open-discussion > Path T1
Showing 1-6 of 6 posts
Mar 30, 2015 09:03 AM | joana pereira - KI
Path T1
Dear all,
I'm trying to run an analysis with PANDA.
In the Network Node Definition, I selected the option T1 images and the following message came out: "Please select T1 in accordance with the order of the FA path".
My DTI images have the path /PANDA/Subj01/.
Inside Subj01 there are 3 folders with dicom files: DTI1 (1st repetition), DTI2 (2nd repetition) and T1.
Could you tell me how to select T1 in accordance with the order of the FA path?
Thanks a lot!
I'm trying to run an analysis with PANDA.
In the Network Node Definition, I selected the option T1 images and the following message came out: "Please select T1 in accordance with the order of the FA path".
My DTI images have the path /PANDA/Subj01/.
Inside Subj01 there are 3 folders with dicom files: DTI1 (1st repetition), DTI2 (2nd repetition) and T1.
Could you tell me how to select T1 in accordance with the order of the FA path?
Thanks a lot!
Apr 4, 2015 09:04 AM | Zaixu Cui
RE: Path T1
Hi,
Thanks for your interest in PANDA. Sorry to reply so late.
You can only put the data of DTI under the subject folder.
Inside Subj01, there should be DTI1 and DTI2.
You should put the DICOM of T1 elsewhere, PANDA doesn't care.
When you input T1 for network node definition, the nifti images of T1 is needed.
And the order of T1 images should be in accordance with the order of the subjectfolder
Best wishes
zaixu
Thanks for your interest in PANDA. Sorry to reply so late.
You can only put the data of DTI under the subject folder.
Inside Subj01, there should be DTI1 and DTI2.
You should put the DICOM of T1 elsewhere, PANDA doesn't care.
When you input T1 for network node definition, the nifti images of T1 is needed.
And the order of T1 images should be in accordance with the order of the subjectfolder
Best wishes
zaixu
Apr 6, 2015 01:04 PM | joana pereira - KI
RE: Path T1
> (
> Dear Zaixu,
>
> Thanks a lot for your answer.
>
> I did as you suggested and launched PANDA.
>
> The job finished without any error but I can't find the Network folder. I
> thought this folder would be generated since I selected the options for
> Network Node Definition and input the T1.nii image as you suggested. Did I
> miss something?
>
> I also noticed something rather strange with the PANDA interface. Many
> options are simply not shown in my mac, they are not visible in the
> interfaces of PANDA. I did write sudo launchctl load -w
> /System/Library/LaunchDaemons/com.apple.atrun.plist and opened matlab
> from the terminal. Have you ever heard of a similar problem? I'm using OS X
> Yosemite version 10.10.2.
>
> Thanks again!
>
> Best wishes,
>
> Joana)
> Dear Zaixu,
>
> Thanks a lot for your answer.
>
> I did as you suggested and launched PANDA.
>
> The job finished without any error but I can't find the Network folder. I
> thought this folder would be generated since I selected the options for
> Network Node Definition and input the T1.nii image as you suggested. Did I
> miss something?
>
> I also noticed something rather strange with the PANDA interface. Many
> options are simply not shown in my mac, they are not visible in the
> interfaces of PANDA. I did write sudo launchctl load -w
> /System/Library/LaunchDaemons/com.apple.atrun.plist and opened matlab
> from the terminal. Have you ever heard of a similar problem? I'm using OS X
> Yosemite version 10.10.2.
>
> Thanks again!
>
> Best wishes,
>
> Joana)
Apr 13, 2015 11:04 AM | Zaixu Cui
RE: Path T1
Dear Joana,
Sorry for reply so late.
Have you selected the options (Deterministic or Probabilistic) in the network construction located in the lowermost of the GUI of TrackingOpt?
Best
Zaixu
Sorry for reply so late.
Have you selected the options (Deterministic or Probabilistic) in the network construction located in the lowermost of the GUI of TrackingOpt?
Best
Zaixu
Apr 21, 2015 01:04 PM | joana pereira - KI
RE: Path T1
Dear Zaixu,
Thank you for your reply.
The option that you mention is not visible when I use PANDA in my mac (OS X 10.10.2), although I followed the manual instructions.
I also have access to an Ubuntu and ran PANDA from there, after selecting the Deterministic option.
Unfortunately, a different problem came out (see below).
The problem seemed to be related with not being able to open libnewimage.so.
However, this file does exist in my path /usr/share/fsl/5.0/bin/
I tried to add this path to my matlab but the same error came out after that.
I read in the forum that another person had a similar problem and that you recommended upgrading to Ubuntu 12.04 or 12.10 but my Ubuntu version is already 12.04.5 LTS.
Do you have any suggestions?
Thanks a lot for your help!
Warning: No display specified. You will not be able to display graphics on the screen.
Warning: No window system found. Java option 'MWT' ignored.
< M A T L A B (R) >
Copyright 1984-2013 The MathWorks, Inc.
R2013b (8.2.0.701) 64-bit (glnxa64)
August 13, 2013
No window system found. Java option 'MWT' ignored.
To get started, type one of these: helpwin, helpdesk, or demo.
For product information, visit http://www.mathworks.com.
/usr/share/fsl/5.0/bin/fslchfiletype_exe: error while loading shared libraries: libnewimage.so: cannot open shared object file: No such file or directory
Invalid file identifier. Use fopen to generate a valid file identifier.
g_DeterministicNetwork_FileOut in /home/joana/Toolboxes/PANDA-1.2.4_64/FileOut/g_DeterministicNetwork_FileOut.m at 24
g_dti_pipeline in /home/joana/Toolboxes/PANDA-1.2.4_64/g_dti_pipeline.m at 1414
Thank you for your reply.
The option that you mention is not visible when I use PANDA in my mac (OS X 10.10.2), although I followed the manual instructions.
I also have access to an Ubuntu and ran PANDA from there, after selecting the Deterministic option.
Unfortunately, a different problem came out (see below).
The problem seemed to be related with not being able to open libnewimage.so.
However, this file does exist in my path /usr/share/fsl/5.0/bin/
I tried to add this path to my matlab but the same error came out after that.
I read in the forum that another person had a similar problem and that you recommended upgrading to Ubuntu 12.04 or 12.10 but my Ubuntu version is already 12.04.5 LTS.
Do you have any suggestions?
Thanks a lot for your help!
Warning: No display specified. You will not be able to display graphics on the screen.
Warning: No window system found. Java option 'MWT' ignored.
< M A T L A B (R) >
Copyright 1984-2013 The MathWorks, Inc.
R2013b (8.2.0.701) 64-bit (glnxa64)
August 13, 2013
No window system found. Java option 'MWT' ignored.
To get started, type one of these: helpwin, helpdesk, or demo.
For product information, visit http://www.mathworks.com.
/usr/share/fsl/5.0/bin/fslchfiletype_exe: error while loading shared libraries: libnewimage.so: cannot open shared object file: No such file or directory
Invalid file identifier. Use fopen to generate a valid file identifier.
g_DeterministicNetwork_FileOut in /home/joana/Toolboxes/PANDA-1.2.4_64/FileOut/g_DeterministicNetwork_FileOut.m at 24
g_dti_pipeline in /home/joana/Toolboxes/PANDA-1.2.4_64/g_dti_pipeline.m at 1414
Apr 25, 2015 04:04 AM | Zaixu Cui
RE: Path T1
Dear Pereira,
I think your fsl is ubuntu debain version.
Please change it to centos version, you can download it in http://fsl.fmrib.ox.ac.uk/fsl/fslwiki/FslInstallation
If you still have any problems, please feel free to contact me.
Best
Zaixu
I think your fsl is ubuntu debain version.
Please change it to centos version, you can download it in http://fsl.fmrib.ox.ac.uk/fsl/fslwiki/FslInstallation
If you still have any problems, please feel free to contact me.
Best
Zaixu