subject:"Re\: \[HCP\-Users\] values in myelin maps"

Re: [HCP-Users] values in myelin maps

2017-06-08 Thread Glasser, Matthew

I’m happy to hear that!

Peace,

Matt.

From: Lisa Kramarenko 
<lisa.kramare...@gmail.com<mailto:lisa.kramare...@gmail.com>>
Date: Thursday, June 8, 2017 at 2:18 PM
To: "Harms, Michael" <mha...@wustl.edu<mailto:mha...@wustl.edu>>
Cc: Matt Glasser <glass...@wustl.edu<mailto:glass...@wustl.edu>>, 
"hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>" 
<hcp-users@humanconnectome.org<mailto: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 
<mha...@wustl.edu<mailto:mha...@wustl.edu>> 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<tel:(314)%20747-6173>
St. Louis, MO  63110Email: mha...@wustl.edu<mailto:mha...@wustl.edu>

From: "Glasser, Matthew" <glass...@wustl.edu<mailto:glass...@wustl.edu>>
Date: Thursday, June 8, 2017 at 8:30 AM
To: Lisa Kramarenko 
<lisa.kramare...@gmail.com<mailto:lisa.kramare...@gmail.com>>
Cc: Michael Harms <mha...@wustl.edu<mailto:mha...@wustl.edu>>, 
"hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>" 
<hcp-users@humanconnectome.org<mailto: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 
<lisa.kramare...@gmail.com<mailto:lisa.kramare...@gmail.com>>
Date: Thursday, June 8, 2017 at 4:21 AM
To: Matt Glasser <glass...@wustl.edu<mailto:glass...@wustl.edu>>
Cc: "Harms, Michael" <mha...@wustl.edu<mailto:mha...@wustl.edu>>, 
"hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>" 
<hcp-users@humanconnectome.org<mailto: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 
<lisa.kramare...@gmail.com<mailto:lisa.kramare...@gmail.com>> 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 
<glass...@wustl.edu<mailto:glass...@wustl.edu>> wrote:
Right she would want to comment out stuff that had already been done.

Matt.

From: "Harms, Michael" <mha...@wustl.edu<mailto:mha...@wustl.edu>>
Date: Wednesday, June 7, 2017 at 12:50 PM
To: Matt Glasser <glass...@wustl.edu<mailto:glass...@w

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 <mha...@wustl.edu> 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" <glass...@wustl.edu>
> Date: Thursday, June 8, 2017 at 8:30 AM
> To: Lisa Kramarenko <lisa.kramare...@gmail.com>
> Cc: Michael Harms <mha...@wustl.edu>, "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 <lisa.kramare...@gmail.com>
> Date: Thursday, June 8, 2017 at 4:21 AM
> To: Matt Glasser <glass...@wustl.edu>
> Cc: "Harms, Michael" <mha...@wustl.edu>, "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 <lisa.kramare...@gmail.com>
> 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 <glass...@wustl.edu> wrote:
>>
>>> Right she would want to comment out stuff that had already been done.
>>>
>>> Matt.
>>>
>>> From: "Harms, Michael" <mha...@wustl.edu>
>>> Date: Wednesday, June 7, 2017 at 12:50 PM
>>> To: Matt Glasser <glass...@wustl.edu>, Lisa Kramarenko <
>>> lisa.kramare...@gmail.com>
>>>
>>> Cc: "hcp-users@humanconnectome.org" <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.  Curre

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" <glass...@wustl.edu<mailto:glass...@wustl.edu>>
Date: Thursday, June 8, 2017 at 8:30 AM
To: Lisa Kramarenko 
<lisa.kramare...@gmail.com<mailto:lisa.kramare...@gmail.com>>
Cc: Michael Harms <mha...@wustl.edu<mailto:mha...@wustl.edu>>, 
"hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>" 
<hcp-users@humanconnectome.org<mailto: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 
<lisa.kramare...@gmail.com<mailto:lisa.kramare...@gmail.com>>
Date: Thursday, June 8, 2017 at 4:21 AM
To: Matt Glasser <glass...@wustl.edu<mailto:glass...@wustl.edu>>
Cc: "Harms, Michael" <mha...@wustl.edu<mailto:mha...@wustl.edu>>, 
"hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>" 
<hcp-users@humanconnectome.org<mailto: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 
<lisa.kramare...@gmail.com<mailto:lisa.kramare...@gmail.com>> 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 
<glass...@wustl.edu<mailto:glass...@wustl.edu>> wrote:
Right she would want to comment out stuff that had already been done.

Matt.

From: "Harms, Michael" <mha...@wustl.edu<mailto:mha...@wustl.edu>>
Date: Wednesday, June 7, 2017 at 12:50 PM
To: Matt Glasser <glass...@wustl.edu<mailto:glass...@wustl.edu>>, Lisa 
Kramarenko <lisa.kramare...@gmail.com<mailto:lisa.kramare...@gmail.com>>

Cc: "hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>" 
<hcp-users@humanconnectome.org<mailto: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 Universit

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 
<lisa.kramare...@gmail.com<mailto:lisa.kramare...@gmail.com>>
Date: Thursday, June 8, 2017 at 4:21 AM
To: Matt Glasser <glass...@wustl.edu<mailto:glass...@wustl.edu>>
Cc: "Harms, Michael" <mha...@wustl.edu<mailto:mha...@wustl.edu>>, 
"hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>" 
<hcp-users@humanconnectome.org<mailto: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 
<lisa.kramare...@gmail.com<mailto:lisa.kramare...@gmail.com>> 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 
<glass...@wustl.edu<mailto:glass...@wustl.edu>> wrote:
Right she would want to comment out stuff that had already been done.

Matt.

From: "Harms, Michael" <mha...@wustl.edu<mailto:mha...@wustl.edu>>
Date: Wednesday, June 7, 2017 at 12:50 PM
To: Matt Glasser <glass...@wustl.edu<mailto:glass...@wustl.edu>>, Lisa 
Kramarenko <lisa.kramare...@gmail.com<mailto:lisa.kramare...@gmail.com>>

Cc: "hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>" 
<hcp-users@humanconnectome.org<mailto: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<tel:(314)%20747-6173>
St. Louis, MO  63110Email: mha...@wustl.edu<mailto:mha...@wustl.edu>

From: "Glasser, Matthew" <glass...@wustl.edu<mailto:glass...@wustl.edu>>
Date: Wednesday, June 7, 2017 at 11:55 AM
To: Lisa Kramarenko 
<lisa.kramare...@gmail.com<mailto:lisa.kramare...@gmail.com>>, Michael Harms 
<mha...@wustl.edu<mailto:mha...@wustl.edu>>
Cc: "hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>" 
<hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>>
Subject: Re: [HCP-Users] 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

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 <lisa.kramare...@gmail.com> 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 <glass...@wustl.edu> wrote:
>
>> Right she would want to comment out stuff that had already been done.
>>
>> Matt.
>>
>> From: "Harms, Michael" <mha...@wustl.edu>
>> Date: Wednesday, June 7, 2017 at 12:50 PM
>> To: Matt Glasser <glass...@wustl.edu>, Lisa Kramarenko <
>> lisa.kramare...@gmail.com>
>>
>> Cc: "hcp-users@humanconnectome.org" <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" <glass...@wustl.edu>
>> Date: Wednesday, June 7, 2017 at 11:55 AM
>> To: Lisa Kramarenko <lisa.kramare...@gmail.com>, Michael Harms <
>> mha...@wustl.edu>
>> Cc: "hcp-users@humanconnectome.org" <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 <lisa.kramare.

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 <glass...@wustl.edu> wrote:

> Right she would want to comment out stuff that had already been done.
>
> Matt.
>
> From: "Harms, Michael" <mha...@wustl.edu>
> Date: Wednesday, June 7, 2017 at 12:50 PM
> To: Matt Glasser <glass...@wustl.edu>, Lisa Kramarenko <
> lisa.kramare...@gmail.com>
>
> Cc: "hcp-users@humanconnectome.org" <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" <glass...@wustl.edu>
> Date: Wednesday, June 7, 2017 at 11:55 AM
> To: Lisa Kramarenko <lisa.kramare...@gmail.com>, Michael Harms <
> mha...@wustl.edu>
> Cc: "hcp-users@humanconnectome.org" <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 <lisa.kramare...@gmail.com>
> Date: Wednesday, June 7, 2017 at 11:16 AM
> To: "Harms, Michael" <mha...@wustl.edu>
> Cc: Matt Glasser <glass...@wustl.edu>, "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 <mha...@wustl.edu> 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: <hcp-users-boun...@humanconnectome.org> on behalf of Lisa
>> Kramarenko <lisa.

Re: [HCP-Users] values in myelin maps

2017-06-07 Thread Glasser, Matthew

Right she would want to comment out stuff that had already been done.

Matt.

From: "Harms, Michael" <mha...@wustl.edu<mailto:mha...@wustl.edu>>
Date: Wednesday, June 7, 2017 at 12:50 PM
To: Matt Glasser <glass...@wustl.edu<mailto:glass...@wustl.edu>>, Lisa 
Kramarenko <lisa.kramare...@gmail.com<mailto:lisa.kramare...@gmail.com>>
Cc: "hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>" 
<hcp-users@humanconnectome.org<mailto: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  63110 Email: mha...@wustl.edu<mailto:mha...@wustl.edu>

From: "Glasser, Matthew" <glass...@wustl.edu<mailto:glass...@wustl.edu>>
Date: Wednesday, June 7, 2017 at 11:55 AM
To: Lisa Kramarenko 
<lisa.kramare...@gmail.com<mailto:lisa.kramare...@gmail.com>>, Michael Harms 
<mha...@wustl.edu<mailto:mha...@wustl.edu>>
Cc: "hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>" 
<hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>>
Subject: Re: [HCP-Users] 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 
<lisa.kramare...@gmail.com<mailto:lisa.kramare...@gmail.com>>
Date: Wednesday, June 7, 2017 at 11:16 AM
To: "Harms, Michael" <mha...@wustl.edu<mailto:mha...@wustl.edu>>
Cc: Matt Glasser <glass...@wustl.edu<mailto:glass...@wustl.edu>>, 
"hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>" 
<hcp-users@humanconnectome.org<mailto: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 
<mha...@wustl.edu<mailto:mha...@wustl.edu>> 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<tel:(314)%20747-6173>
St. Louis, MO  63110Email: mha...@wustl.edu<mailto:mha...@wustl.edu>

From: 
<hcp-users-boun...@humanconnectome.org<mailto:hcp-users-boun...@humanconnectome.org>>
 on behalf of Lisa Kramarenko 
<lisa.kramare...@gmail.com<mailto:lisa.kramare...@gmail.com>>
Date: Wednesday, June 7, 2017 at 11:00 AM
To: "Glasser, Matthew" <glass...@wustl.edu<mailto:glass...@wustl.edu>>, 
"hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>" 
<hcp-users@humanconnectome.org<mailto: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 wm.gmz 
in the /mri I need to start the FreeSurfer Pipeline after the step "# 
Generate brain mask" (meaning starting with the step "# Call recon-all to run 
most of the "-autorecon2"

Re: [HCP-Users] values in myelin maps

2017-06-07 Thread Harms, Michael


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  63110 Email: mha...@wustl.edu

From: "Glasser, Matthew" <glass...@wustl.edu<mailto:glass...@wustl.edu>>
Date: Wednesday, June 7, 2017 at 11:55 AM
To: Lisa Kramarenko 
<lisa.kramare...@gmail.com<mailto:lisa.kramare...@gmail.com>>, Michael Harms 
<mha...@wustl.edu<mailto:mha...@wustl.edu>>
Cc: "hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>" 
<hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>>
Subject: Re: [HCP-Users] 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 
<lisa.kramare...@gmail.com<mailto:lisa.kramare...@gmail.com>>
Date: Wednesday, June 7, 2017 at 11:16 AM
To: "Harms, Michael" <mha...@wustl.edu<mailto:mha...@wustl.edu>>
Cc: Matt Glasser <glass...@wustl.edu<mailto:glass...@wustl.edu>>, 
"hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>" 
<hcp-users@humanconnectome.org<mailto: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 
<mha...@wustl.edu<mailto:mha...@wustl.edu>> 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<tel:(314)%20747-6173>
St. Louis, MO  63110Email: mha...@wustl.edu<mailto:mha...@wustl.edu>

From: 
<hcp-users-boun...@humanconnectome.org<mailto:hcp-users-boun...@humanconnectome.org>>
 on behalf of Lisa Kramarenko 
<lisa.kramare...@gmail.com<mailto:lisa.kramare...@gmail.com>>
Date: Wednesday, June 7, 2017 at 11:00 AM
To: "Glasser, Matthew" <glass...@wustl.edu<mailto:glass...@wustl.edu>>, 
"hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>" 
<hcp-users@humanconnectome.org<mailto: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 wm.gmz 
in the /mri I need to start the FreeSurfer Pipeline after the step "# 
Generate brain mask" (meaning starting with the step "# Call recon-all to run 
most of the "-autorecon2" stages, but turning off smooth2, inflate2, curvstats, 
and segstats stages")?
2. Do I need to use any additional flags in the autorecon after my intervention?
3. I also created some control points to fix missing white matter. Should I put 
the control.dat file in the /tmp folder? Will FreeSurfer see the file 
automatically or should I add some flag for it?

thanks a lot for your help!
Lisa

On 30 May 2017 at 16:38, Lisa Kramarenko 
<lisa.kramare...@gmail.com<mailto:lisa.kramare...@gmail.com>> wrote:
thanks

best,
Lisa

On 30 May 2017 at 16:37, Glasser, Matthew 
<glass...@wustl.edu<mai

Re: [HCP-Users] values in myelin maps

2017-06-07 Thread Glasser, Matthew

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 
<lisa.kramare...@gmail.com<mailto:lisa.kramare...@gmail.com>>
Date: Wednesday, June 7, 2017 at 11:16 AM
To: "Harms, Michael" <mha...@wustl.edu<mailto:mha...@wustl.edu>>
Cc: Matt Glasser <glass...@wustl.edu<mailto:glass...@wustl.edu>>, 
"hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>" 
<hcp-users@humanconnectome.org<mailto: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 
<mha...@wustl.edu<mailto:mha...@wustl.edu>> 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<tel:(314)%20747-6173>
St. Louis, MO  63110Email: mha...@wustl.edu<mailto:mha...@wustl.edu>

From: 
<hcp-users-boun...@humanconnectome.org<mailto:hcp-users-boun...@humanconnectome.org>>
 on behalf of Lisa Kramarenko 
<lisa.kramare...@gmail.com<mailto:lisa.kramare...@gmail.com>>
Date: Wednesday, June 7, 2017 at 11:00 AM
To: "Glasser, Matthew" <glass...@wustl.edu<mailto:glass...@wustl.edu>>, 
"hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>" 
<hcp-users@humanconnectome.org<mailto: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 wm.gmz 
in the /mri I need to start the FreeSurfer Pipeline after the step "# 
Generate brain mask" (meaning starting with the step "# Call recon-all to run 
most of the "-autorecon2" stages, but turning off smooth2, inflate2, curvstats, 
and segstats stages")?
2. Do I need to use any additional flags in the autorecon after my intervention?
3. I also created some control points to fix missing white matter. Should I put 
the control.dat file in the /tmp folder? Will FreeSurfer see the file 
automatically or should I add some flag for it?

thanks a lot for your help!
Lisa

On 30 May 2017 at 16:38, Lisa Kramarenko 
<lisa.kramare...@gmail.com<mailto:lisa.kramare...@gmail.com>> wrote:
thanks

best,
Lisa

On 30 May 2017 at 16:37, Glasser, Matthew 
<glass...@wustl.edu<mailto:glass...@wustl.edu>> wrote:
Yes.

Peace,

Matt.

From: Lisa Kramarenko 
<lisa.kramare...@gmail.com<mailto:lisa.kramare...@gmail.com>>
Date: Tuesday, May 30, 2017 at 9:31 AM

To: Matt Glasser <glass...@wustl.edu<mailto:glass...@wustl.edu>>
Cc: "hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>" 
<hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>>
Subject: Re: [HCP-Users] values in myelin maps

do I find the files I should inspect in the {subject_id}/T1w/{subject_id}/mri/ 
folder?

On 30 May 2017 at 16:28, Lisa Kramarenko 
<lisa.kramare...@gmail.com<mailto:lisa.kramare...@gmail.com>> wrote:
ok. so basically just go through recon-all output and manually correct whatever 
might have gone wrong?

best,
Lisa

On 30 May 2017 at 16:13, Glasser, Matthew 
<glass...@wustl.edu<mailto:glass...@wustl.edu>> wrote:
I would look for locations in which the FreeSurfer aseg is clearly labeling 
things outside of the brain as grey or white matter.

Peace,

Matt.

From: Lisa Kramarenko 
<lisa.kramare...@gmail.com<mailto:l

Re: [HCP-Users] values in myelin maps

2017-06-07 Thread Lisa Kramarenko

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 <mha...@wustl.edu> 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  63110 Email: mha...@wustl.edu
>
> From: <hcp-users-boun...@humanconnectome.org> on behalf of Lisa
> Kramarenko <lisa.kramare...@gmail.com>
> Date: Wednesday, June 7, 2017 at 11:00 AM
> To: "Glasser, Matthew" <glass...@wustl.edu>, "
> hcp-users@humanconnectome.org" <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
> wm.gmz in the /mri I need to start the FreeSurfer Pipeline after
> the step "# Generate brain mask" (meaning starting with the step "# Call
> recon-all to run most of the "-autorecon2" stages, but turning off smooth2,
> inflate2, curvstats, and segstats stages")?
> 2. Do I need to use any additional flags in the autorecon after my
> intervention?
> 3. I also created some control points to fix missing white matter. Should
> I put the control.dat file in the /tmp folder? Will FreeSurfer
> see the file automatically or should I add some flag for it?
>
> thanks a lot for your help!
> Lisa
>
> On 30 May 2017 at 16:38, Lisa Kramarenko <lisa.kramare...@gmail.com>
> wrote:
>
>> thanks
>>
>> best,
>> Lisa
>>
>> On 30 May 2017 at 16:37, Glasser, Matthew <glass...@wustl.edu> wrote:
>>
>>> Yes.
>>>
>>> Peace,
>>>
>>> Matt.
>>>
>>> From: Lisa Kramarenko <lisa.kramare...@gmail.com>
>>> Date: Tuesday, May 30, 2017 at 9:31 AM
>>>
>>> To: Matt Glasser <glass...@wustl.edu>
>>> Cc: "hcp-users@humanconnectome.org" <hcp-users@humanconnectome.org>
>>> Subject: Re: [HCP-Users] values in myelin maps
>>>
>>> do I find the files I should inspect in the
>>> {subject_id}/T1w/{subject_id}/mri/ folder?
>>>
>>> On 30 May 2017 at 16:28, Lisa Kramarenko <lisa.kramare...@gmail.com>
>>> wrote:
>>>
>>>> ok. so basically just go through recon-all output and manually correct
>>>> whatever might have gone wrong?
>>>>
>>>> best,
>>>> Lisa
>>>>
>>>> On 30 May 2017 at 16:13, Glasser, Matthew <glass...@wustl.edu> wrote:
>>>>
>>>>> I would look for locations in which the FreeSurfer aseg is clearly
>>>>> labeling things outside of the brain as grey or white matter.
>>>>>
>>>>> Peace,
>>>>>
>>>>> Matt.
>>>>>
>>>>> From: Lisa Kramarenko <lisa.kramare...@gmail.com>
>>>>> Date: Tuesday, May 30, 2017 at 8:59 AM
>>>>>
>>>>> To: Matt Glasser <glass...@wustl.edu>
>>>>> Cc: "hcp-users@humanconnectome.org" <hcp-users@humanconnectome.org>
>>>>> Subject: Re: [HCP-Users] values in myelin maps
>>>>>
>>>>> Alright, thanks for the quick reply! Should I look for some specific
>>>>> problem with the surfaces which is to be fixed? I mean I imagine a lot of
>>>>> things can go wrong with a surface, so that I need to know what exactly to
>>>>> fix? Or is it something more general like this:
>>>>> http://sites.bu.edu/cnrlab/lab-resources/freesurfer-qu
>>>>> ality-control-guide/freesurfer-quality-control-step-1-fix-pi
>>>>> al-surface/  ?
>>>>>
>>>>> And does it look like it affect both pial and white matter surfaces,
>>>>> so that both need to be fixed?
>>>>>
>>>>> Sorry for the naive questions and thanks again.
>>>>>
>>>>> On 30 Ma

Re: [HCP-Users] values in myelin maps

2017-06-07 Thread Harms, Michael


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
St. Louis, MO  63110 Email: mha...@wustl.edu

From: 
<hcp-users-boun...@humanconnectome.org<mailto:hcp-users-boun...@humanconnectome.org>>
 on behalf of Lisa Kramarenko 
<lisa.kramare...@gmail.com<mailto:lisa.kramare...@gmail.com>>
Date: Wednesday, June 7, 2017 at 11:00 AM
To: "Glasser, Matthew" <glass...@wustl.edu<mailto:glass...@wustl.edu>>, 
"hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>" 
<hcp-users@humanconnectome.org<mailto: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 wm.gmz 
in the /mri I need to start the FreeSurfer Pipeline after the step "# 
Generate brain mask" (meaning starting with the step "# Call recon-all to run 
most of the "-autorecon2" stages, but turning off smooth2, inflate2, curvstats, 
and segstats stages")?
2. Do I need to use any additional flags in the autorecon after my intervention?
3. I also created some control points to fix missing white matter. Should I put 
the control.dat file in the /tmp folder? Will FreeSurfer see the file 
automatically or should I add some flag for it?

thanks a lot for your help!
Lisa

On 30 May 2017 at 16:38, Lisa Kramarenko 
<lisa.kramare...@gmail.com<mailto:lisa.kramare...@gmail.com>> wrote:
thanks

best,
Lisa

On 30 May 2017 at 16:37, Glasser, Matthew 
<glass...@wustl.edu<mailto:glass...@wustl.edu>> wrote:
Yes.

Peace,

Matt.

From: Lisa Kramarenko 
<lisa.kramare...@gmail.com<mailto:lisa.kramare...@gmail.com>>
Date: Tuesday, May 30, 2017 at 9:31 AM

To: Matt Glasser <glass...@wustl.edu<mailto:glass...@wustl.edu>>
Cc: "hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>" 
<hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>>
Subject: Re: [HCP-Users] values in myelin maps

do I find the files I should inspect in the {subject_id}/T1w/{subject_id}/mri/ 
folder?

On 30 May 2017 at 16:28, Lisa Kramarenko 
<lisa.kramare...@gmail.com<mailto:lisa.kramare...@gmail.com>> wrote:
ok. so basically just go through recon-all output and manually correct whatever 
might have gone wrong?

best,
Lisa

On 30 May 2017 at 16:13, Glasser, Matthew 
<glass...@wustl.edu<mailto:glass...@wustl.edu>> wrote:
I would look for locations in which the FreeSurfer aseg is clearly labeling 
things outside of the brain as grey or white matter.

Peace,

Matt.

From: Lisa Kramarenko 
<lisa.kramare...@gmail.com<mailto:lisa.kramare...@gmail.com>>
Date: Tuesday, May 30, 2017 at 8:59 AM

To: Matt Glasser <glass...@wustl.edu<mailto:glass...@wustl.edu>>
Cc: "hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>" 
<hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>>
Subject: Re: [HCP-Users] values in myelin maps

Alright, thanks for the quick reply! Should I look for some specific problem 
with the surfaces which is to be fixed? I mean I imagine a lot of things can go 
wrong with a surface, so that I need to know what exactly to fix? Or is it 
something more general like this: 
http://sites.bu.edu/cnrlab/lab-resources/freesurfer-quality-control-guide/freesurfer-quality-control-step-1-fix-pial-surface/
  ?

And does it look like it affect both pial and white matter surfaces, so that 
both need to be fixed?

Sorry for the naive questions and thanks again.

On 30 May 2017 at 15:51, Glasser, Matthew 
<glass...@wustl.edu<mailto:glass...@wustl.edu>> wrote:
Fat saturation reduces the intensity of the fat within the bone marrow, which 
reduces the chance that FreeSurfer will mistake this fat for white matter.  You 
would need to have this on during acquisition.  As for how to fix the surfaces 
after the fact, I would look at FreeSurfer’s documentation.

Peace,

Matt.

From: Lisa Kramarenko 
<lisa.kramare...@gmail.com<mailto:lisa.kramare...@gmail.com>>
Date: Tuesday, May 30, 2017 at 8:49 AM

To: Matt Glasser <glass...@wustl.edu<mailto:glass...@wustl.edu>>
Cc: "hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>" 
<hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>>

Re: [HCP-Users] values in myelin maps

2017-06-07 Thread Lisa Kramarenko

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
wm.gmz in the /mri I need to start the FreeSurfer Pipeline after
the step "# Generate brain mask" (meaning starting with the step "# Call
recon-all to run most of the "-autorecon2" stages, but turning off smooth2,
inflate2, curvstats, and segstats stages")?
2. Do I need to use any additional flags in the autorecon after my
intervention?
3. I also created some control points to fix missing white matter. Should I
put the control.dat file in the /tmp folder? Will FreeSurfer see
the file automatically or should I add some flag for it?

thanks a lot for your help!
Lisa

On 30 May 2017 at 16:38, Lisa Kramarenko <lisa.kramare...@gmail.com> wrote:

> thanks
>
> best,
> Lisa
>
> On 30 May 2017 at 16:37, Glasser, Matthew <glass...@wustl.edu> wrote:
>
>> Yes.
>>
>> Peace,
>>
>> Matt.
>>
>> From: Lisa Kramarenko <lisa.kramare...@gmail.com>
>> Date: Tuesday, May 30, 2017 at 9:31 AM
>>
>> To: Matt Glasser <glass...@wustl.edu>
>> Cc: "hcp-users@humanconnectome.org" <hcp-users@humanconnectome.org>
>> Subject: Re: [HCP-Users] values in myelin maps
>>
>> do I find the files I should inspect in the 
>> {subject_id}/T1w/{subject_id}/mri/
>> folder?
>>
>> On 30 May 2017 at 16:28, Lisa Kramarenko <lisa.kramare...@gmail.com>
>> wrote:
>>
>>> ok. so basically just go through recon-all output and manually correct
>>> whatever might have gone wrong?
>>>
>>> best,
>>> Lisa
>>>
>>> On 30 May 2017 at 16:13, Glasser, Matthew <glass...@wustl.edu> wrote:
>>>
>>>> I would look for locations in which the FreeSurfer aseg is clearly
>>>> labeling things outside of the brain as grey or white matter.
>>>>
>>>> Peace,
>>>>
>>>> Matt.
>>>>
>>>> From: Lisa Kramarenko <lisa.kramare...@gmail.com>
>>>> Date: Tuesday, May 30, 2017 at 8:59 AM
>>>>
>>>> To: Matt Glasser <glass...@wustl.edu>
>>>> Cc: "hcp-users@humanconnectome.org" <hcp-users@humanconnectome.org>
>>>> Subject: Re: [HCP-Users] values in myelin maps
>>>>
>>>> Alright, thanks for the quick reply! Should I look for some specific
>>>> problem with the surfaces which is to be fixed? I mean I imagine a lot of
>>>> things can go wrong with a surface, so that I need to know what exactly to
>>>> fix? Or is it something more general like this:
>>>> http://sites.bu.edu/cnrlab/lab-resources/freesurfer-qu
>>>> ality-control-guide/freesurfer-quality-control-step-1-fix-pial-surface/
>>>>  ?
>>>>
>>>> And does it look like it affect both pial and white matter surfaces, so
>>>> that both need to be fixed?
>>>>
>>>> Sorry for the naive questions and thanks again.
>>>>
>>>> On 30 May 2017 at 15:51, Glasser, Matthew <glass...@wustl.edu> wrote:
>>>>
>>>>> Fat saturation reduces the intensity of the fat within the bone
>>>>> marrow, which reduces the chance that FreeSurfer will mistake this fat for
>>>>> white matter.  You would need to have this on during acquisition.  As for
>>>>> how to fix the surfaces after the fact, I would look at FreeSurfer’s
>>>>> documentation.
>>>>>
>>>>> Peace,
>>>>>
>>>>> Matt.
>>>>>
>>>>> From: Lisa Kramarenko <lisa.kramare...@gmail.com>
>>>>> Date: Tuesday, May 30, 2017 at 8:49 AM
>>>>>
>>>>> To: Matt Glasser <glass...@wustl.edu>
>>>>> Cc: "hcp-users@humanconnectome.org" <hcp-users@humanconnectome.org>
>>>>> Subject: Re: [HCP-Users] values in myelin maps
>>>>>
>>>>> Yes, this is data of the lab I am in. I assume that I don't have fat
>>>>> saturation as I have never heard about it before... If I understand
>>>>> correctly it can't be done post-hoc after acquisition and should have been
>>>>> done during scanning? Other patients from the same batch (acquired the 
>>>>> same
>>>>> way) don't have this problem.
>>>>> What would be the way to fix the surfaces manually?
>&g

Re: [HCP-Users] values in myelin maps

2017-05-30 Thread Glasser, Matthew

Yes.

Peace,

Matt.

From: Lisa Kramarenko 
<lisa.kramare...@gmail.com<mailto:lisa.kramare...@gmail.com>>
Date: Tuesday, May 30, 2017 at 9:31 AM
To: Matt Glasser <glass...@wustl.edu<mailto:glass...@wustl.edu>>
Cc: "hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>" 
<hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>>
Subject: Re: [HCP-Users] values in myelin maps

do I find the files I should inspect in the {subject_id}/T1w/{subject_id}/mri/ 
folder?

On 30 May 2017 at 16:28, Lisa Kramarenko 
<lisa.kramare...@gmail.com<mailto:lisa.kramare...@gmail.com>> wrote:
ok. so basically just go through recon-all output and manually correct whatever 
might have gone wrong?

best,
Lisa

On 30 May 2017 at 16:13, Glasser, Matthew 
<glass...@wustl.edu<mailto:glass...@wustl.edu>> wrote:
I would look for locations in which the FreeSurfer aseg is clearly labeling 
things outside of the brain as grey or white matter.

Peace,

Matt.

From: Lisa Kramarenko 
<lisa.kramare...@gmail.com<mailto:lisa.kramare...@gmail.com>>
Date: Tuesday, May 30, 2017 at 8:59 AM

To: Matt Glasser <glass...@wustl.edu<mailto:glass...@wustl.edu>>
Cc: "hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>" 
<hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>>
Subject: Re: [HCP-Users] values in myelin maps

Alright, thanks for the quick reply! Should I look for some specific problem 
with the surfaces which is to be fixed? I mean I imagine a lot of things can go 
wrong with a surface, so that I need to know what exactly to fix? Or is it 
something more general like this: 
http://sites.bu.edu/cnrlab/lab-resources/freesurfer-quality-control-guide/freesurfer-quality-control-step-1-fix-pial-surface/
  ?

And does it look like it affect both pial and white matter surfaces, so that 
both need to be fixed?

Sorry for the naive questions and thanks again.

On 30 May 2017 at 15:51, Glasser, Matthew 
<glass...@wustl.edu<mailto:glass...@wustl.edu>> wrote:
Fat saturation reduces the intensity of the fat within the bone marrow, which 
reduces the chance that FreeSurfer will mistake this fat for white matter.  You 
would need to have this on during acquisition.  As for how to fix the surfaces 
after the fact, I would look at FreeSurfer’s documentation.

Peace,

Matt.

From: Lisa Kramarenko 
<lisa.kramare...@gmail.com<mailto:lisa.kramare...@gmail.com>>
Date: Tuesday, May 30, 2017 at 8:49 AM

To: Matt Glasser <glass...@wustl.edu<mailto:glass...@wustl.edu>>
Cc: "hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>" 
<hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>>
Subject: Re: [HCP-Users] values in myelin maps

Yes, this is data of the lab I am in. I assume that I don't have fat saturation 
as I have never heard about it before... If I understand correctly it can't be 
done post-hoc after acquisition and should have been done during scanning? 
Other patients from the same batch (acquired the same way) don't have this 
problem.
What would be the way to fix the surfaces manually?

Thanks a lot!

On 30 May 2017 at 15:42, Glasser, Matthew 
<glass...@wustl.edu<mailto:glass...@wustl.edu>> wrote:
Are these of your own data?  Do you have fat sat on in your T1w?  This looks 
like most likely surface errors because of not using fat sat and you would need 
to exclude these subjects or fix the surfaces manually.

Peace,

Matt.

From: Lisa Kramarenko 
<lisa.kramare...@gmail.com<mailto:lisa.kramare...@gmail.com>>
Date: Tuesday, May 30, 2017 at 7:53 AM
To: Matt Glasser <glass...@wustl.edu<mailto:glass...@wustl.edu>>
Cc: "hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>" 
<hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>>
Subject: Re: [HCP-Users] values in myelin maps

Thanks!
 Another question I have concerning myelin maps is the following: when I was 
doing quality control I noticed that some of them look rather weird (see 
screenshot). Why are some areas grey? And I presume the fact that the values in 
this grey area are negative, indicates that something is wrong... And are the 
black parts normal (they still have positive values)? Do you have an idea of 
what to do?

Thanks a lot!

Lisa

On 29 May 2017 at 15:55, Glasser, Matthew 
<glass...@wustl.edu<mailto:glass...@wustl.edu>> wrote:
They are the ratio of the T1w/T2w images and are a relative measure of myelin 
content.  See this publication for more details:

http://www.jneurosci.org/content/31/32/11597.short

Peace,

Matt.

From: 
<hcp-users-boun...@humanconnectome.org<mailto:hcp-users-boun...@humanconnectome.org>>
 on behalf of Lisa Kramarenko 
<lisa.kramare...@gmail.com<mailto:lisa.kramare...@gmail.co

Re: [HCP-Users] values in myelin maps

2017-05-30 Thread Lisa Kramarenko

ok. so basically just go through recon-all output and manually correct
whatever might have gone wrong?

best,
Lisa

On 30 May 2017 at 16:13, Glasser, Matthew <glass...@wustl.edu> wrote:

> I would look for locations in which the FreeSurfer aseg is clearly
> labeling things outside of the brain as grey or white matter.
>
> Peace,
>
> Matt.
>
> From: Lisa Kramarenko <lisa.kramare...@gmail.com>
> Date: Tuesday, May 30, 2017 at 8:59 AM
>
> To: Matt Glasser <glass...@wustl.edu>
> Cc: "hcp-users@humanconnectome.org" <hcp-users@humanconnectome.org>
> Subject: Re: [HCP-Users] values in myelin maps
>
> Alright, thanks for the quick reply! Should I look for some specific
> problem with the surfaces which is to be fixed? I mean I imagine a lot of
> things can go wrong with a surface, so that I need to know what exactly to
> fix? Or is it something more general like this: http://sites.bu.edu/
> cnrlab/lab-resources/freesurfer-quality-control-guide/freesurfer-quality-
> control-step-1-fix-pial-surface/  ?
>
> And does it look like it affect both pial and white matter surfaces, so
> that both need to be fixed?
>
> Sorry for the naive questions and thanks again.
>
> On 30 May 2017 at 15:51, Glasser, Matthew <glass...@wustl.edu> wrote:
>
>> Fat saturation reduces the intensity of the fat within the bone marrow,
>> which reduces the chance that FreeSurfer will mistake this fat for white
>> matter.  You would need to have this on during acquisition.  As for how to
>> fix the surfaces after the fact, I would look at FreeSurfer’s
>> documentation.
>>
>> Peace,
>>
>> Matt.
>>
>> From: Lisa Kramarenko <lisa.kramare...@gmail.com>
>> Date: Tuesday, May 30, 2017 at 8:49 AM
>>
>> To: Matt Glasser <glass...@wustl.edu>
>> Cc: "hcp-users@humanconnectome.org" <hcp-users@humanconnectome.org>
>> Subject: Re: [HCP-Users] values in myelin maps
>>
>> Yes, this is data of the lab I am in. I assume that I don't have fat
>> saturation as I have never heard about it before... If I understand
>> correctly it can't be done post-hoc after acquisition and should have been
>> done during scanning? Other patients from the same batch (acquired the same
>> way) don't have this problem.
>> What would be the way to fix the surfaces manually?
>>
>> Thanks a lot!
>>
>> On 30 May 2017 at 15:42, Glasser, Matthew <glass...@wustl.edu> wrote:
>>
>>> Are these of your own data?  Do you have fat sat on in your T1w?  This
>>> looks like most likely surface errors because of not using fat sat and you
>>> would need to exclude these subjects or fix the surfaces manually.
>>>
>>> Peace,
>>>
>>> Matt.
>>>
>>> From: Lisa Kramarenko <lisa.kramare...@gmail.com>
>>> Date: Tuesday, May 30, 2017 at 7:53 AM
>>> To: Matt Glasser <glass...@wustl.edu>
>>> Cc: "hcp-users@humanconnectome.org" <hcp-users@humanconnectome.org>
>>> Subject: Re: [HCP-Users] values in myelin maps
>>>
>>> Thanks!
>>>  Another question I have concerning myelin maps is the following: when I
>>> was doing quality control I noticed that some of them look rather weird
>>> (see screenshot). Why are some areas grey? And I presume the fact that the
>>> values in this grey area are negative, indicates that something is wrong...
>>> And are the black parts normal (they still have positive values)? Do you
>>> have an idea of what to do?
>>>
>>> Thanks a lot!
>>>
>>> Lisa
>>>
>>> On 29 May 2017 at 15:55, Glasser, Matthew <glass...@wustl.edu> wrote:
>>>
>>>> They are the ratio of the T1w/T2w images and are a relative measure of
>>>> myelin content.  See this publication for more details:
>>>>
>>>> http://www.jneurosci.org/content/31/32/11597.short
>>>>
>>>> Peace,
>>>>
>>>> Matt.
>>>>
>>>> From: <hcp-users-boun...@humanconnectome.org> on behalf of Lisa
>>>> Kramarenko <lisa.kramare...@gmail.com>
>>>> Date: Monday, May 29, 2017 at 5:29 AM
>>>> To: "hcp-users@humanconnectome.org" <hcp-users@humanconnectome.org>
>>>> Subject: [HCP-Users] values in myelin maps
>>>>
>>>> Hello,
>>>>
>>>> I am not sure what exactly are the values shown for the myelin maps.
>>>> E.g. on the screenshot the values are 0.998 to 1.771. I understand that
>>>> higher values mean higher myelination and vice versa, but what do they mean
>>>> exactly?
>>>> Thanks!
>>>>
>>>> Lisa
>>>>
>>>> ___
>>>> HCP-Users mailing list
>>>> HCP-Users@humanconnectome.org
>>>> http://lists.humanconnectome.org/mailman/listinfo/hcp-users
>>>>
>>>
>>>
>>
>

___
HCP-Users mailing list
HCP-Users@humanconnectome.org
http://lists.humanconnectome.org/mailman/listinfo/hcp-users

Re: [HCP-Users] values in myelin maps

2017-05-30 Thread Glasser, Matthew

I would look for locations in which the FreeSurfer aseg is clearly labeling 
things outside of the brain as grey or white matter.

Peace,

Matt.

From: Lisa Kramarenko 
<lisa.kramare...@gmail.com<mailto:lisa.kramare...@gmail.com>>
Date: Tuesday, May 30, 2017 at 8:59 AM
To: Matt Glasser <glass...@wustl.edu<mailto:glass...@wustl.edu>>
Cc: "hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>" 
<hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>>
Subject: Re: [HCP-Users] values in myelin maps

Alright, thanks for the quick reply! Should I look for some specific problem 
with the surfaces which is to be fixed? I mean I imagine a lot of things can go 
wrong with a surface, so that I need to know what exactly to fix? Or is it 
something more general like this: 
http://sites.bu.edu/cnrlab/lab-resources/freesurfer-quality-control-guide/freesurfer-quality-control-step-1-fix-pial-surface/
  ?

And does it look like it affect both pial and white matter surfaces, so that 
both need to be fixed?

Sorry for the naive questions and thanks again.

On 30 May 2017 at 15:51, Glasser, Matthew 
<glass...@wustl.edu<mailto:glass...@wustl.edu>> wrote:
Fat saturation reduces the intensity of the fat within the bone marrow, which 
reduces the chance that FreeSurfer will mistake this fat for white matter.  You 
would need to have this on during acquisition.  As for how to fix the surfaces 
after the fact, I would look at FreeSurfer’s documentation.

Peace,

Matt.

From: Lisa Kramarenko 
<lisa.kramare...@gmail.com<mailto:lisa.kramare...@gmail.com>>
Date: Tuesday, May 30, 2017 at 8:49 AM

To: Matt Glasser <glass...@wustl.edu<mailto:glass...@wustl.edu>>
Cc: "hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>" 
<hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>>
Subject: Re: [HCP-Users] values in myelin maps

Yes, this is data of the lab I am in. I assume that I don't have fat saturation 
as I have never heard about it before... If I understand correctly it can't be 
done post-hoc after acquisition and should have been done during scanning? 
Other patients from the same batch (acquired the same way) don't have this 
problem.
What would be the way to fix the surfaces manually?

Thanks a lot!

On 30 May 2017 at 15:42, Glasser, Matthew 
<glass...@wustl.edu<mailto:glass...@wustl.edu>> wrote:
Are these of your own data?  Do you have fat sat on in your T1w?  This looks 
like most likely surface errors because of not using fat sat and you would need 
to exclude these subjects or fix the surfaces manually.

Peace,

Matt.

From: Lisa Kramarenko 
<lisa.kramare...@gmail.com<mailto:lisa.kramare...@gmail.com>>
Date: Tuesday, May 30, 2017 at 7:53 AM
To: Matt Glasser <glass...@wustl.edu<mailto:glass...@wustl.edu>>
Cc: "hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>" 
<hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>>
Subject: Re: [HCP-Users] values in myelin maps

Thanks!
 Another question I have concerning myelin maps is the following: when I was 
doing quality control I noticed that some of them look rather weird (see 
screenshot). Why are some areas grey? And I presume the fact that the values in 
this grey area are negative, indicates that something is wrong... And are the 
black parts normal (they still have positive values)? Do you have an idea of 
what to do?

Thanks a lot!

Lisa

On 29 May 2017 at 15:55, Glasser, Matthew 
<glass...@wustl.edu<mailto:glass...@wustl.edu>> wrote:
They are the ratio of the T1w/T2w images and are a relative measure of myelin 
content.  See this publication for more details:

http://www.jneurosci.org/content/31/32/11597.short

Peace,

Matt.

From: 
<hcp-users-boun...@humanconnectome.org<mailto:hcp-users-boun...@humanconnectome.org>>
 on behalf of Lisa Kramarenko 
<lisa.kramare...@gmail.com<mailto:lisa.kramare...@gmail.com>>
Date: Monday, May 29, 2017 at 5:29 AM
To: "hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>" 
<hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>>
Subject: [HCP-Users] values in myelin maps

Hello,

I am not sure what exactly are the values shown for the myelin maps. E.g. on 
the screenshot the values are 0.998 to 1.771. I understand that higher values 
mean higher myelination and vice versa, but what do they mean exactly?
Thanks!

Lisa

___
HCP-Users mailing list
HCP-Users@humanconnectome.org<mailto:HCP-Users@humanconnectome.org>
http://lists.humanconnectome.org/mailman/listinfo/hcp-users

___
HCP-Users mailing list
HCP-Users@humanconnectome.org
http://lists.humanconnectome.org/mailman/listinfo/hcp-users

Re: [HCP-Users] values in myelin maps

2017-05-30 Thread Lisa Kramarenko

Alright, thanks for the quick reply! Should I look for some specific
problem with the surfaces which is to be fixed? I mean I imagine a lot of
things can go wrong with a surface, so that I need to know what exactly to
fix? Or is it something more general like this:
http://sites.bu.edu/cnrlab/lab-resources/freesurfer-quality-control-guide/freesurfer-quality-control-step-1-fix-pial-surface/
 ?

And does it look like it affect both pial and white matter surfaces, so
that both need to be fixed?

Sorry for the naive questions and thanks again.

On 30 May 2017 at 15:51, Glasser, Matthew <glass...@wustl.edu> wrote:

> Fat saturation reduces the intensity of the fat within the bone marrow,
> which reduces the chance that FreeSurfer will mistake this fat for white
> matter.  You would need to have this on during acquisition.  As for how to
> fix the surfaces after the fact, I would look at FreeSurfer’s
> documentation.
>
> Peace,
>
> Matt.
>
> From: Lisa Kramarenko <lisa.kramare...@gmail.com>
> Date: Tuesday, May 30, 2017 at 8:49 AM
>
> To: Matt Glasser <glass...@wustl.edu>
> Cc: "hcp-users@humanconnectome.org" <hcp-users@humanconnectome.org>
> Subject: Re: [HCP-Users] values in myelin maps
>
> Yes, this is data of the lab I am in. I assume that I don't have fat
> saturation as I have never heard about it before... If I understand
> correctly it can't be done post-hoc after acquisition and should have been
> done during scanning? Other patients from the same batch (acquired the same
> way) don't have this problem.
> What would be the way to fix the surfaces manually?
>
> Thanks a lot!
>
> On 30 May 2017 at 15:42, Glasser, Matthew <glass...@wustl.edu> wrote:
>
>> Are these of your own data?  Do you have fat sat on in your T1w?  This
>> looks like most likely surface errors because of not using fat sat and you
>> would need to exclude these subjects or fix the surfaces manually.
>>
>> Peace,
>>
>> Matt.
>>
>> From: Lisa Kramarenko <lisa.kramare...@gmail.com>
>> Date: Tuesday, May 30, 2017 at 7:53 AM
>> To: Matt Glasser <glass...@wustl.edu>
>> Cc: "hcp-users@humanconnectome.org" <hcp-users@humanconnectome.org>
>> Subject: Re: [HCP-Users] values in myelin maps
>>
>> Thanks!
>>  Another question I have concerning myelin maps is the following: when I
>> was doing quality control I noticed that some of them look rather weird
>> (see screenshot). Why are some areas grey? And I presume the fact that the
>> values in this grey area are negative, indicates that something is wrong...
>> And are the black parts normal (they still have positive values)? Do you
>> have an idea of what to do?
>>
>> Thanks a lot!
>>
>> Lisa
>>
>> On 29 May 2017 at 15:55, Glasser, Matthew <glass...@wustl.edu> wrote:
>>
>>> They are the ratio of the T1w/T2w images and are a relative measure of
>>> myelin content.  See this publication for more details:
>>>
>>> http://www.jneurosci.org/content/31/32/11597.short
>>>
>>> Peace,
>>>
>>> Matt.
>>>
>>> From: <hcp-users-boun...@humanconnectome.org> on behalf of Lisa
>>> Kramarenko <lisa.kramare...@gmail.com>
>>> Date: Monday, May 29, 2017 at 5:29 AM
>>> To: "hcp-users@humanconnectome.org" <hcp-users@humanconnectome.org>
>>> Subject: [HCP-Users] values in myelin maps
>>>
>>> Hello,
>>>
>>> I am not sure what exactly are the values shown for the myelin maps.
>>> E.g. on the screenshot the values are 0.998 to 1.771. I understand that
>>> higher values mean higher myelination and vice versa, but what do they mean
>>> exactly?
>>> Thanks!
>>>
>>> Lisa
>>>
>>> ___
>>> 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

2017-05-30 Thread Glasser, Matthew

Fat saturation reduces the intensity of the fat within the bone marrow, which 
reduces the chance that FreeSurfer will mistake this fat for white matter.  You 
would need to have this on during acquisition.  As for how to fix the surfaces 
after the fact, I would look at FreeSurfer’s documentation.

Peace,

Matt.

From: Lisa Kramarenko 
<lisa.kramare...@gmail.com<mailto:lisa.kramare...@gmail.com>>
Date: Tuesday, May 30, 2017 at 8:49 AM
To: Matt Glasser <glass...@wustl.edu<mailto:glass...@wustl.edu>>
Cc: "hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>" 
<hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>>
Subject: Re: [HCP-Users] values in myelin maps

Yes, this is data of the lab I am in. I assume that I don't have fat saturation 
as I have never heard about it before... If I understand correctly it can't be 
done post-hoc after acquisition and should have been done during scanning? 
Other patients from the same batch (acquired the same way) don't have this 
problem.
What would be the way to fix the surfaces manually?

Thanks a lot!

On 30 May 2017 at 15:42, Glasser, Matthew 
<glass...@wustl.edu<mailto:glass...@wustl.edu>> wrote:
Are these of your own data?  Do you have fat sat on in your T1w?  This looks 
like most likely surface errors because of not using fat sat and you would need 
to exclude these subjects or fix the surfaces manually.

Peace,

Matt.

From: Lisa Kramarenko 
<lisa.kramare...@gmail.com<mailto:lisa.kramare...@gmail.com>>
Date: Tuesday, May 30, 2017 at 7:53 AM
To: Matt Glasser <glass...@wustl.edu<mailto:glass...@wustl.edu>>
Cc: "hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>" 
<hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>>
Subject: Re: [HCP-Users] values in myelin maps

Thanks!
 Another question I have concerning myelin maps is the following: when I was 
doing quality control I noticed that some of them look rather weird (see 
screenshot). Why are some areas grey? And I presume the fact that the values in 
this grey area are negative, indicates that something is wrong... And are the 
black parts normal (they still have positive values)? Do you have an idea of 
what to do?

Thanks a lot!

Lisa

On 29 May 2017 at 15:55, Glasser, Matthew 
<glass...@wustl.edu<mailto:glass...@wustl.edu>> wrote:
They are the ratio of the T1w/T2w images and are a relative measure of myelin 
content.  See this publication for more details:

http://www.jneurosci.org/content/31/32/11597.short

Peace,

Matt.

From: 
<hcp-users-boun...@humanconnectome.org<mailto:hcp-users-boun...@humanconnectome.org>>
 on behalf of Lisa Kramarenko 
<lisa.kramare...@gmail.com<mailto:lisa.kramare...@gmail.com>>
Date: Monday, May 29, 2017 at 5:29 AM
To: "hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>" 
<hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>>
Subject: [HCP-Users] values in myelin maps

Hello,

I am not sure what exactly are the values shown for the myelin maps. E.g. on 
the screenshot the values are 0.998 to 1.771. I understand that higher values 
mean higher myelination and vice versa, but what do they mean exactly?
Thanks!

Lisa

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Re: [HCP-Users] values in myelin maps

2017-05-30 Thread Lisa Kramarenko

Yes, this is data of the lab I am in. I assume that I don't have fat
saturation as I have never heard about it before... If I understand
correctly it can't be done post-hoc after acquisition and should have been
done during scanning? Other patients from the same batch (acquired the same
way) don't have this problem.
What would be the way to fix the surfaces manually?

Thanks a lot!

On 30 May 2017 at 15:42, Glasser, Matthew <glass...@wustl.edu> wrote:

> Are these of your own data?  Do you have fat sat on in your T1w?  This
> looks like most likely surface errors because of not using fat sat and you
> would need to exclude these subjects or fix the surfaces manually.
>
> Peace,
>
> Matt.
>
> From: Lisa Kramarenko <lisa.kramare...@gmail.com>
> Date: Tuesday, May 30, 2017 at 7:53 AM
> To: Matt Glasser <glass...@wustl.edu>
> Cc: "hcp-users@humanconnectome.org" <hcp-users@humanconnectome.org>
> Subject: Re: [HCP-Users] values in myelin maps
>
> Thanks!
>  Another question I have concerning myelin maps is the following: when I
> was doing quality control I noticed that some of them look rather weird
> (see screenshot). Why are some areas grey? And I presume the fact that the
> values in this grey area are negative, indicates that something is wrong...
> And are the black parts normal (they still have positive values)? Do you
> have an idea of what to do?
>
> Thanks a lot!
>
> Lisa
>
> On 29 May 2017 at 15:55, Glasser, Matthew <glass...@wustl.edu> wrote:
>
>> They are the ratio of the T1w/T2w images and are a relative measure of
>> myelin content.  See this publication for more details:
>>
>> http://www.jneurosci.org/content/31/32/11597.short
>>
>> Peace,
>>
>> Matt.
>>
>> From: <hcp-users-boun...@humanconnectome.org> on behalf of Lisa
>> Kramarenko <lisa.kramare...@gmail.com>
>> Date: Monday, May 29, 2017 at 5:29 AM
>> To: "hcp-users@humanconnectome.org" <hcp-users@humanconnectome.org>
>> Subject: [HCP-Users] values in myelin maps
>>
>> Hello,
>>
>> I am not sure what exactly are the values shown for the myelin maps. E.g.
>> on the screenshot the values are 0.998 to 1.771. I understand that higher
>> values mean higher myelination and vice versa, but what do they mean
>> exactly?
>> Thanks!
>>
>> Lisa
>>
>> ___
>> 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

2017-05-29 Thread Glasser, Matthew

They are the ratio of the T1w/T2w images and are a relative measure of myelin 
content.  See this publication for more details:

http://www.jneurosci.org/content/31/32/11597.short

Peace,

Matt.

From: 
>
 on behalf of Lisa Kramarenko 
>
Date: Monday, May 29, 2017 at 5:29 AM
To: "hcp-users@humanconnectome.org" 
>
Subject: [HCP-Users] values in myelin maps

Hello,

I am not sure what exactly are the values shown for the myelin maps. E.g. on 
the screenshot the values are 0.998 to 1.771. I understand that higher values 
mean higher myelination and vice versa, but what do they mean exactly?
Thanks!

Lisa

___
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HCP-Users@humanconnectome.org
http://lists.humanconnectome.org/mailman/listinfo/hcp-users

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

Re: [HCP-Users] values in myelin maps

Re: [HCP-Users] values in myelin maps

Re: [HCP-Users] values in myelin maps

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Re: [HCP-Users] values in myelin maps

Re: [HCP-Users] values in myelin maps

Re: [HCP-Users] values in myelin maps

Re: [HCP-Users] values in myelin maps

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Re: [HCP-Users] values in myelin maps

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