Re: [HCP-Users] hcp_fix bug
Please include the error message, I don’t know what you are referring to else. Peace, Matt. From: <hcp-users-boun...@humanconnectome.org<mailto:hcp-users-boun...@humanconnectome.org>> on behalf of Timothy Hendrickson <hendr...@umn.edu<mailto:hendr...@umn.edu>> Date: Wednesday, March 22, 2017 at 5:17 PM To: "hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>" <HCP-Users@humanconnectome.org<mailto:HCP-Users@humanconnectome.org>> Subject: [HCP-Users] hcp_fix bug I am getting very similar errors to Nallin. Has this been resolved? Timothy Hendrickson Department of Psychiatry University of Minnesota Bioinformatics and Computational Biology M.S. Candidate Office: 612-624-6441 Mobile: 507-259-3434 (texts okay) ___ HCP-Users mailing list HCP-Users@humanconnectome.org<mailto:HCP-Users@humanconnectome.org> http://lists.humanconnectome.org/mailman/listinfo/hcp-users 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. ___ HCP-Users mailing list HCP-Users@humanconnectome.org http://lists.humanconnectome.org/mailman/listinfo/hcp-users
[HCP-Users] hcp_fix bug
I am getting very similar errors to Nallin. Has this been resolved? Timothy Hendrickson Department of Psychiatry University of Minnesota Bioinformatics and Computational Biology M.S. Candidate Office: 612-624-6441 Mobile: 507-259-3434 (texts okay) ___ HCP-Users mailing list HCP-Users@humanconnectome.org http://lists.humanconnectome.org/mailman/listinfo/hcp-users
Re: [HCP-Users] hcp_fix bug
You also need the GIFTI toolbox installed for Matlab:
http://www.artefact.tk/software/matlab/gifti/
Peace,
Matt.
From: nailin yao <ynai...@gmail.com<mailto:ynai...@gmail.com>>
Date: Wednesday, October 19, 2016 at 6:58 PM
To: Matt Glasser <glass...@wustl.edu<mailto:glass...@wustl.edu>>
Cc: "hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>"
<hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>>
Subject: Re: [HCP-Users] hcp_fix bug
Hi Matt,
"... " in last Email refer to
/home/fas/glahn/ny87/software/workbench/bin_linux64/
So before running fix_3_clean, I've set
WBC='/home/fas/glahn/ny87/software/workbench/bin_linux64/wb_command' and
CIFTI='/home/fas/glahn/ny87/software/workbench' , which have ciftiopen.m
stored. However, I still met the problem as mentioned before. Do you know what
could be wrong? Thank you!
Best,
Nailin
2016-10-19 19:29 GMT-04:00 Glasser, Matthew
<glass...@wustl.edu<mailto:glass...@wustl.edu>>:
I don’t think three dots is valid.
Peace,
Matt.
From: "ynai...@gmail.com<mailto:ynai...@gmail.com>"
<ynai...@gmail.com<mailto:ynai...@gmail.com>>
Date: Wednesday, October 19, 2016 at 5:04 PM
To: Matt Glasser <glass...@wustl.edu<mailto:glass...@wustl.edu>>
Cc: "hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>"
<hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>>
Subject: Re: [HCP-Users] hcp_fix bug
Hi Matt,
I added all the paths needed in fix_3_clean, but still get the error. Is it
possible because I add WBC as .../wb_command ?
Best,
Nailin
Sent from my iPhone
On Oct 19, 2016, at 5:46 PM, Glasser, Matthew
<glass...@wustl.edu<mailto:glass...@wustl.edu>> wrote:
You could also need to run the add path parts of the command.
Peace,
Matt.
From: nailin yao <ynai...@gmail.com<mailto:ynai...@gmail.com>>
Date: Wednesday, October 19, 2016 at 4:02 PM
To: Matt Glasser <glass...@wustl.edu<mailto:glass...@wustl.edu>>
Cc: "hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>"
<hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>>
Subject: Re: [HCP-Users] hcp_fix bug
Hi Matt,
I tried to run fix_3_clean on matlab directly, and met the error message below:
fix_3_clean('.fix',0,1,2000)
TR =
0.7200
/bin/bash: -cifti-convert: command not found
Undefined function 'gifti' for input arguments of type 'char'.
Error in ciftiopen (line 31)
cifti = gifti([tmpfile '.gii']);
Error in fix_3_clean (line 40)
BO=ciftiopen('Atlas.dtseries.nii',WBC);
Do you know why? Thank you very much!
Best,
Nailin
2016-10-17 20:12 GMT-04:00 Glasser, Matthew
<glass...@wustl.edu<mailto:glass...@wustl.edu>>:
Is it a reproducible error? What happens if you try running the fix_3_clean
function with the parameters mentioned below?
Peace,
Matt.
From: nailin yao <ynai...@gmail.com<mailto:ynai...@gmail.com>>
Date: Monday, October 17, 2016 at 2:58 PM
To: Matt Glasser <glass...@wustl.edu<mailto:glass...@wustl.edu>>
Cc: "hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>"
<hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>>
Subject: Re: [HCP-Users] hcp_fix bug
Hi Matt,
It's not compiled matlab.
Best,
Nailin
2016-10-17 13:53 GMT-04:00 Glasser, Matthew
<glass...@wustl.edu<mailto:glass...@wustl.edu>>:
Is this compiled matlab or not compiled?
Peace,
Matt.
From:
<hcp-users-boun...@humanconnectome.org<mailto:hcp-users-boun...@humanconnectome.org>>
on behalf of nailin yao <ynai...@gmail.com<mailto:ynai...@gmail.com>>
Date: Monday, October 17, 2016 at 11:13 AM
To: "hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>"
<hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>>
Subject: [HCP-Users] hcp_fix bug
Hi ,
I received the bug report when running hcp_fix for the last step:
running FIX
FIX Feature extraction for Melodic output directory:
rfMRI_REST1_LR_nonlin_norm_hp2000.ica
create edge masks
run FAST
registration of standard space masks
extract features
FIX Classifying components in Melodic directory:
rfMRI_REST1_LR_nonlin_norm_hp2000.ica using training file:
/home/fas/glahn/ny87/Pipelines/fix1.06/training_files/HCP_hp2000.RData and
threshold 10
FIX Applying cleanup using cleanup file:
rfMRI_REST1_LR_nonlin_norm_hp2000.ica/fix4melview_HCP_hp2000_thr10.txt and
motion cleanup set to 1
sh: line 1: 24221 Bus error (core dumped)
/gpfs/apps/hpc/Apps/Matlab/R2015b/bin/matlab -nojvm -nodisplay -nodesktop
-nosplash -r "addpath('/home/fas/glahn/ny87/Pipelines/fix1.06');
addpath('/gpfs/apps/hpc/Apps/FSL/5.0.6/fsl/etc/matlab');
fix_3_clean('.fix',0,1,2000)" >&g
Re: [HCP-Users] hcp_fix bug
I don’t think three dots is valid.
Peace,
Matt.
From: "ynai...@gmail.com<mailto:ynai...@gmail.com>"
<ynai...@gmail.com<mailto:ynai...@gmail.com>>
Date: Wednesday, October 19, 2016 at 5:04 PM
To: Matt Glasser <glass...@wustl.edu<mailto:glass...@wustl.edu>>
Cc: "hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>"
<hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>>
Subject: Re: [HCP-Users] hcp_fix bug
Hi Matt,
I added all the paths needed in fix_3_clean, but still get the error. Is it
possible because I add WBC as .../wb_command ?
Best,
Nailin
Sent from my iPhone
On Oct 19, 2016, at 5:46 PM, Glasser, Matthew
<glass...@wustl.edu<mailto:glass...@wustl.edu>> wrote:
You could also need to run the add path parts of the command.
Peace,
Matt.
From: nailin yao <ynai...@gmail.com<mailto:ynai...@gmail.com>>
Date: Wednesday, October 19, 2016 at 4:02 PM
To: Matt Glasser <glass...@wustl.edu<mailto:glass...@wustl.edu>>
Cc: "hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>"
<hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>>
Subject: Re: [HCP-Users] hcp_fix bug
Hi Matt,
I tried to run fix_3_clean on matlab directly, and met the error message below:
fix_3_clean('.fix',0,1,2000)
TR =
0.7200
/bin/bash: -cifti-convert: command not found
Undefined function 'gifti' for input arguments of type 'char'.
Error in ciftiopen (line 31)
cifti = gifti([tmpfile '.gii']);
Error in fix_3_clean (line 40)
BO=ciftiopen('Atlas.dtseries.nii',WBC);
Do you know why? Thank you very much!
Best,
Nailin
2016-10-17 20:12 GMT-04:00 Glasser, Matthew
<glass...@wustl.edu<mailto:glass...@wustl.edu>>:
Is it a reproducible error? What happens if you try running the fix_3_clean
function with the parameters mentioned below?
Peace,
Matt.
From: nailin yao <ynai...@gmail.com<mailto:ynai...@gmail.com>>
Date: Monday, October 17, 2016 at 2:58 PM
To: Matt Glasser <glass...@wustl.edu<mailto:glass...@wustl.edu>>
Cc: "hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>"
<hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>>
Subject: Re: [HCP-Users] hcp_fix bug
Hi Matt,
It's not compiled matlab.
Best,
Nailin
2016-10-17 13:53 GMT-04:00 Glasser, Matthew
<glass...@wustl.edu<mailto:glass...@wustl.edu>>:
Is this compiled matlab or not compiled?
Peace,
Matt.
From:
<hcp-users-boun...@humanconnectome.org<mailto:hcp-users-boun...@humanconnectome.org>>
on behalf of nailin yao <ynai...@gmail.com<mailto:ynai...@gmail.com>>
Date: Monday, October 17, 2016 at 11:13 AM
To: "hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>"
<hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>>
Subject: [HCP-Users] hcp_fix bug
Hi ,
I received the bug report when running hcp_fix for the last step:
running FIX
FIX Feature extraction for Melodic output directory:
rfMRI_REST1_LR_nonlin_norm_hp2000.ica
create edge masks
run FAST
registration of standard space masks
extract features
FIX Classifying components in Melodic directory:
rfMRI_REST1_LR_nonlin_norm_hp2000.ica using training file:
/home/fas/glahn/ny87/Pipelines/fix1.06/training_files/HCP_hp2000.RData and
threshold 10
FIX Applying cleanup using cleanup file:
rfMRI_REST1_LR_nonlin_norm_hp2000.ica/fix4melview_HCP_hp2000_thr10.txt and
motion cleanup set to 1
sh: line 1: 24221 Bus error (core dumped)
/gpfs/apps/hpc/Apps/Matlab/R2015b/bin/matlab -nojvm -nodisplay -nodesktop
-nosplash -r "addpath('/home/fas/glahn/ny87/Pipelines/fix1.06');
addpath('/gpfs/apps/hpc/Apps/FSL/5.0.6/fsl/etc/matlab');
fix_3_clean('.fix',0,1,2000)" >> .fix.log 2>&1
Does anyone know what's the problem? Thank you very much!
Best,
Nailin
--
Nailin Yao, PhD
Postdoctoral Associate
Department of Psychiatry, Yale University
___
HCP-Users mailing list
HCP-Users@humanconnectome.org<mailto:HCP-Users@humanconnectome.org>
http://lists.humanconnectome.org/mailman/listinfo/hcp-users
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.
--
Nailin Yao, PhD
Postdoctoral Associate
Department of Psychiatry, Yale University
The materials in this message are private and may contain
Re: [HCP-Users] hcp_fix bug
Hi Matt,
I added all the paths needed in fix_3_clean, but still get the error. Is it
possible because I add WBC as .../wb_command ?
Best,
Nailin
Sent from my iPhone
> On Oct 19, 2016, at 5:46 PM, Glasser, Matthew <glass...@wustl.edu> wrote:
>
> You could also need to run the add path parts of the command.
>
> Peace,
>
> Matt.
>
> From: nailin yao <ynai...@gmail.com>
> Date: Wednesday, October 19, 2016 at 4:02 PM
> To: Matt Glasser <glass...@wustl.edu>
> Cc: "hcp-users@humanconnectome.org" <hcp-users@humanconnectome.org>
> Subject: Re: [HCP-Users] hcp_fix bug
>
> Hi Matt,
>
>
> I tried to run fix_3_clean on matlab directly, and met the error message
> below:
>
>
> fix_3_clean('.fix',0,1,2000)
>
> TR =
>
> 0.7200
>
> /bin/bash: -cifti-convert: command not found
>
> Undefined function 'gifti' for input arguments of type 'char'.
>
> Error in ciftiopen (line 31)
>
> cifti = gifti([tmpfile '.gii']);
>
> Error in fix_3_clean (line 40)
>
> BO=ciftiopen('Atlas.dtseries.nii',WBC);
>
>
> Do you know why? Thank you very much!
>
> Best,
> Nailin
>
> 2016-10-17 20:12 GMT-04:00 Glasser, Matthew <glass...@wustl.edu>:
>> Is it a reproducible error? What happens if you try running the fix_3_clean
>> function with the parameters mentioned below?
>>
>> Peace,
>>
>> Matt.
>>
>> From: nailin yao <ynai...@gmail.com>
>> Date: Monday, October 17, 2016 at 2:58 PM
>> To: Matt Glasser <glass...@wustl.edu>
>> Cc: "hcp-users@humanconnectome.org" <hcp-users@humanconnectome.org>
>> Subject: Re: [HCP-Users] hcp_fix bug
>>
>> Hi Matt,
>>
>> It's not compiled matlab.
>>
>> Best,
>> Nailin
>>
>> 2016-10-17 13:53 GMT-04:00 Glasser, Matthew <glass...@wustl.edu>:
>>> Is this compiled matlab or not compiled?
>>>
>>> Peace,
>>>
>>> Matt.
>>>
>>> From: <hcp-users-boun...@humanconnectome.org> on behalf of nailin yao
>>> <ynai...@gmail.com>
>>> Date: Monday, October 17, 2016 at 11:13 AM
>>> To: "hcp-users@humanconnectome.org" <hcp-users@humanconnectome.org>
>>> Subject: [HCP-Users] hcp_fix bug
>>>
>>> Hi ,
>>>
>>> I received the bug report when running hcp_fix for the last step:
>>>
>>> running FIX
>>>
>>> FIX Feature extraction for Melodic output directory:
>>> rfMRI_REST1_LR_nonlin_norm_hp2000.ica
>>>
>>> create edge masks
>>>
>>> run FAST
>>>
>>> registration of standard space masks
>>>
>>> extract features
>>>
>>> FIX Classifying components in Melodic directory:
>>> rfMRI_REST1_LR_nonlin_norm_hp2000.ica using training file:
>>> /home/fas/glahn/ny87/Pipelines/fix1.06/training_files/HCP_hp2000.RData and
>>> threshold 10
>>>
>>> FIX Applying cleanup using cleanup file:
>>> rfMRI_REST1_LR_nonlin_norm_hp2000.ica/fix4melview_HCP_hp2000_thr10.txt and
>>> motion cleanup set to 1
>>>
>>> sh: line 1: 24221 Bus error (core dumped)
>>> /gpfs/apps/hpc/Apps/Matlab/R2015b/bin/matlab -nojvm -nodisplay -nodesktop
>>> -nosplash -r "addpath('/home/fas/glahn/ny87/Pipelines/fix1.06');
>>> addpath('/gpfs/apps/hpc/Apps/FSL/5.0.6/fsl/etc/matlab');
>>> fix_3_clean('.fix',0,1,2000)" >> .fix.log 2>&1
>>>
>>>
>>> Does anyone know what's the problem? Thank you very much!
>>>
>>> Best,
>>> Nailin
>>>
>>> --
>>> Nailin Yao, PhD
>>>
>>> Postdoctoral Associate
>>> Department of Psychiatry, Yale University
>>>
>>> ___
>>> HCP-Users mailing list
>>> HCP-Users@humanconnectome.org
>>> http://lists.humanconnectome.org/mailman/listinfo/hcp-users
>>>
>>>
>>>
>>> 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.
>>>
>>
>&
Re: [HCP-Users] hcp_fix bug
You could also need to run the add path parts of the command.
Peace,
Matt.
From: nailin yao <ynai...@gmail.com<mailto:ynai...@gmail.com>>
Date: Wednesday, October 19, 2016 at 4:02 PM
To: Matt Glasser <glass...@wustl.edu<mailto:glass...@wustl.edu>>
Cc: "hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>"
<hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>>
Subject: Re: [HCP-Users] hcp_fix bug
Hi Matt,
I tried to run fix_3_clean on matlab directly, and met the error message below:
fix_3_clean('.fix',0,1,2000)
TR =
0.7200
/bin/bash: -cifti-convert: command not found
Undefined function 'gifti' for input arguments of type 'char'.
Error in ciftiopen (line 31)
cifti = gifti([tmpfile '.gii']);
Error in fix_3_clean (line 40)
BO=ciftiopen('Atlas.dtseries.nii',WBC);
Do you know why? Thank you very much!
Best,
Nailin
2016-10-17 20:12 GMT-04:00 Glasser, Matthew
<glass...@wustl.edu<mailto:glass...@wustl.edu>>:
Is it a reproducible error? What happens if you try running the fix_3_clean
function with the parameters mentioned below?
Peace,
Matt.
From: nailin yao <ynai...@gmail.com<mailto:ynai...@gmail.com>>
Date: Monday, October 17, 2016 at 2:58 PM
To: Matt Glasser <glass...@wustl.edu<mailto:glass...@wustl.edu>>
Cc: "hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>"
<hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>>
Subject: Re: [HCP-Users] hcp_fix bug
Hi Matt,
It's not compiled matlab.
Best,
Nailin
2016-10-17 13:53 GMT-04:00 Glasser, Matthew
<glass...@wustl.edu<mailto:glass...@wustl.edu>>:
Is this compiled matlab or not compiled?
Peace,
Matt.
From:
<hcp-users-boun...@humanconnectome.org<mailto:hcp-users-boun...@humanconnectome.org>>
on behalf of nailin yao <ynai...@gmail.com<mailto:ynai...@gmail.com>>
Date: Monday, October 17, 2016 at 11:13 AM
To: "hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>"
<hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>>
Subject: [HCP-Users] hcp_fix bug
Hi ,
I received the bug report when running hcp_fix for the last step:
running FIX
FIX Feature extraction for Melodic output directory:
rfMRI_REST1_LR_nonlin_norm_hp2000.ica
create edge masks
run FAST
registration of standard space masks
extract features
FIX Classifying components in Melodic directory:
rfMRI_REST1_LR_nonlin_norm_hp2000.ica using training file:
/home/fas/glahn/ny87/Pipelines/fix1.06/training_files/HCP_hp2000.RData and
threshold 10
FIX Applying cleanup using cleanup file:
rfMRI_REST1_LR_nonlin_norm_hp2000.ica/fix4melview_HCP_hp2000_thr10.txt and
motion cleanup set to 1
sh: line 1: 24221 Bus error (core dumped)
/gpfs/apps/hpc/Apps/Matlab/R2015b/bin/matlab -nojvm -nodisplay -nodesktop
-nosplash -r "addpath('/home/fas/glahn/ny87/Pipelines/fix1.06');
addpath('/gpfs/apps/hpc/Apps/FSL/5.0.6/fsl/etc/matlab');
fix_3_clean('.fix',0,1,2000)" >> .fix.log 2>&1
Does anyone know what's the problem? Thank you very much!
Best,
Nailin
--
Nailin Yao, PhD
Postdoctoral Associate
Department of Psychiatry, Yale University
___
HCP-Users mailing list
HCP-Users@humanconnectome.org<mailto:HCP-Users@humanconnectome.org>
http://lists.humanconnectome.org/mailman/listinfo/hcp-users
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.
--
Nailin Yao, PhD
Postdoctoral Associate
Department of Psychiatry, Yale University
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.
--
Nailin Yao, PhD
Postdoctoral Associate
Department of Psychiatry, Yale University
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
Re: [HCP-Users] hcp_fix bug
Hi Matt,
I tried to run fix_3_clean on matlab directly, and met the error message
below:
fix_3_clean('.fix',0,1,2000)
TR =
0.7200
/bin/bash: -cifti-convert: command not found
Undefined function 'gifti' for input arguments of type 'char'.
Error in ciftiopen (line 31)
cifti = gifti([tmpfile '.gii']);
Error in fix_3_clean (line 40)
BO=ciftiopen('Atlas.dtseries.nii',WBC);
Do you know why? Thank you very much!
Best,
Nailin
2016-10-17 20:12 GMT-04:00 Glasser, Matthew <glass...@wustl.edu>:
> Is it a reproducible error? What happens if you try running the
> fix_3_clean function with the parameters mentioned below?
>
> Peace,
>
> Matt.
>
> From: nailin yao <ynai...@gmail.com>
> Date: Monday, October 17, 2016 at 2:58 PM
> To: Matt Glasser <glass...@wustl.edu>
> Cc: "hcp-users@humanconnectome.org" <hcp-users@humanconnectome.org>
> Subject: Re: [HCP-Users] hcp_fix bug
>
> Hi Matt,
>
> It's not compiled matlab.
>
> Best,
> Nailin
>
> 2016-10-17 13:53 GMT-04:00 Glasser, Matthew <glass...@wustl.edu>:
>
>> Is this compiled matlab or not compiled?
>>
>> Peace,
>>
>> Matt.
>>
>> From: <hcp-users-boun...@humanconnectome.org> on behalf of nailin yao <
>> ynai...@gmail.com>
>> Date: Monday, October 17, 2016 at 11:13 AM
>> To: "hcp-users@humanconnectome.org" <hcp-users@humanconnectome.org>
>> Subject: [HCP-Users] hcp_fix bug
>>
>> Hi ,
>>
>> I received the bug report when running hcp_fix for the last step:
>>
>> running FIX
>>
>> FIX Feature extraction for Melodic output directory:
>> rfMRI_REST1_LR_nonlin_norm_hp2000.ica
>>
>> create edge masks
>>
>> run FAST
>>
>> registration of standard space masks
>>
>> extract features
>>
>> FIX Classifying components in Melodic directory:
>> rfMRI_REST1_LR_nonlin_norm_hp2000.ica using training file:
>> /home/fas/glahn/ny87/Pipelines/fix1.06/training_files/HCP_hp2000.RData
>> and threshold 10
>>
>> FIX Applying cleanup using cleanup file: rfMRI_REST1_LR_nonlin_norm_hp2
>> 000.ica/fix4melview_HCP_hp2000_thr10.txt and motion cleanup set to 1
>>
>> sh: line 1: 24221 Bus error (core dumped)
>> /gpfs/apps/hpc/Apps/Matlab/R2015b/bin/matlab -nojvm -nodisplay
>> -nodesktop -nosplash -r "addpath('/home/fas/glahn/ny87/Pipelines/fix1.06');
>> addpath('/gpfs/apps/hpc/Apps/FSL/5.0.6/fsl/etc/matlab');
>> fix_3_clean('.fix',0,1,2000)" >> .fix.log 2>&1
>>
>> Does anyone know what's the problem? Thank you very much!
>>
>> Best,
>> Nailin
>>
>> --
>> Nailin Yao, PhD
>>
>> Postdoctoral Associate
>> Department of Psychiatry, Yale University
>>
>> ___
>> HCP-Users mailing list
>> HCP-Users@humanconnectome.org
>> http://lists.humanconnectome.org/mailman/listinfo/hcp-users
>>
>>
>> --
>>
>> 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.
>>
>
>
>
> --
> Nailin Yao, PhD
>
> Postdoctoral Associate
> Department of Psychiatry, Yale University
>
>
> --
>
> 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.
>
--
Nailin Yao, PhD
Postdoctoral Associate
Department of Psychiatry, Yale University
___
HCP-Users mailing list
HCP-Users@humanconnectome.org
http://lists.humanconnectome.org/mailman/listinfo/hcp-users
Re: [HCP-Users] hcp_fix bug
Is this compiled matlab or not compiled?
Peace,
Matt.
From:
<hcp-users-boun...@humanconnectome.org<mailto:hcp-users-boun...@humanconnectome.org>>
on behalf of nailin yao <ynai...@gmail.com<mailto:ynai...@gmail.com>>
Date: Monday, October 17, 2016 at 11:13 AM
To: "hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>"
<hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>>
Subject: [HCP-Users] hcp_fix bug
Hi ,
I received the bug report when running hcp_fix for the last step:
running FIX
FIX Feature extraction for Melodic output directory:
rfMRI_REST1_LR_nonlin_norm_hp2000.ica
create edge masks
run FAST
registration of standard space masks
extract features
FIX Classifying components in Melodic directory:
rfMRI_REST1_LR_nonlin_norm_hp2000.ica using training file:
/home/fas/glahn/ny87/Pipelines/fix1.06/training_files/HCP_hp2000.RData and
threshold 10
FIX Applying cleanup using cleanup file:
rfMRI_REST1_LR_nonlin_norm_hp2000.ica/fix4melview_HCP_hp2000_thr10.txt and
motion cleanup set to 1
sh: line 1: 24221 Bus error (core dumped)
/gpfs/apps/hpc/Apps/Matlab/R2015b/bin/matlab -nojvm -nodisplay -nodesktop
-nosplash -r "addpath('/home/fas/glahn/ny87/Pipelines/fix1.06');
addpath('/gpfs/apps/hpc/Apps/FSL/5.0.6/fsl/etc/matlab');
fix_3_clean('.fix',0,1,2000)" >> .fix.log 2>&1
Does anyone know what's the problem? Thank you very much!
Best,
Nailin
--
Nailin Yao, PhD
Postdoctoral Associate
Department of Psychiatry, Yale University
___
HCP-Users mailing list
HCP-Users@humanconnectome.org<mailto:HCP-Users@humanconnectome.org>
http://lists.humanconnectome.org/mailman/listinfo/hcp-users
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.
___
HCP-Users mailing list
HCP-Users@humanconnectome.org
http://lists.humanconnectome.org/mailman/listinfo/hcp-users
[HCP-Users] hcp_fix bug
Hi ,
I received the bug report when running hcp_fix for the last step:
running FIX
FIX Feature extraction for Melodic output directory:
rfMRI_REST1_LR_nonlin_norm_hp2000.ica
create edge masks
run FAST
registration of standard space masks
extract features
FIX Classifying components in Melodic directory:
rfMRI_REST1_LR_nonlin_norm_hp2000.ica using training file:
/home/fas/glahn/ny87/Pipelines/fix1.06/training_files/HCP_hp2000.RData and
threshold 10
FIX Applying cleanup using cleanup file:
rfMRI_REST1_LR_nonlin_norm_hp2000.ica/fix4melview_HCP_hp2000_thr10.txt and
motion cleanup set to 1
sh: line 1: 24221 Bus error (core dumped)
/gpfs/apps/hpc/Apps/Matlab/R2015b/bin/matlab -nojvm -nodisplay -nodesktop
-nosplash -r "addpath('/home/fas/glahn/ny87/Pipelines/fix1.06');
addpath('/gpfs/apps/hpc/Apps/FSL/5.0.6/fsl/etc/matlab');
fix_3_clean('.fix',0,1,2000)" >> .fix.log 2>&1
Does anyone know what's the problem? Thank you very much!
Best,
Nailin
--
Nailin Yao, PhD
Postdoctoral Associate
Department of Psychiatry, Yale University
___
HCP-Users mailing list
HCP-Users@humanconnectome.org
http://lists.humanconnectome.org/mailman/listinfo/hcp-users
