Re: [HCP-Users] drawing borders

2018-10-10 Thread Gaurav Patel 
Thanks; drawing borders will be easier and more accurate with smaller sphere 
sizes

_
 gaurav patel
 gauravpa...@gmail.com
 pateldsclab.net

> On Oct 10, 2018, at 6:45 PM, Timothy Coalson  wrote:
> 
> To clarify the phrasing: the existing release doesn't have a way to change 
> the size of these symbols.  We will consider making the size controllable in 
> the next release, but that may be a while off.
> 
> Tim
> 
> 
>> On Wed, Oct 10, 2018 at 12:15 PM, Harwell, John  wrote:
>> When drawing a border, I am able to reproduce the border sizes displayed in 
>> your image.  I would describe the border symbols as a little bigger, but not 
>> huge.  We understand this is not optimal for you, but there is nothing we 
>> can do to immediately change the border drawing symbol size.
>> 
>> > On Oct 10, 2018, at 9:57 AM, Gaurav Patel  wrote:
>> > 
>> > this is the tutorial 1.0 brain 
>> > (Q1-Q6_R440.R.veryinflated.32k_fs_LR.surf.gii).  2mm was actually much 
>> > smaller than the current 3% standard for the adult brain.  Are you able to 
>> > reproduce the issue with the same surface?
>> > 
>> > gaurav patel
>> > gauravpa...@gmail.com
>> > pateldsclab.net
>> > 
>> >> On Oct 10, 2018, at 9:50 AM, Harwell, John  wrote:
>> >> 
>> >> There is nothing in the user interface to adjust the size of the spheres 
>> >> while drawing a border.  In a previous version of Workbench, the size was 
>> >> 2mm.  However, 2mm was far too large when drawing borders on very small 
>> >> brains (babies, mice, etc) so the size was changed to 3% of the longest 
>> >> surface axis (typically posterior-to-anterior).
>> >> 
>> >> John
>> >> 
>> >>> On Oct 9, 2018, at 12:58 PM, Gaurav Patel  wrote:
>> >>> 
>> >>> here’s a screen shot of the draw borders output vs. a finished border 
>> >>> (symbol diameter set to 2mm).  I tried to change the ID sphere size 
>> >>> property, and that did not change.  On a machine with 1.23 still 
>> >>> installed, the draw borders output is the same size as the 2mm diameter 
>> >>> finalized borders.  I am drawing this on the tutorial surface
>> >>> 
>> >>> 
>> >>> 
>> >>> gaurav patel
>> >>> gauravpa...@gmail.com
>> >>> pateldsclab.net
>> >>> 
>>  On Oct 9, 2018, at 1:07 PM, Harwell, John  wrote:
>>  
>>  How huge is huge?  When drawing a new border, the symbol size should be 
>>  about 3% of the longest surface axis.  On a human surface, that appears 
>>  be about 5mm.  There is no way for the user to adjust the symbol size 
>>  when drawing.
>>  
>>  I am using Workbench version 1.3.2 and the size should be the same in 
>>  1.3.1.
>>  
>>  John Harwell
>>  
>> > On Oct 9, 2018, at 11:37 AM, Gaurav Patel  
>> > wrote:
>> > 
>> > Hi—when I am drawing borders in wb_view 1.31, the diameters of the red 
>> > spheres is huge, making is difficult to see what I am drawing.  This 
>> > was not the case in 1.23.  Is there a way to change that setting?  
>> > Finishing the border reduces the size of the spheres to the setting in 
>> > the borders menu, so that setting doesn’t make a difference.  Thanks
>> > 
>> > gaurav patel
>> > gauravpa...@gmail.com
>> > pateldsclab.net
>> > 
>> > 
>> > ___
>> > HCP-Users mailing list
>> > HCP-Users@humanconnectome.org
>> > http://lists.humanconnectome.org/mailman/listinfo/hcp-users
>>  
>> >>> 
>> >> 
>> > 
>> 
>> 
>> ___
>> HCP-Users mailing list
>> HCP-Users@humanconnectome.org
>> http://lists.humanconnectome.org/mailman/listinfo/hcp-users
> 

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Re: [HCP-Users] hcp_fix_multi_fix errors

2018-10-10 Thread Glasser, Matthew 
It might fix the problem.

Matt.

On 10/10/18, 4:42 PM, "Shankar Tumati"  wrote:

>Hi Matt,
>
>No, its 3.14.
>Is the latest (3.15, I believe) needed for the script?
>
>Best,
>Shankar
>
>From: Glasser, Matthew [glass...@wustl.edu]
>Sent: Wednesday, October 10, 2018 4:28 PM
>To: Shankar Tumati; hcp-users@humanconnectome.org
>Subject: Re: [HCP-Users] hcp_fix_multi_fix errors
>
>Is this with the latest melodic?
>
>Matt.
>
>On 10/10/18, 2:54 PM, "hcp-users-boun...@humanconnectome.org on behalf of
>Shankar Tumati" shankar.tum...@theroyal.ca> wrote:
>
>>Hi
>>
>>We get these seemingly random errors when implementing the
>>hcp_fix_multi_run code on the task data with some subjects. We need help
>>to figure it out.
>>
>>Below is the output for two of the subjects. It the same error in all
>>cases but with different column numbers.
>>
>>Thanks,
>>Shankar
>>-
>>
>>Wed Oct 10 13:40:11 EDT 2018 - hcp_fix_multi_run - INFORM - melodic_cmd:
>>/usr/local/fsl-5.0/bin/melodic -i day2_hp2000_vnf -o
>>day2_hp2000.ica/filtered_func_data.ica --nobet --report --Oall
>>--tr=0.72  --vn --dim=160 --verbose --debug -m
>>/group/northoff/share/hcp_task_prep_fix/104416/MNINonLinear/Results/day2/
>>d
>>ay2_brain_mask
>>
>>Melodic Version 3.14
>>
>>Melodic results will be in day2_hp2000.ica/filtered_func_data.ica
>>
>>START: setup
>>START: setup_misc
>>Mask provided :
>>/group/northoff/share/hcp_task_prep_fix/104416/MNINonLinear/Results/day2/
>>d
>>ay2_brain_mask
>>
>>END: setup_misc
>> after setup_misc START: setup_classic
>>START: process_file
>> before reading file day2_hp2000_vnfReading data file day2_hp2000_vnf
>>...  done
>> after reading file day2_hp2000_vnf before est smoothness   Estimating
>>data smoothness ...  done
>> after smoothness  before reshape  after reshape   Removing mean image
>>... before remmean  after remmean  done
>>END: process_file
>> after process_file Excluding voxels with constant value ... done
>>  day2_hp2000.ica/filtered_func_data.ica/alldat
>>
>>
>>
>>An exception has been thrown
>>Logic error:- detected by Newmat: index error: requested index = 0
>>
>>MatrixType = Rect   # Rows = 1; # Cols = 1994
>>
>>Wed Oct 10 14:41:57 EDT 2018 - hcp_fix_multi_run - INFORM - melodic has
>>been run: return_code = 0
>>-
>>-
>>-
>>-
>>--
>>
>>Wed Oct 10 14:07:43 EDT 2018 - hcp_fix_multi_run - INFORM - melodic_cmd:
>>/usr/local/fsl-5.0/bin/melodic -i day1_hp2000_vnf -o
>>day1_hp2000.ica/filtered_func_data.ica --nobet --report --Oall
>>--tr=0.72  --vn --dim=139 --verbose --debug -m
>>/group/northoff/share/hcp_task_prep_fix/130114/MNINonLinear/Results/day1/
>>d
>>ay1_brain_mask
>>
>>Melodic Version 3.14
>>
>>Melodic results will be in day1_hp2000.ica/filtered_func_data.ica
>>
>>START: setup
>>START: setup_misc
>>Mask provided :
>>/group/northoff/share/hcp_task_prep_fix/130114/MNINonLinear/Results/day1/
>>d
>>ay1_brain_mask
>>
>>END: setup_misc
>> after setup_misc START: setup_classic
>>START: process_file
>> before reading file day1_hp2000_vnfReading data file day1_hp2000_vnf
>>...  done
>> after reading file day1_hp2000_vnf before est smoothness   Estimating
>>data smoothness ...  done
>> after smoothness  before reshape  after reshape   Removing mean image
>>... before remmean  after remmean  done
>>END: process_file
>> after process_file Excluding voxels with constant value ... done
>>  day1_hp2000.ica/filtered_func_data.ica/alldat
>>
>>
>>
>>An exception has been thrown
>>Logic error:- detected by Newmat: index error: requested index = 0
>>
>>MatrixType = Rect   # Rows = 1; # Cols = 1882
>>
>>Wed Oct 10 14:57:27 EDT 2018 - hcp_fix_multi_run - INFORM - melodic has
>>been run: return_code = 0
>>
>>
>>___
>>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.



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 
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Re: [HCP-Users] Error Running HCP's PostFreeSurferPipelineBatch.sh

2018-10-10 Thread Glasser, Matthew 
Is it having problems reading files (in the D state?).

Matt.

From: ARMAN PRAFUL KULKARNI mailto:apkulkar...@wisc.edu>>
Date: Wednesday, October 10, 2018 at 3:55 PM
To: Matt Glasser mailto:glass...@wustl.edu>>, Timothy 
Coalson mailto:tsc...@mst.edu>>
Cc: "hcp-users@humanconnectome.org" 
mailto:hcp-users@humanconnectome.org>>
Subject: Re: [HCP-Users] Error Running HCP's PostFreeSurferPipelineBatch.sh


Hi Matt,


Currently, this process is using 0.7% of the CPU--it doesn't appear to be the 
issue. In terms of where the pipeline is currently at, from the output script 
(PostFreeSurferPipeline.sh.o) it has been stuck on the following for the past 
hour or greater:



parsed 'var * -1' as '(var*(-1))'
parsed 'var * -1' as '(var*(-1))'
parsed 'var * -1' as '(var*(-1))'
parsed 'abs(thickness)' as 'abs(thickness)'
parsed 'thickness > 0' as '(thickness>0)'
parsed 'ln(spherereg / sphere) / ln(2)' as '(ln((spherereg/sphere))/ln(2))'
parsed 'ln(var) / ln (2)' as '(ln(var)/ln(2))'
parsed 'ln(var) / ln (2)' as '(ln(var)/ln(2))'
parsed '(atlas + individual) > 0' as '((atlas+individual)>0)'
parsed 'var * -1' as '(var*(-1))'
parsed 'var * -1' as '(var*(-1))'
parsed 'var * -1' as '(var*(-1))'
parsed 'abs(thickness)' as 'abs(thickness)'
parsed 'thickness > 0' as '(thickness>0)'
parsed 'ln(spherereg / sphere) / ln(2)' as '(ln((spherereg/sphere))/ln(2))'
parsed 'ln(var) / ln (2)' as '(ln(var)/ln(2))'
parsed 'ln(var) / ln (2)' as '(ln(var)/ln(2))'
parsed '(atlas + individual) > 0' as '((atlas+individual)>0)'




Also, for the error output file (PostFreeSurferPipeline.sh.e), this seems to be 
the most recent output:




WARNING: name collision in input name 'WM-RH-UNKNOWN', changing one to 
'WM-RH-UNKNOWN_1'

reading colortable from annotation file...
colortable with 36 entries read (originally 
/autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt)
reading colortable from annotation file...
colortable with 76 entries read (originally 
/autofs/space/birn_044/users/christophe_atlas_rebuild//scripts_2008/Simple_surface_labels2009.txt)
reading colortable from annotation file...
colortable with 36 entries read (originally 
/autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt)
reading colortable from annotation file...
colortable with 76 entries read (originally 
/autofs/space/birn_044/users/christophe_atlas_rebuild//scripts_2008/Simple_surface_labels2009.txt)




Sincerely,

Arman


From: Glasser, Matthew mailto:glass...@wustl.edu>>
Sent: Wednesday, October 10, 2018 3:28:28 PM
To: ARMAN PRAFUL KULKARNI; NEUROSCIENCE tim
Cc: hcp-users@humanconnectome.org
Subject: Re: [HCP-Users] Error Running HCP's PostFreeSurferPipelineBatch.sh

What is using the CPU?

Matt.

From: 
mailto:hcp-users-boun...@humanconnectome.org>>
 on behalf of ARMAN PRAFUL KULKARNI 
mailto:apkulkar...@wisc.edu>>
Date: Wednesday, October 10, 2018 at 3:27 PM
To: Timothy Coalson mailto:tsc...@mst.edu>>
Cc: "hcp-users@humanconnectome.org" 
mailto:hcp-users@humanconnectome.org>>
Subject: Re: [HCP-Users] Error Running HCP's PostFreeSurferPipelineBatch.sh


Hi Tim,


I have the updated version of workbench now, and have tried running the 
pipeline again. PostFreeSurferPipelineBatch.sh has now been running for over 5 
hours. To my knowledge, prior to this update, it only took around 45 minutes 
when successful. Is this normal for this version of the pipeline to take this 
long? Thanks again.


Sincerely,

Arman


From: Timothy Coalson mailto:tsc...@mst.edu>>
Sent: Tuesday, October 9, 2018 6:13:44 PM
To: ARMAN PRAFUL KULKARNI
Cc: hcp-users@humanconnectome.org
Subject: Re: [HCP-Users] Error Running HCP's PostFreeSurferPipelineBatch.sh

You need to update workbench to the latest release, that option is a recent 
addition to the command that is failing.

Tim


On Tue, Oct 9, 2018 at 6:08 PM, ARMAN PRAFUL KULKARNI 
mailto:apkulkar...@wisc.edu>> wrote:

Hi,

I have been running the HCP Pipeline (v 3.27.0) on one subject's unprocessed 
data from the HCP-1200 dataset. Below is what I have in the SetUpHCPPipeline.sh 
file. I have been able to run PreFreeSurferPipelineBatch.sh and 
FreeSurferPipelineBatch.sh with no issues. However, when running 
PostFreeSurferPipelineBatch.sh, I get the following error after around 10 
minutes of the script running: "ERROR: Unexpected parameter: 
-local-affine-method", and I am not sure how to proceed. I appreciate any 
insight into this problem.

Sincerely,
Arman
---

#!/bin/bash

echo "This script must be SOURCED to correctly setup the environment prior to 
running any of the other HCP scripts contained here"

# Set up FSL (if not already done so in the running environment)
# Uncomment the following 2 lines (remove the leading

Re: [HCP-Users] drawing borders

2018-10-10 Thread Timothy Coalson 
To clarify the phrasing: the existing release doesn't have a way to change
the size of these symbols.  We will consider making the size controllable
in the next release, but that may be a while off.

Tim


On Wed, Oct 10, 2018 at 12:15 PM, Harwell, John  wrote:

> When drawing a border, I am able to reproduce the border sizes displayed
> in your image.  I would describe the border symbols as a little bigger, but
> not huge.  We understand this is not optimal for you, but there is nothing
> we can do to immediately change the border drawing symbol size.
>
> > On Oct 10, 2018, at 9:57 AM, Gaurav Patel  wrote:
> >
> > this is the tutorial 1.0 brain 
> > (Q1-Q6_R440.R.veryinflated.32k_fs_LR.surf.gii).
> 2mm was actually much smaller than the current 3% standard for the adult
> brain.  Are you able to reproduce the issue with the same surface?
> > 
> > gaurav patel
> > gauravpa...@gmail.com
> > pateldsclab.net
> >
> >> On Oct 10, 2018, at 9:50 AM, Harwell, John  wrote:
> >>
> >> There is nothing in the user interface to adjust the size of the
> spheres while drawing a border.  In a previous version of Workbench, the
> size was 2mm.  However, 2mm was far too large when drawing borders on very
> small brains (babies, mice, etc) so the size was changed to 3% of the
> longest surface axis (typically posterior-to-anterior).
> >>
> >> John
> >>
> >>> On Oct 9, 2018, at 12:58 PM, Gaurav Patel 
> wrote:
> >>>
> >>> here’s a screen shot of the draw borders output vs. a finished border
> (symbol diameter set to 2mm).  I tried to change the ID sphere size
> property, and that did not change.  On a machine with 1.23 still installed,
> the draw borders output is the same size as the 2mm diameter finalized
> borders.  I am drawing this on the tutorial surface
> >>>
> >>> 
> >>> 
> >>> gaurav patel
> >>> gauravpa...@gmail.com
> >>> pateldsclab.net
> >>>
>  On Oct 9, 2018, at 1:07 PM, Harwell, John  wrote:
> 
>  How huge is huge?  When drawing a new border, the symbol size should
> be about 3% of the longest surface axis.  On a human surface, that appears
> be about 5mm.  There is no way for the user to adjust the symbol size when
> drawing.
> 
>  I am using Workbench version 1.3.2 and the size should be the same in
> 1.3.1.
> 
>  John Harwell
> 
> > On Oct 9, 2018, at 11:37 AM, Gaurav Patel 
> wrote:
> >
> > Hi—when I am drawing borders in wb_view 1.31, the diameters of the
> red spheres is huge, making is difficult to see what I am drawing.  This
> was not the case in 1.23.  Is there a way to change that setting?
> Finishing the border reduces the size of the spheres to the setting in the
> borders menu, so that setting doesn’t make a difference.  Thanks
> > 
> > gaurav patel
> > gauravpa...@gmail.com
> > pateldsclab.net
> >
> >
> > ___
> > HCP-Users mailing list
> > HCP-Users@humanconnectome.org
> > http://lists.humanconnectome.org/mailman/listinfo/hcp-users
> 
> >>>
> >>
> >
>
>
> ___
> HCP-Users mailing list
> HCP-Users@humanconnectome.org
> http://lists.humanconnectome.org/mailman/listinfo/hcp-users
>

___
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Re: [HCP-Users] hcp_fix_multi_fix errors

2018-10-10 Thread Shankar Tumati 
Hi Matt,

No, its 3.14.
Is the latest (3.15, I believe) needed for the script?

Best,
Shankar 

From: Glasser, Matthew [glass...@wustl.edu]
Sent: Wednesday, October 10, 2018 4:28 PM
To: Shankar Tumati; hcp-users@humanconnectome.org
Subject: Re: [HCP-Users] hcp_fix_multi_fix errors

Is this with the latest melodic?

Matt.

On 10/10/18, 2:54 PM, "hcp-users-boun...@humanconnectome.org on behalf of
Shankar Tumati"  wrote:

>Hi
>
>We get these seemingly random errors when implementing the
>hcp_fix_multi_run code on the task data with some subjects. We need help
>to figure it out.
>
>Below is the output for two of the subjects. It the same error in all
>cases but with different column numbers.
>
>Thanks,
>Shankar
>-
>
>Wed Oct 10 13:40:11 EDT 2018 - hcp_fix_multi_run - INFORM - melodic_cmd:
>/usr/local/fsl-5.0/bin/melodic -i day2_hp2000_vnf -o
>day2_hp2000.ica/filtered_func_data.ica --nobet --report --Oall
>--tr=0.72  --vn --dim=160 --verbose --debug -m
>/group/northoff/share/hcp_task_prep_fix/104416/MNINonLinear/Results/day2/d
>ay2_brain_mask
>
>Melodic Version 3.14
>
>Melodic results will be in day2_hp2000.ica/filtered_func_data.ica
>
>START: setup
>START: setup_misc
>Mask provided :
>/group/northoff/share/hcp_task_prep_fix/104416/MNINonLinear/Results/day2/d
>ay2_brain_mask
>
>END: setup_misc
> after setup_misc START: setup_classic
>START: process_file
> before reading file day2_hp2000_vnfReading data file day2_hp2000_vnf
>...  done
> after reading file day2_hp2000_vnf before est smoothness   Estimating
>data smoothness ...  done
> after smoothness  before reshape  after reshape   Removing mean image
>... before remmean  after remmean  done
>END: process_file
> after process_file Excluding voxels with constant value ... done
>  day2_hp2000.ica/filtered_func_data.ica/alldat
>
>
>
>An exception has been thrown
>Logic error:- detected by Newmat: index error: requested index = 0
>
>MatrixType = Rect   # Rows = 1; # Cols = 1994
>
>Wed Oct 10 14:41:57 EDT 2018 - hcp_fix_multi_run - INFORM - melodic has
>been run: return_code = 0
>--
>--
>--
>
>Wed Oct 10 14:07:43 EDT 2018 - hcp_fix_multi_run - INFORM - melodic_cmd:
>/usr/local/fsl-5.0/bin/melodic -i day1_hp2000_vnf -o
>day1_hp2000.ica/filtered_func_data.ica --nobet --report --Oall
>--tr=0.72  --vn --dim=139 --verbose --debug -m
>/group/northoff/share/hcp_task_prep_fix/130114/MNINonLinear/Results/day1/d
>ay1_brain_mask
>
>Melodic Version 3.14
>
>Melodic results will be in day1_hp2000.ica/filtered_func_data.ica
>
>START: setup
>START: setup_misc
>Mask provided :
>/group/northoff/share/hcp_task_prep_fix/130114/MNINonLinear/Results/day1/d
>ay1_brain_mask
>
>END: setup_misc
> after setup_misc START: setup_classic
>START: process_file
> before reading file day1_hp2000_vnfReading data file day1_hp2000_vnf
>...  done
> after reading file day1_hp2000_vnf before est smoothness   Estimating
>data smoothness ...  done
> after smoothness  before reshape  after reshape   Removing mean image
>... before remmean  after remmean  done
>END: process_file
> after process_file Excluding voxels with constant value ... done
>  day1_hp2000.ica/filtered_func_data.ica/alldat
>
>
>
>An exception has been thrown
>Logic error:- detected by Newmat: index error: requested index = 0
>
>MatrixType = Rect   # Rows = 1; # Cols = 1882
>
>Wed Oct 10 14:57:27 EDT 2018 - hcp_fix_multi_run - INFORM - melodic has
>been run: return_code = 0
>
>
>___
>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.

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Re: [HCP-Users] Error Running HCP's PostFreeSurferPipelineBatch.sh

2018-10-10 Thread ARMAN PRAFUL KULKARNI 
Hi Matt,


Currently, this process is using 0.7% of the CPU--it doesn't appear to be the 
issue. In terms of where the pipeline is currently at, from the output script 
(PostFreeSurferPipeline.sh.o) it has been stuck on the following for the past 
hour or greater:



parsed 'var * -1' as '(var*(-1))'
parsed 'var * -1' as '(var*(-1))'
parsed 'var * -1' as '(var*(-1))'
parsed 'abs(thickness)' as 'abs(thickness)'
parsed 'thickness > 0' as '(thickness>0)'
parsed 'ln(spherereg / sphere) / ln(2)' as '(ln((spherereg/sphere))/ln(2))'
parsed 'ln(var) / ln (2)' as '(ln(var)/ln(2))'
parsed 'ln(var) / ln (2)' as '(ln(var)/ln(2))'
parsed '(atlas + individual) > 0' as '((atlas+individual)>0)'
parsed 'var * -1' as '(var*(-1))'
parsed 'var * -1' as '(var*(-1))'
parsed 'var * -1' as '(var*(-1))'
parsed 'abs(thickness)' as 'abs(thickness)'
parsed 'thickness > 0' as '(thickness>0)'
parsed 'ln(spherereg / sphere) / ln(2)' as '(ln((spherereg/sphere))/ln(2))'
parsed 'ln(var) / ln (2)' as '(ln(var)/ln(2))'
parsed 'ln(var) / ln (2)' as '(ln(var)/ln(2))'
parsed '(atlas + individual) > 0' as '((atlas+individual)>0)'




Also, for the error output file (PostFreeSurferPipeline.sh.e), this seems to be 
the most recent output:




WARNING: name collision in input name 'WM-RH-UNKNOWN', changing one to 
'WM-RH-UNKNOWN_1'

reading colortable from annotation file...
colortable with 36 entries read (originally 
/autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt)
reading colortable from annotation file...
colortable with 76 entries read (originally 
/autofs/space/birn_044/users/christophe_atlas_rebuild//scripts_2008/Simple_surface_labels2009.txt)
reading colortable from annotation file...
colortable with 36 entries read (originally 
/autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt)
reading colortable from annotation file...
colortable with 76 entries read (originally 
/autofs/space/birn_044/users/christophe_atlas_rebuild//scripts_2008/Simple_surface_labels2009.txt)




Sincerely,

Arman


From: Glasser, Matthew 
Sent: Wednesday, October 10, 2018 3:28:28 PM
To: ARMAN PRAFUL KULKARNI; NEUROSCIENCE tim
Cc: hcp-users@humanconnectome.org
Subject: Re: [HCP-Users] Error Running HCP's PostFreeSurferPipelineBatch.sh

What is using the CPU?

Matt.

From: 
mailto:hcp-users-boun...@humanconnectome.org>>
 on behalf of ARMAN PRAFUL KULKARNI 
mailto:apkulkar...@wisc.edu>>
Date: Wednesday, October 10, 2018 at 3:27 PM
To: Timothy Coalson mailto:tsc...@mst.edu>>
Cc: "hcp-users@humanconnectome.org" 
mailto:hcp-users@humanconnectome.org>>
Subject: Re: [HCP-Users] Error Running HCP's PostFreeSurferPipelineBatch.sh


Hi Tim,


I have the updated version of workbench now, and have tried running the 
pipeline again. PostFreeSurferPipelineBatch.sh has now been running for over 5 
hours. To my knowledge, prior to this update, it only took around 45 minutes 
when successful. Is this normal for this version of the pipeline to take this 
long? Thanks again.


Sincerely,

Arman


From: Timothy Coalson mailto:tsc...@mst.edu>>
Sent: Tuesday, October 9, 2018 6:13:44 PM
To: ARMAN PRAFUL KULKARNI
Cc: hcp-users@humanconnectome.org
Subject: Re: [HCP-Users] Error Running HCP's PostFreeSurferPipelineBatch.sh

You need to update workbench to the latest release, that option is a recent 
addition to the command that is failing.

Tim


On Tue, Oct 9, 2018 at 6:08 PM, ARMAN PRAFUL KULKARNI 
mailto:apkulkar...@wisc.edu>> wrote:

Hi,

I have been running the HCP Pipeline (v 3.27.0) on one subject's unprocessed 
data from the HCP-1200 dataset. Below is what I have in the SetUpHCPPipeline.sh 
file. I have been able to run PreFreeSurferPipelineBatch.sh and 
FreeSurferPipelineBatch.sh with no issues. However, when running 
PostFreeSurferPipelineBatch.sh, I get the following error after around 10 
minutes of the script running: "ERROR: Unexpected parameter: 
-local-affine-method", and I am not sure how to proceed. I appreciate any 
insight into this problem.

Sincerely,
Arman
---

#!/bin/bash

echo "This script must be SOURCED to correctly setup the environment prior to 
running any of the other HCP scripts contained here"

# Set up FSL (if not already done so in the running environment)
# Uncomment the following 2 lines (remove the leading #) and correct the FSLDIR 
setting for your setup
#export FSLDIR=/usr/share/fsl/5.0
#. ${FSLDIR}/etc/fslconf/fsl.sh

# Let FreeSurfer know what version of FSL to use
# FreeSurfer uses FSL_DIR instead of FSLDIR to determine the FSL version
export FSL_DIR="${FSLDIR}"

# Set up FreeSurfer (if not already done so in the running environment)
# Uncomment the following 2 lines (remove the leading #) and correct the 
FREESURFER_HOME setting for your setup
#export FREESURFER_HOME=/usr/local/bin/freesurfer
#source

Re: [HCP-Users] Error Running HCP's PostFreeSurferPipelineBatch.sh

2018-10-10 Thread Glasser, Matthew 
What is using the CPU?

Matt.

From: 
mailto:hcp-users-boun...@humanconnectome.org>>
 on behalf of ARMAN PRAFUL KULKARNI 
mailto:apkulkar...@wisc.edu>>
Date: Wednesday, October 10, 2018 at 3:27 PM
To: Timothy Coalson mailto:tsc...@mst.edu>>
Cc: "hcp-users@humanconnectome.org" 
mailto:hcp-users@humanconnectome.org>>
Subject: Re: [HCP-Users] Error Running HCP's PostFreeSurferPipelineBatch.sh


Hi Tim,


I have the updated version of workbench now, and have tried running the 
pipeline again. PostFreeSurferPipelineBatch.sh has now been running for over 5 
hours. To my knowledge, prior to this update, it only took around 45 minutes 
when successful. Is this normal for this version of the pipeline to take this 
long? Thanks again.


Sincerely,

Arman


From: Timothy Coalson mailto:tsc...@mst.edu>>
Sent: Tuesday, October 9, 2018 6:13:44 PM
To: ARMAN PRAFUL KULKARNI
Cc: hcp-users@humanconnectome.org
Subject: Re: [HCP-Users] Error Running HCP's PostFreeSurferPipelineBatch.sh

You need to update workbench to the latest release, that option is a recent 
addition to the command that is failing.

Tim


On Tue, Oct 9, 2018 at 6:08 PM, ARMAN PRAFUL KULKARNI 
mailto:apkulkar...@wisc.edu>> wrote:

Hi,

I have been running the HCP Pipeline (v 3.27.0) on one subject's unprocessed 
data from the HCP-1200 dataset. Below is what I have in the SetUpHCPPipeline.sh 
file. I have been able to run PreFreeSurferPipelineBatch.sh and 
FreeSurferPipelineBatch.sh with no issues. However, when running 
PostFreeSurferPipelineBatch.sh, I get the following error after around 10 
minutes of the script running: "ERROR: Unexpected parameter: 
-local-affine-method", and I am not sure how to proceed. I appreciate any 
insight into this problem.

Sincerely,
Arman
---

#!/bin/bash

echo "This script must be SOURCED to correctly setup the environment prior to 
running any of the other HCP scripts contained here"

# Set up FSL (if not already done so in the running environment)
# Uncomment the following 2 lines (remove the leading #) and correct the FSLDIR 
setting for your setup
#export FSLDIR=/usr/share/fsl/5.0
#. ${FSLDIR}/etc/fslconf/fsl.sh

# Let FreeSurfer know what version of FSL to use
# FreeSurfer uses FSL_DIR instead of FSLDIR to determine the FSL version
export FSL_DIR="${FSLDIR}"

# Set up FreeSurfer (if not already done so in the running environment)
# Uncomment the following 2 lines (remove the leading #) and correct the 
FREESURFER_HOME setting for your setup
#export FREESURFER_HOME=/usr/local/bin/freesurfer
#source ${FREESURFER_HOME}/SetUpFreeSurfer.sh > /dev/null 2>&1

# Set up specific environment variables for the HCP Pipeline
export HCPPIPEDIR=${HOME}//HCP/Pipelines
#export CARET7DIR=${HOME}/tools/workbench/bin_rh_linux64
export CARET7DIR=/usr/local/workbench/bin_linux64

export HCPPIPEDIR_Templates=${HCPPIPEDIR}/global/templates
export HCPPIPEDIR_Bin=${HCPPIPEDIR}/global/binaries
export HCPPIPEDIR_Config=${HCPPIPEDIR}/global/config

export HCPPIPEDIR_PreFS=${HCPPIPEDIR}/PreFreeSurfer/scripts
export HCPPIPEDIR_FS=${HCPPIPEDIR}/FreeSurfer/scripts
export HCPPIPEDIR_PostFS=${HCPPIPEDIR}/PostFreeSurfer/scripts
export HCPPIPEDIR_fMRISurf=${HCPPIPEDIR}/fMRISurface/scripts
export HCPPIPEDIR_fMRIVol=${HCPPIPEDIR}/fMRIVolume/scripts
export HCPPIPEDIR_tfMRI=${HCPPIPEDIR}/tfMRI/scripts
export HCPPIPEDIR_dMRI=${HCPPIPEDIR}/DiffusionPreprocessing/scripts
export HCPPIPEDIR_dMRITract=${HCPPIPEDIR}/DiffusionTractography/scripts
export HCPPIPEDIR_Global=${HCPPIPEDIR}/global/scripts
export HCPPIPEDIR_tfMRIAnalysis=${HCPPIPEDIR}/TaskfMRIAnalysis/scripts
export MSMBINDIR=${HCPPIPEDIR}/global/templates/MSMAll


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Re: [HCP-Users] hcp_fix_multi_fix errors

2018-10-10 Thread Glasser, Matthew 
Is this with the latest melodic?

Matt.

On 10/10/18, 2:54 PM, "hcp-users-boun...@humanconnectome.org on behalf of
Shankar Tumati"  wrote:

>Hi
>
>We get these seemingly random errors when implementing the
>hcp_fix_multi_run code on the task data with some subjects. We need help
>to figure it out.
>
>Below is the output for two of the subjects. It the same error in all
>cases but with different column numbers.
>
>Thanks,
>Shankar
>-
>
>Wed Oct 10 13:40:11 EDT 2018 - hcp_fix_multi_run - INFORM - melodic_cmd:
>/usr/local/fsl-5.0/bin/melodic -i day2_hp2000_vnf -o
>day2_hp2000.ica/filtered_func_data.ica --nobet --report --Oall
>--tr=0.72  --vn --dim=160 --verbose --debug -m
>/group/northoff/share/hcp_task_prep_fix/104416/MNINonLinear/Results/day2/d
>ay2_brain_mask
>
>Melodic Version 3.14
>
>Melodic results will be in day2_hp2000.ica/filtered_func_data.ica
>
>START: setup
>START: setup_misc
>Mask provided :
>/group/northoff/share/hcp_task_prep_fix/104416/MNINonLinear/Results/day2/d
>ay2_brain_mask
>
>END: setup_misc
> after setup_misc START: setup_classic
>START: process_file
> before reading file day2_hp2000_vnfReading data file day2_hp2000_vnf
>...  done
> after reading file day2_hp2000_vnf before est smoothness   Estimating
>data smoothness ...  done
> after smoothness  before reshape  after reshape   Removing mean image
>... before remmean  after remmean  done
>END: process_file
> after process_file Excluding voxels with constant value ... done
>  day2_hp2000.ica/filtered_func_data.ica/alldat
>
>
>
>An exception has been thrown
>Logic error:- detected by Newmat: index error: requested index = 0
>
>MatrixType = Rect   # Rows = 1; # Cols = 1994
>
>Wed Oct 10 14:41:57 EDT 2018 - hcp_fix_multi_run - INFORM - melodic has
>been run: return_code = 0
>--
>--
>--
>
>Wed Oct 10 14:07:43 EDT 2018 - hcp_fix_multi_run - INFORM - melodic_cmd:
>/usr/local/fsl-5.0/bin/melodic -i day1_hp2000_vnf -o
>day1_hp2000.ica/filtered_func_data.ica --nobet --report --Oall
>--tr=0.72  --vn --dim=139 --verbose --debug -m
>/group/northoff/share/hcp_task_prep_fix/130114/MNINonLinear/Results/day1/d
>ay1_brain_mask
>
>Melodic Version 3.14
>
>Melodic results will be in day1_hp2000.ica/filtered_func_data.ica
>
>START: setup
>START: setup_misc
>Mask provided :
>/group/northoff/share/hcp_task_prep_fix/130114/MNINonLinear/Results/day1/d
>ay1_brain_mask
>
>END: setup_misc
> after setup_misc START: setup_classic
>START: process_file
> before reading file day1_hp2000_vnfReading data file day1_hp2000_vnf
>...  done
> after reading file day1_hp2000_vnf before est smoothness   Estimating
>data smoothness ...  done
> after smoothness  before reshape  after reshape   Removing mean image
>... before remmean  after remmean  done
>END: process_file
> after process_file Excluding voxels with constant value ... done
>  day1_hp2000.ica/filtered_func_data.ica/alldat
>
>
>
>An exception has been thrown
>Logic error:- detected by Newmat: index error: requested index = 0
>
>MatrixType = Rect   # Rows = 1; # Cols = 1882
>
>Wed Oct 10 14:57:27 EDT 2018 - hcp_fix_multi_run - INFORM - melodic has
>been run: return_code = 0
>
>
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The materials in this message are private and may contain Protected Healthcare 
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Re: [HCP-Users] Error Running HCP's PostFreeSurferPipelineBatch.sh

2018-10-10 Thread ARMAN PRAFUL KULKARNI 
Hi Tim,


I have the updated version of workbench now, and have tried running the 
pipeline again. PostFreeSurferPipelineBatch.sh has now been running for over 5 
hours. To my knowledge, prior to this update, it only took around 45 minutes 
when successful. Is this normal for this version of the pipeline to take this 
long? Thanks again.


Sincerely,

Arman


From: Timothy Coalson 
Sent: Tuesday, October 9, 2018 6:13:44 PM
To: ARMAN PRAFUL KULKARNI
Cc: hcp-users@humanconnectome.org
Subject: Re: [HCP-Users] Error Running HCP's PostFreeSurferPipelineBatch.sh

You need to update workbench to the latest release, that option is a recent 
addition to the command that is failing.

Tim


On Tue, Oct 9, 2018 at 6:08 PM, ARMAN PRAFUL KULKARNI 
mailto:apkulkar...@wisc.edu>> wrote:

Hi,

I have been running the HCP Pipeline (v 3.27.0) on one subject's unprocessed 
data from the HCP-1200 dataset. Below is what I have in the SetUpHCPPipeline.sh 
file. I have been able to run PreFreeSurferPipelineBatch.sh and 
FreeSurferPipelineBatch.sh with no issues. However, when running 
PostFreeSurferPipelineBatch.sh, I get the following error after around 10 
minutes of the script running: "ERROR: Unexpected parameter: 
-local-affine-method", and I am not sure how to proceed. I appreciate any 
insight into this problem.

Sincerely,
Arman
---

#!/bin/bash

echo "This script must be SOURCED to correctly setup the environment prior to 
running any of the other HCP scripts contained here"

# Set up FSL (if not already done so in the running environment)
# Uncomment the following 2 lines (remove the leading #) and correct the FSLDIR 
setting for your setup
#export FSLDIR=/usr/share/fsl/5.0
#. ${FSLDIR}/etc/fslconf/fsl.sh

# Let FreeSurfer know what version of FSL to use
# FreeSurfer uses FSL_DIR instead of FSLDIR to determine the FSL version
export FSL_DIR="${FSLDIR}"

# Set up FreeSurfer (if not already done so in the running environment)
# Uncomment the following 2 lines (remove the leading #) and correct the 
FREESURFER_HOME setting for your setup
#export FREESURFER_HOME=/usr/local/bin/freesurfer
#source ${FREESURFER_HOME}/SetUpFreeSurfer.sh > /dev/null 2>&1

# Set up specific environment variables for the HCP Pipeline
export HCPPIPEDIR=${HOME}//HCP/Pipelines
#export CARET7DIR=${HOME}/tools/workbench/bin_rh_linux64
export CARET7DIR=/usr/local/workbench/bin_linux64

export HCPPIPEDIR_Templates=${HCPPIPEDIR}/global/templates
export HCPPIPEDIR_Bin=${HCPPIPEDIR}/global/binaries
export HCPPIPEDIR_Config=${HCPPIPEDIR}/global/config

export HCPPIPEDIR_PreFS=${HCPPIPEDIR}/PreFreeSurfer/scripts
export HCPPIPEDIR_FS=${HCPPIPEDIR}/FreeSurfer/scripts
export HCPPIPEDIR_PostFS=${HCPPIPEDIR}/PostFreeSurfer/scripts
export HCPPIPEDIR_fMRISurf=${HCPPIPEDIR}/fMRISurface/scripts
export HCPPIPEDIR_fMRIVol=${HCPPIPEDIR}/fMRIVolume/scripts
export HCPPIPEDIR_tfMRI=${HCPPIPEDIR}/tfMRI/scripts
export HCPPIPEDIR_dMRI=${HCPPIPEDIR}/DiffusionPreprocessing/scripts
export HCPPIPEDIR_dMRITract=${HCPPIPEDIR}/DiffusionTractography/scripts
export HCPPIPEDIR_Global=${HCPPIPEDIR}/global/scripts
export HCPPIPEDIR_tfMRIAnalysis=${HCPPIPEDIR}/TaskfMRIAnalysis/scripts
export MSMBINDIR=${HCPPIPEDIR}/global/templates/MSMAll


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[HCP-Users] hcp_fix_multi_fix errors

2018-10-10 Thread Shankar Tumati 
Hi

We get these seemingly random errors when implementing the hcp_fix_multi_run 
code on the task data with some subjects. We need help to figure it out.

Below is the output for two of the subjects. It the same error in all cases but 
with different column numbers.

Thanks,
Shankar
-

Wed Oct 10 13:40:11 EDT 2018 - hcp_fix_multi_run - INFORM - melodic_cmd: 
/usr/local/fsl-5.0/bin/melodic -i day2_hp2000_vnf -o 
day2_hp2000.ica/filtered_func_data.ica --nobet --report --Oall --tr=0.72  
--vn --dim=160 --verbose --debug -m 
/group/northoff/share/hcp_task_prep_fix/104416/MNINonLinear/Results/day2/day2_brain_mask

Melodic Version 3.14

Melodic results will be in day2_hp2000.ica/filtered_func_data.ica

START: setup
START: setup_misc
Mask provided : 
/group/northoff/share/hcp_task_prep_fix/104416/MNINonLinear/Results/day2/day2_brain_mask

END: setup_misc
 after setup_misc START: setup_classic
START: process_file
 before reading file day2_hp2000_vnfReading data file day2_hp2000_vnf  ...  done
 after reading file day2_hp2000_vnf before est smoothness   Estimating data 
smoothness ...  done 
 after smoothness  before reshape  after reshape   Removing mean image ... 
before remmean  after remmean  done
END: process_file
 after process_file Excluding voxels with constant value ... done
  day2_hp2000.ica/filtered_func_data.ica/alldat



An exception has been thrown
Logic error:- detected by Newmat: index error: requested index = 0

MatrixType = Rect   # Rows = 1; # Cols = 1994

Wed Oct 10 14:41:57 EDT 2018 - hcp_fix_multi_run - INFORM - melodic has been 
run: return_code = 0
--

Wed Oct 10 14:07:43 EDT 2018 - hcp_fix_multi_run - INFORM - melodic_cmd: 
/usr/local/fsl-5.0/bin/melodic -i day1_hp2000_vnf -o 
day1_hp2000.ica/filtered_func_data.ica --nobet --report --Oall --tr=0.72  
--vn --dim=139 --verbose --debug -m 
/group/northoff/share/hcp_task_prep_fix/130114/MNINonLinear/Results/day1/day1_brain_mask

Melodic Version 3.14

Melodic results will be in day1_hp2000.ica/filtered_func_data.ica

START: setup
START: setup_misc
Mask provided : 
/group/northoff/share/hcp_task_prep_fix/130114/MNINonLinear/Results/day1/day1_brain_mask

END: setup_misc
 after setup_misc START: setup_classic
START: process_file
 before reading file day1_hp2000_vnfReading data file day1_hp2000_vnf  ...  done
 after reading file day1_hp2000_vnf before est smoothness   Estimating data 
smoothness ...  done 
 after smoothness  before reshape  after reshape   Removing mean image ... 
before remmean  after remmean  done
END: process_file
 after process_file Excluding voxels with constant value ... done
  day1_hp2000.ica/filtered_func_data.ica/alldat



An exception has been thrown
Logic error:- detected by Newmat: index error: requested index = 0

MatrixType = Rect   # Rows = 1; # Cols = 1882

Wed Oct 10 14:57:27 EDT 2018 - hcp_fix_multi_run - INFORM - melodic has been 
run: return_code = 0


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Re: [HCP-Users] Visualizing Greyordinate Masks

2018-10-10 Thread Timothy Coalson 
The surfaces are fine, we generally recommend very_inflated for viewing
data.  To expand on what Matt said, the data in the map you are displaying
in that image appears to have an unusual distribution, with most values
near the minimum value, and a few spots with higher values (or perhaps the
palette coloring in the file doesn't match that map well).  Clicking the
wrench icon on the layer will show you a histogram of the values in that
map, and let you change the settings for how the values get colored.  You
may also want to look at a volume view to see if anything shows up in the
subcortical structures or cerebellum.

Tim


On Wed, Oct 10, 2018 at 2:20 PM, Glasser, Matthew 
wrote:

> Try changing the color windowing.
>
> Matt.
>
> From: Cathy Chen 
> Date: Wednesday, October 10, 2018 at 7:55 AM
> To: Matt Glasser 
> Cc: "hcp-users@humanconnectome.org" 
> Subject: Re: [HCP-Users] Visualizing Greyordinate Masks
>
> Hi Matt,
>
> I loaded the file as an overlay with the various .surf.gii files in the
> folder "100206_3T_Structural_preproc\100206\MNINonLinear\fsaverage_LR32k". 
> When
> I step through the 15 images corresponding to the 15 parcellation
> dimensions, I see very sparse visualizations. For example, this is the
> visualization I got corresponding to one of the parcellation dimensions:
> [image: image.png]
> I'm not sure if I'm using the wrong surface files, or if I need to re-save
> the .dtseries.nii file (to have 1s and 0s rather than the regression
> coeffecients), or if there is something else I need to change or add.
>
> Best,
> Cathy
>
> Am Mi., 10. Okt. 2018 um 04:14 Uhr schrieb Glasser, Matthew <
> glass...@wustl.edu>:
>
>> Steve and I think you have the right file, but are not understanding what
>> is confusing about viewing that file in Connectome Workbench, assuming you
>> have loaded the appropriate surfaces and volumes.
>>
>> Matt.
>>
>> From:  on behalf of Cathy Chen <
>> c...@alumni.princeton.edu>
>> Date: Tuesday, October 9, 2018 at 9:11 AM
>> To: "hcp-users@humanconnectome.org" 
>> Subject: [HCP-Users] Visualizing Greyordinate Masks
>>
>> Dear HCP experts,
>>
>> I'm working with subject-specific parcellations (for instance, "
>> HCP_S1200_PTNmaps_d15_25_50_100\3T_HCP1200_MSMAll_d15_ts2_
>> Z\100206.dtseries.nii" ) and would like to visualize the greyordinates
>> corresponding to each of the 15 (or 25, 50, or 100) spatial maps.
>>
>> I've been using Connectome Workbench, but have not been able to figure
>> out a way to do this based on online tutorials -- is it possible to
>> visualize these maps with Connectome Workbench? Would I need to save new
>> versions of the data, so that the maps lie in a [num_grayordinates x
>> num_maps] matrix rather than a [num_maps x num_grayordinates] matrix?
>>
>> Best,
>> Cathy
>>
>> ___
>> 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.
>>
>
> --
>
> 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
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>

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Re: [HCP-Users] Visualizing Greyordinate Masks

2018-10-10 Thread Glasser, Matthew 
Try changing the color windowing.

Matt.

From: Cathy Chen mailto:c...@alumni.princeton.edu>>
Date: Wednesday, October 10, 2018 at 7:55 AM
To: Matt Glasser mailto:glass...@wustl.edu>>
Cc: "hcp-users@humanconnectome.org" 
mailto:hcp-users@humanconnectome.org>>
Subject: Re: [HCP-Users] Visualizing Greyordinate Masks

Hi Matt,

I loaded the file as an overlay with the various .surf.gii files in the folder 
"100206_3T_Structural_preproc\100206\MNINonLinear\fsaverage_LR32k". When I step 
through the 15 images corresponding to the 15 parcellation dimensions, I see 
very sparse visualizations. For example, this is the visualization I got 
corresponding to one of the parcellation dimensions:
[image.png]
I'm not sure if I'm using the wrong surface files, or if I need to re-save the 
.dtseries.nii file (to have 1s and 0s rather than the regression coeffecients), 
or if there is something else I need to change or add.

Best,
Cathy

Am Mi., 10. Okt. 2018 um 04:14 Uhr schrieb Glasser, Matthew 
mailto:glass...@wustl.edu>>:
Steve and I think you have the right file, but are not understanding what is 
confusing about viewing that file in Connectome Workbench, assuming you have 
loaded the appropriate surfaces and volumes.

Matt.

From: 
mailto:hcp-users-boun...@humanconnectome.org>>
 on behalf of Cathy Chen 
mailto:c...@alumni.princeton.edu>>
Date: Tuesday, October 9, 2018 at 9:11 AM
To: "hcp-users@humanconnectome.org" 
mailto:hcp-users@humanconnectome.org>>
Subject: [HCP-Users] Visualizing Greyordinate Masks

Dear HCP experts,

I'm working with subject-specific parcellations (for instance, 
"HCP_S1200_PTNmaps_d15_25_50_100\3T_HCP1200_MSMAll_d15_ts2_Z\100206.dtseries.nii"
 ) and would like to visualize the greyordinates corresponding to each of the 
15 (or 25, 50, or 100) spatial maps.

I've been using Connectome Workbench, but have not been able to figure out a 
way to do this based on online tutorials -- is it possible to visualize these 
maps with Connectome Workbench? Would I need to save new versions of the data, 
so that the maps lie in a [num_grayordinates x num_maps] matrix rather than a 
[num_maps x num_grayordinates] matrix?

Best,
Cathy

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[HCP-Users] Postdoctoral positions available

2018-10-10 Thread Manish Saggar 
[https://tr.cloudmagic.com/h/v6/emailtag/tag/2.0/1539197810/b66430ca7e69eb44a2365b99bb8d8527/2/37dc7c4101057d665b3af19baa29b2ed/91e47bcc09b97ecb510bd665381a6240/9efab2399c7c560b34de477b9aa0a465/newton.gif]
[Apologies for cross-posting]

The Brain Dynamics Lab (http://bdl.stanford.edu) at Stanford is looking to hire 
1-2 postdocs with expertise in neuroimaging data analysis to develop/apply 
computational methods that can quantify transitions in brain activity (or 
connectivity) in health and disease (specifically, major depression and ADHD).

We use a number of neuroimaging modalities including simultaneous EEG-fMRI and 
EEG-fNIRS, structural/functional connectivity, and independent fMRI/fNIRS/EEG. 
We also use computational modeling (e.g., The Virtual Brain) for realistic 
bio-physical network model simulations and neuromodulation (e.g., TMS) to gain 
mechanistic understandings for the observed aberrant brain dynamics in patients 
with psychiatric illness. Other computational tools used in the lab include 
Topological Data Analysis (TDA) - including Mapper and Persistent Homology - 
and Deep Learning (DL). Stanford University is located in sunny northern 
California, deep in the heart of Silicon Valley and a short train ride to San 
Francisco.

The postdoc will be able to contribute to a number of ongoing research projects 
in our lab and collaborating labs by analyzing neuroimaging data from those 
studies. In addition, the postdoc will have the opportunity to develop their 
own research program with the domain of scientific or methodological problems 
currently being investigated within the lab (http://bdl.stanford.edu).

The successful candidate should:
• Have a PhD in a relevant field of study and demonstrated experience with the 
processing and statistical analysis of neuroimaging data.
• Have strong and demonstrated computer programming skills, including Python.  
Experience with Nipype is preferred.
• Have strong skills in statistics and machine learning (esp. TDA, DL, etc.)
• Have solid experience with computational data analysis, including strong 
UNIX/Linux skills and experience using high performance computing clusters.

Our lab is strongly committed to diversity in science, and we particularly 
welcome applications from members of traditionally underrepresented groups.

Interested candidates should email the following to sag...@stanford.edu:
• A cover letter describing your background and research interests
• CV
• Names and email addresses of two references

The initial position is for one year, with the option to renew for 2-3 years, 
given satisfactory performance and available funding. The positions are 
available immediately and applicants will be considered on a rolling basis.


m-

Manish Saggar, Ph.D.
Assistant Professor, Psychiatry
Stanford University
http://bdl.stanford.edu



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Re: [HCP-Users] drawing borders

2018-10-10 Thread Harwell, John 
Borders are not annotations and that is why borders are not in the annotations 
guide.  Borders are always attached to a surface whereas annotations may or may 
not be attached to a surface.  Visualizing borders is covered in the Workbench 
1.0 - 1.3.2 Tutorial 
(https://www.humanconnectome.org/software/connectome-workbench).  There is a 
description in the Workbench Help for border drawing (Help Menu—> Workbench 
Help), look for “Toolbar -> Mode -> Border Drawing.   Borders are simply a 
sequence of points that may be closed, it just depends upon how the border is 
drawn.

On Oct 10, 2018, at 10:01 AM, Demian Wassermann 
mailto:demian.wasserm...@inria.fr>> wrote:

This is an interesting topic. Despite the 3% being a good idea the border 
depends more on the structure being traced than on the brain itself (arguably 
those two are also related). I haven’t managed to find border tracing on the 
tutorial of annotations. Am I looking on the wrong place? Also are the 
traceable borders closed curves or can be also simple curves? Ie lines instead 
of borders?

Best and thanks for all this work


Demian

--
Demian Wassermann, PhD
demian.wasserm...@inria.fr
Associate Research Professor (CRN)
Parietal Lab
INRIA Saclay Ile-de-France
1 Rue Honoré d'Estienne d'Orves, 91120 Palaiseau

On 10 Oct 2018, at 10:51, Harwell, John 
mailto:jharw...@wustl.edu>> wrote:

There is nothing in the user interface to adjust the size of the spheres while 
drawing a border.  In a previous version of Workbench, the size was 2mm.  
However, 2mm was far too large when drawing borders on very small brains 
(babies, mice, etc) so the size was changed to 3% of the longest surface axis 
(typically posterior-to-anterior).

John

On Oct 9, 2018, at 12:58 PM, Gaurav Patel 
mailto:gauravpa...@gmail.com>> wrote:

here’s a screen shot of the draw borders output vs. a finished border (symbol 
diameter set to 2mm).  I tried to change the ID sphere size property, and that 
did not change.  On a machine with 1.23 still installed, the draw borders 
output is the same size as the 2mm diameter finalized borders.  I am drawing 
this on the tutorial surface



 gaurav patel
 gauravpa...@gmail.com
 pateldsclab.net

On Oct 9, 2018, at 1:07 PM, Harwell, John 
mailto:jharw...@wustl.edu>> wrote:

How huge is huge?  When drawing a new border, the symbol size should be about 
3% of the longest surface axis.  On a human surface, that appears be about 5mm. 
 There is no way for the user to adjust the symbol size when drawing.

I am using Workbench version 1.3.2 and the size should be the same in 1.3.1.

John Harwell

On Oct 9, 2018, at 11:37 AM, Gaurav Patel 
mailto:gauravpa...@gmail.com>> wrote:

Hi—when I am drawing borders in wb_view 1.31, the diameters of the red spheres 
is huge, making is difficult to see what I am drawing.  This was not the case 
in 1.23.  Is there a way to change that setting?  Finishing the border reduces 
the size of the spheres to the setting in the borders menu, so that setting 
doesn’t make a difference.  Thanks

gaurav patel
gauravpa...@gmail.com
pateldsclab.net


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Re: [HCP-Users] drawing borders

2018-10-10 Thread Harwell, John 
When drawing a border, I am able to reproduce the border sizes displayed in 
your image.  I would describe the border symbols as a little bigger, but not 
huge.  We understand this is not optimal for you, but there is nothing we can 
do to immediately change the border drawing symbol size.

> On Oct 10, 2018, at 9:57 AM, Gaurav Patel  wrote:
> 
> this is the tutorial 1.0 brain 
> (Q1-Q6_R440.R.veryinflated.32k_fs_LR.surf.gii).  2mm was actually much 
> smaller than the current 3% standard for the adult brain.  Are you able to 
> reproduce the issue with the same surface?
> 
> gaurav patel
> gauravpa...@gmail.com
> pateldsclab.net
> 
>> On Oct 10, 2018, at 9:50 AM, Harwell, John  wrote:
>> 
>> There is nothing in the user interface to adjust the size of the spheres 
>> while drawing a border.  In a previous version of Workbench, the size was 
>> 2mm.  However, 2mm was far too large when drawing borders on very small 
>> brains (babies, mice, etc) so the size was changed to 3% of the longest 
>> surface axis (typically posterior-to-anterior).
>> 
>> John
>> 
>>> On Oct 9, 2018, at 12:58 PM, Gaurav Patel  wrote:
>>> 
>>> here’s a screen shot of the draw borders output vs. a finished border 
>>> (symbol diameter set to 2mm).  I tried to change the ID sphere size 
>>> property, and that did not change.  On a machine with 1.23 still installed, 
>>> the draw borders output is the same size as the 2mm diameter finalized 
>>> borders.  I am drawing this on the tutorial surface
>>> 
>>> 
>>> 
>>> gaurav patel
>>> gauravpa...@gmail.com
>>> pateldsclab.net
>>> 
 On Oct 9, 2018, at 1:07 PM, Harwell, John  wrote:
 
 How huge is huge?  When drawing a new border, the symbol size should be 
 about 3% of the longest surface axis.  On a human surface, that appears be 
 about 5mm.  There is no way for the user to adjust the symbol size when 
 drawing.
 
 I am using Workbench version 1.3.2 and the size should be the same in 
 1.3.1.
 
 John Harwell
 
> On Oct 9, 2018, at 11:37 AM, Gaurav Patel  wrote:
> 
> Hi—when I am drawing borders in wb_view 1.31, the diameters of the red 
> spheres is huge, making is difficult to see what I am drawing.  This was 
> not the case in 1.23.  Is there a way to change that setting?  Finishing 
> the border reduces the size of the spheres to the setting in the borders 
> menu, so that setting doesn’t make a difference.  Thanks
> 
> gaurav patel
> gauravpa...@gmail.com
> pateldsclab.net
> 
> 
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>>> 
>> 
> 


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Re: [HCP-Users] drawing borders

2018-10-10 Thread Demian Wassermann 
This is an interesting topic. Despite the 3% being a good idea the border 
depends more on the structure being traced than on the brain itself (arguably 
those two are also related). I haven’t managed to find border tracing on the 
tutorial of annotations. Am I looking on the wrong place? Also are the 
traceable borders closed curves or can be also simple curves? Ie lines instead 
of borders?

Best and thanks for all this work


Demian

--
Demian Wassermann, PhD
demian.wasserm...@inria.fr
Associate Research Professor (CRN)
Parietal Lab
INRIA Saclay Ile-de-France
1 Rue Honoré d'Estienne d'Orves, 91120 Palaiseau

> On 10 Oct 2018, at 10:51, Harwell, John  wrote:
> 
> There is nothing in the user interface to adjust the size of the spheres 
> while drawing a border.  In a previous version of Workbench, the size was 
> 2mm.  However, 2mm was far too large when drawing borders on very small 
> brains (babies, mice, etc) so the size was changed to 3% of the longest 
> surface axis (typically posterior-to-anterior).
> 
> John
> 
>> On Oct 9, 2018, at 12:58 PM, Gaurav Patel  wrote:
>> 
>> here’s a screen shot of the draw borders output vs. a finished border 
>> (symbol diameter set to 2mm).  I tried to change the ID sphere size 
>> property, and that did not change.  On a machine with 1.23 still installed, 
>> the draw borders output is the same size as the 2mm diameter finalized 
>> borders.  I am drawing this on the tutorial surface
>> 
>> 
>> 
>>  gaurav patel
>>  gauravpa...@gmail.com
>>  pateldsclab.net
>> 
>>> On Oct 9, 2018, at 1:07 PM, Harwell, John  wrote:
>>> 
>>> How huge is huge?  When drawing a new border, the symbol size should be 
>>> about 3% of the longest surface axis.  On a human surface, that appears be 
>>> about 5mm.  There is no way for the user to adjust the symbol size when 
>>> drawing.
>>> 
>>> I am using Workbench version 1.3.2 and the size should be the same in 1.3.1.
>>> 
>>> John Harwell
>>> 
 On Oct 9, 2018, at 11:37 AM, Gaurav Patel  wrote:
 
 Hi—when I am drawing borders in wb_view 1.31, the diameters of the red 
 spheres is huge, making is difficult to see what I am drawing.  This was 
 not the case in 1.23.  Is there a way to change that setting?  Finishing 
 the border reduces the size of the spheres to the setting in the borders 
 menu, so that setting doesn’t make a difference.  Thanks
 
 gaurav patel
 gauravpa...@gmail.com
 pateldsclab.net
 
 
 ___
 HCP-Users mailing list
 HCP-Users@humanconnectome.org
 http://lists.humanconnectome.org/mailman/listinfo/hcp-users
>>> 
>> 
> 
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Re: [HCP-Users] drawing borders

2018-10-10 Thread Gaurav Patel 
this is the tutorial 1.0 brain (Q1-Q6_R440.R.veryinflated.32k_fs_LR.surf.gii).  
2mm was actually much smaller than the current 3% standard for the adult brain. 
 Are you able to reproduce the issue with the same surface?

 gaurav patel
 gauravpa...@gmail.com
 pateldsclab.net

> On Oct 10, 2018, at 9:50 AM, Harwell, John  wrote:
> 
> There is nothing in the user interface to adjust the size of the spheres 
> while drawing a border.  In a previous version of Workbench, the size was 
> 2mm.  However, 2mm was far too large when drawing borders on very small 
> brains (babies, mice, etc) so the size was changed to 3% of the longest 
> surface axis (typically posterior-to-anterior).
> 
> John
> 
>> On Oct 9, 2018, at 12:58 PM, Gaurav Patel  wrote:
>> 
>> here’s a screen shot of the draw borders output vs. a finished border 
>> (symbol diameter set to 2mm).  I tried to change the ID sphere size 
>> property, and that did not change.  On a machine with 1.23 still installed, 
>> the draw borders output is the same size as the 2mm diameter finalized 
>> borders.  I am drawing this on the tutorial surface
>> 
>> 
>> 
>>  gaurav patel
>>  gauravpa...@gmail.com
>>  pateldsclab.net
>> 
>>> On Oct 9, 2018, at 1:07 PM, Harwell, John  wrote:
>>> 
>>> How huge is huge?  When drawing a new border, the symbol size should be 
>>> about 3% of the longest surface axis.  On a human surface, that appears be 
>>> about 5mm.  There is no way for the user to adjust the symbol size when 
>>> drawing.
>>> 
>>> I am using Workbench version 1.3.2 and the size should be the same in 1.3.1.
>>> 
>>> John Harwell
>>> 
 On Oct 9, 2018, at 11:37 AM, Gaurav Patel  wrote:
 
 Hi—when I am drawing borders in wb_view 1.31, the diameters of the red 
 spheres is huge, making is difficult to see what I am drawing.  This was 
 not the case in 1.23.  Is there a way to change that setting?  Finishing 
 the border reduces the size of the spheres to the setting in the borders 
 menu, so that setting doesn’t make a difference.  Thanks
 
 gaurav patel
 gauravpa...@gmail.com
 pateldsclab.net
 
 
 ___
 HCP-Users mailing list
 HCP-Users@humanconnectome.org
 http://lists.humanconnectome.org/mailman/listinfo/hcp-users
>>> 
>> 
> 


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Re: [HCP-Users] drawing borders

2018-10-10 Thread Harwell, John 
There is nothing in the user interface to adjust the size of the spheres while 
drawing a border.  In a previous version of Workbench, the size was 2mm.  
However, 2mm was far too large when drawing borders on very small brains 
(babies, mice, etc) so the size was changed to 3% of the longest surface axis 
(typically posterior-to-anterior).

John

On Oct 9, 2018, at 12:58 PM, Gaurav Patel 
mailto:gauravpa...@gmail.com>> wrote:

here’s a screen shot of the draw borders output vs. a finished border (symbol 
diameter set to 2mm).  I tried to change the ID sphere size property, and that 
did not change.  On a machine with 1.23 still installed, the draw borders 
output is the same size as the 2mm diameter finalized borders.  I am drawing 
this on the tutorial surface



 gaurav patel
 gauravpa...@gmail.com
 pateldsclab.net

On Oct 9, 2018, at 1:07 PM, Harwell, John 
mailto:jharw...@wustl.edu>> wrote:

How huge is huge?  When drawing a new border, the symbol size should be about 
3% of the longest surface axis.  On a human surface, that appears be about 5mm. 
 There is no way for the user to adjust the symbol size when drawing.

I am using Workbench version 1.3.2 and the size should be the same in 1.3.1.

John Harwell

On Oct 9, 2018, at 11:37 AM, Gaurav Patel 
mailto:gauravpa...@gmail.com>> wrote:

Hi—when I am drawing borders in wb_view 1.31, the diameters of the red spheres 
is huge, making is difficult to see what I am drawing.  This was not the case 
in 1.23.  Is there a way to change that setting?  Finishing the border reduces 
the size of the spheres to the setting in the borders menu, so that setting 
doesn’t make a difference.  Thanks

gaurav patel
gauravpa...@gmail.com
pateldsclab.net


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Re: [HCP-Users] Visualizing Greyordinate Masks

2018-10-10 Thread Cathy Chen 
Hi Matt,

I loaded the file as an overlay with the various .surf.gii files in the
folder "100206_3T_Structural_preproc\100206\MNINonLinear\fsaverage_LR32k". When
I step through the 15 images corresponding to the 15 parcellation
dimensions, I see very sparse visualizations. For example, this is the
visualization I got corresponding to one of the parcellation dimensions:
[image: image.png]
I'm not sure if I'm using the wrong surface files, or if I need to re-save
the .dtseries.nii file (to have 1s and 0s rather than the regression
coeffecients), or if there is something else I need to change or add.

Best,
Cathy

Am Mi., 10. Okt. 2018 um 04:14 Uhr schrieb Glasser, Matthew <
glass...@wustl.edu>:

> Steve and I think you have the right file, but are not understanding what
> is confusing about viewing that file in Connectome Workbench, assuming you
> have loaded the appropriate surfaces and volumes.
>
> Matt.
>
> From:  on behalf of Cathy Chen <
> c...@alumni.princeton.edu>
> Date: Tuesday, October 9, 2018 at 9:11 AM
> To: "hcp-users@humanconnectome.org" 
> Subject: [HCP-Users] Visualizing Greyordinate Masks
>
> Dear HCP experts,
>
> I'm working with subject-specific parcellations (for instance, "
> HCP_S1200_PTNmaps_d15_25_50_100\3T_HCP1200_MSMAll_d15_ts2_Z\100206.dtseries.nii"
> ) and would like to visualize the greyordinates corresponding to each of
> the 15 (or 25, 50, or 100) spatial maps.
>
> I've been using Connectome Workbench, but have not been able to figure out
> a way to do this based on online tutorials -- is it possible to visualize
> these maps with Connectome Workbench? Would I need to save new versions of
> the data, so that the maps lie in a [num_grayordinates x num_maps] matrix
> rather than a [num_maps x num_grayordinates] matrix?
>
> Best,
> Cathy
>
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>
>
> --
>
> 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.
>

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