date:20170608

Re: [HCP-Users] values in myelin maps

2017-06-08 Thread Lisa Kramarenko

I am sorry, I have made a mistake in the mail above. It seems that the
Pipeline ended in the end of the "FreeSurferHiresPial.sh" script and not
the Intermediate recon-all steps. It ended after

Reading surface file /Users/user/Desktop/003/T1w/
003/surf/rh.pial.postT2.pass2

Applying linear registration transform

 1.000   0.000   0.000   0.000;

 0.000   0.000  -1.000   0.350;

 0.000   1.000   0.000   0.000;

 0.000   0.000   0.000   1.000;

INFO: trgsubject = srcsubject

Saving target data

mkdir: ribbon.postT2.pass1: File exists


So as I understand it, the only part that didn't finish are the Final
Recon-all Steps. Should I delete the folder "ribbon.postT2.pass1" before
running the pipeline the way I described above, so that it can be created
again (and the ribbon files moved there) and the pipeline can end?

Sorry for naive questions and thanks again.

Lisa

On 8 June 2017 at 09:59, Lisa Kramarenko  wrote:

> I wasn't sure about the exact hacking process and just naively commented
> out lines 133-167 in the FreeSurfer script, so that I started with
> recon-all -subjid $SubjectID -sd $SubjectDIR -autorecon2 -nosmooth2
> -noinflate2 -nocurvstats -nosegstats -openmp ${num_cores}
> ${seed_cmd_appendix}   (with brainmask and wm being edited)
>
> It ran without problems, but stopped after saying
>
> "mkdir: ribbon.postT2.pass1: File exists" in the Intermediate Recon-all
> Steps. So it was rewriting everything up to this point but for some reason
> stopped there.
>
> Nevertheless, seeing that surfaces seemed to have been regenerated, I
> tried to run PostFreeSurfer and apart from the warnings ("annot file:
> /Users/user/Desktop/003/T1w/003/label/lh.BA.annot MRISreadAnnotationIntoArray:
> vertex index out of range: 146448 i=00190519, in_array_size=146066) it went
> without error and my myelin map looks good now.
>
> What do you think? Can I use it or should I change something else so that
> the complete pipeline finishes?
>
> Thanks!
>
> Lisa
>
> On 7 June 2017 at 19:53, Glasser, Matthew  wrote:
>
>> Right she would want to comment out stuff that had already been done.
>>
>> Matt.
>>
>> From: "Harms, Michael" 
>> Date: Wednesday, June 7, 2017 at 12:50 PM
>> To: Matt Glasser , Lisa Kramarenko <
>> lisa.kramare...@gmail.com>
>>
>> Cc: "hcp-users@humanconnectome.org" 
>> Subject: Re: [HCP-Users] values in myelin maps
>>
>>
>> I haven’t thought this all through, but I think that one of the main
>> things you’d need to hack is to be able to make use of an already existing
>> FS output.  Currently, I believe that re-running the pipeline will simply
>> overwrite any existing FS files, as if you were running FS de-novo.
>>
>> cheers,
>> -MH
>>
>> --
>> Michael Harms, Ph.D.
>> ---
>> Conte Center for the Neuroscience of Mental Disorders
>> Washington University School of Medicine
>> Department of Psychiatry, Box 8134
>> 660 South Euclid Ave. Tel: 314-747-6173 <(314)%20747-6173>
>> St. Louis, MO  63110 Email: mha...@wustl.edu
>>
>> From: "Glasser, Matthew" 
>> Date: Wednesday, June 7, 2017 at 11:55 AM
>> To: Lisa Kramarenko , Michael Harms <
>> mha...@wustl.edu>
>> Cc: "hcp-users@humanconnectome.org" 
>> Subject: Re: [HCP-Users] values in myelin maps
>>
>> Hi Lisa,
>>
>> I was going to suggest that you hack the pipeline yourself if you are
>> comfortable with that.  You might try starting at line 167 of the
>> FreeSurfer pipeline to incorporate the brainmask edits (the WM edits might
>> not be needed then).  As for the control points, I don’t know enough about
>> that to advise you so you’ll need to consult the FreeSurfer documentation
>> to see where to add them in.
>>
>> The main things we do to modify the recon-all script is to assist with
>> brain masking, to fine tune the white surface to be placed based on high
>> res data, and place the pial surface based on highres T1w and T2w data
>> using the script modules.
>>
>> The white surface tuning happens in between –white and –smooth2 whereas
>> the pial surface tuning happens between -pial and -surfvolume on this
>> table: http://surfer.nmr.mgh.harvard.edu/fswiki/ReconAllTableStableV5.3
>>
>> Peace,
>> Matt.
>>
>> From: Lisa Kramarenko 
>> Date: Wednesday, June 7, 2017 at 11:16 AM
>> To: "Harms, Michael" 
>> Cc: Matt Glasser , "hcp-users@humanconnectome.org" <
>> hcp-users@humanconnectome.org>
>> Subject: Re: [HCP-Users] values in myelin maps
>>
>> so that means if something went wrong with the skull strip and surfaces
>> during the FreeSurfer Pipeline there is no other alternative than to
>> exclude these subjects?
>>
>> On 7 June 2017 at 18:04, Harms, Michael  wrote:
>>
>>>
>>> Unfortunately, the HCP Pipelines do not currently support

[HCP-Users] Matching field map resolutions to images

2017-06-08 Thread Grant Sutcliffe

Hi,

just to check, for the preprocessing pipelines, is it necessary or
advisable to match the resolutions between field map images and the images
to be corrected? Specifically I am interested in the case of gradient echo
field maps and fMRI timeseries.

Regards,
Grant

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Re: [HCP-Users] values in myelin maps

2017-06-08 Thread Lisa Kramarenko

I wasn't sure about the exact hacking process and just naively commented
out lines 133-167 in the FreeSurfer script, so that I started with
recon-all -subjid $SubjectID -sd $SubjectDIR -autorecon2 -nosmooth2
-noinflate2 -nocurvstats -nosegstats -openmp ${num_cores}
${seed_cmd_appendix}   (with brainmask and wm being edited)

It ran without problems, but stopped after saying

"mkdir: ribbon.postT2.pass1: File exists" in the Intermediate Recon-all
Steps. So it was rewriting everything up to this point but for some reason
stopped there.

Nevertheless, seeing that surfaces seemed to have been regenerated, I tried
to run PostFreeSurfer and apart from the warnings ("annot file:
/Users/user/Desktop/003/T1w/003/label/lh.BA.annot MRISreadAnnotationIntoArray:
vertex index out of range: 146448 i=00190519, in_array_size=146066) it went
without error and my myelin map looks good now.

What do you think? Can I use it or should I change something else so that
the complete pipeline finishes?

Thanks!

Lisa

On 7 June 2017 at 19:53, Glasser, Matthew  wrote:

> Right she would want to comment out stuff that had already been done.
>
> Matt.
>
> From: "Harms, Michael" 
> Date: Wednesday, June 7, 2017 at 12:50 PM
> To: Matt Glasser , Lisa Kramarenko <
> lisa.kramare...@gmail.com>
>
> Cc: "hcp-users@humanconnectome.org" 
> Subject: Re: [HCP-Users] values in myelin maps
>
>
> I haven’t thought this all through, but I think that one of the main
> things you’d need to hack is to be able to make use of an already existing
> FS output.  Currently, I believe that re-running the pipeline will simply
> overwrite any existing FS files, as if you were running FS de-novo.
>
> cheers,
> -MH
>
> --
> Michael Harms, Ph.D.
> ---
> Conte Center for the Neuroscience of Mental Disorders
> Washington University School of Medicine
> Department of Psychiatry, Box 8134
> 660 South Euclid Ave. Tel: 314-747-6173 <(314)%20747-6173>
> St. Louis, MO  63110 Email: mha...@wustl.edu
>
> From: "Glasser, Matthew" 
> Date: Wednesday, June 7, 2017 at 11:55 AM
> To: Lisa Kramarenko , Michael Harms <
> mha...@wustl.edu>
> Cc: "hcp-users@humanconnectome.org" 
> Subject: Re: [HCP-Users] values in myelin maps
>
> Hi Lisa,
>
> I was going to suggest that you hack the pipeline yourself if you are
> comfortable with that.  You might try starting at line 167 of the
> FreeSurfer pipeline to incorporate the brainmask edits (the WM edits might
> not be needed then).  As for the control points, I don’t know enough about
> that to advise you so you’ll need to consult the FreeSurfer documentation
> to see where to add them in.
>
> The main things we do to modify the recon-all script is to assist with
> brain masking, to fine tune the white surface to be placed based on high
> res data, and place the pial surface based on highres T1w and T2w data
> using the script modules.
>
> The white surface tuning happens in between –white and –smooth2 whereas
> the pial surface tuning happens between -pial and -surfvolume on this
> table: http://surfer.nmr.mgh.harvard.edu/fswiki/ReconAllTableStableV5.3
>
> Peace,
> Matt.
>
> From: Lisa Kramarenko 
> Date: Wednesday, June 7, 2017 at 11:16 AM
> To: "Harms, Michael" 
> Cc: Matt Glasser , "hcp-users@humanconnectome.org" <
> hcp-users@humanconnectome.org>
> Subject: Re: [HCP-Users] values in myelin maps
>
> so that means if something went wrong with the skull strip and surfaces
> during the FreeSurfer Pipeline there is no other alternative than to
> exclude these subjects?
>
> On 7 June 2017 at 18:04, Harms, Michael  wrote:
>
>>
>> Unfortunately, the HCP Pipelines do not currently support rerunning
>> FreeSurfer after editing.  It is on our list of “things to do” to add that
>> functionality.
>>
>> cheers,
>> -MH
>>
>> --
>> Michael Harms, Ph.D.
>> ---
>> Conte Center for the Neuroscience of Mental Disorders
>> Washington University School of Medicine
>> Department of Psychiatry, Box 8134
>> 660 South Euclid Ave.Tel: 314-747-6173 <(314)%20747-6173>
>> St. Louis, MO  63110Email: mha...@wustl.edu
>>
>> From:  on behalf of Lisa
>> Kramarenko 
>> Date: Wednesday, June 7, 2017 at 11:00 AM
>> To: "Glasser, Matthew" , "
>> hcp-users@humanconnectome.org" 
>>
>> Subject: Re: [HCP-Users] values in myelin maps
>>
>> Dear Matthew,
>>
>> I have now manually edited brainmask.gmz ans wm.gmz to remove dura that
>> was still mistaken for a surface. Now I am not sure from which step to
>> re-run these participants.
>> 1. Do I understand it correctly that after replacing brainmask.gmz and

Re: [HCP-Users] Question about unprocessed fMRI data

2017-06-08 Thread Xu, Junqian

Hi Ben,

Yes, the CMRR multiband sequence incorporates "dynamic off-resonance in 
k-space” (DORK)” method as in Pfeuffer et al., MRM 2002, which has already been 
implemented in the Siemens product EPI sequence ICE recon.

Gordon
 
> On Jun 8, 2017, at 12:05 PM, Benjamin Risk  wrote:
> 
> Dear HCP experts,
> 
> I am trying to better understand the unprocessed fMRI data. Does the online 
> reconstruction include corrections for spatial shifts due to B0 fluctuations? 
> There is a note about this in Ugurbil et al 2013 but I am wondering if this 
> applies to the final HCP acquisition protocol. 
> 
> Thank you!
> Ben Risk
> 
> ___
> HCP-Users mailing list
> HCP-Users@humanconnectome.org
> http://lists.humanconnectome.org/mailman/listinfo/hcp-users
> 


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Re: [HCP-Users] Matching field map resolutions to images

2017-06-08 Thread Glasser, Matthew

What is most important is that they both cover the whole brain for gradient 
echo field maps.  Matching geometry more exactly is nice but not necessary.

Peace,

Matt.

From: 
>
 on behalf of Grant Sutcliffe >
Date: Thursday, June 8, 2017 at 4:32 AM
To: "hcp-users@humanconnectome.org" 
>
Subject: [HCP-Users] Matching field map resolutions to images

Hi,

just to check, for the preprocessing pipelines, is it necessary or advisable to 
match the resolutions between field map images and the images to be corrected? 
Specifically I am interested in the case of gradient echo field maps and fMRI 
timeseries.

Regards,
Grant

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Re: [HCP-Users] values in myelin maps

2017-06-08 Thread Harms, Michael

‘mkdir’ is telling you that the directory already exists.  Normally that won’t 
abort a script, but it does in this case because of the “set -e” at the top of 
the script.
The easy solution is to add the -p flag to the mkdir command, so that it is no 
longer considered an error if the directory already exists.

cheers,
-MH

--
Michael Harms, Ph.D.
---
Conte Center for the Neuroscience of Mental Disorders
Washington University School of Medicine
Department of Psychiatry, Box 8134
660 South Euclid Ave. Tel: 314-747-6173
St. Louis, MO  63110 Email: mha...@wustl.edu

From: "Glasser, Matthew" >
Date: Thursday, June 8, 2017 at 8:30 AM
To: Lisa Kramarenko 
>
Cc: Michael Harms >, 
"hcp-users@humanconnectome.org" 
>
Subject: Re: [HCP-Users] values in myelin maps

You could delete that or make the mkdir a conditional if it doesn’t already 
exist.

Peace,

Matt.

From: Lisa Kramarenko 
>
Date: Thursday, June 8, 2017 at 4:21 AM
To: Matt Glasser >
Cc: "Harms, Michael" >, 
"hcp-users@humanconnectome.org" 
>
Subject: Re: [HCP-Users] values in myelin maps

I am sorry, I have made a mistake in the mail above. It seems that the Pipeline 
ended in the end of the "FreeSurferHiresPial.sh" script and not the 
Intermediate recon-all steps. It ended after

Reading surface file /Users/user/Desktop/003/T1w/003/surf/rh.pial.postT2.pass2

Applying linear registration transform

 1.000   0.000   0.000   0.000;

 0.000   0.000  -1.000   0.350;

 0.000   1.000   0.000   0.000;

 0.000   0.000   0.000   1.000;

INFO: trgsubject = srcsubject

Saving target data

mkdir: ribbon.postT2.pass1: File exists

So as I understand it, the only part that didn't finish are the Final Recon-all 
Steps. Should I delete the folder "ribbon.postT2.pass1" before running the 
pipeline the way I described above, so that it can be created again (and the 
ribbon files moved there) and the pipeline can end?

Sorry for naive questions and thanks again.

Lisa

On 8 June 2017 at 09:59, Lisa Kramarenko 
> wrote:
I wasn't sure about the exact hacking process and just naively commented out 
lines 133-167 in the FreeSurfer script, so that I started with
recon-all -subjid $SubjectID -sd $SubjectDIR -autorecon2 -nosmooth2 -noinflate2 
-nocurvstats -nosegstats -openmp ${num_cores} ${seed_cmd_appendix}   (with 
brainmask and wm being edited)

It ran without problems, but stopped after saying

"mkdir: ribbon.postT2.pass1: File exists" in the Intermediate Recon-all Steps. 
So it was rewriting everything up to this point but for some reason stopped 
there.

Nevertheless, seeing that surfaces seemed to have been regenerated, I tried to 
run PostFreeSurfer and apart from the warnings ("annot file: 
/Users/user/Desktop/003/T1w/003/label/lh.BA.annot MRISreadAnnotationIntoArray: 
vertex index out of range: 146448 i=00190519, in_array_size=146066) it went 
without error and my myelin map looks good now.

What do you think? Can I use it or should I change something else so that the 
complete pipeline finishes?

Thanks!

Lisa

On 7 June 2017 at 19:53, Glasser, Matthew 
> wrote:
Right she would want to comment out stuff that had already been done.

Matt.

From: "Harms, Michael" >
Date: Wednesday, June 7, 2017 at 12:50 PM
To: Matt Glasser >, Lisa 
Kramarenko >

Cc: "hcp-users@humanconnectome.org" 
>
Subject: Re: [HCP-Users] values in myelin maps

I haven’t thought this all through, but I think that one of the main things 
you’d need to hack is to be able to make use of an already existing FS output.  
Currently, I believe that re-running the pipeline will simply overwrite any 
existing FS files, as if you were running FS de-novo.

cheers,
-MH

--
Michael Harms, Ph.D.
---
Conte Center for the Neuroscience of Mental Disorders
Washington University School of Medicine
Department of Psychiatry, Box 8134
660 South Euclid Ave.Tel: 314-747-6173
St. Louis, MO  63110Email: mha...@wustl.edu

From: "Glasser, Matthew" >
Date: Wednesday, June

Re: [HCP-Users] values in myelin maps

2017-06-08 Thread Glasser, Matthew

You could delete that or make the mkdir a conditional if it doesn’t already 
exist.

Peace,

Matt.

From: Lisa Kramarenko 
>
Date: Thursday, June 8, 2017 at 4:21 AM
To: Matt Glasser >
Cc: "Harms, Michael" >, 
"hcp-users@humanconnectome.org" 
>
Subject: Re: [HCP-Users] values in myelin maps

I am sorry, I have made a mistake in the mail above. It seems that the Pipeline 
ended in the end of the "FreeSurferHiresPial.sh" script and not the 
Intermediate recon-all steps. It ended after

Reading surface file /Users/user/Desktop/003/T1w/003/surf/rh.pial.postT2.pass2

Applying linear registration transform

 1.000   0.000   0.000   0.000;

 0.000   0.000  -1.000   0.350;

 0.000   1.000   0.000   0.000;

 0.000   0.000   0.000   1.000;

INFO: trgsubject = srcsubject

Saving target data

mkdir: ribbon.postT2.pass1: File exists

So as I understand it, the only part that didn't finish are the Final Recon-all 
Steps. Should I delete the folder "ribbon.postT2.pass1" before running the 
pipeline the way I described above, so that it can be created again (and the 
ribbon files moved there) and the pipeline can end?

Sorry for naive questions and thanks again.

Lisa

On 8 June 2017 at 09:59, Lisa Kramarenko 
> wrote:
I wasn't sure about the exact hacking process and just naively commented out 
lines 133-167 in the FreeSurfer script, so that I started with
recon-all -subjid $SubjectID -sd $SubjectDIR -autorecon2 -nosmooth2 -noinflate2 
-nocurvstats -nosegstats -openmp ${num_cores} ${seed_cmd_appendix}   (with 
brainmask and wm being edited)

It ran without problems, but stopped after saying

"mkdir: ribbon.postT2.pass1: File exists" in the Intermediate Recon-all Steps. 
So it was rewriting everything up to this point but for some reason stopped 
there.

Nevertheless, seeing that surfaces seemed to have been regenerated, I tried to 
run PostFreeSurfer and apart from the warnings ("annot file: 
/Users/user/Desktop/003/T1w/003/label/lh.BA.annot MRISreadAnnotationIntoArray: 
vertex index out of range: 146448 i=00190519, in_array_size=146066) it went 
without error and my myelin map looks good now.

What do you think? Can I use it or should I change something else so that the 
complete pipeline finishes?

Thanks!

Lisa

On 7 June 2017 at 19:53, Glasser, Matthew 
> wrote:
Right she would want to comment out stuff that had already been done.

Matt.

From: "Harms, Michael" >
Date: Wednesday, June 7, 2017 at 12:50 PM
To: Matt Glasser >, Lisa 
Kramarenko >

Cc: "hcp-users@humanconnectome.org" 
>
Subject: Re: [HCP-Users] values in myelin maps

I haven’t thought this all through, but I think that one of the main things 
you’d need to hack is to be able to make use of an already existing FS output.  
Currently, I believe that re-running the pipeline will simply overwrite any 
existing FS files, as if you were running FS de-novo.

cheers,
-MH

--
Michael Harms, Ph.D.
---
Conte Center for the Neuroscience of Mental Disorders
Washington University School of Medicine
Department of Psychiatry, Box 8134
660 South Euclid Ave.Tel: 314-747-6173
St. Louis, MO  63110Email: mha...@wustl.edu

From: "Glasser, Matthew" >
Date: Wednesday, June 7, 2017 at 11:55 AM
To: Lisa Kramarenko 
>, Michael Harms 
>
Cc: "hcp-users@humanconnectome.org" 
>
Subject: Re: [HCP-Users] values in myelin maps

Hi Lisa,

I was going to suggest that you hack the pipeline yourself if you are 
comfortable with that.  You might try starting at line 167 of the FreeSurfer 
pipeline to incorporate the brainmask edits (the WM edits might not be needed 
then).  As for the control points, I don’t know enough about that to advise you 
so you’ll need to consult the FreeSurfer documentation to see where to add them 
in.

The main things we do to modify the recon-all script is to assist with brain 
masking, to fine tune the white surface to be placed based on high res data, 
and place the pial surface based on highres T1w and T2w data using the script 
modules.

The white surface tuning happens in between –white and –smooth2

Re: [HCP-Users] Matching field map resolutions to images

2017-06-08 Thread Harms, Michael


In theory, the resolutions and matrix size don’t need to match.  But I thought 
that, as a practical matter, the Pipelines don’t work if they don’t match.  At 
least that was the case at some point in the past...

--
Michael Harms, Ph.D.
---
Conte Center for the Neuroscience of Mental Disorders
Washington University School of Medicine
Department of Psychiatry, Box 8134
660 South Euclid Ave. Tel: 314-747-6173
St. Louis, MO  63110 Email: mha...@wustl.edu

From: 
>
 on behalf of "Glasser, Matthew" >
Date: Thursday, June 8, 2017 at 8:29 AM
To: Grant Sutcliffe >, 
"hcp-users@humanconnectome.org" 
>
Subject: Re: [HCP-Users] Matching field map resolutions to images

What is most important is that they both cover the whole brain for gradient 
echo field maps.  Matching geometry more exactly is nice but not necessary.

Peace,

Matt.

From: 
>
 on behalf of Grant Sutcliffe >
Date: Thursday, June 8, 2017 at 4:32 AM
To: "hcp-users@humanconnectome.org" 
>
Subject: [HCP-Users] Matching field map resolutions to images

Hi,

just to check, for the preprocessing pipelines, is it necessary or advisable to 
match the resolutions between field map images and the images to be corrected? 
Specifically I am interested in the case of gradient echo field maps and fMRI 
timeseries.

Regards,
Grant

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Re: [HCP-Users] values in myelin maps

2017-06-08 Thread Lisa Kramarenko

thanks so much, it works and myelin maps look good now!

Lisa

On 8 June 2017 at 16:15, Harms, Michael  wrote:

>
> ‘mkdir’ is telling you that the directory already exists.  Normally that
> won’t abort a script, but it does in this case because of the “set -e” at
> the top of the script.
> The easy solution is to add the -p flag to the mkdir command, so that it
> is no longer considered an error if the directory already exists.
>
> cheers,
> -MH
>
> --
> Michael Harms, Ph.D.
> ---
> Conte Center for the Neuroscience of Mental Disorders
> Washington University School of Medicine
> Department of Psychiatry, Box 8134
> 660 South Euclid Ave. Tel: 314-747-6173 <(314)%20747-6173>
> St. Louis, MO  63110 Email: mha...@wustl.edu
>
> From: "Glasser, Matthew" 
> Date: Thursday, June 8, 2017 at 8:30 AM
> To: Lisa Kramarenko 
> Cc: Michael Harms , "hcp-users@humanconnectome.org" <
> hcp-users@humanconnectome.org>
>
> Subject: Re: [HCP-Users] values in myelin maps
>
> You could delete that or make the mkdir a conditional if it doesn’t
> already exist.
>
> Peace,
>
> Matt.
>
> From: Lisa Kramarenko 
> Date: Thursday, June 8, 2017 at 4:21 AM
> To: Matt Glasser 
> Cc: "Harms, Michael" , "hcp-users@humanconnectome.org" <
> hcp-users@humanconnectome.org>
> Subject: Re: [HCP-Users] values in myelin maps
>
> I am sorry, I have made a mistake in the mail above. It seems that the
> Pipeline ended in the end of the "FreeSurferHiresPial.sh" script and not
> the Intermediate recon-all steps. It ended after
>
> Reading surface file /Users/user/Desktop/003/T1w/00
> 3/surf/rh.pial.postT2.pass2
>
> Applying linear registration transform
>
>  1.000   0.000   0.000   0.000;
>
>  0.000   0.000  -1.000   0.350;
>
>  0.000   1.000   0.000   0.000;
>
>  0.000   0.000   0.000   1.000;
>
> INFO: trgsubject = srcsubject
>
> Saving target data
>
> mkdir: ribbon.postT2.pass1: File exists
>
>
> So as I understand it, the only part that didn't finish are the Final
> Recon-all Steps. Should I delete the folder "ribbon.postT2.pass1" before
> running the pipeline the way I described above, so that it can be created
> again (and the ribbon files moved there) and the pipeline can end?
>
> Sorry for naive questions and thanks again.
>
> Lisa
>
> On 8 June 2017 at 09:59, Lisa Kramarenko 
> wrote:
>
>> I wasn't sure about the exact hacking process and just naively commented
>> out lines 133-167 in the FreeSurfer script, so that I started with
>> recon-all -subjid $SubjectID -sd $SubjectDIR -autorecon2 -nosmooth2
>> -noinflate2 -nocurvstats -nosegstats -openmp ${num_cores}
>> ${seed_cmd_appendix}   (with brainmask and wm being edited)
>>
>> It ran without problems, but stopped after saying
>>
>> "mkdir: ribbon.postT2.pass1: File exists" in the Intermediate Recon-all
>> Steps. So it was rewriting everything up to this point but for some reason
>> stopped there.
>>
>> Nevertheless, seeing that surfaces seemed to have been regenerated, I
>> tried to run PostFreeSurfer and apart from the warnings ("annot file:
>> /Users/user/Desktop/003/T1w/003/label/lh.BA.annot 
>> MRISreadAnnotationIntoArray:
>> vertex index out of range: 146448 i=00190519, in_array_size=146066) it went
>> without error and my myelin map looks good now.
>>
>> What do you think? Can I use it or should I change something else so that
>> the complete pipeline finishes?
>>
>> Thanks!
>>
>> Lisa
>>
>> On 7 June 2017 at 19:53, Glasser, Matthew  wrote:
>>
>>> Right she would want to comment out stuff that had already been done.
>>>
>>> Matt.
>>>
>>> From: "Harms, Michael" 
>>> Date: Wednesday, June 7, 2017 at 12:50 PM
>>> To: Matt Glasser , Lisa Kramarenko <
>>> lisa.kramare...@gmail.com>
>>>
>>> Cc: "hcp-users@humanconnectome.org" 
>>> Subject: Re: [HCP-Users] values in myelin maps
>>>
>>>
>>> I haven’t thought this all through, but I think that one of the main
>>> things you’d need to hack is to be able to make use of an already existing
>>> FS output.  Currently, I believe that re-running the pipeline will simply
>>> overwrite any existing FS files, as if you were running FS de-novo.
>>>
>>> cheers,
>>> -MH
>>>
>>> --
>>> Michael Harms, Ph.D.
>>> ---
>>> Conte Center for the Neuroscience of Mental Disorders
>>> Washington University School of Medicine
>>> Department of Psychiatry, Box 8134
>>> 660 South Euclid Ave.Tel: 314-747-6173 <(314)%20747-6173>
>>> St. Louis, MO  63110Email: mha...@wustl.edu
>>>
>>> From: "Glasser, Matthew" 
>>> Date: Wednesday, June 7, 2017 at 11:55 AM
>>> To: Lisa Kramarenko , Michael Harms <
>>> mha...@wustl.edu>
>>> Cc: "hcp-users@humanconnectome.org"

Re: [HCP-Users] Question about unprocessed fMRI data

2017-06-08 Thread Harms, Michael


This is via Essa:

It is the same as what is done in the Siemens product - these are Siemens 
code/algorithms. But yes - they do B0 corrections, including in post-processing.

--
Michael Harms, Ph.D.
---
Conte Center for the Neuroscience of Mental Disorders
Washington University School of Medicine
Department of Psychiatry, Box 8134
660 South Euclid Ave. Tel: 314-747-6173
St. Louis, MO  63110 Email: mha...@wustl.edu

From: 
>
 on behalf of Benjamin Risk >
Date: Thursday, June 8, 2017 at 11:05 AM
To: "hcp-users@humanconnectome.org" 
>
Subject: [HCP-Users] Question about unprocessed fMRI data

Dear HCP experts,

I am trying to better understand the unprocessed fMRI data. Does the online 
reconstruction include corrections for spatial shifts due to B0 fluctuations? 
There is a note about this in Ugurbil et al 2013 but I am wondering if this 
applies to the final HCP acquisition protocol.

Thank you!
Ben Risk


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Re: [HCP-Users] Question about unprocessed fMRI data

2017-06-08 Thread Glasser, Matthew

I suppose it isn’t good enough given what we see in some subjects FD traces 
however…

Matt.

From: 
>
 on behalf of "Harms, Michael" >
Date: Thursday, June 8, 2017 at 2:05 PM
To: Benjamin Risk >, 
"hcp-users@humanconnectome.org" 
>
Cc: Essa Yacoub >
Subject: Re: [HCP-Users] Question about unprocessed fMRI data

This is via Essa:

It is the same as what is done in the Siemens product - these are Siemens 
code/algorithms. But yes - they do B0 corrections, including in post-processing.

--
Michael Harms, Ph.D.
---
Conte Center for the Neuroscience of Mental Disorders
Washington University School of Medicine
Department of Psychiatry, Box 8134
660 South Euclid Ave. Tel: 314-747-6173
St. Louis, MO  63110 Email: mha...@wustl.edu

From: 
>
 on behalf of Benjamin Risk >
Date: Thursday, June 8, 2017 at 11:05 AM
To: "hcp-users@humanconnectome.org" 
>
Subject: [HCP-Users] Question about unprocessed fMRI data

Dear HCP experts,

I am trying to better understand the unprocessed fMRI data. Does the online 
reconstruction include corrections for spatial shifts due to B0 fluctuations? 
There is a note about this in Ugurbil et al 2013 but I am wondering if this 
applies to the final HCP acquisition protocol.

Thank you!
Ben Risk

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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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Re: [HCP-Users] values in myelin maps

2017-06-08 Thread Glasser, Matthew

I’m happy to hear that!

Peace,

Matt.

From: Lisa Kramarenko 
>
Date: Thursday, June 8, 2017 at 2:18 PM
To: "Harms, Michael" >
Cc: Matt Glasser >, 
"hcp-users@humanconnectome.org" 
>
Subject: Re: [HCP-Users] values in myelin maps

thanks so much, it works and myelin maps look good now!

Lisa

On 8 June 2017 at 16:15, Harms, Michael 
> wrote:

‘mkdir’ is telling you that the directory already exists.  Normally that won’t 
abort a script, but it does in this case because of the “set -e” at the top of 
the script.
The easy solution is to add the -p flag to the mkdir command, so that it is no 
longer considered an error if the directory already exists.

cheers,
-MH

--
Michael Harms, Ph.D.
---
Conte Center for the Neuroscience of Mental Disorders
Washington University School of Medicine
Department of Psychiatry, Box 8134
660 South Euclid Ave.Tel: 314-747-6173
St. Louis, MO  63110Email: mha...@wustl.edu

From: "Glasser, Matthew" >
Date: Thursday, June 8, 2017 at 8:30 AM
To: Lisa Kramarenko 
>
Cc: Michael Harms >, 
"hcp-users@humanconnectome.org" 
>

Subject: Re: [HCP-Users] values in myelin maps

You could delete that or make the mkdir a conditional if it doesn’t already 
exist.

Peace,

Matt.

From: Lisa Kramarenko 
>
Date: Thursday, June 8, 2017 at 4:21 AM
To: Matt Glasser >
Cc: "Harms, Michael" >, 
"hcp-users@humanconnectome.org" 
>
Subject: Re: [HCP-Users] values in myelin maps

I am sorry, I have made a mistake in the mail above. It seems that the Pipeline 
ended in the end of the "FreeSurferHiresPial.sh" script and not the 
Intermediate recon-all steps. It ended after

Reading surface file /Users/user/Desktop/003/T1w/003/surf/rh.pial.postT2.pass2

Applying linear registration transform

 1.000   0.000   0.000   0.000;

 0.000   0.000  -1.000   0.350;

 0.000   1.000   0.000   0.000;

 0.000   0.000   0.000   1.000;

INFO: trgsubject = srcsubject

Saving target data

mkdir: ribbon.postT2.pass1: File exists

So as I understand it, the only part that didn't finish are the Final Recon-all 
Steps. Should I delete the folder "ribbon.postT2.pass1" before running the 
pipeline the way I described above, so that it can be created again (and the 
ribbon files moved there) and the pipeline can end?

Sorry for naive questions and thanks again.

Lisa

On 8 June 2017 at 09:59, Lisa Kramarenko 
> wrote:
I wasn't sure about the exact hacking process and just naively commented out 
lines 133-167 in the FreeSurfer script, so that I started with
recon-all -subjid $SubjectID -sd $SubjectDIR -autorecon2 -nosmooth2 -noinflate2 
-nocurvstats -nosegstats -openmp ${num_cores} ${seed_cmd_appendix}   (with 
brainmask and wm being edited)

It ran without problems, but stopped after saying

"mkdir: ribbon.postT2.pass1: File exists" in the Intermediate Recon-all Steps. 
So it was rewriting everything up to this point but for some reason stopped 
there.

Nevertheless, seeing that surfaces seemed to have been regenerated, I tried to 
run PostFreeSurfer and apart from the warnings ("annot file: 
/Users/user/Desktop/003/T1w/003/label/lh.BA.annot MRISreadAnnotationIntoArray: 
vertex index out of range: 146448 i=00190519, in_array_size=146066) it went 
without error and my myelin map looks good now.

What do you think? Can I use it or should I change something else so that the 
complete pipeline finishes?

Thanks!

Lisa

On 7 June 2017 at 19:53, Glasser, Matthew 
> wrote:
Right she would want to comment out stuff that had already been done.

Matt.

From: "Harms, Michael" >
Date: Wednesday, June 7, 2017 at 12:50 PM
To: Matt Glasser >, Lisa 
Kramarenko >

Cc: "hcp-users@humanconnectome.org" 
>
Subject: Re: [HCP-Users] values in myelin maps

I haven’t thought this all through, but I think that

Re: [HCP-Users] Matching field map resolutions to images

2017-06-08 Thread Glasser, Matthew

Hi Mike,

That is for spin echo field maps.

Matt.

From: "Harms, Michael" >
Date: Thursday, June 8, 2017 at 9:26 AM
To: Matt Glasser >, Grant 
Sutcliffe >, 
"hcp-users@humanconnectome.org" 
>
Subject: Re: [HCP-Users] Matching field map resolutions to images

In theory, the resolutions and matrix size don’t need to match.  But I thought 
that, as a practical matter, the Pipelines don’t work if they don’t match.  At 
least that was the case at some point in the past...

--
Michael Harms, Ph.D.
---
Conte Center for the Neuroscience of Mental Disorders
Washington University School of Medicine
Department of Psychiatry, Box 8134
660 South Euclid Ave. Tel: 314-747-6173
St. Louis, MO  63110 Email: mha...@wustl.edu

From: 
>
 on behalf of "Glasser, Matthew" >
Date: Thursday, June 8, 2017 at 8:29 AM
To: Grant Sutcliffe >, 
"hcp-users@humanconnectome.org" 
>
Subject: Re: [HCP-Users] Matching field map resolutions to images

What is most important is that they both cover the whole brain for gradient 
echo field maps.  Matching geometry more exactly is nice but not necessary.

Peace,

Matt.

From: 
>
 on behalf of Grant Sutcliffe >
Date: Thursday, June 8, 2017 at 4:32 AM
To: "hcp-users@humanconnectome.org" 
>
Subject: [HCP-Users] Matching field map resolutions to images

Hi,

just to check, for the preprocessing pipelines, is it necessary or advisable to 
match the resolutions between field map images and the images to be corrected? 
Specifically I am interested in the case of gradient echo field maps and fMRI 
timeseries.

Regards,
Grant

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[HCP-Users] Question about unprocessed fMRI data

2017-06-08 Thread Benjamin Risk

Dear HCP experts,

I am trying to better understand the unprocessed fMRI data. Does the online
reconstruction include corrections for spatial shifts due to B0
fluctuations? There is a note about this in Ugurbil et al 2013 but I am
wondering if this applies to the final HCP acquisition protocol.

Thank you!
Ben Risk

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Re: [HCP-Users] [HCP-Info] [Contact Form]: Transforming Group MPM Parcellations to fsaverage

2017-06-08 Thread Glasser, Matthew

The parcellation file is available here: https://balsa.wustl.edu/file/show/3VLx

Note that the preferred venue for asking questions about HCP data is the 
HCP-Users mailing list so that all list members have the benefit of the answer.

Peace,

Matt.


From: info-boun...@humanconnectome.org 
> on 
behalf of i...@humanconnectome.org 
>
Sent: Thursday, June 8, 2017 12:36 PM
To: i...@humanconnectome.org
Subject: [HCP-Info] [Contact Form]: Transforming Group MPM Parcellations to 
fsaverage

Name: Ian Kennedy

Email: ikenn...@avidrp.com

Institution: Avid Radiopharmaceuticals

Area of Scientific Interest: Relationships between PET/volumetrics, Alzheimer's 
Disease

Subject: [Contact Form]: Transforming Group MPM Parcellations to fsaverage

Comments:
 Good Afternoon,

I'm interested in exploring tau and amyloid PET concentrations within the group 
MPM parcellations from the Glasser et al publication from 2016, but I was 
hoping I could project the labels onto FreeSurfer's fsaverage standard template 
for use as VOIs. I located the document "hcp-users FAQ #9: How do I map data 
between FreeSurfer and HCP?" and have a good idea how to go about transforming 
the parcellations, but I'm unable to locate the correct file with the 
parcellations. I downloaded the Group MPM Parcellations scene file, but there 
doesn't appear to be hemisphere-specific parcellations that I could use when I 
follow along with the FAQ. Are these files located elsewhere, or is it easy for 
me to extract them from the scene file myself? I'm new to the HCP pipelines and 
may just be missing something.

Best,

Ian


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Re: [HCP-Users] Question about unprocessed fMRI data

2017-06-08 Thread Benjamin Risk

I see, thank you!

On Thu, Jun 8, 2017 at 3:08 PM, Glasser, Matthew  wrote:

> I suppose it isn’t good enough given what we see in some subjects FD
> traces however…
>
> Matt.
>
> From:  on behalf of "Harms,
> Michael" 
> Date: Thursday, June 8, 2017 at 2:05 PM
> To: Benjamin Risk , "hcp-users@humanconnectome.org" <
> hcp-users@humanconnectome.org>
> Cc: Essa Yacoub 
> Subject: Re: [HCP-Users] Question about unprocessed fMRI data
>
>
> This is via Essa:
>
> It is the same as what is done in the Siemens product - these are Siemens
> code/algorithms. But yes - they do B0 corrections, including in
> post-processing.
>
> --
> Michael Harms, Ph.D.
> ---
> Conte Center for the Neuroscience of Mental Disorders
> Washington University School of Medicine
> Department of Psychiatry, Box 8134
> 660 South Euclid Ave. Tel: 314-747-6173 <(314)%20747-6173>
> St. Louis, MO  63110 Email: mha...@wustl.edu
>
> From:  on behalf of Benjamin Risk <
> bb...@cornell.edu>
> Date: Thursday, June 8, 2017 at 11:05 AM
> To: "hcp-users@humanconnectome.org" 
> Subject: [HCP-Users] Question about unprocessed fMRI data
>
> Dear HCP experts,
>
> I am trying to better understand the unprocessed fMRI data. Does the
> online reconstruction include corrections for spatial shifts due to B0
> fluctuations? There is a note about this in Ugurbil et al 2013 but I am
> wondering if this applies to the final HCP acquisition protocol.
>
> Thank you!
> Ben Risk
>
> ___
> 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.
>
> ___
> HCP-Users mailing list
> HCP-Users@humanconnectome.org
> http://lists.humanconnectome.org/mailman/listinfo/hcp-users
>

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Re: [HCP-Users] values in myelin maps

[HCP-Users] Matching field map resolutions to images

Re: [HCP-Users] values in myelin maps

Re: [HCP-Users] Question about unprocessed fMRI data

Re: [HCP-Users] Matching field map resolutions to images

Re: [HCP-Users] values in myelin maps

Re: [HCP-Users] values in myelin maps

Re: [HCP-Users] Matching field map resolutions to images

Re: [HCP-Users] values in myelin maps

Re: [HCP-Users] Question about unprocessed fMRI data

Re: [HCP-Users] Question about unprocessed fMRI data

Re: [HCP-Users] values in myelin maps

Re: [HCP-Users] Matching field map resolutions to images

[HCP-Users] Question about unprocessed fMRI data

Re: [HCP-Users] [HCP-Info] [Contact Form]: Transforming Group MPM Parcellations to fsaverage

Re: [HCP-Users] Question about unprocessed fMRI data

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