all-info

ProgramName: mri_convert  ProgramArguments: --all-info  ProgramVersion: $Name:  
$  TimeStamp: 2016/03/29-13:00:54-GMT  BuildTimeStamp: Aug 16 2014 05:13:24 
CVS: $Id: mri_convert.c,v 1.213 2014/07/29 19:22:31 fischl Exp $  User: fsl  
Machine: localhost.localdomain  Platform: Linux  PlatformVersion:
2.6.18-128.1.6.el5  CompilerName: GCC  CompilerVersion: 30400

FLIRT version 6.0

$Id: bbregister,v 1.49.2.3 2013/03/25 18:04:53 greve Exp $

$Id: mri_cvs_register,v 1.15.2.12 2013/02/09 00:37:37 nicks Exp $

ProgramName: dmri_motion  ProgramArguments: --all-info  ProgramVersion: $Name:  
$  TimeStamp: 2016/03/29-13:00:54-GMT  BuildTimeStamp: Feb  2 2013 22:46:06 
CVS:   User: fsl  Machine: localhost.localdomain  Platform: Linux  
PlatformVersion: 2.6.18-128.1.6.el5  CompilerName: GCC  CompilerVersion: 30400

ProgramName: dmri_train  ProgramArguments: --all-info  ProgramVersion: $Name:  
$  TimeStamp: 2016/03/29-13:00:54-GMT  BuildTimeStamp: May 23 2014 05:15:35 
CVS:   User: fsl  Machine: localhost.localdomain  Platform: Linux  
PlatformVersion: 2.6.18-128.1.6.el5  CompilerName: GCC  CompilerVersion: 30400

ProgramName: dmri_paths  ProgramArguments: --all-info  ProgramVersion: $Name:  
$  TimeStamp: 2016/03/29-13:00:54-GMT  BuildTimeStamp: May 23 2014 05:15:35 
CVS:   User: fsl  Machine: localhost.localdomain  Platform: Linux  
PlatformVersion: 2.6.18-128.1.6.el5  CompilerName: GCC  CompilerVersion: 30400

ProgramName: dmri_pathstats  ProgramArguments: --all-info  ProgramVersion: 
$Name:  $  TimeStamp: 2016/03/29-13:00:54-GMT  BuildTimeStamp: Feb  2 2013
22:46:06  CVS:   User: fsl  Machine: localhost.localdomain  Platform: Linux  
PlatformVersion: 2.6.18-128.1.6.el5  CompilerName: GCC  CompilerVersion: 30400

ProgramName: dmri_mergepaths  ProgramArguments: --all-info  ProgramVersion: 
$Name:  $  TimeStamp: 2016/03/29-13:00:54-GMT  BuildTimeStamp: May 23 2014
05:15:35  CVS:   User: fsl  Machine: localhost.localdomain  Platform: Linux  
PlatformVersion: 2.6.18-128.1.6.el5  CompilerName: GCC  CompilerVersion: 30400

ProgramName: dmri_group  ProgramArguments: --all-info  ProgramVersion: $Name:  
$  TimeStamp: 2016/03/29-13:00:54-GMT  BuildTimeStamp:

[Freesurfer] Tracula problems (creating symbolic link)

2016-03-29 Thread Efrat Kliper

Dear Freesurfer experts,


I upgraded to Freesurfer 5.3 from Freesurfer 5.1 (all of the preprocessing
has already been completed in Freesurfer 5.1) in order to run some new
functions of Tracula (I have also installed the latest Tracula update
(tracula.update.centos4_x86_64.5.3.2014_05_26).


I am using:

FREESURFER_HOME: /usr/local/freesurfer

Build stamp: freesurfer-Linux-centos4_x86_64-stable-pub-v5.3.0

RedHat release: CentOS release 5.3 (Final)

Kernel info: Linux 2.6.18-128.1.6.el5 x86_64



 I encountered two problems:


1.  When I run the initial code of Tracula: trac-all –prep code:

/home/fsl/

usr/local/freesurfer/bin/trac-all -prep -c
/mnt/hgfs/linux_share/Scripts/FreeSurfersScript/config_2.txt

Subject TB_480

SUBJECTS_DIR /mnt/hgfs/linux_share/subjects

FREESURFER_HOME /usr/local/freesurfer

Actual FREESURFER_HOME /usr/local/freesurfer

build-stamp.txt: freesurfer-Linux-centos4_x86_64-stable-pub-v5.3.0

fsl

localhost.localdomain

Linux localhost.localdomain 2.6.18-128.1.6.el5 #1 SMP Wed Apr 1 09:10:25
EDT 2009 x86_64 x86_64 x86_64 GNU/Linux



*I am getting the following message:* ln -sf
/mnt/hgfs/linux_share/subjects/TB_480/dmri/dwi.nii.gz
/mnt/hgfs/linux_share/subjects/TB_480/dmri/data.nii.gz



ln: creating symbolic link
`/mnt/hgfs/linux_share/subjects/TB_480/dmri/data.nii.gz' to
`/mnt/hgfs/linux_share/subjects/TB_480/dmri/dwi.nii.gz': Operation not
supported



2.  If I run the trac-all –bedp command of Tracula (on already trac-all
data which was preproc on Freesurfer version 5.1. /home/fsl

/usr/local/freesurfer/bin/trac-all

-bedp -c /home/fsl/Desktop/xxx.txt

Subject TB_201

SUBJECTS_DIR /mnt/hgfs/linux_share/subjects

FREESURFER_HOME /usr/local/freesurfer

Actual FREESURFER_HOME /usr/local/freesurfer

build-stamp.txt: freesurfer-Linux-centos4_x86_64-stable-pub-v5.3.0

fsl

localhost.localdomain

Linux localhost.localdomain 2.6.18-128.1.6.el5 #1 SMP Wed Apr 1 09:10:25
EDT 2009 x86_64 x86_64 x86_64 GNU/Linux



*I am getting the following message:*

Program versions:

$Id: trac-all,v 1.56 2014/05/26 08:28:32 ayendiki Exp $

mri_convert --all-info

ProgramName: mri_convert  ProgramArguments: --all-info  ProgramVersion:
$Name:  $  TimeStamp: 2016/03/29-13:00:54-GMT  BuildTimeStamp: Aug 16 2014
05:13:24  CVS: $Id: mri_convert.c,v 1.213 2014/07/29 19:22:31 fischl Exp $
User: fsl  Machine: localhost.localdomain  Platform: Linux
PlatformVersion: 2.6.18-128.1.6.el5  CompilerName: GCC  CompilerVersion:
30400

FLIRT version 6.0

$Id: bbregister,v 1.49.2.3 2013/03/25 18:04:53 greve Exp $

$Id: mri_cvs_register,v 1.15.2.12 2013/02/09 00:37:37 nicks Exp $

ProgramName: dmri_motion  ProgramArguments: --all-info  ProgramVersion:
$Name:  $  TimeStamp: 2016/03/29-13:00:54-GMT  BuildTimeStamp: Feb  2 2013
22:46:06  CVS:   User: fsl  Machine: localhost.localdomain  Platform:
Linux  PlatformVersion: 2.6.18-128.1.6.el5  CompilerName: GCC
CompilerVersion: 30400

ProgramName: dmri_train  ProgramArguments: --all-info  ProgramVersion:
$Name:  $  TimeStamp: 2016/03/29-13:00:54-GMT  BuildTimeStamp: May 23 2014
05:15:35  CVS:   User: fsl  Machine: localhost.localdomain  Platform:
Linux  PlatformVersion: 2.6.18-128.1.6.el5  CompilerName: GCC
CompilerVersion: 30400

ProgramName: dmri_paths  ProgramArguments: --all-info  ProgramVersion:
$Name:  $  TimeStamp: 2016/03/29-13:00:54-GMT  BuildTimeStamp: May 23 2014
05:15:35  CVS:   User: fsl  Machine: localhost.localdomain  Platform:
Linux  PlatformVersion: 2.6.18-128.1.6.el5  CompilerName: GCC
CompilerVersion: 30400

ProgramName: dmri_pathstats  ProgramArguments: --all-info  ProgramVersion:
$Name:  $  TimeStamp: 2016/03/29-13:00:54-GMT  BuildTimeStamp: Feb  2 2013
22:46:06  CVS:   User: fsl  Machine: localhost.localdomain  Platform:
Linux  PlatformVersion: 2.6.18-128.1.6.el5  CompilerName: GCC
CompilerVersion: 30400

ProgramName: dmri_mergepaths  ProgramArguments: --all-info  ProgramVersion:
$Name:  $  TimeStamp: 2016/03/29-13:00:54-GMT  BuildTimeStamp: May 23 2014
05:15:35  CVS:   User: fsl  Machine: localhost.localdomain  Platform:
Linux  PlatformVersion: 2.6.18-128.1.6.el5  CompilerName: GCC
CompilerVersion: 30400

ProgramName: dmri_group  ProgramArguments: --all-info  ProgramVersion:
$Name:  $  TimeStamp: 2016/03/29-13:00:54-GMT  BuildTimeStamp: May 23 2014
05:15:35  CVS:   User: fsl  Machine: localhost.localdomain  Platform:
Linux  PlatformVersion: 2.6.18-128.1.6.el5  CompilerName: GCC
CompilerVersion: 30400

WARN: Running FSL's bedbost locally - this might take a while

WARN: It is recommended to run this step on a cluster

bedpostx_mgh -n 2 /mnt/hgfs/linux_share/subjects/TB_201/dmri

subjectdir is /mnt/hgfs/linux_share/subjects/TB_201/dmri

/mnt/hgfs/linux_share/subjects/TB_201/dmri/data not found



I am guessing those problems are from the same source.

Do you have any suggestions on how can I resolve these issues?

Is there a way to overcome the "ln" command and to create this data file
without it?

(I have also tried to run it from local OS linux and

[Freesurfer] Tracula problems initializing pathway

2013-01-14 Thread Cat Chong

 
Hello Experts

I am still at the first pre-proc step
for Tracula and although the script is running, it seems to have
difficulty initializing the first pathway (1 out of 18)

Please see below script excerpt:
Is that normal that it takes this many
trials to initiate a pathway?
Cheers,
Catherine
WARN: Could not find satisfactory
control point fit - try 171
Finding center streamline
INFO: Step is 5 voxels
WARN: Turning off FA check for center
streamline
INFO: Step is 5 voxels
INFO: Length of center streamline is
111 voxels
Selecting 5 points on center streamline
INFO: Step is 4 voxels
WARN: Defaulting to equidistant control
points
INFO: Selected control points are
96 100 30
106 108 58
116 109 87
113 102 115
108 105 146
INFO: Distances between consecutive
points are 31 31 29 32
WARN: Could not find satisfactory
control point fit - try 172
Finding center streamline
INFO: Step is 5 voxels
WARN: Turning off FA check for center
streamline
INFO: Step is 5 voxels
INFO: Length of center streamline is
107 voxels
Selecting 5 points on center streamline
INFO: Step is 4 voxels___
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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
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Re: [Freesurfer] Tracula problems initializing pathway

2013-01-14 Thread Anastasia Yendiki


Hi Cat - 1 out of 18 is the left CST. That one usually isn't hard to 
initialize b/c it's not a part of the brain where it's especially 
difficult to align a typical individual to the atlas. I'd wait to see the 
final outcome before declaring defeat, but is there any chance that the 
top of the brain or the brainstem are cut off in this subject?

a.y

On Mon, 14 Jan 2013, Cat Chong wrote:

 Hello Experts
 
 I am still at the first pre-proc step for Tracula and although the script is
 running, it seems to have difficulty initializing the first pathway (1 out
 of 18)
 
 Please see below script excerpt:
 Is that normal that it takes this many trials to initiate a pathway?
 Cheers,
 Catherine
 WARN: Could not find satisfactory control point fit - try 171
 Finding center streamline
 INFO: Step is 5 voxels
 WARN: Turning off FA check for center streamline
 INFO: Step is 5 voxels
 INFO: Length of center streamline is 111 voxels
 Selecting 5 points on center streamline
 INFO: Step is 4 voxels
 WARN: Defaulting to equidistant control points
 INFO: Selected control points are
 96 100 30
 106 108 58
 116 109 87
 113 102 115
 108 105 146
 INFO: Distances between consecutive points are 31 31 29 32
 WARN: Could not find satisfactory control point fit - try 172
 Finding center streamline
 INFO: Step is 5 voxels
 WARN: Turning off FA check for center streamline
 INFO: Step is 5 voxels
 INFO: Length of center streamline is 107 voxels
 Selecting 5 points on center streamline
 INFO: Step is 4 voxels
 

___
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] TRACULA problems

Re: [Freesurfer] Tracula problems (creating symbolic link)

Re: [Freesurfer] Tracula problems (creating symbolic link)

Re: [Freesurfer] Tracula problems (creating symbolic link)

[Freesurfer] Tracula problems (creating symbolic link)

[Freesurfer] Tracula problems initializing pathway

Re: [Freesurfer] Tracula problems initializing pathway

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