Hi Sabrina, sorry, I was working on a grant, and now I'm out of town
until Monday. I can try to push you forward on this now, but I have to
be brief. Those images where made from data created with the pctsurfcon
scriopt. If you run it with --help, you will get some docs on it. This
is already run by default with output {lr}h.w-g.pct.mgh which is the
GM/WM intensity in Figure 1. This script will also create the GM and WM
intensity files but deletes them by default. You can re-run it and
specify the temporary folder with --tmp, and those files will be in
there. I don't know what they will be called but hopefully it will be
obvious.
doug
On 2/4/16 2:14 PM, Sabrina Yu wrote:
> Hi sorry, haven't heard back yet from Freesurfers. Just following up on how
> to generate gray matter & white matter intensity maps overlaid onto brain
> like in Salat paper.
>
> http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2750073/#R57
>
> Figure 1 (c). The mean maps of signal intensity.
>
> Thanks!
> ________________________________________
> From: Sabrina Yu
> Sent: Thursday, January 28, 2016 10:51 AM
> To: Freesurfer support list
> Subject: Re: [Freesurfer] Fw: Gray matter intensity
>
> http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2750073/#R57
>
> Figure 1 (c). The mean maps of signal intensity.
>
> ________________________________________
> From: freesurfer-boun...@nmr.mgh.harvard.edu
> <freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Douglas N Greve
> <gr...@nmr.mgh.harvard.edu>
> Sent: Thursday, January 28, 2016 10:47 AM
> To: freesurfer@nmr.mgh.harvard.edu
> Subject: Re: [Freesurfer] Fw: Gray matter intensity
>
> which figure(s) in particular?
>
> On 01/28/2016 01:41 PM, Sabrina Yu wrote:
>> Hi,
>>
>> Sorry for bringing this thread up again. Referring back to the figure in the
>> Salat paper, what map do I load as an overlay to get the intensity maps? How
>> do I generate these maps?
>>
>> Thank you,
>> Sabrina
>>
>> ________________________________________
>> From: freesurfer-boun...@nmr.mgh.harvard.edu
>> <freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Douglas N Greve
>> <gr...@nmr.mgh.harvard.edu>
>> Sent: Monday, December 21, 2015 10:08 AM
>> To: freesurfer@nmr.mgh.harvard.edu
>> Subject: Re: [Freesurfer] Fw: Gray matter intensity
>>
>> freeview or tksurfer. Load the relevant map as an overlay
>>
>> On 12/21/2015 12:57 PM, Sabrina Yu wrote:
>>> Hello,
>>>
>>> Thank you for the very helpful replies! I have another quick question.
>>> Which commands would I use to generate images like the ones in Figure 1
>>> (C) generated in the Salat paper
>>> (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2750073/#R57)?
>>>
>>> Thank you
>>> Sabrina
>>>
>>> ________________________________________
>>> From: freesurfer-boun...@nmr.mgh.harvard.edu
>>> <freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Douglas N Greve
>>> <gr...@nmr.mgh.harvard.edu>
>>> Sent: Tuesday, December 15, 2015 10:10 AM
>>> To: freesurfer@nmr.mgh.harvard.edu
>>> Subject: Re: [Freesurfer] Fw: Gray matter intensity
>>>
>>> On 12/15/2015 01:00 PM, Sabrina Yu wrote:
>>>> Hi,
>>>>
>>>>
>>>> Just following up on my previous email (see below) as I have not yet
>>>> heard back. I also have another question regarding the lh.wm.mgh and
>>>> rh.wm.mgh generated by pctsurfcon. How do I view these as surface
>>>> overlays on T1 brain scans?
>>>>
>>> If you want to view them on a volume instead of a surface, you can use
>>> mri_surf2vol
>>>> Thank you very much.
>>>>
>>>>
>>>>
>>>> ------------------------------------------------------------------------
>>>> *From:* Sabrina Yu
>>>> *Sent:* Thursday, December 10, 2015 2:47 PM
>>>> *To:* Freesurfer support list
>>>> *Subject:* Gray matter intensity
>>>>
>>>> Hello,
>>>>
>>>>
>>>>
>>>> I have been following the instructions in this email thread:
>>>> https://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/2014-April/037240.html.
>>>> <https://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/2014-April/037240.html>
>>>> And
>>>> have successfully gotten the wm-gm signal intensity contrast, but
>>>> now have a few questions regarding signal intensity for white matter
>>>> and gray matter intensity.
>>>>
>>>>
>>>> 1) Does the wmparc.stats contain mean white matter intensity values
>>>> for each ROI?
>>>>
>>> Yes
>>>> 2) Is it possible to extract these same mean intensity values for gray
>>>> matter? There is no gmparc.stats file. We know that it's possible to
>>>> calculate these from the WM/GM ratio from pctsurfcon, but it'd be
>>>> great if there was a more direct way to get this data.
>>>>
>>> There is not one by default that includes the cortical parcellation. You
>>> can create your own with mri_segstats passing it the aparc+aseg.mgz as
>>> the segmentation. Look in the recon-all.log file for the command line
>>> that creates the aseg.stats or wmparc.stats. You will probably need to
>>> change the --ctab flag to --ctab-default (no argument)
>>>> Thank you,
>>>>
>>>> Sabrina Yu
>>>>
>>>>
>>>>
>>>> _______________________________________________
>>>> Freesurfer mailing list
>>>> Freesurfer@nmr.mgh.harvard.edu
>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>> --
>>> Douglas N. Greve, Ph.D.
>>> MGH-NMR Center
>>> gr...@nmr.mgh.harvard.edu
>>> Phone Number: 617-724-2358
>>> Fax: 617-726-7422
>>>
>>> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
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>>> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
>>>
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>>>
>>>
>>> The information in this e-mail is intended only for the person to whom it is
>>> addressed. If you believe this e-mail was sent to you in error and the
>>> e-mail
>>> contains patient information, please contact the Partners Compliance
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>>>
>> --
>> Douglas N. Greve, Ph.D.
>> MGH-NMR Center
>> gr...@nmr.mgh.harvard.edu
>> Phone Number: 617-724-2358
>> Fax: 617-726-7422
>>
>> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
>> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
>> www.nmr.mgh.harvard.edu/facility/filedrop/index.html
>> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
>>
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>> Freesurfer mailing list
>> Freesurfer@nmr.mgh.harvard.edu
>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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>> Freesurfer mailing list
>> Freesurfer@nmr.mgh.harvard.edu
>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>
>>
> --
> Douglas N. Greve, Ph.D.
> MGH-NMR Center
> gr...@nmr.mgh.harvard.edu
> Phone Number: 617-724-2358
> Fax: 617-726-7422
>
> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
> www.nmr.mgh.harvard.edu/facility/filedrop/index.html
> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
>
> _______________________________________________
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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>
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