Hi Yan,
There are lots of ways to split up the brain -- "parcellations". For example,
the Conte69 atlas
(http://brainvis.wustl.edu/wiki/index.php/Caret:Conte69_Atlas) comes with two
label.gii files per hemisphere, e.g.:
parcellations_VGD11b.R.164k_fs_LR.label.gii
RSN-networks.R.164k_fs_LR.label.gii
The first includes two parcellations:
Composite Parcellation-rh (FRB08_OFP03_retinotopic)
Brodmann rh (from colin.R via pals_R-to-fs_LR)
The second includes four parcellations:
7 RSN Networks (YKS11 - Yeo et al., JNP, 2011)
17 RSN Networks (YKS11 - Yeo et al., JNP, 2011)
RSN consensus communities (holes filled) (PCN11 - Power_Neuron11)
RSN consensus communities (PCN11 - Power_Neuron11)
And lots more have been published since, and will continue to be published. ;-)
So you have to decide which one you want. Then you can either load that
parcellation in wb_view (or caret5) and click on nodes interactively, or if you
want to write a script that queries regions, there is a lookup table that maps
the label key to a label name in the front of the label file, e.g.:
<Label Key="0" Red="0.667" Green="0.667" Blue="0.667"
Alpha="0"><![CDATA[???]]></Label>
<Label Key="1" Red="1" Green="1" Blue="1"
Alpha="1"><![CDATA[u1_Unassigned]]></Label>
<Label Key="2" Red="0.502" Green="0.502" Blue="0.502"
Alpha="1"><![CDATA[u2_Ventral_frontal_temporal]]></Label>
<Label Key="3" Red="1" Green="0" Blue="0"
Alpha="1"><![CDATA[a3_Default_mode]]></Label>
<Label Key="4" Red="0" Green="1" Blue="1"
Alpha="1"><![CDATA[a4_"Hand"_somatosensory-motor]]></Label>
<Label Key="5" Red="0" Green="0" Blue="1"
Alpha="1"><![CDATA[a5_Visual]]></Label>
<Label Key="6" Red="0.961" Green="0.961" Blue="0.059"
Alpha="1"><![CDATA[a6_Fronto-parietal_task_control]]></Label>
<Label Key="7" Red="0" Green="0.502" Blue="0.502"
Alpha="1"><![CDATA[a7_Ventral_attention]]></Label>
<Label Key="8" Red="0" Green="0.275" Blue="0.157"
Alpha="1"><![CDATA[a8_Caudate_putamen]]></Label>
<Label Key="9" Red="1" Green="0.722" Blue="0.831"
Alpha="1"><![CDATA[a9_Superior_temporal_gyrus]]></Label>
<Label Key="10" Red="0.675" Green="0.675" Blue="0.675"
Alpha="1"><![CDATA[u10_Inferior_temporal_pole]]></Label>
You can also export the label table as ASCII text. But each vertex is
associated with one of these keys in the label.gii file.
Donna
On Aug 28, 2014, at 2:27 PM, "Tang, Yan" <[email protected]> wrote:
> I still have problem. How can I know which brain region is every vertex
> belonged to?
> ________________________________________
> From: Tang, Yan
> Sent: Friday, August 15, 2014 12:27 PM
> To: Caret, SureFit, and SuMS software users
> Subject: RE: [caret-users] projecting functional MRI to gii surfaces
>
> Thank all of you. Thank you very much.
> ________________________________________
> From: [email protected]
> [[email protected]] on behalf of Donna Dierker
> [[email protected]]
> Sent: Wednesday, August 13, 2014 2:27 PM
> To: Caret, SureFit, and SuMS software users
> Subject: Re: [caret-users] projecting functional MRI to gii surfaces
>
> Hi Yan,
>
> I'm not sure about wb_import, but I know it won't downsample for you. This
> will, I hope:
>
> http://brainmap.wustl.edu/pub/donna/ATLASES/HUMAN/FSLR/downsample164_to_32k.zip
> login pub
> password download
>
> There is a script in there you will need to tweak to put in your pathnames
> and subject list. I tried it on some freesurfer_to_fs_LR output I had lying
> around, and it worked. The zip file also contains the spheres you need:
>
> ExtractDir=/home/donna/downsample164_to_32k
> SubjectDir=/mnt/myelin/donna/SUBJ/fs_LR_output_directory
> ResamplingMethod=BARYCENTRIC
>
> for Subject in $SubjList
> do
> for Hemisphere in L R
> do
>
> CoordInput=$SubjectDir/$Subject/"$Subject".$Hemisphere.midthickness_orig.164k_fs_LR.coord.gii
> TopoInput=$SubjectDir/$Subject/"$Subject".$Hemisphere.164k_fs_LR.topo.gii
>
> SurfaceInput=$SubjectDir/$Subject/"$Subject".$Hemisphere.midthickness_orig.164k_fs_LR.surf.gii
> caret_command -file-convert -sc -is CARET $CoordInput $TopoInput -os
> GS $SurfaceInput
>
> CurrentSphere=$ExtractDir/spheres/standard.$Hemisphere.sphere.164k_fs_LR.surf.gii
> NewSphere=$ExtractDir/spheres/standard.$Hemisphere.sphere.32k_fs_LR.surf.gii
>
> SurfaceOutput=$SubjectDir/$Subject/"$Subject".$Hemisphere.midthickness_orig.32k_fs_LR.surf.gii
> wb_command -surface-resample \
> $SurfaceInput \
> $CurrentSphere \
> $NewSphere \
> $ResamplingMethod \
> $SurfaceOutput
> done
> done
>
> Donna
>
>
> On Aug 13, 2014, at 10:42 AM, "Tang, Yan" <[email protected]> wrote:
>
>> You means I can finish this work by using the Connectome Workbench. So, the
>> first thing I need to do is to convert all files to Workbench format by
>> using wb_import. Is it true?
>> From: [email protected]
>> [[email protected]] on behalf of Timothy Coalson
>> [[email protected]]
>> Sent: Tuesday, August 12, 2014 7:16 PM
>> To: Caret, SureFit, and SuMS software users; Donna Dierker
>> Subject: Re: [caret-users] projecting functional MRI to gii surfaces
>>
>> -spec-file-change-resolution will not get you to the fs_LR 32k atlas from
>> fs_LR 164k (but it may get you deceptively close, making it even more
>> treacherous). Those messages aren't errors, and the reasons behind them are
>> better left alone, as this isn't the command you want.
>>
>> What you need to do is to use the fs_LR atlas files for resampling the
>> surface. In caret5, this requires deformation map files, which we have
>> probably already made for going between fs_LR 32k and 164k (Donna, do you
>> know if these are available?), with the -deformation-map-apply command.
>> However, we now do this in Connectome Workbench using atlas spheres directly
>> with the -surface-resample command (the fs_LR 32k and 164k spheres are
>> aligned by definition, but going to or from other atlases will need a
>> cross-atlas registered sphere).
>>
>> Tim
>>
>>
>>
>> On Tue, Aug 12, 2014 at 4:33 PM, Tang, Yan <[email protected]> wrote:
>> Sorry, I meet another problem. I used the Freesurfer_to_fs_LR Pipeline to
>> get 164k fs_LR surface. I think the vertex too much. So I want to
>> down-sampled to a 32,492 vertex surface. I used the caret_command
>> -spec-file-change-resolution.
>> But, the error was followed:
>> "Nonstandard resolution specified...
>> Using closest divided icosahedron, with 32492 nodes."
>> Can you explain it?
>> if I change the number, I find only a few files be created such as
>> def_sphere.coord, def_sphere.deform_map,study1.R.2k_fs_LR.topo.gii and
>> study1.R.mini+orig.2k_fs_LR.spc. Many files such as curvature.shape.gii,
>> inflated.coord.gii, midthickness.coord.gii, pial.coord.gii,
>> thickness.shape.gii and white.coord.gii all aren't changed. So, I do some
>> wrong steps. How should I do it?
>> From: [email protected]
>> [[email protected]] on behalf of Timothy Coalson
>> [[email protected]]
>> Sent: Monday, August 11, 2014 3:54 PM
>>
>> To: Caret, SureFit, and SuMS software users
>> Subject: Re: [caret-users] projecting functional MRI to gii surfaces
>>
>>
>> On Mon, Aug 11, 2014 at 2:14 PM, Tang, Yan <[email protected]> wrote:
>> Yes，I have a lot of volumes which need be projected to surface. I only know
>> how to use the 'map volume to surface '. I don't know how to use the
>> command. Could you give me an example?
>> Can the file of *.coord.gii be thought as the <coordinate-file-name> file?
>> But I only found .coord file can be used in the menu of "caret command
>> executor" . How about "topo"?
>>
>> .coord.gii should work, if it doesn't rename or copy the file to end in just
>> .coord . The topo is the same file you need to load to be able to view the
>> surface.
>>
>> another thing is how to set the <input-metric-or-paint-file-name>?
>>
>> From the pasted help:
>>
>> "If the input metric or paint file name is not an empty string (""), the
>> newly create metric or paint columns will be appended to the file and then
>> written with the output file name."
>>
>> In other words, if you don't want to append the columns to an existing
>> metric file, use "" (a pair of double quotes) for the argument.
>>
>> Since you asked something related on the hcp_users list (wb_command volume
>> to surface mapping), I will recommend that you try using wb_command for
>> this, as caret5 is no longer under active development. The main hurdle in
>> moving to Workbench is converting the separate coord/topo files into the
>> combined .surf.gii format (with caret_command -file-convert with the -sc
>> option).
>>
>> ________________________________________
>> From: [email protected]
>> [[email protected]] on behalf of Donna Dierker
>> [[email protected]]
>> Sent: Tuesday, August 05, 2014 9:14 AM
>> To: Caret, SureFit, and SuMS software users
>> Cc: Tang, Yiyuan
>> Subject: Re: [caret-users] projecting functional MRI to gii surfaces
>>
>> I'm not clear on what you mean by "I want get fMRI time course for surface
>> vertices of every subject."
>>
>> If you just mean how do you scale up -- map that many volumes to all your
>> subjects -- then I recommend scripting it and using caret_command. (Note
>> that Workbench, the software that is superseding Caret 5.*, has more robust
>> mapping features than caret_command, but I am going to provide the
>> caret_command usage, since this is the caret-users list. There is also a
>> hcp-users list that covers workbench.)
>>
>> Here is the usage for the command that maps volumes onto surfaces:
>>
>> caret_command -volume-map-to-surface
>> <coordinate-file-name>
>> <topology-file-name>
>> <input-metric-or-paint-file-name>
>> <output-metric-or-paint-file-name>
>> <algorithm>
>> <input-volume-file-names>
>> [-av average-voxel-neighbor-cube-size (mm)]
>> [-bf brain-fish-max-distance
>> brain-fish-splat factor]
>> [-g gaussian-neighbor-cube-size (mm)
>> sigma-norm
>> sigma-tang
>> norm below cutoff (mm)
>> norm above cutoff (mm)
>> tang-cutoff (mm)]
>> [-mv maximum-voxel-neighbor-cube-size (mm)]
>> [-sv strongest-voxel-neighbor-cube-size (mm)]
>>
>> Map volume(s) to a surface metric or paint file.
>>
>> For successful mapping, both the surface and the volume
>> must be in the same stereotaxic space.
>>
>> "algorithm" is one of:
>> METRIC_AVERAGE_NODES
>> METRIC_AVERAGE_VOXEL
>> METRIC_ENCLOSING_VOXEL
>> METRIC_GAUSSIAN
>> METRIC_INTERPOLATED_VOXEL
>> METRIC_MAXIMUM_VOXEL
>> METRIC_MCW_BRAIN_FISH
>> METRIC_STRONGEST_VOXEL
>> PAINT_ENCLOSING_VOXEL
>>
>> If the input metric or paint file name is not an empty string
>> (""), the newly create metric or paint columns will be
>> appended to the file and then written with the output file
>> name.
>>
>>
>>
>> On Aug 4, 2014, at 3:49 PM, "Tang, Yan" <[email protected]> wrote:
>>
>>> Thank you for your help. Now, I meet another problem. I project all
>>> functional MRI to 164k fs_LR surface. Every subject have 135 volumes. I
>>> want get fMRI time course for surface vertices of every subject. How should
>>> I do?
>>> ________________________________________
>>> From: [email protected]
>>> [[email protected]] on behalf of Donna Dierker
>>> [[email protected]]
>>> Sent: Friday, August 01, 2014 5:34 PM
>>> To: Caret, SureFit, and SuMS software users
>>> Cc: Tang, Yiyuan
>>> Subject: Re: [caret-users] projecting functional MRI to gii surfaces
>>>
>>> Push Toolbar: D/C and make sure the primary overlay is Metric.
>>>
>>> Make sure the right column is selected.
>>>
>>> If that check out okay, then I would do:
>>>
>>> File: Open Data File: Volume Functional File
>>> Load the volume you just mapped
>>> Switch to volume view and select view All (as opposed to H (horizontal or
>>> axial).
>>> Select D/C and on the page selection drop-down menu, scroll all the way to
>>> the bottom
>>> something like volume surface outline
>>> Toggle on the fiducial surface used for the mapping, so that you can see
>>> how the surface aligns with the volume.
>>>
>>> Sometimes there are header issues, and the origin is not set correctly,
>>> resulting in faulty volume-surface alignment.
>>>
>>>
>>> On Aug 1, 2014, at 4:29 PM, "Tang, Yan" <[email protected]> wrote:
>>>
>>>> When I open the spec file and mapped the Metric, only the surface was
>>>> displayed. The result is in the attachment. How should I do?
>>>> ________________________________________
>>>> From: [email protected]
>>>> [[email protected]] on behalf of Donna Dierker
>>>> [[email protected]]
>>>> Sent: Friday, August 01, 2014 4:02 PM
>>>> To: Caret, SureFit, and SuMS software users
>>>> Cc: Tang, Yiyuan
>>>> Subject: Re: [caret-users] projecting functional MRI to gii surfaces
>>>>
>>>> Hmmm. Sounds like more than a header to me.
>>>>
>>>> When you open the spec file you selected when you mapped the data, and
>>>> select the output file that is 446kb, what happens?
>>>>
>>>> You must make sure you select Metric on the D/C: Overlay/Underlay Surface
>>>> menu (primary or secondary, typically). Else it won't display.
>>>>
>>>>
>>>> On Aug 1, 2014, at 2:47 PM, "Tang, Yan" <[email protected]> wrote:
>>>>
>>>>> I am sure that the file exist and the size of file is 446KB. Is It
>>>>> correct?
>>>>> ________________________________________
>>>>> From: [email protected]
>>>>> [[email protected]] on behalf of Donna Dierker
>>>>> [[email protected]]
>>>>> Sent: Friday, August 01, 2014 10:10 AM
>>>>> To: Caret, SureFit, and SuMS software users
>>>>> Cc: Tang, Yiyuan
>>>>> Subject: Re: [caret-users] projecting functional MRI to gii surfaces
>>>>>
>>>>> Hi Yan,
>>>>>
>>>>> Could you use a terminal window or file manager to check whether the file
>>>>> exists, and if so, what its size is.
>>>>>
>>>>> We have seen cases before where the file was just a header -- no data.
>>>>> Inexplicably, the presence of a non-english character set on the system
>>>>> used has caused this sort of trouble. If there is a system nearby that
>>>>> does not have a non-english character set installed, you might see if
>>>>> Caret works there. Or remove any non-english character sets on your
>>>>> system and see if it helps.
>>>>>
>>>>> Donna
>>>>>
>>>>>
>>>>> On Jul 31, 2014, at 3:52 PM, "Tang, Yan" <[email protected]> wrote:
>>>>>
>>>>>> Dear all,
>>>>>>
>>>>>> I used the Freesurfer_to_fs_LR Pipeline to get 164k fs_LR surface. Now
>>>>>> I want to map functional volumes to surfaces.
>>>>>> In volume selection page, I choose my file 'ff001_010.nii'; In spec file
>>>>>> and surface selection page, I choose the file
>>>>>> 'study1.L.orig.164k_fs_LR'. I get a file
>>>>>> 'map_data_0_31_Jul_2014_15_10_13.metric'. But I find I couldn't open
>>>>>> this file. Which step is wrong? How can you do it?
>>>>>> _______________________________________________
>>>>>> caret-users mailing list
>>>>>> [email protected]
>>>>>> http://brainvis.wustl.edu/mailman/listinfo/caret-users
>>>>>
>>>>>
>>>>> _______________________________________________
>>>>> caret-users mailing list
>>>>> [email protected]
>>>>> http://brainvis.wustl.edu/mailman/listinfo/caret-users
>>>>>
>>>>> _______________________________________________
>>>>> caret-users mailing list
>>>>> [email protected]
>>>>> http://brainvis.wustl.edu/mailman/listinfo/caret-users
>>>>
>>>>
>>>> _______________________________________________
>>>> caret-users mailing list
>>>> [email protected]
>>>> http://brainvis.wustl.edu/mailman/listinfo/caret-users
>>>> <QQ截图20140801162715.png>_______________________________________________
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>>>
>>>
>>> _______________________________________________
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>>>
>>> _______________________________________________
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>>> http://brainvis.wustl.edu/mailman/listinfo/caret-users
>>
>>
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>>
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>
>
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