Re: [HCP-Users] ERROR: surface exceeds the bounding box of the warpfield
Great thank you Matt,
Working with 160mm in the acpc stage seems to work.
Thank you for everyone's help!
Cheers,
Barbara
On 16/01/2016 14:50, Glasser, Matthew wrote:
It won’t create any biases, it just might help you get the acpc step
to work on the two subjects it hasn’t.
Peace,
Matt.
From: Barbara Kreilkamp <mailto:bakk@googlemail.com>>
Date: Friday, January 15, 2016 at 9:46 AM
To: Matt Glasser mailto:glass...@wustl.edu>>
Cc: "Van Essen, David" <mailto:vanes...@wustl.edu>>, Timothy Coalson <mailto:tsc...@mst.edu>>, "hcp-users@humanconnectome.org
<mailto:hcp-users@humanconnectome.org>" <mailto:hcp-users@humanconnectome.org>>
Subject: Re: [HCP-Users] ERROR: surface exceeds the bounding box of
the warpfield
Dear Matt,
Thank you, I found the brain size parameter, but do you think it is
okay to tweak this, when I leave it at the default value for all the
other subjects (which ran through fine by the way, 58 participants
were fine for the whole myelin pipeline, just 1 patient and 1 control
failed in our dataset, potentially as you pointed out in the
acpc-alignment step.
Thank you,
Best wishes,
Barbara
On 15/01/2016 03:08, Glasser, Matthew wrote:
Maybe post your PreFreeSurfer pipeline launch variables.
Peace,
Matt.
From: Barbara Kreilkamp <mailto:bakk@googlemail.com>>
Date: Thursday, January 14, 2016 at 6:11 AM
To: Matt Glasser
Cc: "Van Essen, David" <mailto:vanes...@wustl.edu>>, Timothy Coalson <mailto:tsc...@mst.edu>>, "hcp-users@humanconnectome.org"
mailto:hcp-users@humanconnectome.org>>
Subject: Re: [HCP-Users] ERROR: surface exceeds the bounding box of
the warpfield
Dear Matt, David and Tim,
Thanks for looking into it, I've got the 1mm templates with their
correct paths, however I am unsure of how to test performance
implementing these as "down sampled, and brain mask" as well as where
to change the brain size parameter.
Would you guide me on this please?
Thank you,
Best wishes,
Barbara
On Wed, Jan 13, 2016 at 11:07 AM, Glasser, Matthew
mailto:glass...@wustl.edu>> wrote:
Indeed sorry Barbara!
Matt.
From: David Van Essen mailto:vanes...@wustl.edu>>
Date: Tuesday, January 12, 2016 at 11:27 PM
To: Matt Glasser mailto:glass...@wustl.edu>>
Cc: Timothy Coalson mailto:tsc...@mst.edu>>,
Barbara Kreilkamp mailto:bakk@googlemail.com>>, "hcp-users@humanconnectome.org
<mailto:hcp-users@humanconnectome.org>"
mailto:hcp-users@humanconnectome.org>>
Subject: Re: [HCP-Users] ERROR: surface exceeds the bounding box
of the warpfield
Thanks for the suggestions, Matt, which are excellent even though
accidentally addressed to the wrong gender - said your mentor,
(s)heepishly.
David :<)
On Jan 12, 2016, at 10:23 PM, Glasser, Matthew
wrote:
Indeed the acpc registration is failing. He might check to be
sure he is using the right templates (1mm, correct ones for
original, down sampled, and brain mask). He could also try
fiddling with the brain size parameter (trying values 10mm
larger and smaller than 150mm). The acpc stage is most
vulnerable to failure. If it works, usually everything else
will after it.
Matt.
From: on behalf of
Timothy Coalson
Date: Friday, January 8, 2016 at 6:42 PM
To: Barbara Kreilkamp
Cc: "hcp-users@humanconnectome.org"
Subject: Re: [HCP-Users] ERROR: surface exceeds the bounding box
of the warpfield
Well, somewhere along the line, volume registration got messed
up, and clipped off some cortex, as in the attached capture. We
think it might be in the ACPC alignment step, as it has caused
some problems before. Could you next zip up the following files
so we can take a look, and upload them the same way:
Pipelines_ExampleData/C10/T1w/ACPCAlignment (the entire directory)
Pipelines_ExampleData/C10/T1w/T1w.nii.gz
Pipelines_ExampleData/C10/T1w/T1w_acpc.nii.gz
Tim
On Fri, Jan 8, 2016 at 6:15 AM, Barbara Kreilkamp
wrote:
They are in the file HCP_Boundig_Box_error
Thank you,
Best wishes,
Barbara
On Fri, Jan 8, 2016 at 12:12 PM, Barbara Kreilkamp
wrote:
Thank you very much for looking into it.
I have now uploaded the files.
Thank you,
Best wishes,
Barbara
On Wed, Jan 6, 2016 at 11:19 PM, Timothy Coalson
wrote:
After some brief internal discussion, we think it would be
fastest to figure out what went wrong if we had a look at the
files. To start with, can you zip up the following 3 files:
Pipelines_ExampleData/C10/T1w/Native/C10.L.white.native.surf.gii
Pipelines_ExampleData/C10/MNINonLinear/xfms/standard2acpc_dc.nii.gz
Pipelines_ExampleData/C10/T1w/T1w_acpc_dc_restore.nii.gz
Re: [HCP-Users] ERROR: surface exceeds the bounding box of the warpfield
It won’t create any biases, it just might help you get the acpc step to work on the two subjects it hasn’t. Peace, Matt. From: Barbara Kreilkamp mailto:bakk@googlemail.com>> Date: Friday, January 15, 2016 at 9:46 AM To: Matt Glasser mailto:glass...@wustl.edu>> Cc: "Van Essen, David" mailto:vanes...@wustl.edu>>, Timothy Coalson mailto:tsc...@mst.edu>>, "hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>" mailto:hcp-users@humanconnectome.org>> Subject: Re: [HCP-Users] ERROR: surface exceeds the bounding box of the warpfield Dear Matt, Thank you, I found the brain size parameter, but do you think it is okay to tweak this, when I leave it at the default value for all the other subjects (which ran through fine by the way, 58 participants were fine for the whole myelin pipeline, just 1 patient and 1 control failed in our dataset, potentially as you pointed out in the acpc-alignment step. Thank you, Best wishes, Barbara On 15/01/2016 03:08, Glasser, Matthew wrote: Maybe post your PreFreeSurfer pipeline launch variables. Peace, Matt. From: Barbara Kreilkamp mailto:bakk@googlemail.com>> Date: Thursday, January 14, 2016 at 6:11 AM To: Matt Glasser <<mailto:glass...@wustl.edu>glass...@wustl.edu<mailto:glass...@wustl.edu>> Cc: "Van Essen, David" mailto:vanes...@wustl.edu>>, Timothy Coalson mailto:tsc...@mst.edu>>, "<mailto:hcp-users@humanconnectome.org>hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>" mailto:hcp-users@humanconnectome.org>> Subject: Re: [HCP-Users] ERROR: surface exceeds the bounding box of the warpfield Dear Matt, David and Tim, Thanks for looking into it, I've got the 1mm templates with their correct paths, however I am unsure of how to test performance implementing these as "down sampled, and brain mask" as well as where to change the brain size parameter. Would you guide me on this please? Thank you, Best wishes, Barbara On Wed, Jan 13, 2016 at 11:07 AM, Glasser, Matthew mailto:glass...@wustl.edu>> wrote: Indeed sorry Barbara! Matt. From: David Van Essen mailto:vanes...@wustl.edu>> Date: Tuesday, January 12, 2016 at 11:27 PM To: Matt Glasser mailto:glass...@wustl.edu>> Cc: Timothy Coalson mailto:tsc...@mst.edu>>, Barbara Kreilkamp mailto:bakk@googlemail.com>>, "hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>" mailto:hcp-users@humanconnectome.org>> Subject: Re: [HCP-Users] ERROR: surface exceeds the bounding box of the warpfield Thanks for the suggestions, Matt, which are excellent even though accidentally addressed to the wrong gender - said your mentor, (s)heepishly. David :<) On Jan 12, 2016, at 10:23 PM, Glasser, Matthew <<mailto:glass...@wustl.edu>glass...@wustl.edu<mailto:glass...@wustl.edu>> wrote: Indeed the acpc registration is failing. He might check to be sure he is using the right templates (1mm, correct ones for original, down sampled, and brain mask). He could also try fiddling with the brain size parameter (trying values 10mm larger and smaller than 150mm). The acpc stage is most vulnerable to failure. If it works, usually everything else will after it. Matt. From: <<mailto:hcp-users-boun...@humanconnectome.org>hcp-users-boun...@humanconnectome.org<mailto:hcp-users-boun...@humanconnectome.org>> on behalf of Timothy Coalson <<mailto:tsc...@mst.edu>tsc...@mst.edu<mailto:tsc...@mst.edu>> Date: Friday, January 8, 2016 at 6:42 PM To: Barbara Kreilkamp <<mailto:bakk@googlemail.com>bakk@googlemail.com<mailto:bakk....@googlemail.com>> Cc: "<mailto:hcp-users@humanconnectome.org>hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>" <<mailto:hcp-users@humanconnectome.org>hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>> Subject: Re: [HCP-Users] ERROR: surface exceeds the bounding box of the warpfield Well, somewhere along the line, volume registration got messed up, and clipped off some cortex, as in the attached capture. We think it might be in the ACPC alignment step, as it has caused some problems before. Could you next zip up the following files so we can take a look, and upload them the same way: Pipelines_ExampleData/C10/T1w/ACPCAlignment (the entire directory) Pipelines_ExampleData/C10/T1w/T1w.nii.gz Pipelines_ExampleData/C10/T1w/T1w_acpc.nii.gz Tim On Fri, Jan 8, 2016 at 6:15 AM, Barbara Kreilkamp <<mailto:bakk@googlemail.com>bakk@googlemail.com<mailto:bakk@googlemail.com>> wrote: They are in the file HCP_Boundig_Box_error Thank you, Best wishes, Barbara On Fri, Jan 8, 2016 at 12:12 PM, Barbara Kreilkamp <<mailto:bakk@googlemail.com>bakk@g
Re: [HCP-Users] ERROR: surface exceeds the bounding box of the warpfield
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Dear Matt,
Thank you, I found the brain size parameter, but do you think it is okay
to tweak this, when I leave it at the default value for all the other
subjects (which ran through fine by the way, 58 participants were fine
for the whole myelin pipeline, just 1 patient and 1 control failed in
our dataset, potentially as you pointed out in the acpc-alignment step.
Thank you,
Best wishes,
Barbara
On 15/01/2016 03:08, Glasser, Matthew wrote:
Maybe post your PreFreeSurfer pipeline launch variables.
Peace,
Matt.
From: Barbara Kreilkamp <mailto:bakk@googlemail.com>>
Date: Thursday, January 14, 2016 at 6:11 AM
To: Matt Glasser mailto:glass...@wustl.edu>>
Cc: "Van Essen, David" <mailto:vanes...@wustl.edu>>, Timothy Coalson <mailto:tsc...@mst.edu>>, "hcp-users@humanconnectome.org
<mailto:hcp-users@humanconnectome.org>" <mailto:hcp-users@humanconnectome.org>>
Subject: Re: [HCP-Users] ERROR: surface exceeds the bounding box of
the warpfield
Dear Matt, David and Tim,
Thanks for looking into it, I've got the 1mm templates with their
correct paths, however I am unsure of how to test performance
implementing these as "down sampled, and brain mask" as well as where
to change the brain size parameter.
Would you guide me on this please?
Thank you,
Best wishes,
Barbara
On Wed, Jan 13, 2016 at 11:07 AM, Glasser, Matthew <mailto:glass...@wustl.edu>> wrote:
Indeed sorry Barbara!
Matt.
From: David Van Essen mailto:vanes...@wustl.edu>>
Date: Tuesday, January 12, 2016 at 11:27 PM
To: Matt Glasser mailto:glass...@wustl.edu>>
Cc: Timothy Coalson mailto:tsc...@mst.edu>>,
Barbara Kreilkamp mailto:bakk@googlemail.com>>, "hcp-users@humanconnectome.org
<mailto:hcp-users@humanconnectome.org>"
mailto:hcp-users@humanconnectome.org>>
Subject: Re: [HCP-Users] ERROR: surface exceeds the bounding box
of the warpfield
Thanks for the suggestions, Matt, which are excellent even though
accidentally addressed to the wrong gender - said your mentor,
(s)heepishly.
David :<)
On Jan 12, 2016, at 10:23 PM, Glasser, Matthew
mailto:glass...@wustl.edu>> wrote:
Indeed the acpc registration is failing. He might check to be
sure he is using the right templates (1mm, correct ones for
original, down sampled, and brain mask). He could also try
fiddling with the brain size parameter (trying values 10mm larger
and smaller than 150mm). The acpc stage is most vulnerable to
failure. If it works, usually everything else will after it.
Matt.
From: mailto:hcp-users-boun...@humanconnectome.org>> on behalf of
Timothy Coalson mailto:tsc...@mst.edu>>
Date: Friday, January 8, 2016 at 6:42 PM
To: Barbara Kreilkamp mailto:bakk....@googlemail.com>>
Cc: "hcp-users@humanconnectome.org
<mailto:hcp-users@humanconnectome.org>"
mailto:hcp-users@humanconnectome.org>>
Subject: Re: [HCP-Users] ERROR: surface exceeds the bounding box
of the warpfield
Well, somewhere along the line, volume registration got messed
up, and clipped off some cortex, as in the attached capture. We
think it might be in the ACPC alignment step, as it has caused
some problems before. Could you next zip up the following files
so we can take a look, and upload them the same way:
Pipelines_ExampleData/C10/T1w/ACPCAlignment (the entire directory)
Pipelines_ExampleData/C10/T1w/T1w.nii.gz
Pipelines_ExampleData/C10/T1w/T1w_acpc.nii.gz
Tim
On Fri, Jan 8, 2016 at 6:15 AM, Barbara Kreilkamp
mailto:bakk@googlemail.com>> wrote:
They are in the file HCP_Boundig_Box_error
Thank you,
Best wishes,
Barbara
On Fri, Jan 8, 2016 at 12:12 PM, Barbara Kreilkamp
mailto:bakk@googlemail.com>> wrote:
Thank you very much for looking into it.
I have now uploaded the files.
Thank you,
Best wishes,
Barbara
On Wed, Jan 6, 2016 at 11:19 PM, Timothy Coalson
mailto:tsc...@mst.edu>> wrote:
After some brief int
Re: [HCP-Users] ERROR: surface exceeds the bounding box of the warpfield
Maybe post your PreFreeSurfer pipeline launch variables. Peace, Matt. From: Barbara Kreilkamp mailto:bakk@googlemail.com>> Date: Thursday, January 14, 2016 at 6:11 AM To: Matt Glasser mailto:glass...@wustl.edu>> Cc: "Van Essen, David" mailto:vanes...@wustl.edu>>, Timothy Coalson mailto:tsc...@mst.edu>>, "hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>" mailto:hcp-users@humanconnectome.org>> Subject: Re: [HCP-Users] ERROR: surface exceeds the bounding box of the warpfield Dear Matt, David and Tim, Thanks for looking into it, I've got the 1mm templates with their correct paths, however I am unsure of how to test performance implementing these as "down sampled, and brain mask" as well as where to change the brain size parameter. Would you guide me on this please? Thank you, Best wishes, Barbara On Wed, Jan 13, 2016 at 11:07 AM, Glasser, Matthew mailto:glass...@wustl.edu>> wrote: Indeed sorry Barbara! Matt. From: David Van Essen mailto:vanes...@wustl.edu>> Date: Tuesday, January 12, 2016 at 11:27 PM To: Matt Glasser mailto:glass...@wustl.edu>> Cc: Timothy Coalson mailto:tsc...@mst.edu>>, Barbara Kreilkamp mailto:bakk@googlemail.com>>, "hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>" mailto:hcp-users@humanconnectome.org>> Subject: Re: [HCP-Users] ERROR: surface exceeds the bounding box of the warpfield Thanks for the suggestions, Matt, which are excellent even though accidentally addressed to the wrong gender - said your mentor, (s)heepishly. David :<) On Jan 12, 2016, at 10:23 PM, Glasser, Matthew mailto:glass...@wustl.edu>> wrote: Indeed the acpc registration is failing. He might check to be sure he is using the right templates (1mm, correct ones for original, down sampled, and brain mask). He could also try fiddling with the brain size parameter (trying values 10mm larger and smaller than 150mm). The acpc stage is most vulnerable to failure. If it works, usually everything else will after it. Matt. From: mailto:hcp-users-boun...@humanconnectome.org>> on behalf of Timothy Coalson mailto:tsc...@mst.edu>> Date: Friday, January 8, 2016 at 6:42 PM To: Barbara Kreilkamp mailto:bakk....@googlemail.com>> Cc: "hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>" mailto:hcp-users@humanconnectome.org>> Subject: Re: [HCP-Users] ERROR: surface exceeds the bounding box of the warpfield Well, somewhere along the line, volume registration got messed up, and clipped off some cortex, as in the attached capture. We think it might be in the ACPC alignment step, as it has caused some problems before. Could you next zip up the following files so we can take a look, and upload them the same way: Pipelines_ExampleData/C10/T1w/ACPCAlignment (the entire directory) Pipelines_ExampleData/C10/T1w/T1w.nii.gz Pipelines_ExampleData/C10/T1w/T1w_acpc.nii.gz Tim On Fri, Jan 8, 2016 at 6:15 AM, Barbara Kreilkamp mailto:bakk@googlemail.com>> wrote: They are in the file HCP_Boundig_Box_error Thank you, Best wishes, Barbara On Fri, Jan 8, 2016 at 12:12 PM, Barbara Kreilkamp mailto:bakk@googlemail.com>> wrote: Thank you very much for looking into it. I have now uploaded the files. Thank you, Best wishes, Barbara On Wed, Jan 6, 2016 at 11:19 PM, Timothy Coalson mailto:tsc...@mst.edu>> wrote: After some brief internal discussion, we think it would be fastest to figure out what went wrong if we had a look at the files. To start with, can you zip up the following 3 files: Pipelines_ExampleData/C10/T1w/Native/C10.L.white.native.surf.gii Pipelines_ExampleData/C10/MNINonLinear/xfms/standard2acpc_dc.nii.gz Pipelines_ExampleData/C10/T1w/T1w_acpc_dc_restore.nii.gz And upload them here: http://brainvis.wustl.edu/cgi-bin/upload.cgi Tim On Wed, Jan 6, 2016 at 4:04 PM, Timothy Coalson mailto:tsc...@mst.edu>> wrote: I'm not sure what could have gone wrong in the script, but as you may have guessed, that error means the input surface to -surface-apply-warpfield is too large for the specified warpfield volume, and thus some vertices would have undefined coordinates if it proceeded with the transformation. Tim On Wed, Jan 6, 2016 at 4:47 AM, Barbara Kreilkamp mailto:bakk@googlemail.com>> wrote: Dear HCP experts, Thank you for all your help so far. Unfortunately I am running into an error in PostFreeSurferPipelineBatch.sh I wonder if you could please help me solve this issue? Other participants with the same data have run without any issues, and the FreeSurferPipelineBatch.sh completed without any issues as well. Thank you, Best wishes, Barbara ./PostFreeSurferPipelineBatch.sh This script must be SOURCED to correctly setup the environment prior to running any of the other HCP scripts contained here C10
Re: [HCP-Users] ERROR: surface exceeds the bounding box of the warpfield
Dear Matt, David and Tim, Thanks for looking into it, I've got the 1mm templates with their correct paths, however I am unsure of how to test performance implementing these as "down sampled, and brain mask" as well as where to change the brain size parameter. Would you guide me on this please? Thank you, Best wishes, Barbara On Wed, Jan 13, 2016 at 11:07 AM, Glasser, Matthew wrote: > Indeed sorry Barbara! > > Matt. > > From: David Van Essen > Date: Tuesday, January 12, 2016 at 11:27 PM > To: Matt Glasser > Cc: Timothy Coalson , Barbara Kreilkamp < > bakk@googlemail.com>, "hcp-users@humanconnectome.org" < > hcp-users@humanconnectome.org> > > Subject: Re: [HCP-Users] ERROR: surface exceeds the bounding box of the > warpfield > > Thanks for the suggestions, Matt, which are excellent even though > accidentally addressed to the wrong gender - said your mentor, > (s)heepishly. > > David :<) > > On Jan 12, 2016, at 10:23 PM, Glasser, Matthew wrote: > > Indeed the acpc registration is failing. He might check to be sure he is > using the right templates (1mm, correct ones for original, down sampled, > and brain mask). He could also try fiddling with the brain size parameter > (trying values 10mm larger and smaller than 150mm). The acpc stage is most > vulnerable to failure. If it works, usually everything else will after it. > > Matt. > > From: on behalf of Timothy > Coalson > Date: Friday, January 8, 2016 at 6:42 PM > To: Barbara Kreilkamp > Cc: "hcp-users@humanconnectome.org" > Subject: Re: [HCP-Users] ERROR: surface exceeds the bounding box of the > warpfield > > Well, somewhere along the line, volume registration got messed up, and > clipped off some cortex, as in the attached capture. We think it might be > in the ACPC alignment step, as it has caused some problems before. Could > you next zip up the following files so we can take a look, and upload them > the same way: > > Pipelines_ExampleData/C10/T1w/ACPCAlignment (the entire directory) > Pipelines_ExampleData/C10/T1w/T1w.nii.gz > Pipelines_ExampleData/C10/T1w/T1w_acpc.nii.gz > > Tim > > > On Fri, Jan 8, 2016 at 6:15 AM, Barbara Kreilkamp > wrote: > >> They are in the file HCP_Boundig_Box_error >> Thank you, >> Best wishes, >> Barbara >> >> On Fri, Jan 8, 2016 at 12:12 PM, Barbara Kreilkamp < >> bakk@googlemail.com> wrote: >> >>> Thank you very much for looking into it. >>> I have now uploaded the files. >>> >>> Thank you, >>> Best wishes, >>> Barbara >>> >>> On Wed, Jan 6, 2016 at 11:19 PM, Timothy Coalson wrote: >>> >>>> After some brief internal discussion, we think it would be fastest to >>>> figure out what went wrong if we had a look at the files. To start with, >>>> can you zip up the following 3 files: >>>> >>>> Pipelines_ExampleData/C10/T1w/Native/C10.L.white.native.surf.gii >>>> Pipelines_ExampleData/C10/MNINonLinear/xfms/standard2acpc_dc.nii.gz >>>> Pipelines_ExampleData/C10/T1w/T1w_acpc_dc_restore.nii.gz >>>> >>>> And upload them here: >>>> >>>> http://brainvis.wustl.edu/cgi-bin/upload.cgi >>>> >>>> Tim >>>> >>>> >>>> On Wed, Jan 6, 2016 at 4:04 PM, Timothy Coalson wrote: >>>> >>>>> I'm not sure what could have gone wrong in the script, but as you may >>>>> have guessed, that error means the input surface to >>>>> -surface-apply-warpfield is too large for the specified warpfield volume, >>>>> and thus some vertices would have undefined coordinates if it proceeded >>>>> with the transformation. >>>>> >>>>> Tim >>>>> >>>>> >>>>> On Wed, Jan 6, 2016 at 4:47 AM, Barbara Kreilkamp < >>>>> bakk@googlemail.com> wrote: >>>>> >>>>>> Dear HCP experts, >>>>>> >>>>>> Thank you for all your help so far. >>>>>> Unfortunately I am running into an error in >>>>>> PostFreeSurferPipelineBatch.sh >>>>>> I wonder if you could please help me solve this issue? Other >>>>>> participants with the same data have run without any issues, and the >>>>>> FreeSurferPipelineBatch.sh completed without any issues as well. >>>>>> >>>>>> Thank you, >>>>>> Best wishes, >>>>>> Barbara >>>>>&
Re: [HCP-Users] ERROR: surface exceeds the bounding box of the warpfield
Indeed sorry Barbara! Matt. From: David Van Essen mailto:vanes...@wustl.edu>> Date: Tuesday, January 12, 2016 at 11:27 PM To: Matt Glasser mailto:glass...@wustl.edu>> Cc: Timothy Coalson mailto:tsc...@mst.edu>>, Barbara Kreilkamp mailto:bakk@googlemail.com>>, "hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>" mailto:hcp-users@humanconnectome.org>> Subject: Re: [HCP-Users] ERROR: surface exceeds the bounding box of the warpfield Thanks for the suggestions, Matt, which are excellent even though accidentally addressed to the wrong gender - said your mentor, (s)heepishly. David :<) On Jan 12, 2016, at 10:23 PM, Glasser, Matthew mailto:glass...@wustl.edu>> wrote: Indeed the acpc registration is failing. He might check to be sure he is using the right templates (1mm, correct ones for original, down sampled, and brain mask). He could also try fiddling with the brain size parameter (trying values 10mm larger and smaller than 150mm). The acpc stage is most vulnerable to failure. If it works, usually everything else will after it. Matt. From: mailto:hcp-users-boun...@humanconnectome.org>> on behalf of Timothy Coalson mailto:tsc...@mst.edu>> Date: Friday, January 8, 2016 at 6:42 PM To: Barbara Kreilkamp mailto:bakk@googlemail.com>> Cc: "hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>" mailto:hcp-users@humanconnectome.org>> Subject: Re: [HCP-Users] ERROR: surface exceeds the bounding box of the warpfield Well, somewhere along the line, volume registration got messed up, and clipped off some cortex, as in the attached capture. We think it might be in the ACPC alignment step, as it has caused some problems before. Could you next zip up the following files so we can take a look, and upload them the same way: Pipelines_ExampleData/C10/T1w/ACPCAlignment (the entire directory) Pipelines_ExampleData/C10/T1w/T1w.nii.gz Pipelines_ExampleData/C10/T1w/T1w_acpc.nii.gz Tim On Fri, Jan 8, 2016 at 6:15 AM, Barbara Kreilkamp mailto:bakk@googlemail.com>> wrote: They are in the file HCP_Boundig_Box_error Thank you, Best wishes, Barbara On Fri, Jan 8, 2016 at 12:12 PM, Barbara Kreilkamp mailto:bakk@googlemail.com>> wrote: Thank you very much for looking into it. I have now uploaded the files. Thank you, Best wishes, Barbara On Wed, Jan 6, 2016 at 11:19 PM, Timothy Coalson mailto:tsc...@mst.edu>> wrote: After some brief internal discussion, we think it would be fastest to figure out what went wrong if we had a look at the files. To start with, can you zip up the following 3 files: Pipelines_ExampleData/C10/T1w/Native/C10.L.white.native.surf.gii Pipelines_ExampleData/C10/MNINonLinear/xfms/standard2acpc_dc.nii.gz Pipelines_ExampleData/C10/T1w/T1w_acpc_dc_restore.nii.gz And upload them here: http://brainvis.wustl.edu/cgi-bin/upload.cgi Tim On Wed, Jan 6, 2016 at 4:04 PM, Timothy Coalson mailto:tsc...@mst.edu>> wrote: I'm not sure what could have gone wrong in the script, but as you may have guessed, that error means the input surface to -surface-apply-warpfield is too large for the specified warpfield volume, and thus some vertices would have undefined coordinates if it proceeded with the transformation. Tim On Wed, Jan 6, 2016 at 4:47 AM, Barbara Kreilkamp mailto:bakk@googlemail.com>> wrote: Dear HCP experts, Thank you for all your help so far. Unfortunately I am running into an error in PostFreeSurferPipelineBatch.sh I wonder if you could please help me solve this issue? Other participants with the same data have run without any issues, and the FreeSurferPipelineBatch.sh completed without any issues as well. Thank you, Best wishes, Barbara ./PostFreeSurferPipelineBatch.sh This script must be SOURCED to correctly setup the environment prior to running any of the other HCP scripts contained here C10 About to use fsl_sub to queue or run /Users/projects/Pipelines/PostFreeSurfer/PostFreeSurferPipeline.sh WARNING: name collision in input name 'CTX-LH-UNKNOWN', changing one to 'CTX-LH-UNKNOWN_1' WARNING: name collision in input name 'CTX-RH-UNKNOWN', changing one to 'CTX-RH-UNKNOWN_1' WARNING: name collision in input name 'WM-LH-UNKNOWN', changing one to 'WM-LH-UNKNOWN_1' WARNING: name collision in input name 'WM-RH-UNKNOWN', changing one to 'WM-RH-UNKNOWN_1' WARNING: name collision in input name 'CTX-LH-UNKNOWN', changing one to 'CTX-LH-UNKNOWN_1' WARNING: name collision in input name 'CTX-RH-UNKNOWN', changing one to 'CTX-RH-UNKNOWN_1' WARNING: name collision in input name 'WM-LH-UNKNOWN', changing one to 'WM-LH-UNKNOWN_1' WARNING: name collision in input name 'WM-RH-UNKNOWN', changing one to 'WM-RH-UNKNOWN_1'
Re: [HCP-Users] ERROR: surface exceeds the bounding box of the warpfield
Thanks for the suggestions, Matt, which are excellent even though accidentally addressed to the wrong gender - said your mentor, (s)heepishly. David :<) > On Jan 12, 2016, at 10:23 PM, Glasser, Matthew wrote: > > Indeed the acpc registration is failing. He might check to be sure he is > using the right templates (1mm, correct ones for original, down sampled, and > brain mask). He could also try fiddling with the brain size parameter > (trying values 10mm larger and smaller than 150mm). The acpc stage is most > vulnerable to failure. If it works, usually everything else will after it. > > Matt. > > From: <mailto:hcp-users-boun...@humanconnectome.org>> on behalf of Timothy Coalson > mailto:tsc...@mst.edu>> > Date: Friday, January 8, 2016 at 6:42 PM > To: Barbara Kreilkamp <mailto:bakk@googlemail.com>> > Cc: "hcp-users@humanconnectome.org <mailto:hcp-users@humanconnectome.org>" > mailto:hcp-users@humanconnectome.org>> > Subject: Re: [HCP-Users] ERROR: surface exceeds the bounding box of the > warpfield > > Well, somewhere along the line, volume registration got messed up, and > clipped off some cortex, as in the attached capture. We think it might be in > the ACPC alignment step, as it has caused some problems before. Could you > next zip up the following files so we can take a look, and upload them the > same way: > > Pipelines_ExampleData/C10/T1w/ACPCAlignment (the entire directory) > Pipelines_ExampleData/C10/T1w/T1w.nii.gz > Pipelines_ExampleData/C10/T1w/T1w_acpc.nii.gz > > Tim > > > On Fri, Jan 8, 2016 at 6:15 AM, Barbara Kreilkamp <mailto:bakk@googlemail.com>> wrote: >> They are in the file HCP_Boundig_Box_error >> Thank you, >> Best wishes, >> Barbara >> >> On Fri, Jan 8, 2016 at 12:12 PM, Barbara Kreilkamp > <mailto:bakk@googlemail.com>> wrote: >>> Thank you very much for looking into it. >>> I have now uploaded the files. >>> >>> Thank you, >>> Best wishes, >>> Barbara >>> >>> On Wed, Jan 6, 2016 at 11:19 PM, Timothy Coalson >> <mailto:tsc...@mst.edu>> wrote: >>>> After some brief internal discussion, we think it would be fastest to >>>> figure out what went wrong if we had a look at the files. To start with, >>>> can you zip up the following 3 files: >>>> >>>> Pipelines_ExampleData/C10/T1w/Native/C10.L.white.native.surf.gii >>>> Pipelines_ExampleData/C10/MNINonLinear/xfms/standard2acpc_dc.nii.gz >>>> Pipelines_ExampleData/C10/T1w/T1w_acpc_dc_restore.nii.gz >>>> >>>> And upload them here: >>>> >>>> http://brainvis.wustl.edu/cgi-bin/upload.cgi >>>> <http://brainvis.wustl.edu/cgi-bin/upload.cgi> >>>> >>>> Tim >>>> >>>> >>>> On Wed, Jan 6, 2016 at 4:04 PM, Timothy Coalson >>> <mailto:tsc...@mst.edu>> wrote: >>>>> I'm not sure what could have gone wrong in the script, but as you may >>>>> have guessed, that error means the input surface to >>>>> -surface-apply-warpfield is too large for the specified warpfield volume, >>>>> and thus some vertices would have undefined coordinates if it proceeded >>>>> with the transformation. >>>>> >>>>> Tim >>>>> >>>>> >>>>> On Wed, Jan 6, 2016 at 4:47 AM, Barbara Kreilkamp >>>>> mailto:bakk@googlemail.com>> wrote: >>>>>> Dear HCP experts, >>>>>> >>>>>> Thank you for all your help so far. >>>>>> Unfortunately I am running into an error in >>>>>> PostFreeSurferPipelineBatch.sh >>>>>> I wonder if you could please help me solve this issue? Other >>>>>> participants with the same data have run without any issues, and the >>>>>> FreeSurferPipelineBatch.sh completed without any issues as well. >>>>>> >>>>>> Thank you, >>>>>> Best wishes, >>>>>> Barbara >>>>>> >>>>>> ./PostFreeSurferPipelineBatch.sh >>>>>> This script must be SOURCED to correctly setup the environment prior to >>>>>> running any of the other HCP scripts contained here >>>>>> >>>>>> C10 >>>>>> About to use fsl_sub to queue or run >>>>>> /Users/projects/Pipelines/PostFreeSurfer/PostFreeSurferPipelin
Re: [HCP-Users] ERROR: surface exceeds the bounding box of the warpfield
Indeed the acpc registration is failing. He might check to be sure he is using the right templates (1mm, correct ones for original, down sampled, and brain mask). He could also try fiddling with the brain size parameter (trying values 10mm larger and smaller than 150mm). The acpc stage is most vulnerable to failure. If it works, usually everything else will after it. Matt. From: mailto:hcp-users-boun...@humanconnectome.org>> on behalf of Timothy Coalson mailto:tsc...@mst.edu>> Date: Friday, January 8, 2016 at 6:42 PM To: Barbara Kreilkamp mailto:bakk@googlemail.com>> Cc: "hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>" mailto:hcp-users@humanconnectome.org>> Subject: Re: [HCP-Users] ERROR: surface exceeds the bounding box of the warpfield Well, somewhere along the line, volume registration got messed up, and clipped off some cortex, as in the attached capture. We think it might be in the ACPC alignment step, as it has caused some problems before. Could you next zip up the following files so we can take a look, and upload them the same way: Pipelines_ExampleData/C10/T1w/ACPCAlignment (the entire directory) Pipelines_ExampleData/C10/T1w/T1w.nii.gz Pipelines_ExampleData/C10/T1w/T1w_acpc.nii.gz Tim On Fri, Jan 8, 2016 at 6:15 AM, Barbara Kreilkamp mailto:bakk@googlemail.com>> wrote: They are in the file HCP_Boundig_Box_error Thank you, Best wishes, Barbara On Fri, Jan 8, 2016 at 12:12 PM, Barbara Kreilkamp mailto:bakk@googlemail.com>> wrote: Thank you very much for looking into it. I have now uploaded the files. Thank you, Best wishes, Barbara On Wed, Jan 6, 2016 at 11:19 PM, Timothy Coalson mailto:tsc...@mst.edu>> wrote: After some brief internal discussion, we think it would be fastest to figure out what went wrong if we had a look at the files. To start with, can you zip up the following 3 files: Pipelines_ExampleData/C10/T1w/Native/C10.L.white.native.surf.gii Pipelines_ExampleData/C10/MNINonLinear/xfms/standard2acpc_dc.nii.gz Pipelines_ExampleData/C10/T1w/T1w_acpc_dc_restore.nii.gz And upload them here: http://brainvis.wustl.edu/cgi-bin/upload.cgi Tim On Wed, Jan 6, 2016 at 4:04 PM, Timothy Coalson mailto:tsc...@mst.edu>> wrote: I'm not sure what could have gone wrong in the script, but as you may have guessed, that error means the input surface to -surface-apply-warpfield is too large for the specified warpfield volume, and thus some vertices would have undefined coordinates if it proceeded with the transformation. Tim On Wed, Jan 6, 2016 at 4:47 AM, Barbara Kreilkamp mailto:bakk@googlemail.com>> wrote: Dear HCP experts, Thank you for all your help so far. Unfortunately I am running into an error in PostFreeSurferPipelineBatch.sh I wonder if you could please help me solve this issue? Other participants with the same data have run without any issues, and the FreeSurferPipelineBatch.sh completed without any issues as well. Thank you, Best wishes, Barbara ./PostFreeSurferPipelineBatch.sh This script must be SOURCED to correctly setup the environment prior to running any of the other HCP scripts contained here C10 About to use fsl_sub to queue or run /Users/projects/Pipelines/PostFreeSurfer/PostFreeSurferPipeline.sh WARNING: name collision in input name 'CTX-LH-UNKNOWN', changing one to 'CTX-LH-UNKNOWN_1' WARNING: name collision in input name 'CTX-RH-UNKNOWN', changing one to 'CTX-RH-UNKNOWN_1' WARNING: name collision in input name 'WM-LH-UNKNOWN', changing one to 'WM-LH-UNKNOWN_1' WARNING: name collision in input name 'WM-RH-UNKNOWN', changing one to 'WM-RH-UNKNOWN_1' WARNING: name collision in input name 'CTX-LH-UNKNOWN', changing one to 'CTX-LH-UNKNOWN_1' WARNING: name collision in input name 'CTX-RH-UNKNOWN', changing one to 'CTX-RH-UNKNOWN_1' WARNING: name collision in input name 'WM-LH-UNKNOWN', changing one to 'WM-LH-UNKNOWN_1' WARNING: name collision in input name 'WM-RH-UNKNOWN', changing one to 'WM-RH-UNKNOWN_1' WARNING: name collision in input name 'CTX-LH-UNKNOWN', changing one to 'CTX-LH-UNKNOWN_1' WARNING: name collision in input name 'CTX-RH-UNKNOWN', changing one to 'CTX-RH-UNKNOWN_1' WARNING: name collision in input name 'WM-LH-UNKNOWN', changing one to 'WM-LH-UNKNOWN_1' WARNING: name collision in input name 'WM-RH-UNKNOWN', changing one to 'WM-RH-UNKNOWN_1' WARNING: name collision in input name 'CTX-LH-UNKNOWN', changing one to 'CTX-LH-UNKNOWN_1' WARNING: name collision in input name 'CTX-RH-UNKNOWN', changing one to 'CTX-RH-UNKNOWN_1' WARNING: name collision in input name 'WM-LH-UNK
Re: [HCP-Users] ERROR: surface exceeds the bounding box of the warpfield
Dear Tim, Thank you very much, I have uploaded HCP_bounding_box_error2.zip to the link you sent me. Really do appreciate your help on this, that's great, thanks! Best wishes, Barbara On Sat, Jan 9, 2016 at 12:42 AM, Timothy Coalson wrote: > Well, somewhere along the line, volume registration got messed up, and > clipped off some cortex, as in the attached capture. We think it might be > in the ACPC alignment step, as it has caused some problems before. Could > you next zip up the following files so we can take a look, and upload them > the same way: > > Pipelines_ExampleData/C10/T1w/ACPCAlignment (the entire directory) > Pipelines_ExampleData/C10/T1w/T1w.nii.gz > Pipelines_ExampleData/C10/T1w/T1w_acpc.nii.gz > > Tim > > > On Fri, Jan 8, 2016 at 6:15 AM, Barbara Kreilkamp > wrote: > >> They are in the file HCP_Boundig_Box_error >> Thank you, >> Best wishes, >> Barbara >> >> On Fri, Jan 8, 2016 at 12:12 PM, Barbara Kreilkamp < >> bakk@googlemail.com> wrote: >> >>> Thank you very much for looking into it. >>> I have now uploaded the files. >>> >>> Thank you, >>> Best wishes, >>> Barbara >>> >>> On Wed, Jan 6, 2016 at 11:19 PM, Timothy Coalson wrote: >>> After some brief internal discussion, we think it would be fastest to figure out what went wrong if we had a look at the files. To start with, can you zip up the following 3 files: Pipelines_ExampleData/C10/T1w/Native/C10.L.white.native.surf.gii Pipelines_ExampleData/C10/MNINonLinear/xfms/standard2acpc_dc.nii.gz Pipelines_ExampleData/C10/T1w/T1w_acpc_dc_restore.nii.gz And upload them here: http://brainvis.wustl.edu/cgi-bin/upload.cgi Tim On Wed, Jan 6, 2016 at 4:04 PM, Timothy Coalson wrote: > I'm not sure what could have gone wrong in the script, but as you may > have guessed, that error means the input surface to > -surface-apply-warpfield is too large for the specified warpfield volume, > and thus some vertices would have undefined coordinates if it proceeded > with the transformation. > > Tim > > > On Wed, Jan 6, 2016 at 4:47 AM, Barbara Kreilkamp < > bakk@googlemail.com> wrote: > >> Dear HCP experts, >> >> Thank you for all your help so far. >> Unfortunately I am running into an error in >> PostFreeSurferPipelineBatch.sh >> I wonder if you could please help me solve this issue? Other >> participants with the same data have run without any issues, and the >> FreeSurferPipelineBatch.sh completed without any issues as well. >> >> Thank you, >> Best wishes, >> Barbara >> >> ./PostFreeSurferPipelineBatch.sh >> >> This script must be SOURCED to correctly setup the environment prior >> to running any of the other HCP scripts contained here >> >> >> C10 >> >> About to use fsl_sub to queue or run >> /Users/projects/Pipelines/PostFreeSurfer/PostFreeSurferPipeline.sh >> >> >> WARNING: name collision in input name 'CTX-LH-UNKNOWN', changing one >> to 'CTX-LH-UNKNOWN_1' >> >> >> >> WARNING: name collision in input name 'CTX-RH-UNKNOWN', changing one >> to 'CTX-RH-UNKNOWN_1' >> >> >> >> WARNING: name collision in input name 'WM-LH-UNKNOWN', changing one >> to 'WM-LH-UNKNOWN_1' >> >> >> >> WARNING: name collision in input name 'WM-RH-UNKNOWN', changing one >> to 'WM-RH-UNKNOWN_1' >> >> >> >> WARNING: name collision in input name 'CTX-LH-UNKNOWN', changing one >> to 'CTX-LH-UNKNOWN_1' >> >> >> >> WARNING: name collision in input name 'CTX-RH-UNKNOWN', changing one >> to 'CTX-RH-UNKNOWN_1' >> >> >> >> WARNING: name collision in input name 'WM-LH-UNKNOWN', changing one >> to 'WM-LH-UNKNOWN_1' >> >> >> >> WARNING: name collision in input name 'WM-RH-UNKNOWN', changing one >> to 'WM-RH-UNKNOWN_1' >> >> >> >> WARNING: name collision in input name 'CTX-LH-UNKNOWN', changing one >> to 'CTX-LH-UNKNOWN_1' >> >> >> >> WARNING: name collision in input name 'CTX-RH-UNKNOWN', changing one >> to 'CTX-RH-UNKNOWN_1' >> >> >> >> WARNING: name collision in input name 'WM-LH-UNKNOWN', changing one >> to 'WM-LH-UNKNOWN_1' >> >> >> >> WARNING: name collision in input name 'WM-RH-UNKNOWN', changing one >> to 'WM-RH-UNKNOWN_1' >> >> >> >> WARNING: name collision in input name 'CTX-LH-UNKNOWN', changing one >> to 'CTX-LH-UNKNOWN_1' >> >> >> >> WARNING: name collision in input name 'CTX-RH-UNKNOWN', changing one >> to 'CTX-RH-UNKNOWN_1' >> >> >> >> WARNING: name collision in input name 'WM-LH-UNKNOWN', changing one >> to 'WM-LH-UNKNOWN_1' >> >> >> >> WARNING: name collision in input name 'WM-RH-UNKNOWN', changing one >> to 'WM-RH-UNKNOWN_1' >
Re: [HCP-Users] ERROR: surface exceeds the bounding box of the warpfield
They are in the file HCP_Boundig_Box_error Thank you, Best wishes, Barbara On Fri, Jan 8, 2016 at 12:12 PM, Barbara Kreilkamp wrote: > Thank you very much for looking into it. > I have now uploaded the files. > > Thank you, > Best wishes, > Barbara > > On Wed, Jan 6, 2016 at 11:19 PM, Timothy Coalson wrote: > >> After some brief internal discussion, we think it would be fastest to >> figure out what went wrong if we had a look at the files. To start with, >> can you zip up the following 3 files: >> >> Pipelines_ExampleData/C10/T1w/Native/C10.L.white.native.surf.gii >> Pipelines_ExampleData/C10/MNINonLinear/xfms/standard2acpc_dc.nii.gz >> Pipelines_ExampleData/C10/T1w/T1w_acpc_dc_restore.nii.gz >> >> And upload them here: >> >> http://brainvis.wustl.edu/cgi-bin/upload.cgi >> >> Tim >> >> >> On Wed, Jan 6, 2016 at 4:04 PM, Timothy Coalson wrote: >> >>> I'm not sure what could have gone wrong in the script, but as you may >>> have guessed, that error means the input surface to >>> -surface-apply-warpfield is too large for the specified warpfield volume, >>> and thus some vertices would have undefined coordinates if it proceeded >>> with the transformation. >>> >>> Tim >>> >>> >>> On Wed, Jan 6, 2016 at 4:47 AM, Barbara Kreilkamp < >>> bakk@googlemail.com> wrote: >>> Dear HCP experts, Thank you for all your help so far. Unfortunately I am running into an error in PostFreeSurferPipelineBatch.sh I wonder if you could please help me solve this issue? Other participants with the same data have run without any issues, and the FreeSurferPipelineBatch.sh completed without any issues as well. Thank you, Best wishes, Barbara ./PostFreeSurferPipelineBatch.sh This script must be SOURCED to correctly setup the environment prior to running any of the other HCP scripts contained here C10 About to use fsl_sub to queue or run /Users/projects/Pipelines/PostFreeSurfer/PostFreeSurferPipeline.sh WARNING: name collision in input name 'CTX-LH-UNKNOWN', changing one to 'CTX-LH-UNKNOWN_1' WARNING: name collision in input name 'CTX-RH-UNKNOWN', changing one to 'CTX-RH-UNKNOWN_1' WARNING: name collision in input name 'WM-LH-UNKNOWN', changing one to 'WM-LH-UNKNOWN_1' WARNING: name collision in input name 'WM-RH-UNKNOWN', changing one to 'WM-RH-UNKNOWN_1' WARNING: name collision in input name 'CTX-LH-UNKNOWN', changing one to 'CTX-LH-UNKNOWN_1' WARNING: name collision in input name 'CTX-RH-UNKNOWN', changing one to 'CTX-RH-UNKNOWN_1' WARNING: name collision in input name 'WM-LH-UNKNOWN', changing one to 'WM-LH-UNKNOWN_1' WARNING: name collision in input name 'WM-RH-UNKNOWN', changing one to 'WM-RH-UNKNOWN_1' WARNING: name collision in input name 'CTX-LH-UNKNOWN', changing one to 'CTX-LH-UNKNOWN_1' WARNING: name collision in input name 'CTX-RH-UNKNOWN', changing one to 'CTX-RH-UNKNOWN_1' WARNING: name collision in input name 'WM-LH-UNKNOWN', changing one to 'WM-LH-UNKNOWN_1' WARNING: name collision in input name 'WM-RH-UNKNOWN', changing one to 'WM-RH-UNKNOWN_1' WARNING: name collision in input name 'CTX-LH-UNKNOWN', changing one to 'CTX-LH-UNKNOWN_1' WARNING: name collision in input name 'CTX-RH-UNKNOWN', changing one to 'CTX-RH-UNKNOWN_1' WARNING: name collision in input name 'WM-LH-UNKNOWN', changing one to 'WM-LH-UNKNOWN_1' WARNING: name collision in input name 'WM-RH-UNKNOWN', changing one to 'WM-RH-UNKNOWN_1' WARNING: name collision in input name 'CTX-LH-UNKNOWN', changing one to 'CTX-LH-UNKNOWN_1' WARNING: name collision in input name 'CTX-RH-UNKNOWN', changing one to 'CTX-RH-UNKNOWN_1' WARNING: name collision in input name 'WM-LH-UNKNOWN', changing one to 'WM-LH-UNKNOWN_1' WARNING: name collision in input name 'WM-RH-UNKNOWN', changing one to 'WM-RH-UNKNOWN_1' WARNING: name collision in input name 'CTX-LH-UNKNOWN', changing one to 'CTX-LH-UNKNOWN_1' WARNING: name collision in input name 'CTX-RH-UNKNOWN', changing one to 'CTX-RH-UNKNOWN_1' WARNING: name collision in input name 'WM-LH-UNKNOWN', changing one to 'WM-LH-UNKNOWN_1' WARNING: name collision in input name 'WM-RH-UNKNOWN', changing one to 'WM-RH-UNKNOWN_1' WARNING: name collision in input name 'CTX-LH-UNKNOWN', changing one to 'CTX-LH-UNKNOWN_1' WARNING: name collision in input name 'CTX-RH-UNKNOWN', changing one to '
Re: [HCP-Users] ERROR: surface exceeds the bounding box of the warpfield
Thank you very much for looking into it. I have now uploaded the files. Thank you, Best wishes, Barbara On Wed, Jan 6, 2016 at 11:19 PM, Timothy Coalson wrote: > After some brief internal discussion, we think it would be fastest to > figure out what went wrong if we had a look at the files. To start with, > can you zip up the following 3 files: > > Pipelines_ExampleData/C10/T1w/Native/C10.L.white.native.surf.gii > Pipelines_ExampleData/C10/MNINonLinear/xfms/standard2acpc_dc.nii.gz > Pipelines_ExampleData/C10/T1w/T1w_acpc_dc_restore.nii.gz > > And upload them here: > > http://brainvis.wustl.edu/cgi-bin/upload.cgi > > Tim > > > On Wed, Jan 6, 2016 at 4:04 PM, Timothy Coalson wrote: > >> I'm not sure what could have gone wrong in the script, but as you may >> have guessed, that error means the input surface to >> -surface-apply-warpfield is too large for the specified warpfield volume, >> and thus some vertices would have undefined coordinates if it proceeded >> with the transformation. >> >> Tim >> >> >> On Wed, Jan 6, 2016 at 4:47 AM, Barbara Kreilkamp < >> bakk@googlemail.com> wrote: >> >>> Dear HCP experts, >>> >>> Thank you for all your help so far. >>> Unfortunately I am running into an error in >>> PostFreeSurferPipelineBatch.sh >>> I wonder if you could please help me solve this issue? Other >>> participants with the same data have run without any issues, and the >>> FreeSurferPipelineBatch.sh completed without any issues as well. >>> >>> Thank you, >>> Best wishes, >>> Barbara >>> >>> ./PostFreeSurferPipelineBatch.sh >>> >>> This script must be SOURCED to correctly setup the environment prior to >>> running any of the other HCP scripts contained here >>> >>> >>> C10 >>> >>> About to use fsl_sub to queue or run >>> /Users/projects/Pipelines/PostFreeSurfer/PostFreeSurferPipeline.sh >>> >>> >>> WARNING: name collision in input name 'CTX-LH-UNKNOWN', changing one to >>> 'CTX-LH-UNKNOWN_1' >>> >>> >>> >>> WARNING: name collision in input name 'CTX-RH-UNKNOWN', changing one to >>> 'CTX-RH-UNKNOWN_1' >>> >>> >>> >>> WARNING: name collision in input name 'WM-LH-UNKNOWN', changing one to >>> 'WM-LH-UNKNOWN_1' >>> >>> >>> >>> WARNING: name collision in input name 'WM-RH-UNKNOWN', changing one to >>> 'WM-RH-UNKNOWN_1' >>> >>> >>> >>> WARNING: name collision in input name 'CTX-LH-UNKNOWN', changing one to >>> 'CTX-LH-UNKNOWN_1' >>> >>> >>> >>> WARNING: name collision in input name 'CTX-RH-UNKNOWN', changing one to >>> 'CTX-RH-UNKNOWN_1' >>> >>> >>> >>> WARNING: name collision in input name 'WM-LH-UNKNOWN', changing one to >>> 'WM-LH-UNKNOWN_1' >>> >>> >>> >>> WARNING: name collision in input name 'WM-RH-UNKNOWN', changing one to >>> 'WM-RH-UNKNOWN_1' >>> >>> >>> >>> WARNING: name collision in input name 'CTX-LH-UNKNOWN', changing one to >>> 'CTX-LH-UNKNOWN_1' >>> >>> >>> >>> WARNING: name collision in input name 'CTX-RH-UNKNOWN', changing one to >>> 'CTX-RH-UNKNOWN_1' >>> >>> >>> >>> WARNING: name collision in input name 'WM-LH-UNKNOWN', changing one to >>> 'WM-LH-UNKNOWN_1' >>> >>> >>> >>> WARNING: name collision in input name 'WM-RH-UNKNOWN', changing one to >>> 'WM-RH-UNKNOWN_1' >>> >>> >>> >>> WARNING: name collision in input name 'CTX-LH-UNKNOWN', changing one to >>> 'CTX-LH-UNKNOWN_1' >>> >>> >>> >>> WARNING: name collision in input name 'CTX-RH-UNKNOWN', changing one to >>> 'CTX-RH-UNKNOWN_1' >>> >>> >>> >>> WARNING: name collision in input name 'WM-LH-UNKNOWN', changing one to >>> 'WM-LH-UNKNOWN_1' >>> >>> >>> >>> WARNING: name collision in input name 'WM-RH-UNKNOWN', changing one to >>> 'WM-RH-UNKNOWN_1' >>> >>> >>> >>> WARNING: name collision in input name 'CTX-LH-UNKNOWN', changing one to >>> 'CTX-LH-UNKNOWN_1' >>> >>> >>> >>> WARNING: name collision in input name 'CTX-RH-UNKNOWN', changing one to >>> 'CTX-RH-UNKNOWN_1' >>> >>> >>> >>> WARNING: name collision in input name 'WM-LH-UNKNOWN', changing one to >>> 'WM-LH-UNKNOWN_1' >>> >>> >>> >>> WARNING: name collision in input name 'WM-RH-UNKNOWN', changing one to >>> 'WM-RH-UNKNOWN_1' >>> >>> >>> >>> WARNING: name collision in input name 'CTX-LH-UNKNOWN', changing one to >>> 'CTX-LH-UNKNOWN_1' >>> >>> >>> >>> WARNING: name collision in input name 'CTX-RH-UNKNOWN', changing one to >>> 'CTX-RH-UNKNOWN_1' >>> >>> >>> >>> WARNING: name collision in input name 'WM-LH-UNKNOWN', changing one to >>> 'WM-LH-UNKNOWN_1' >>> >>> >>> >>> WARNING: name collision in input name 'WM-RH-UNKNOWN', changing one to >>> 'WM-RH-UNKNOWN_1' >>> >>> >>> >>> WARNING: name collision in input name 'CTX-LH-UNKNOWN', changing one to >>> 'CTX-LH-UNKNOWN_1' >>> >>> >>> >>> WARNING: name collision in input name 'CTX-RH-UNKNOWN', changing one to >>> 'CTX-RH-UNKNOWN_1' >>> >>> >>> >>> WARNING: name collision in input name 'WM-LH-UNKNOWN', changing one to >>> 'WM-LH-UNKNOWN_1' >>> >>> >>> >>> WARNING: name collision in input name 'WM-RH-UNKNOWN', changing one to >>> 'WM-RH-UNKNOWN_1' >>> >>> >>> >>> WARNING: name collision in input name 'CTX-LH-UNKNOWN', changing one to >>> 'CTX
Re: [HCP-Users] ERROR: surface exceeds the bounding box of the warpfield
After some brief internal discussion, we think it would be fastest to figure out what went wrong if we had a look at the files. To start with, can you zip up the following 3 files: Pipelines_ExampleData/C10/T1w/Native/C10.L.white.native.surf.gii Pipelines_ExampleData/C10/MNINonLinear/xfms/standard2acpc_dc.nii.gz Pipelines_ExampleData/C10/T1w/T1w_acpc_dc_restore.nii.gz And upload them here: http://brainvis.wustl.edu/cgi-bin/upload.cgi Tim On Wed, Jan 6, 2016 at 4:04 PM, Timothy Coalson wrote: > I'm not sure what could have gone wrong in the script, but as you may have > guessed, that error means the input surface to -surface-apply-warpfield is > too large for the specified warpfield volume, and thus some vertices would > have undefined coordinates if it proceeded with the transformation. > > Tim > > > On Wed, Jan 6, 2016 at 4:47 AM, Barbara Kreilkamp > wrote: > >> Dear HCP experts, >> >> Thank you for all your help so far. >> Unfortunately I am running into an error in PostFreeSurferPipelineBatch.sh >> I wonder if you could please help me solve this issue? Other participants >> with the same data have run without any issues, and the >> FreeSurferPipelineBatch.sh completed without any issues as well. >> >> Thank you, >> Best wishes, >> Barbara >> >> ./PostFreeSurferPipelineBatch.sh >> >> This script must be SOURCED to correctly setup the environment prior to >> running any of the other HCP scripts contained here >> >> >> C10 >> >> About to use fsl_sub to queue or run >> /Users/projects/Pipelines/PostFreeSurfer/PostFreeSurferPipeline.sh >> >> >> WARNING: name collision in input name 'CTX-LH-UNKNOWN', changing one to >> 'CTX-LH-UNKNOWN_1' >> >> >> >> WARNING: name collision in input name 'CTX-RH-UNKNOWN', changing one to >> 'CTX-RH-UNKNOWN_1' >> >> >> >> WARNING: name collision in input name 'WM-LH-UNKNOWN', changing one to >> 'WM-LH-UNKNOWN_1' >> >> >> >> WARNING: name collision in input name 'WM-RH-UNKNOWN', changing one to >> 'WM-RH-UNKNOWN_1' >> >> >> >> WARNING: name collision in input name 'CTX-LH-UNKNOWN', changing one to >> 'CTX-LH-UNKNOWN_1' >> >> >> >> WARNING: name collision in input name 'CTX-RH-UNKNOWN', changing one to >> 'CTX-RH-UNKNOWN_1' >> >> >> >> WARNING: name collision in input name 'WM-LH-UNKNOWN', changing one to >> 'WM-LH-UNKNOWN_1' >> >> >> >> WARNING: name collision in input name 'WM-RH-UNKNOWN', changing one to >> 'WM-RH-UNKNOWN_1' >> >> >> >> WARNING: name collision in input name 'CTX-LH-UNKNOWN', changing one to >> 'CTX-LH-UNKNOWN_1' >> >> >> >> WARNING: name collision in input name 'CTX-RH-UNKNOWN', changing one to >> 'CTX-RH-UNKNOWN_1' >> >> >> >> WARNING: name collision in input name 'WM-LH-UNKNOWN', changing one to >> 'WM-LH-UNKNOWN_1' >> >> >> >> WARNING: name collision in input name 'WM-RH-UNKNOWN', changing one to >> 'WM-RH-UNKNOWN_1' >> >> >> >> WARNING: name collision in input name 'CTX-LH-UNKNOWN', changing one to >> 'CTX-LH-UNKNOWN_1' >> >> >> >> WARNING: name collision in input name 'CTX-RH-UNKNOWN', changing one to >> 'CTX-RH-UNKNOWN_1' >> >> >> >> WARNING: name collision in input name 'WM-LH-UNKNOWN', changing one to >> 'WM-LH-UNKNOWN_1' >> >> >> >> WARNING: name collision in input name 'WM-RH-UNKNOWN', changing one to >> 'WM-RH-UNKNOWN_1' >> >> >> >> WARNING: name collision in input name 'CTX-LH-UNKNOWN', changing one to >> 'CTX-LH-UNKNOWN_1' >> >> >> >> WARNING: name collision in input name 'CTX-RH-UNKNOWN', changing one to >> 'CTX-RH-UNKNOWN_1' >> >> >> >> WARNING: name collision in input name 'WM-LH-UNKNOWN', changing one to >> 'WM-LH-UNKNOWN_1' >> >> >> >> WARNING: name collision in input name 'WM-RH-UNKNOWN', changing one to >> 'WM-RH-UNKNOWN_1' >> >> >> >> WARNING: name collision in input name 'CTX-LH-UNKNOWN', changing one to >> 'CTX-LH-UNKNOWN_1' >> >> >> >> WARNING: name collision in input name 'CTX-RH-UNKNOWN', changing one to >> 'CTX-RH-UNKNOWN_1' >> >> >> >> WARNING: name collision in input name 'WM-LH-UNKNOWN', changing one to >> 'WM-LH-UNKNOWN_1' >> >> >> >> WARNING: name collision in input name 'WM-RH-UNKNOWN', changing one to >> 'WM-RH-UNKNOWN_1' >> >> >> >> WARNING: name collision in input name 'CTX-LH-UNKNOWN', changing one to >> 'CTX-LH-UNKNOWN_1' >> >> >> >> WARNING: name collision in input name 'CTX-RH-UNKNOWN', changing one to >> 'CTX-RH-UNKNOWN_1' >> >> >> >> WARNING: name collision in input name 'WM-LH-UNKNOWN', changing one to >> 'WM-LH-UNKNOWN_1' >> >> >> >> WARNING: name collision in input name 'WM-RH-UNKNOWN', changing one to >> 'WM-RH-UNKNOWN_1' >> >> >> >> WARNING: name collision in input name 'CTX-LH-UNKNOWN', changing one to >> 'CTX-LH-UNKNOWN_1' >> >> >> >> WARNING: name collision in input name 'CTX-RH-UNKNOWN', changing one to >> 'CTX-RH-UNKNOWN_1' >> >> >> >> WARNING: name collision in input name 'WM-LH-UNKNOWN', changing one to >> 'WM-LH-UNKNOWN_1' >> >> >> >> WARNING: name collision in input name 'WM-RH-UNKNOWN', changing one to >> 'WM-RH-UNKNOWN_1' >> >> >> >> While running: >> >> /Applications/workbench/bin_macosx64/..
Re: [HCP-Users] ERROR: surface exceeds the bounding box of the warpfield
I'm not sure what could have gone wrong in the script, but as you may have guessed, that error means the input surface to -surface-apply-warpfield is too large for the specified warpfield volume, and thus some vertices would have undefined coordinates if it proceeded with the transformation. Tim On Wed, Jan 6, 2016 at 4:47 AM, Barbara Kreilkamp wrote: > Dear HCP experts, > > Thank you for all your help so far. > Unfortunately I am running into an error in PostFreeSurferPipelineBatch.sh > I wonder if you could please help me solve this issue? Other participants > with the same data have run without any issues, and the > FreeSurferPipelineBatch.sh completed without any issues as well. > > Thank you, > Best wishes, > Barbara > > ./PostFreeSurferPipelineBatch.sh > > This script must be SOURCED to correctly setup the environment prior to > running any of the other HCP scripts contained here > > > C10 > > About to use fsl_sub to queue or run > /Users/projects/Pipelines/PostFreeSurfer/PostFreeSurferPipeline.sh > > > WARNING: name collision in input name 'CTX-LH-UNKNOWN', changing one to > 'CTX-LH-UNKNOWN_1' > > > > WARNING: name collision in input name 'CTX-RH-UNKNOWN', changing one to > 'CTX-RH-UNKNOWN_1' > > > > WARNING: name collision in input name 'WM-LH-UNKNOWN', changing one to > 'WM-LH-UNKNOWN_1' > > > > WARNING: name collision in input name 'WM-RH-UNKNOWN', changing one to > 'WM-RH-UNKNOWN_1' > > > > WARNING: name collision in input name 'CTX-LH-UNKNOWN', changing one to > 'CTX-LH-UNKNOWN_1' > > > > WARNING: name collision in input name 'CTX-RH-UNKNOWN', changing one to > 'CTX-RH-UNKNOWN_1' > > > > WARNING: name collision in input name 'WM-LH-UNKNOWN', changing one to > 'WM-LH-UNKNOWN_1' > > > > WARNING: name collision in input name 'WM-RH-UNKNOWN', changing one to > 'WM-RH-UNKNOWN_1' > > > > WARNING: name collision in input name 'CTX-LH-UNKNOWN', changing one to > 'CTX-LH-UNKNOWN_1' > > > > WARNING: name collision in input name 'CTX-RH-UNKNOWN', changing one to > 'CTX-RH-UNKNOWN_1' > > > > WARNING: name collision in input name 'WM-LH-UNKNOWN', changing one to > 'WM-LH-UNKNOWN_1' > > > > WARNING: name collision in input name 'WM-RH-UNKNOWN', changing one to > 'WM-RH-UNKNOWN_1' > > > > WARNING: name collision in input name 'CTX-LH-UNKNOWN', changing one to > 'CTX-LH-UNKNOWN_1' > > > > WARNING: name collision in input name 'CTX-RH-UNKNOWN', changing one to > 'CTX-RH-UNKNOWN_1' > > > > WARNING: name collision in input name 'WM-LH-UNKNOWN', changing one to > 'WM-LH-UNKNOWN_1' > > > > WARNING: name collision in input name 'WM-RH-UNKNOWN', changing one to > 'WM-RH-UNKNOWN_1' > > > > WARNING: name collision in input name 'CTX-LH-UNKNOWN', changing one to > 'CTX-LH-UNKNOWN_1' > > > > WARNING: name collision in input name 'CTX-RH-UNKNOWN', changing one to > 'CTX-RH-UNKNOWN_1' > > > > WARNING: name collision in input name 'WM-LH-UNKNOWN', changing one to > 'WM-LH-UNKNOWN_1' > > > > WARNING: name collision in input name 'WM-RH-UNKNOWN', changing one to > 'WM-RH-UNKNOWN_1' > > > > WARNING: name collision in input name 'CTX-LH-UNKNOWN', changing one to > 'CTX-LH-UNKNOWN_1' > > > > WARNING: name collision in input name 'CTX-RH-UNKNOWN', changing one to > 'CTX-RH-UNKNOWN_1' > > > > WARNING: name collision in input name 'WM-LH-UNKNOWN', changing one to > 'WM-LH-UNKNOWN_1' > > > > WARNING: name collision in input name 'WM-RH-UNKNOWN', changing one to > 'WM-RH-UNKNOWN_1' > > > > WARNING: name collision in input name 'CTX-LH-UNKNOWN', changing one to > 'CTX-LH-UNKNOWN_1' > > > > WARNING: name collision in input name 'CTX-RH-UNKNOWN', changing one to > 'CTX-RH-UNKNOWN_1' > > > > WARNING: name collision in input name 'WM-LH-UNKNOWN', changing one to > 'WM-LH-UNKNOWN_1' > > > > WARNING: name collision in input name 'WM-RH-UNKNOWN', changing one to > 'WM-RH-UNKNOWN_1' > > > > WARNING: name collision in input name 'CTX-LH-UNKNOWN', changing one to > 'CTX-LH-UNKNOWN_1' > > > > WARNING: name collision in input name 'CTX-RH-UNKNOWN', changing one to > 'CTX-RH-UNKNOWN_1' > > > > WARNING: name collision in input name 'WM-LH-UNKNOWN', changing one to > 'WM-LH-UNKNOWN_1' > > > > WARNING: name collision in input name 'WM-RH-UNKNOWN', changing one to > 'WM-RH-UNKNOWN_1' > > > > While running: > > /Applications/workbench/bin_macosx64/../macosx64_apps/wb_command.app/Contents/MacOS/wb_command > -surface-apply-warpfield > /Users/projects/Pipelines_ExampleData/C10/T1w/Native/C10.L.white.native.surf.gii > /Users/projects/Pipelines_ExampleData/C10/MNINonLinear/xfms/standard2acpc_dc.nii.gz > /Users/projects/Pipelines_ExampleData/C10/MNINonLinear/Native/C10.L.white.native.surf.gii > -fnirt > /Users/projects/Pipelines_ExampleData/C10/MNINonLinear/xfms/acpc_dc2standard.nii.gz > > > ERROR: surface exceeds the bounding box of the warpfield > > > set -- --path=/Users/projects/Pipelines_ExampleData --subject=C10 > > --surfatlasdir=/Users/projects/Pipelines/global/templates/standard_mesh_atlases > > --grayordinatesdir=/Users/projects/Pipeline
