--pt

On Wed, Nov 9, 2016 at 3:34 PM, Douglas N Greve <greve@nmr.mgh.harvard.edu> wrote:

That looks like a good list, but we don't keep track of all these
things. To add to it, we have wmparc.mgz which is segmented WM
(3000-3035, 4000-4035).

On 11/09/2016 03:00 PM, P Taylor wrote:
> The FreeSurferColorLUT.txt file has over 1,200 regions listed in it,
> but I assume that not all of those could be output in those default
> recon-all aparc+aseg* files. For example, I don't think I have ever
> seen a region:
> "3001 wm-lh-bankssts 230 155 215 0"
> output.
>
> So, I assume that there exists some set S of size N<1200 regions
> *could* be output in standard recon-all output aparc+aseg and
> aparc+aseg2009 files. I am interested in having a list of regions in S.
>
> You provided a list of region numbers for WM+CSF that can be expected
> in standard recon-all output aparc+aseg and aparc+aseg2009. So, those
> regions are part of what I am calling S, and presumably the rest of
> the regions in S are all GM ROIs, since I can subtract the list of
> WM+CSF regions from the aparc+aseg* outputs and have a GM mask (->
> what "mri_binarize --gm ..." does).
>
> I was trying to guess what portions of the FreeSurferColorLUT.txt
> table might form S, by looking at the groupings of regions presented
> in the file, as well as the list of WM+CSF regions you had provided
> and some recon-all output files that I had.
>
> So, I was wondering if S is made up of the following regions:
> numbers [0-255] and [1000-2035] for aparc+aseg (i.e., lines 5-231 and
> 430-502 in the LUT),
> and
> numbers [0-255], [1000-2035] and [11100-12175] for aparc+aseg2009
> (i.e., lines 5-231, 430-502 and 1089-1241 in the LUT)
> ?
>
> Thanks,
> pt
>
>
>
>
> On Wed, Nov 9, 2016 at 9:41 AM, Douglas Greve

> <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> wrote:
>
> Sorry, I'm not sure what your question is here?
>
>
> On 11/8/16 5:25 PM, P Taylor wrote:
>> OK, thanks for that list of complementary ROIs.
>>
>> I've always wondered what is the maximal set of regions that can
>> be returned by the standard recon-all with no other options for
>> aparc+aseg and aparc+aseg2009? Looking at the
>> FreeSurferColorLUT.txt, I guess there is a batch from lines 1-231
>> (spanning integer range 0-255), then some groupings of regions
>> get skipped, picking up again at ~line 415 with the comment about
>> mri_aparc2aseg (integer range 1000-2035, the max of which seems
>> to be the largest int in the aparc+aseg), and then is there a
>> jump again to line 1079, starting with the comment about the
>> --a2009s flag (integer range 11100-12175, the last of which seems
>> to be the largest int in the aparc+aseg2009)?
>>
>> Is that a correct set of regions that are returned? And out of
>> that combined set, we can deselect any of the "MatchValues" of
>> WM/CSF/background/etc. to be left with GM?
>>
>> Thanks,
>> pt
>>
>>
>> On Tue, Nov 8, 2016 at 1:32 PM, Douglas Greve

>> <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> wrote:
>>
>> Actually, what it does is to binarize all the labels that it
>> thinks are not GM, and then invert the mask to give GM. for
>> what it is worth, there are the non-GM numbers
>>
>> MatchValues[nMatch++] = 2;
>> MatchValues[nMatch++] = 41;
>> MatchValues[nMatch++] = 77;
>> MatchValues[nMatch++] = 251;
>> MatchValues[nMatch++] = 252;
>> MatchValues[nMatch++] = 253;
>> MatchValues[nMatch++] = 254;
>> MatchValues[nMatch++] = 255;
>> MatchValues[nMatch++] = 7; // Cerebellar WM
>> MatchValues[nMatch++] = 46; // Cerebellar WM
>> MatchValues[nMatch++] = 4; // Left-Lateral-Ventricle
>> MatchValues[nMatch++] = 5; // Left-Inf-Lat-Vent
>> MatchValues[nMatch++] = 14; // 3rd-Ventricle
>> MatchValues[nMatch++] = 43; // Right-Lateral-Ventricle
>> MatchValues[nMatch++] = 44; // Right-Inf-Lat-Vent
>> MatchValues[nMatch++] = 15; // 4th-Ventricle
>> MatchValues[nMatch++] = 72; // 5th-Ventricle
>> MatchValues[nMatch++] = 31; // Left-choroid-plexus
>> MatchValues[nMatch++] = 63; // Right-choroid-plexus
>> MatchValues[nMatch++] = 0; // Background
>> MatchValues[nMatch++] = 24; // CSF
>>
>>
>> On 11/8/16 1:06 PM, P Taylor wrote:
>>> OK. But going back to my question that kicked this thread
>>> off, actually what I was looking for was just such a rule.
>>>
>>> I could make a fairly solid list of GM from using this new
>>> "mri_binarize --gm ...." on several recon-all outputs. Would
>>> it be possible to have the rule (presumably a list of
>>> numbers corresponding to GM ROIs?) so I can have as secure a
>>> set of GM labels as possible?
>>>
>>> Thanks,
>>> pt
>>>
>>>
>>> On Tue, Nov 8, 2016 at 12:29 PM, Douglas Greve
>>> <greve@nmr.mgh.harvard.edu

>>> <mailto:greve@nmr.mgh.harvard.edu>> wrote:
>>>
>>> Yes. It just uses a rule on the numbers that it expects
>>> to be GM. At some point, I'll add both tissue type and
>>> laterality info to the ROIs, but not for version 6
>>>
>>>
>>> On 11/8/16 12:03 PM, P Taylor wrote:
>>>> And a final question, which might be a silly one--
>>>> This GM map applies to both the aparc.a2009s+aseg.mgz
>>>> and aparc+aseg.mgz files, right?
>>>>
>>>> Running "mri_binarize --gm ..." on each of those files
>>>> separately gave the same mask-- I believe this should
>>>> be a general property?
>>>>
>>>> Thanks,
>>>> pt
>>>>
>>>>
>>>> On Tue, Nov 8, 2016 at 11:57 AM, Douglas Greve
>>>> <greve@nmr.mgh.harvard.edu
>>>> <mailto:greve@nmr.mgh.harvard.edu>> wrote:
>>>>
>>>> yes
>>>>
>>>>
>>>> On 11/8/16 11:51 AM, P Taylor wrote:
>>>>> Ah, cool, that looks like it does the trick--
>>>>> thanks much.
>>>>>
>>>>> Will that version of mri_binarize be in the next
>>>>> release of FS?
>>>>>
>>>>> Thanks,
>>>>> pt
>>>>>
>>>>>
>>>>>
>>>>> On Tue, Nov 8, 2016 at 11:35 AM, Douglas Greve
>>>>> <greve@nmr.mgh.harvard.edu

>>>>> <mailto:greve@nmr.mgh.harvard.edu>> wrote:
>>>>>
>>>>> Try this one
>>>>> https://gate.nmr.mgh.harvard.edu/safelinks/greve/mri_binarize
>>>>> <https://gate.nmr.mgh.harvard.edu/safelinks/greve/mri_binarize>
>>>>>
>>>>>
>>>>> On 11/8/16 11:26 AM, P Taylor wrote:
>>>>>> Thanks, I'd like to try that. However, my
>>>>>> mri_binarize doesn't show that option, and
>>>>>> when I try running it, that option isn't
>>>>>> recognized:
>>>>>>
>>>>>> $ mri_binarize --gm --o map_gm.nii --i
>>>>>> aparc+aseg.mgz
>>>>>> ERROR: Option --gm unknown
>>>>>>
>>>>>> Looking at the mri_binarize help, I see
>>>>>> '--wm' exists, and that does, indeed, produce
>>>>>> a WM-looking volume. I also see an option
>>>>>> "--wm+vcsf"; would subtracting that resulting
>>>>>> map leave only GM?
>>>>>>
>>>>>> My version of FS is:
>>>>>> ----------------------------------------------------------------------
>>>>>> You are running this version of FreeSurfer:
>>>>>>
>>>>>> freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0
>>>>>> ----------------------------------------------------------------------
>>>>>>
>>>>>> In the online description of mri_binarize:
>>>>>> https://surfer.nmr.mgh.harvard.edu/fswiki/mri_binarize
>>>>>> <https://surfer.nmr.mgh.harvard.edu/fswiki/mri_binarize>
>>>>>> I see a "--subcort-gm" option that doesn't
>>>>>> appear to work for me, but I guess that isn't
>>>>>> full WM.
>>>>>>
>>>>>> So, am I somehow behind the times? From the
>>>>>> download page:
>>>>>> https://surfer.nmr.mgh.harvard.edu/fswiki/DownloadAndInstall
>>>>>> <https://surfer.nmr.mgh.harvard.edu/fswiki/DownloadAndInstall>
>>>>>> it looks like my v5.3 is the most currently
>>>>>> available?
>>>>>>
>>>>>> ... and, in case it's useful, the explicit
>>>>>> version of my mri_binarize (bottom line of
>>>>>> the help) is:
>>>>>> $Id: mri_binarize.c,v 1.26.2.1 2011/04/08
>>>>>> 15:40:50 greve Exp $
>>>>>>
>>>>>> Thanks,
>>>>>> pt
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>> On Tue, Nov 8, 2016 at 11:08 AM, Douglas
>>>>>> Greve <greve@nmr.mgh.harvard.edu

>>>>>> <mailto:greve@nmr.mgh.harvard.edu>> wrote:
>>>>>>
>>>>>>
>>>>>> We don't currently have that information
>>>>>> (ie, tissue type) stored with the ROI.
>>>>>> One thing you can do is to run
>>>>>> mri_binarize with the --gm option on
>>>>>> aparc+aseg.mgz This uses some rules to
>>>>>> determine what is GM and creates a mask
>>>>>> of GM. You can then feed this into
>>>>>> mri_segstats with --mask, and it should
>>>>>> only return ROIs that are in the GM mask.
>>>>>>
>>>>>>
>>>>>> On 11/7/16 8:10 PM, P Taylor wrote:
>>>>>>> Thanks, that's useful for getting the
>>>>>>> ROI volumes and a list of all that's
>>>>>>> been found for a particular data set.
>>>>>>>
>>>>>>> I would still like to have a way to
>>>>>>> identify a listed region as gray matter
>>>>>>> or not so that I can parse the file for
>>>>>>> only GM regions that have been returned,
>>>>>>> particularly as different numbers of
>>>>>>> ROIs are typically returned in an
>>>>>>> aparc+aseg file.
>>>>>>>
>>>>>>> I see in the aseg.stats file that there
>>>>>>> are volumetric summations for GM
>>>>>>> quantities, such as:
>>>>>>> # Measure lhCortex, lhCortexVol, Left
>>>>>>> hemisphere cortical gray matter volume,
>>>>>>> 238183.759207, mm^3
>>>>>>> # Measure rhCortex, rhCortexVol, Right
>>>>>>> hemisphere cortical gray matter volume,
>>>>>>> 240824.502797, mm^3
>>>>>>> # Measure Cortex, CortexVol, Total
>>>>>>> cortical gray matter volume,
>>>>>>> 479008.262004, mm^3
>>>>>>> ....
>>>>>>> # Measure SubCortGray, SubCortGrayVol,
>>>>>>> Subcortical gray matter volume,
>>>>>>> 57815.000000, mm^3
>>>>>>> # Measure TotalGray, TotalGrayVol, Total
>>>>>>> gray matter volume, 643956.262004, mm^3
>>>>>>>
>>>>>>> Are these calculated by summing
>>>>>>> individual ROI volumes, so that a list
>>>>>>> of all possible GM volumes does already
>>>>>>> exist somewhere?
>>>>>>>
>>>>>>> Thanks,
>>>>>>> pt
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>> On Mon, Nov 7, 2016 at 3:39 PM, Douglas
>>>>>>> N Greve <greve@nmr.mgh.harvard.edu

>>>>>>> <mailto:greve@nmr.mgh.harvard.edu>> wrote:
>>>>>>>
>>>>>>> I don't know that we have a complete
>>>>>>> list in one place of just the
>>>>>>> aparc+aseg ROIs, but you can get one
>>>>>>> by running
>>>>>>>
>>>>>>> mri_segstats --seg aparc+aseg.mgz
>>>>>>> --ctab-default --sum sum.dat
>>>>>>>
>>>>>>> then look in the sum.dat file
>>>>>>>
>>>>>>>
>>>>>>> On 11/03/2016 04:32 PM, P Taylor wrote:
>>>>>>> > Is there an available list of GM
>>>>>>> regions within the list of regions in
>>>>>>> > the FreeSurferColorLUT.txt?
>>>>>>> >
>>>>>>> > (In particular, I am interested in
>>>>>>> a list of GM regions output in a
>>>>>>> > default run of recon-all, which
>>>>>>> seems to have a maximum regionnumber
>>>>>>> > of 2035. But a full list is great,
>>>>>>> too-- I'm not sure which might be
>>>>>>> > already available or easier to
>>>>>>> generate.)
>>>>>>> >
>>>>>>> > I had thought of using the
>>>>>>> segmentation volumes to help me
>>>>>>> > differentiate ROIs. For example, I
>>>>>>> could get rid of regions that
>>>>>>> > overlap with the WM volume, but I
>>>>>>> think that the segmentation might
>>>>>>> > come from a slightly different bit
>>>>>>> of information than the sum of
>>>>>>> > segmented regions. As shown in
>>>>>>> the attached slice image, if I
>>>>>>> > underlay the WM segmentation
>>>>>>> volume (color = white), and overlay a
>>>>>>> > "recon-all"
>>>>>>> parcellation+segmentation map (color
>>>>>>> = red for GM on
>>>>>>> > right, yellow for GM on left, and
>>>>>>> green for non-GM) to look for
>>>>>>> > overlap, I see that some of the WM
>>>>>>> seg volume overlaps with GM ROIs
>>>>>>> > (overlaps are isolated pink-ish
>>>>>>> voxels and light yellow voxels; one
>>>>>>> > highlighted in cross hairs). I
>>>>>>> guess this difference occurs because
>>>>>>> > the segmentation volume comes from
>>>>>>> the surfaces themselves?
>>>>>>> >
>>>>>>> > Anyways, this makes me think that
>>>>>>> I can't automate finding the GM, and
>>>>>>> > I would rather go from LUT
>>>>>>> numbers, and hence the above question.
>>>>>>> >
>>>>>>> > Thanks,
>>>>>>> > pt
>>>>>>> >
>>>>>>> >
>>>>>>> >
>>>>>>> >
>>>>>>> _______________________________________________
>>>>>>> > Freesurfer mailing list
>>>>>>> > Freesurfer@nmr.mgh.harvard.edu

>>>>>>> <mailto:Freesurfer@nmr.mgh.harvard.edu>
>>>>>>> >
>>>>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>>>>>> <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>
>>>>>>>
>>>>>>> --
>>>>>>> Douglas N. Greve, Ph.D.
>>>>>>> MGH-NMR Center
>>>>>>> greve@nmr.mgh.harvard.edu
>>>>>>> <mailto:greve@nmr.mgh.harvard.edu>
>>>>>>> Phone Number: 617-724-2358
>>>>>>> <tel:617-724-2358>
>>>>>>> Fax: 617-726-7422 <tel:617-726-7422>
>>>>>>>
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