Re: [HCP-Users] failed running preprocessed dMRI data with FSL dtifit

2017-08-28 Thread Xinyang Liu 
Ok, thanks a lot for the information. We will surely use the command line after 
starting with the GUI as a new learner. ;)


Best regards,
Xinyang




At 2017-08-29 11:07:50, "Glasser, Matthew"  wrote:

The reason I suggest the FSL list is that I don’t think those of us who answer 
questions on this list know much about the FSL GUIs.  We generally are more 
knowledgable about the FSL command line.


Peace,


Matt.


From: Xinyang Liu 
Date: Monday, August 28, 2017 at 10:04 PM
To: Matt Glasser 
Cc: "HCP-Users@humanconnectome.org" 
Subject: Re: [HCP-Users] failed running preprocessed dMRI data with FSL dtifit



Dear Matthew,


Oh, I just found out the reason, which is due to the very limited internal 
storage of my virtual machine. Now it runs very well after I enlarged it. :)
Thanks a lot for your suggestion about the FSL list, which provides a new way 
to me when I have FSL running problems in the future. 


Best regards,
Xinyang



At 2017-08-29 10:29:57, "Glasser, Matthew"  wrote:

If this is with FSL’s GUI, you might need to ask about it on the FSL list.


Peace,


Matt.


From:  on behalf of Xinyang Liu 

Date: Monday, August 28, 2017 at 9:27 PM
To: "HCP-Users@humanconnectome.org" 
Subject: [HCP-Users] failed running preprocessed dMRI data with FSL dtifit



Dear HCP fellows,


Hi. Could I ask for some help? When I ran the HCP preprocessed diffusion data 
with the "dtifit" function in FSL, it always failed in the middle with a window 
came out saying "signal killed", which is strange. I then used another software 
called PANDA to check the detailed procedure, and found that the processing 
stopped at "extract B0", the log informations are as follows:


***
The job starts now !

fslroi 
/home/panda/ShareFolder/HCPDATA/output4_sub2/4/tmp/test100206_4_DWI_01.nii.gz
 /home/panda/ShareFolder/HCPDATA/output4_sub2/4/tmp/data_b0.nii.gz 0 1
Killed
fslroi 
/home/panda/ShareFolder/HCPDATA/output4_sub2/4/tmp/test100206_4_DWI_01.nii.gz
 /home/panda/ShareFolder/HCPDATA/output4_sub2/4/tmp/data_b0.nii.gz 0 1: 
Killed
extracting b0 volume is done!


Checking outputs

The output file or directory 
/home/panda/ShareFolder/HCPDATA/output4_sub2/4/tmp/data_b0.nii.gz has not 
been generated!
The output file or directory 
/home/panda/ShareFolder/HCPDATA/output4_sub2/4/tmp/OutputDone/extractB0_4.done
 was successfully generated!


Could you suggest possible reasons of how this happened? Thanks a lot!


Best regards,
Xinyang Liu













 

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Re: [HCP-Users] failed running preprocessed dMRI data with FSL dtifit

2017-08-28 Thread Glasser, Matthew 
The reason I suggest the FSL list is that I don’t think those of us who answer 
questions on this list know much about the FSL GUIs.  We generally are more 
knowledgable about the FSL command line.

Peace,

Matt.

From: Xinyang Liu >
Date: Monday, August 28, 2017 at 10:04 PM
To: Matt Glasser >
Cc: "HCP-Users@humanconnectome.org" 
>
Subject: Re: [HCP-Users] failed running preprocessed dMRI data with FSL dtifit

Dear Matthew,

Oh, I just found out the reason, which is due to the very limited internal 
storage of my virtual machine. Now it runs very well after I enlarged it. :)
Thanks a lot for your suggestion about the FSL list, which provides a new way 
to me when I have FSL running problems in the future.

Best regards,
Xinyang


At 2017-08-29 10:29:57, "Glasser, Matthew" 
> wrote:
If this is with FSL’s GUI, you might need to ask about it on the FSL list.

Peace,

Matt.

From: 
>
 on behalf of Xinyang Liu >
Date: Monday, August 28, 2017 at 9:27 PM
To: "HCP-Users@humanconnectome.org" 
>
Subject: [HCP-Users] failed running preprocessed dMRI data with FSL dtifit

Dear HCP fellows,

Hi. Could I ask for some help? When I ran the HCP preprocessed diffusion data 
with the "dtifit" function in FSL, it always failed in the middle with a window 
came out saying "signal killed", which is strange. I then used another software 
called PANDA to check the detailed procedure, and found that the processing 
stopped at "extract B0", the log informations are as follows:

***
The job starts now !

fslroi 
/home/panda/ShareFolder/HCPDATA/output4_sub2/4/tmp/test100206_4_DWI_01.nii.gz
 /home/panda/ShareFolder/HCPDATA/output4_sub2/4/tmp/data_b0.nii.gz 0 1
Killed
fslroi 
/home/panda/ShareFolder/HCPDATA/output4_sub2/4/tmp/test100206_4_DWI_01.nii.gz
 /home/panda/ShareFolder/HCPDATA/output4_sub2/4/tmp/data_b0.nii.gz 0 1: 
Killed
extracting b0 volume is done!


Checking outputs

The output file or directory 
/home/panda/ShareFolder/HCPDATA/output4_sub2/4/tmp/data_b0.nii.gz has not 
been generated!
The output file or directory 
/home/panda/ShareFolder/HCPDATA/output4_sub2/4/tmp/OutputDone/extractB0_4.done
 was successfully generated!

Could you suggest possible reasons of how this happened? Thanks a lot!

Best regards,
Xinyang Liu











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HCP-Users mailing list
HCP-Users@humanconnectome.org
http://lists.humanconnectome.org/mailman/listinfo/hcp-users









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HCP-Users@humanconnectome.org
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Re: [HCP-Users] failed running preprocessed dMRI data with FSL dtifit

2017-08-28 Thread Xinyang Liu 
Dear Matthew,


Oh, I just found out the reason, which is due to the very limited internal 
storage of my virtual machine. Now it runs very well after I enlarged it. :)
Thanks a lot for your suggestion about the FSL list, which provides a new way 
to me when I have FSL running problems in the future. 


Best regards,
Xinyang



At 2017-08-29 10:29:57, "Glasser, Matthew"  wrote:

If this is with FSL’s GUI, you might need to ask about it on the FSL list.


Peace,


Matt.


From:  on behalf of Xinyang Liu 

Date: Monday, August 28, 2017 at 9:27 PM
To: "HCP-Users@humanconnectome.org" 
Subject: [HCP-Users] failed running preprocessed dMRI data with FSL dtifit



Dear HCP fellows,


Hi. Could I ask for some help? When I ran the HCP preprocessed diffusion data 
with the "dtifit" function in FSL, it always failed in the middle with a window 
came out saying "signal killed", which is strange. I then used another software 
called PANDA to check the detailed procedure, and found that the processing 
stopped at "extract B0", the log informations are as follows:


***
The job starts now !

fslroi 
/home/panda/ShareFolder/HCPDATA/output4_sub2/4/tmp/test100206_4_DWI_01.nii.gz
 /home/panda/ShareFolder/HCPDATA/output4_sub2/4/tmp/data_b0.nii.gz 0 1
Killed
fslroi 
/home/panda/ShareFolder/HCPDATA/output4_sub2/4/tmp/test100206_4_DWI_01.nii.gz
 /home/panda/ShareFolder/HCPDATA/output4_sub2/4/tmp/data_b0.nii.gz 0 1: 
Killed
extracting b0 volume is done!


Checking outputs

The output file or directory 
/home/panda/ShareFolder/HCPDATA/output4_sub2/4/tmp/data_b0.nii.gz has not 
been generated!
The output file or directory 
/home/panda/ShareFolder/HCPDATA/output4_sub2/4/tmp/OutputDone/extractB0_4.done
 was successfully generated!


Could you suggest possible reasons of how this happened? Thanks a lot!


Best regards,
Xinyang Liu













 

___
HCP-Users mailing list
HCP-Users@humanconnectome.org
http://lists.humanconnectome.org/mailman/listinfo/hcp-users





 
___
HCP-Users mailing list
HCP-Users@humanconnectome.org
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Re: [HCP-Users] failed running preprocessed dMRI data with FSL dtifit

2017-08-28 Thread Glasser, Matthew 
If this is with FSL’s GUI, you might need to ask about it on the FSL list.

Peace,

Matt.

From: 
>
 on behalf of Xinyang Liu >
Date: Monday, August 28, 2017 at 9:27 PM
To: "HCP-Users@humanconnectome.org" 
>
Subject: [HCP-Users] failed running preprocessed dMRI data with FSL dtifit

Dear HCP fellows,

Hi. Could I ask for some help? When I ran the HCP preprocessed diffusion data 
with the "dtifit" function in FSL, it always failed in the middle with a window 
came out saying "signal killed", which is strange. I then used another software 
called PANDA to check the detailed procedure, and found that the processing 
stopped at "extract B0", the log informations are as follows:

***
The job starts now !

fslroi 
/home/panda/ShareFolder/HCPDATA/output4_sub2/4/tmp/test100206_4_DWI_01.nii.gz
 /home/panda/ShareFolder/HCPDATA/output4_sub2/4/tmp/data_b0.nii.gz 0 1
Killed
fslroi 
/home/panda/ShareFolder/HCPDATA/output4_sub2/4/tmp/test100206_4_DWI_01.nii.gz
 /home/panda/ShareFolder/HCPDATA/output4_sub2/4/tmp/data_b0.nii.gz 0 1: 
Killed
extracting b0 volume is done!


Checking outputs

The output file or directory 
/home/panda/ShareFolder/HCPDATA/output4_sub2/4/tmp/data_b0.nii.gz has not 
been generated!
The output file or directory 
/home/panda/ShareFolder/HCPDATA/output4_sub2/4/tmp/OutputDone/extractB0_4.done
 was successfully generated!

Could you suggest possible reasons of how this happened? Thanks a lot!

Best regards,
Xinyang Liu











___
HCP-Users mailing list
HCP-Users@humanconnectome.org
http://lists.humanconnectome.org/mailman/listinfo/hcp-users

___
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HCP-Users@humanconnectome.org
http://lists.humanconnectome.org/mailman/listinfo/hcp-users

[HCP-Users] failed running preprocessed dMRI data with FSL dtifit

2017-08-28 Thread Xinyang Liu 
Dear HCP fellows,


Hi. Could I ask for some help? When I ran the HCP preprocessed diffusion data 
with the "dtifit" function in FSL, it always failed in the middle with a window 
came out saying "signal killed", which is strange. I then used another software 
called PANDA to check the detailed procedure, and found that the processing 
stopped at "extract B0", the log informations are as follows:


***
The job starts now !

fslroi 
/home/panda/ShareFolder/HCPDATA/output4_sub2/4/tmp/test100206_4_DWI_01.nii.gz
 /home/panda/ShareFolder/HCPDATA/output4_sub2/4/tmp/data_b0.nii.gz 0 1
Killed
fslroi 
/home/panda/ShareFolder/HCPDATA/output4_sub2/4/tmp/test100206_4_DWI_01.nii.gz
 /home/panda/ShareFolder/HCPDATA/output4_sub2/4/tmp/data_b0.nii.gz 0 1: 
Killed
extracting b0 volume is done!


Checking outputs

The output file or directory 
/home/panda/ShareFolder/HCPDATA/output4_sub2/4/tmp/data_b0.nii.gz has not 
been generated!
The output file or directory 
/home/panda/ShareFolder/HCPDATA/output4_sub2/4/tmp/OutputDone/extractB0_4.done
 was successfully generated!


Could you suggest possible reasons of how this happened? Thanks a lot!


Best regards,
Xinyang Liu









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HCP-Users mailing list
HCP-Users@humanconnectome.org
http://lists.humanconnectome.org/mailman/listinfo/hcp-users