Thanks for letting us know.

Matt.

From: Shachar Gal <gal.shac...@gmail.com<mailto:gal.shac...@gmail.com>>
Date: Monday, April 8, 2019 at 6:34 AM
To: Timothy Coalson <tsc...@mst.edu<mailto:tsc...@mst.edu>>
Cc: Matt Glasser <glass...@wustl.edu<mailto:glass...@wustl.edu>>, Ido Tavor 
<idota...@gmail.com<mailto:idota...@gmail.com>>
Subject: Re: [HCP-Users] wb_command -cifti-resample in sub-cortical processing 
taking suspiciously long while

Hey Tim,

Sorry for the belated response.
The opm_num_threads solution worked great! It runs in a few minutes now.

Thanks,
Shachar


On Fri, Apr 5, 2019, 21:12 Timothy Coalson 
<tsc...@mst.edu<mailto:tsc...@mst.edu> wrote:
Have you had a chance to try this?  If nothing else, you can export 
OMP_NUM_THREADS=1 and see if that command finishes in less than an hour.

Tim


On Tue, Apr 2, 2019 at 2:47 AM Shachar Gal 
<gal.shac...@gmail.com<mailto:gal.shac...@gmail.com>> wrote:
sounds reasonable
we'll try to run the process again and restrict it to one socket, and see if it 
speeds things up, and let you know

thanks!

Shachar

On Mon, 1 Apr 2019 at 23:04, Timothy Coalson 
<tsc...@mst.edu<mailto:tsc...@mst.edu>> wrote:
This finished in just over 2 minutes on my quad-core, so I am betting it is the 
multi-socket or other architecture issue:

tim@timsdev:~/Downloads$ time nice released_wb_command -cifti-resample 
rfMRI_REST_AP_temp_subject_smooth.dtseries.nii COLUMN 
rfMRI_REST_AP_temp_template.dlabel.nii COLUMN ADAP_BARY_AREA CUBIC 
test.dtseries.nii -volume-predilate 10

real 2m12.248s
user 16m42.659s
sys 0m1.365s

tim@timsdev:~/Downloads$ released_wb_command -version
Connectome Workbench
Type: Command Line Application
Version: 1.3.2
Qt Compiled Version: 5.7.0
Qt Runtime Version: 5.7.0
Commit: 1c774d37d6cb5a179e0de3cbe1081cd1f698963a
Commit Date: 2018-08-28 08:50:51 -0500
Compiled with OpenMP: YES
Compiler: g++ (/home/caret/gcc/install/gcc-4.8.5/bin)
Compiler Version: 4.8.5
Compiled Debug: NO
Operating System: Linux

Tim


On Mon, Apr 1, 2019 at 2:01 PM Timothy Coalson 
<tsc...@mst.edu<mailto:tsc...@mst.edu>> wrote:
Sorry, that is only one physical CPU per process - you can run one instance of 
wb_command on each CPU just fine, it is simply when a single wb_command process 
has threads on more than one physical CPU that things get very slow.

Tim


On Mon, Apr 1, 2019 at 1:05 PM Timothy Coalson 
<tsc...@mst.edu<mailto:tsc...@mst.edu>> wrote:
Does the computer you were running this on have multiple CPU sockets?  
Synchronizing code across physical sockets is quite expensive in terms of time, 
and on such systems we strongly recommend using cpusets or restricting the 
number of threads to try to use only one physical CPU.

Tim


On Mon, Apr 1, 2019 at 2:15 AM Shachar Gal 
<gal.shac...@gmail.com<mailto:gal.shac...@gmail.com>> wrote:
well, it took 13 hours, but it completed the execution, and the final 
atlas.dtseries output looks good..
so it just takes a REALLY long time, and it takes a crazy amount of CPU
[image.png]

let me know if anything else happens when you run it I your environment?

Shachar

On Mon, 1 Apr 2019 at 00:19, Glasser, Matthew 
<glass...@wustl.edu<mailto:glass...@wustl.edu>> wrote:
We’ll have a look tomorrow and let you know what we find.

Matt.

From: Shachar Gal <gal.shac...@gmail.com<mailto:gal.shac...@gmail.com>>
Date: Sunday, March 31, 2019 at 4:17 PM
To: Matt Glasser <glass...@wustl.edu<mailto:glass...@wustl.edu>>
Cc: Timothy Coalson <tsc...@mst.edu<mailto:tsc...@mst.edu>>
Subject: Re: [HCP-Users] wb_command -cifti-resample in sub-cortical processing 
taking suspiciously long while

It does, and I've uploaded it as well to the drive, so you could have a look 
yourself

Shachar

On Mon, Apr 1, 2019, 00:12 Glasser, Matthew 
<glass...@wustl.edu<mailto:glass...@wustl.edu> wrote:
Well in that case this confirms that what Tim was thinking is not the issue and 
that we will need to look at the files themselves.  Again, we didn’t really 
change stuff in the fMRISurface pipeline recently, so this is quite puzzling…

Does the output of fMRIVolume look okay to you?

Matt.

From: Shachar Gal <gal.shac...@gmail.com<mailto:gal.shac...@gmail.com>>
Date: Sunday, March 31, 2019 at 4:09 PM
To: Matt Glasser <glass...@wustl.edu<mailto:glass...@wustl.edu>>
Cc: Timothy Coalson <tsc...@mst.edu<mailto:tsc...@mst.edu>>
Subject: Re: [HCP-Users] wb_command -cifti-resample in sub-cortical processing 
taking suspiciously long while

sure
this specific command is identical as far as i can tell, so maybe the 
difference is more upstream than this, and has to do with the way the input 
files were constructed (whether its the volume input to this pipeline, or 
upstream inside the fMRISurface pipeline)...

#!/bin/bash
set -e
script_name="SubcorticalProcessing.sh"
echo "${script_name}: START"

AtlasSpaceFolder="$1"
echo "${script_name}: AtlasSpaceFolder: ${AtlasSpaceFolder}"

ROIFolder="$2"
echo "${script_name}: ROIFolder: ${ROIFolder}"

FinalfMRIResolution="$3"
echo "${script_name}: FinalfMRIResolution: ${FinalfMRIResolution}"

ResultsFolder="$4"
echo "${script_name}: ResultsFolder: ${ResultsFolder}"

NameOffMRI="$5"
echo "${script_name}: NameOffMRI: ${NameOffMRI}"

SmoothingFWHM="$6"
echo "${script_name}: SmoothingFWHM: ${SmoothingFWHM}"

BrainOrdinatesResolution="$7"
echo "${script_name}: BrainOrdinatesResolution: ${BrainOrdinatesResolution}"

VolumefMRI="${ResultsFolder}/${NameOffMRI}"
echo "${script_name}: VolumefMRI: ${VolumefMRI}"

Sigma=`echo "$SmoothingFWHM / ( 2 * ( sqrt ( 2 * l ( 2 ) ) ) )" | bc -l`
echo "${script_name}: Sigma: ${Sigma}"

#NOTE: wmparc has dashes in structure names, which -cifti-create-* won't accept
#ROIs files have acceptable structure names

#deal with fsl_sub being silly when we want to use numeric equality on decimals
unset POSIXLY_CORRECT

#generate subject-roi space fMRI cifti for subcortical
if [[ `echo "$BrainOrdinatesResolution == $FinalfMRIResolution" | bc -l | cut 
-f1 -d.` == "1" ]]
then
    echo "${script_name}: Creating subject-roi subcortical cifti at same 
resolution as output"
    ${CARET7DIR}/wb_command -cifti-create-dense-timeseries 
${ResultsFolder}/${NameOffMRI}_temp_subject.dtseries.nii -volume 
"$VolumefMRI".nii.gz "$ROIFolder"/ROIs."$BrainOrdinatesResolution".nii.gz
else
    echo "${script_name}: Creating subject-roi subcortical cifti at differing 
fMRI resolution"
    ${CARET7DIR}/wb_command -volume-affine-resample 
"$ROIFolder"/ROIs."$BrainOrdinatesResolution".nii.gz 
$FSLDIR/etc/flirtsch/ident.mat "$VolumefMRI".nii.gz ENCLOSING_VOXEL 
"$ResultsFolder"/ROIs."$FinalfMRIResolution".nii.gz
    ${CARET7DIR}/wb_command -cifti-create-dense-timeseries 
${ResultsFolder}/${NameOffMRI}_temp_subject.dtseries.nii -volume 
"$VolumefMRI".nii.gz "$ResultsFolder"/ROIs."$FinalfMRIResolution".nii.gz
    rm -f "$ResultsFolder"/ROIs."$FinalfMRIResolution".nii.gz
fi

echo "${script_name}: Dilating out zeros"
#dilate out any exact zeros in the input data, for instance if the brain mask 
is wrong
${CARET7DIR}/wb_command -cifti-dilate 
${ResultsFolder}/${NameOffMRI}_temp_subject.dtseries.nii COLUMN 0 10 
${ResultsFolder}/${NameOffMRI}_temp_subject_dilate.dtseries.nii
rm -f ${ResultsFolder}/${NameOffMRI}_temp_subject.dtseries.nii

echo "${script_name}: Generate atlas subcortical template cifti"
${CARET7DIR}/wb_command -cifti-create-label 
${ResultsFolder}/${NameOffMRI}_temp_template.dlabel.nii -volume 
"$ROIFolder"/Atlas_ROIs."$BrainOrdinatesResolution".nii.gz 
"$ROIFolder"/Atlas_ROIs."$BrainOrdinatesResolution".nii.gz

if [[ `echo "${Sigma} > 0" | bc -l | cut -f1 -d.` == "1" ]]
then
    echo "${script_name}: Smoothing and resampling"
    #this is the whole timeseries, so don't overwrite, in order to allow 
on-disk writing, then delete temporary
    ${CARET7DIR}/wb_command -cifti-smoothing 
${ResultsFolder}/${NameOffMRI}_temp_subject_dilate.dtseries.nii 0 ${Sigma} 
COLUMN ${ResultsFolder}/${NameOffMRI}_temp_subject_smooth.dtseries.nii 
-fix-zeros-volume
    #resample, delete temporary
    ${CARET7DIR}/wb_command -cifti-resample 
${ResultsFolder}/${NameOffMRI}_temp_subject_smooth.dtseries.nii COLUMN 
${ResultsFolder}/${NameOffMRI}_temp_template.dlabel.nii COLUMN ADAP_BARY_AREA 
CUBIC ${ResultsFolder}/${NameOffMRI}_temp_atlas.dtseries.nii -volume-predilate 
10
    rm -f ${ResultsFolder}/${NameOffMRI}_temp_subject_smooth.dtseries.nii
else
    echo "${script_name}: Resampling"
    ${CARET7DIR}/wb_command -cifti-resample 
${ResultsFolder}/${NameOffMRI}_temp_subject_dilate.dtseries.nii COLUMN 
${ResultsFolder}/${NameOffMRI}_temp_template.dlabel.nii COLUMN ADAP_BARY_AREA 
CUBIC ${ResultsFolder}/${NameOffMRI}_temp_atlas.dtseries.nii -volume-predilate 
10
fi

#delete common temporaries
rm -f ${ResultsFolder}/${NameOffMRI}_temp_subject_dilate.dtseries.nii
rm -f ${ResultsFolder}/${NameOffMRI}_temp_template.dlabel.nii

#write output volume, delete temporary
#NOTE: $VolumefMRI contains a path in it, it is not a file in the current 
directory
${CARET7DIR}/wb_command -cifti-separate 
${ResultsFolder}/${NameOffMRI}_temp_atlas.dtseries.nii COLUMN -volume-all 
"$VolumefMRI"_AtlasSubcortical_s"$SmoothingFWHM".nii.gz
rm -f ${ResultsFolder}/${NameOffMRI}_temp_atlas.dtseries.nii

echo "${script_name}: END"


On Mon, 1 Apr 2019 at 00:02, Glasser, Matthew 
<glass...@wustl.edu<mailto:glass...@wustl.edu>> wrote:
Can you paste in the contents of this file in your old version?

HCPpipelines<https://github.com/Washington-University/HCPpipelines/tree/89c9f1d48174c1e6ed85c35391287c706ab86d88>/fMRISurface<https://github.com/Washington-University/HCPpipelines/tree/89c9f1d48174c1e6ed85c35391287c706ab86d88/fMRISurface>/scripts<https://github.com/Washington-University/HCPpipelines/tree/89c9f1d48174c1e6ed85c35391287c706ab86d88/fMRISurface/scripts>/SubcorticalProcessing.sh

Matt.

From: Shachar Gal <gal.shac...@gmail.com<mailto:gal.shac...@gmail.com>>
Date: Sunday, March 31, 2019 at 3:57 PM
To: Matt Glasser <glass...@wustl.edu<mailto:glass...@wustl.edu>>
Cc: Timothy Coalson <tsc...@mst.edu<mailto:tsc...@mst.edu>>
Subject: Re: [HCP-Users] wb_command -cifti-resample in sub-cortical processing 
taking suspiciously long while

As I mentioned, I'm using the latest release of the pipelines (version 4).

Using the previous release, which I downloaded around August, and used up until 
recently, this did not occur.

Regarding the multithreading, I'll have to check tomorrow. Depends on our 
server, and I'm not sure.

Shachar

On Sun, Mar 31, 2019, 23:50 Glasser, Matthew 
<glass...@wustl.edu<mailto:glass...@wustl.edu> wrote:
Also what version of the code (ideally when did you download it) are you using? 
 3 years ago there was a change here, but I am surprised this is the first 
report of a problem.

Matt.

From: Matt Glasser <glass...@wustl.edu<mailto:glass...@wustl.edu>>
Date: Sunday, March 31, 2019 at 3:41 PM
To: Shachar Gal <gal.shac...@gmail.com<mailto:gal.shac...@gmail.com>>
Cc: Timothy Coalson <tsc...@mst.edu<mailto:tsc...@mst.edu>>
Subject: Re: [HCP-Users] wb_command -cifti-resample in sub-cortical processing 
taking suspiciously long while

We’ll also have a look at the files.  If this is really the explanation we will 
have to fix this.

Is it running multi-threaded?

Matt.

From: Shachar Gal <gal.shac...@gmail.com<mailto:gal.shac...@gmail.com>>
Date: Sunday, March 31, 2019 at 3:38 PM
To: Timothy Coalson <tsc...@mst.edu<mailto:tsc...@mst.edu>>
Cc: Matt Glasser <glass...@wustl.edu<mailto:glass...@wustl.edu>>
Subject: Re: [HCP-Users] wb_command -cifti-resample in sub-cortical processing 
taking suspiciously long while

ok, so i guess i'll just wait a while longer, and let you know in the morning 
if it finished running
though i must point out that it has been running for over 12 hours now.. makes 
you wonder if everything is right

did you manage getting the files from the drive?

cheers,
Shachar

On Sun, 31 Mar 2019 at 22:37, Timothy Coalson 
<tsc...@mst.edu<mailto:tsc...@mst.edu>> wrote:
The newer subcortical processing script is expected to take longer than it used 
to, by a fairly substantial factor.  This is partly due to dilation, intended 
to reduce edge effects from the cubic resampling.  I was working on making this 
need less dilation, but was interrupted by other things.

Cifti commands do create their output files partly in advance, and they may 
even be most of the size of the final file, but that does not mean all of the 
data has been written to them.

Tim


On Sun, Mar 31, 2019, 11:00 AM Glasser, Matthew 
<glass...@wustl.edu<mailto:glass...@wustl.edu>> wrote:
I’d like Tim’s input on where to upload if you don’t have your own convenient 
spot.

Matt.

From: Shachar Gal <gal.shac...@gmail.com<mailto:gal.shac...@gmail.com>>
Date: Sunday, March 31, 2019 at 10:58 AM
To: Matt Glasser <glass...@wustl.edu<mailto:glass...@wustl.edu>>
Subject: Re: [HCP-Users] wb_command -cifti-resample in sub-cortical processing 
taking suspiciously long while

yes, it happened for each of my subjects.
these are the input files for the command -  temp_subject_smooth.dtseries.nii, 
temp_template.dlabel.nii
 where should i upload them to?


On Sun, 31 Mar 2019 at 18:56, Glasser, Matthew 
<glass...@wustl.edu<mailto:glass...@wustl.edu>> wrote:
We need the input files to the command that is taking too long.  Also, does the 
problem happen reproducibly?

Matt.

From: Shachar Gal <gal.shac...@gmail.com<mailto:gal.shac...@gmail.com>>
Date: Sunday, March 31, 2019 at 10:53 AM
To: Matt Glasser <glass...@wustl.edu<mailto:glass...@wustl.edu>>
Subject: Re: [HCP-Users] wb_command -cifti-resample in sub-cortical processing 
taking suspiciously long while

so ive connected to our server and visually examined the rfMRI_REST_AP.nii.gz 
file, the output from the fMRIVolume pipeline, and it looks great.

where would you like me to upload the files, and which files exactly, other 
than temp_subject_smooth.dtseries.nii, temp_template.dlabel.nii and the 
registered volume?

thanks,
Shachar

On Sun, 31 Mar 2019 at 18:37, Glasser, Matthew 
<glass...@wustl.edu<mailto:glass...@wustl.edu>> wrote:
Perhaps you should upload the various input files to the specific wb_command 
command somewhere so we can test them if this issue is reproducible (i.e. is 
not a random thing from bad RAM or something like that).

Matt.

From: Shachar Gal <gal.shac...@gmail.com<mailto:gal.shac...@gmail.com>>
Date: Sunday, March 31, 2019 at 10:32 AM
To: Matt Glasser <glass...@wustl.edu<mailto:glass...@wustl.edu>>
Subject: Re: [HCP-Users] wb_command -cifti-resample in sub-cortical processing 
taking suspiciously long while

Its 500 time points.
I'll have a look at the volume input tommorow when I get back to the office. I 
ran them serially, the fmri pipelines..

Cheers
Shachar

On Sun, Mar 31, 2019, 18:13 Glasser, Matthew 
<glass...@wustl.edu<mailto:glass...@wustl.edu> wrote:
How many volumes and did you look at the data being input yet?

This code didn’t change so we don’t expect any difference.

Matt.

From: Shachar Gal <gal.shac...@gmail.com<mailto:gal.shac...@gmail.com>>
Date: Sunday, March 31, 2019 at 10:10 AM
To: Matt Glasser <glass...@wustl.edu<mailto:glass...@wustl.edu>>
Subject: Re: [HCP-Users] wb_command -cifti-resample in sub-cortical processing 
taking suspiciously long while

hey matt,
this is the call to the pipeline:

/root/hcppilelines/HCPpipelines-master/fMRISurface/GenericfMRISurfaceProcessingPipeline.sh
 --path=/root/hcppilelines/piano_hcp/working_directory --subject=101 
--fmriname=rfMRI_REST_AP --lowresmesh=32 --fmrires=2 --smoothingFWHM=4 
--grayordinatesres=2 --regname=MSMSulc

the TR is 0.75, and the resolution is 2 mm isometric.
as i wrote, this went smoothly with the previous release of the pipelines, and 
resulted in data that looked great

thanks,
Shachar




On Sun, 31 Mar 2019 at 17:53, Glasser, Matthew 
<glass...@wustl.edu<mailto:glass...@wustl.edu>> wrote:
How did you call fMRISurface and what kind of data is this in terms of spatial 
and temporal resolution?  Do the input and template data line up and look 
reasonable?

Matt

From: 
<hcp-users-boun...@humanconnectome.org<mailto:hcp-users-boun...@humanconnectome.org>>
 on behalf of Shachar Gal <gal.shac...@gmail.com<mailto:gal.shac...@gmail.com>>
Date: Sunday, March 31, 2019 at 8:27 AM
To: "hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>" 
<hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>>
Subject: Re: [HCP-Users] wb_command -cifti-resample in sub-cortical processing 
taking suspiciously long while

some further information that might be useful - the output file 
rfMRI_REST_AP_temp_atlas.dtseries.nii, has already been created. its in the 
target folder. but the command won't stop "running"

On Sun, 31 Mar 2019 at 16:13, Shachar Gal 
<gal.shac...@gmail.com<mailto:gal.shac...@gmail.com>> wrote:
Dear experts,

while running the fMRISurface pipeline (using the latest pipeline release) I 
encountered an issue where the subcortical-processing script takes a really 
long while (now running for more than 6 hours).
this is the command on which it is stuck

    ${CARET7DIR}/wb_command -cifti-resample 
${ResultsFolder}/${NameOffMRI}_temp_subject_smooth.dtseries.nii COLUMN 
${ResultsFolder}/${NameOffMRI}_temp_template.dlabel.nii COLUMN ADAP_BARY_AREA 
CUBIC ${ResultsFolder}/${NameOffMRI}_temp_atlas.dtseries.nii -volume-predilate 
10
    rm -f ${ResultsFolder}/${NameOffMRI}_temp_subject_smooth.dtseries.nii

the wb_command version is 1.3.2
there is no error being raise or anything. its still running, but its ages...
the thing is, when running the older version of the pipeline (but the same 
workbench version), there was no problem.
any ideas?

ill report later on if it completes the command eventually....

thanks,
Shachar



_______________________________________________
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.

________________________________
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.

On Mar 31, 2019 18:13, "Glasser, Matthew" 
<glass...@wustl.edu<mailto:glass...@wustl.edu>> wrote:
How many volumes and did you look at the data being input yet?

This code didn’t change so we don’t expect any difference.

Matt.

From: Shachar Gal <gal.shac...@gmail.com<mailto:gal.shac...@gmail.com>>
Date: Sunday, March 31, 2019 at 10:10 AM
To: Matt Glasser <glass...@wustl.edu<mailto:glass...@wustl.edu>>
Subject: Re: [HCP-Users] wb_command -cifti-resample in sub-cortical processing 
taking suspiciously long while

hey matt,
this is the call to the pipeline:

/root/hcppilelines/HCPpipelines-master/fMRISurface/GenericfMRISurfaceProcessingPipeline.sh
 --path=/root/hcppilelines/piano_hcp/working_directory --subject=101 
--fmriname=rfMRI_REST_AP --lowresmesh=32 --fmrires=2 --smoothingFWHM=4 
--grayordinatesres=2 --regname=MSMSulc

the TR is 0.75, and the resolution is 2 mm isometric.
as i wrote, this went smoothly with the previous release of the pipelines, and 
resulted in data that looked great

thanks,
Shachar




On Sun, 31 Mar 2019 at 17:53, Glasser, Matthew 
<glass...@wustl.edu<mailto:glass...@wustl.edu>> wrote:
How did you call fMRISurface and what kind of data is this in terms of spatial 
and temporal resolution?  Do the input and template data line up and look 
reasonable?

Matt

From: 
<hcp-users-boun...@humanconnectome.org<mailto:hcp-users-boun...@humanconnectome.org>>
 on behalf of Shachar Gal <gal.shac...@gmail.com<mailto:gal.shac...@gmail.com>>
Date: Sunday, March 31, 2019 at 8:27 AM
To: "hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>" 
<hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>>
Subject: Re: [HCP-Users] wb_command -cifti-resample in sub-cortical processing 
taking suspiciously long while

some further information that might be useful - the output file 
rfMRI_REST_AP_temp_atlas.dtseries.nii, has already been created. its in the 
target folder. but the command won't stop "running"

On Sun, 31 Mar 2019 at 16:13, Shachar Gal 
<gal.shac...@gmail.com<mailto:gal.shac...@gmail.com>> wrote:
Dear experts,

while running the fMRISurface pipeline (using the latest pipeline release) I 
encountered an issue where the subcortical-processing script takes a really 
long while (now running for more than 6 hours).
this is the command on which it is stuck

    ${CARET7DIR}/wb_command -cifti-resample 
${ResultsFolder}/${NameOffMRI}_temp_subject_smooth.dtseries.nii COLUMN 
${ResultsFolder}/${NameOffMRI}_temp_template.dlabel.nii COLUMN ADAP_BARY_AREA 
CUBIC ${ResultsFolder}/${NameOffMRI}_temp_atlas.dtseries.nii -volume-predilate 
10
    rm -f ${ResultsFolder}/${NameOffMRI}_temp_subject_smooth.dtseries.nii

the wb_command version is 1.3.2
there is no error being raise or anything. its still running, but its ages...
the thing is, when running the older version of the pipeline (but the same 
workbench version), there was no problem.
any ideas?

ill report later on if it completes the command eventually....

thanks,
Shachar



_______________________________________________
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.

________________________________
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.


________________________________
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.

________________________________
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.

________________________________
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.

________________________________
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 
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