Thanks Doug. Does mri_seg2annot come w/ the latest FS distribution?
It doesn't seem to be available (I can't launch the help and receive
"command not found" when I try to run the command). mri_binarize
worked fine.
On Tue, Mar 15, 2011 at 12:33 PM, Douglas N Greve
<gr...@nmr.mgh.harvard.edu> wrote:
> No, you'll have to merge them into one map (and you'll probably want it to
> be an annotation). To do this, you'll need to run several programs.
>
> 1. mri_binarize -- threshold your two raw maps, give one a "--binval 1" the
> other "--binval 2"
> 2. Add them together: fscalc binmap1.nii add binmap2.nii -o binmap12.nii
> This will cause voxels only in binmap1 to be one, only in binmap2 to be 2,
> and voxels in both to be 3
> 3. Create a lookup table like $FREESURFER_HOME/FreeSurferColorLUT.txt with 4
> entries (0, 1, 2, 3), and give them the color you want.
> 4. mri_seg2annot --seg binmap12.nii --ctab yourcolortable ...
>
> doug
>
> Scott Hayes wrote:
>>
>> Hi Doug,
>> I was trying to load the maps so I could examine each map and the
>> overlap, as in the attached example (in this image, red is one map,
>> blue is the other, and pink is the overlap--done in MRICRON. I think
>> it's a nice way to view similarities and differences in activation for
>> different groups. Although this might be achievable by merging the
>> maps as you suggest, I was wondering if it was possible to view them
>> in tksurfer without trying to merge them into a single map.
>> Thanks,
>> Scott
>>
>> On Tue, Mar 15, 2011 at 11:09 AM, Douglas N Greve
>> <gr...@nmr.mgh.harvard.edu> wrote:
>>
>>>
>>> Hi Scott, I'm not sure what you are trying to do. How can you display two
>>> different z-values at the same voxel at the same time? Or do you want to
>>> merge the maps in some way?
>>> doug
>>>
>>> Scott Hayes wrote:
>>>
>>>>
>>>> Hi,
>>>> I have 2 functional maps (Patient > Controls and Controls > Patients)
>>>> and I would like to view both maps simultaneously on the surface (one
>>>> with "normal" values and the other using the "inverse" values so that
>>>> I get a "warm" and "cool" map simultaneously displayed on the
>>>> surface).
>>>> I'm using FS 5.0 and mac os 10.6.6
>>>> command from the mac terminal: > tksurfer fsaverage/ lh inflated
>>>> -overlay
>>>>
>>>> PCC_nosmooth_level3_FE_8matched_vs_MA016.gfeat/cope1.feat/thresh_zstat1.nii.gz
>>>> -overlay
>>>>
>>>> PCC_nosmooth_level3_FE_8matched_vs_MA016.gfeat/cope1.feat/thresh_zstat2.nii.gz
>>>>
>>>> Both maps load, but I have to click on one or the other (rather than
>>>> both being overlaid simultaneously), and the options (selecting
>>>> inverse) seem to be applied to both layers (even though I have not
>>>> selected "apply changes to all layers").
>>>>
>>>> Is it possible to view these maps at the same time using tksurfer and
>>>> apply normal values to one map and inverse values to the other?
>>>>
>>>> It was also suggested that freeview *might* be able to do this, but
>>>> this does not launch from the command line (FS, tkmedit and tksurfer
>>>> all work fine).
>>>>
>>>> I've copied the first few lines from the freeview crash if that helps.
>>>>
>>>> Any suggestions/guidance would be appreciated.
>>>>
>>>> Thanks,
>>>> Scott
>>>>
>>>> Process: freeview.bin [36175]
>>>> Path:
>>>> /Applications/freesurfer/bin/Freeview.app/Contents/MacOS/freeview.bin
>>>> Identifier: freeview.bin
>>>> Version: 'latest trunk' ('latest trunk')
>>>> Code Type: X86 (Native)
>>>> Parent Process: bash [30033]
>>>>
>>>> Date/Time: 2011-03-15 08:57:43.954 -0400
>>>> OS Version: Mac OS X 10.6.6 (10J567)
>>>> Report Version: 6
>>>>
>>>> Interval Since Last Report: 1791542 sec
>>>> Crashes Since Last Report: 39
>>>> Per-App Crashes Since Last Report: 3
>>>> Anonymous UUID:
>>>> E5903541-C168-4ED7-92B6-6741CD098D1A
>>>>
>>>> Exception Type: EXC_BAD_ACCESS (SIGBUS)
>>>> Exception Codes: KERN_PROTECTION_FAILURE at 0x0000000000000000
>>>> Crashed Thread: 0 Dispatch queue: com.apple.main-thread
>>>>
>>>> Thread 0 Crashed: Dispatch queue: com.apple.main-thread
>>>> 0 ??? 0000000000 0 + 0
>>>> 1 libvtkRendering.5.2.dylib 0x02b3d1a9
>>>> vtkCarbonRenderWindow::CreateAWindow() + 281
>>>> 2 libvtkRendering.5.2.dylib 0x02b3bfa4
>>>> vtkCarbonRenderWindow::WindowInitialize() + 52
>>>> 3 libvtkRendering.5.2.dylib 0x02b3a435
>>>> vtkCarbonRenderWindow::Start() + 21
>>>> 4 libvtkRendering.5.2.dylib 0x02aa11db
>>>> vtkRenderWindow::DoStereoRender() + 27
>>>> 5 libvtkRendering.5.2.dylib 0x02aa13a9
>>>> vtkRenderWindow::DoFDRender() + 153
>>>> 6 libvtkRendering.5.2.dylib 0x02aa1832
>>>> vtkRenderWindow::DoAARender() + 98
>>>> 7 libvtkRendering.5.2.dylib 0x02a9fc54
>>>> vtkRenderWindow::Render() + 644
>>>> 8 freeview.bin 0x0011d547
>>>> wxVTKRenderWindowInteractor::OnPaint(wxPaintEvent&) + 151
>>>> 9 freeview.bin 0x00407b53
>>>> wxAppConsole::HandleEvent(wxEvtHandler*, void
>>>> (wxEvtHandler::*)(wxEvent&), wxEvent&) const + 65
>>>> 10 freeview.bin 0x00452f30
>>>> wxEvtHandler::ProcessEventIfMatches(wxEventTableEntryBase const&,
>>>> wxEvtHandler*, wxEvent&) + 212
>>>> 11 freeview.bin 0x004532d4
>>>> wxEventHashTable::HandleEvent(wxEvent&, wxEvtHandler*) + 204
>>>> 12 freeview.bin 0x00453f5e
>>>> wxEvtHandler::ProcessEvent(wxEvent&) + 240
>>>> 13 freeview.bin 0x003525e3
>>>> wxWindow::MacDoRedraw(void*, long) + 975
>>>> 14 freeview.bin 0x00353985
>>>> wxMacWindowControlEventHandler(OpaqueEventHandlerCallRef*,
>>>> OpaqueEventRef*, void*) + 815
>>>> 15 freeview.bin 0x00354135
>>>> wxMacWindowEventHandler(OpaqueEventHandlerCallRef*, OpaqueEventRef*,
>>>> void*) + 181
>>>> 16 com.apple.HIToolbox 0x95953ecf
>>>> DispatchEventToHandlers(EventTargetRec*, OpaqueEventRef*,
>>>> HandlerCallRec*) + 1567
>>>> 17 com.apple.HIToolbox 0x95953196
>>>> SendEventToEventTargetInternal(OpaqueEventRef*, OpaqueEventTargetRef*,
>>>> HandlerCallRec*) + 411
>>>> _______________________________________________
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>>>> 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: www.nmr.mgh.harvard.edu/facility/filedrop/index.html
>>>
>>>
>>>
>>> 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
>>> HelpLine at
>>> http://www.partners.org/complianceline . If the e-mail was sent to you in
>>> error
>>> but does not contain patient information, please contact the sender and
>>> properly
>>> dispose of the e-mail.
>>>
>>>
>>>
>>
>>
>>
>>
>> ------------------------------------------------------------------------
>>
>
> --
> 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: www.nmr.mgh.harvard.edu/facility/filedrop/index.html
>
>
--
Scott M. Hayes, Ph.D.
Memory Disorders Research Center
Neuroimaging Research Center
VA Boston Healthcare System
Assistant Professor
Department of Psychiatry
Boston University School of Medicine
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