We don't have a version of the Conte69 midthickness in talairach space, but we
do have a PALS version that is in T&T space. Use the AFNI PALS surface.
But this would not cause the mesh error (wrong number of vertices) issue that
you were having. If you tried to view a 74k PALS mesh metric on a Conte69 164k
mesh surface, then you'd get a problem like the one you had.
________________________________
From: Audrey-Anne Dubé <[email protected]>
To: "Caret, SureFit, and SuMS software users" <[email protected]>
Sent: Wednesday, May 7, 2014 1:20 PM
Subject: Re: [caret-users] mapping ALE on surface: error for number of nodes
Hi,
My volume is in Tal space. Is this a problem?
Audrey-Anne Dubé
Candidate au PhD R/I neuropsychologie
Université de Montréal
On Wed, May 7, 2014 at 11:30 AM, Donna Dierker <[email protected]> wrote:
Another thought occurred to me: If you select a 32k version of the Conte69
atlas as your spec file, then you'll get an error when you try to open the 164k
vertex metric file. I'm sure there is a way to downsample the metric file, and
there are also mapping features in Workbench's wb_command, if you want to map
directly to 32k mesh surfaces. But we don't have a 32k version of Conte69 in
caret5.
>
>
>
>On May 7, 2014, at 9:58 AM, Donna Dierker <[email protected]> wrote:
>
>> Hi Audrey-Anne,
>>
>> Erin and I tried to do that, but you can't see the menu picks very clearly
>> in the video:
>>
>> https://www.youtube.com/watch?v=jED8sg9szdU
>>
>> But here are the steps:
>>
>> Download conte69 atlas:
>>
>> http://sumsdb.wustl.edu/sums/archivelist.do?archive_id=8293720&archive_name=Conte69_atlas_v2.LR.164k_fs_LR.c5.zip
>>
>> Unpack and cd to the Conte69_164k_fs_LR.c5 directory.
>>
>> Launch caret5.
>>
>> Cancel when spec file dialog comes up.
>>
>> Attributes: Map volume to surface
>>
>> Data mapping type: Metric; Next
>>
>> Add volumes from disk; select volume in MNI space; next
>>
>> Map to spec file with atlas
>> Note: If you don't see this, then your caret installation is incomplete
>> or confused about its parent directory. Launch from command line.
>>
>> Output spec file: select Conte69_atlas-v2.L.164k_fs_LR.c5.spec
>> Space: FNIRT
>> Atlas: Conte69 Map LEFT midthickness...
>>
>> Next
>>
>> Accept default metric filename
>>
>> Mapping Algorithm: Enclosing and interpolated are the most popular
>>
>> Next
>>
>> Close when Summary appears
>>
>> File: Open Spec File: Conte69_atlas-v2.L.164k_fs_LR.c5.spec
>>
>> Load scenes
>>
>> Double-click first scene (Conte69 midthickness and inflated...)
>>
>> Toolbar: Spec: Metric: map_data_0_Conte69...
>> Erase all existing columns
>>
>> Toolbar: D/C: Page Selection: Overlay/underlay Surface
>> Primary overlay
>> Data type metric metric
>>
>> You should see it.
>>
>> Donna
>>
>>
>> On May 6, 2014, at 7:36 PM, Audrey-Anne Dubé <[email protected]>
>> wrote:
>>
>>> Hi Donna,
>>>
>>> As you suggested, I tried with the Conte69 atlas (164k and 74k), but same
>>> results. The metric file is recorded in the spec file, but the same error
>>> shows about different number of nodes.
>>>
>>> Thanks for paying attention to my problem.
>>>
>>> Would it be possible for you to make an online demonstration, with a screen
>>> sharing or a screen cast tool? In this way, we may find a way to solve the
>>> issue faster.
>>>
>>>
>>>
>>>
>>> Audrey-Anne Dubé
>>> Candidate au PhD R/I neuropsychologie
>>> Université de Montréal
>>>
>>>
>>> On Tue, May 6, 2014 at 9:50 AM, Donna Dierker <[email protected]>
>>> wrote:
>>> Audrey,
>>>
>>> I will look at this more closely later, but this is the step where you
>>> should be downloading the Conte69 atlas and using one of its visualization
>>> specs instead of this spec out of the distribution directory:
>>>
>>>> 8. select in fmri_mapping_files >
>>>> Human.Conte69.midthickness_FNIRT_fMRI-MAPPER.LEFT.164k_fs_LR.spec as you
>>>> suggested
>>>
>>> The Conte69 atlas is here:
>>>
>>> http://brainvis.wustl.edu/wiki/index.php/Caret:Atlases:Conte69_Atlas
>>>
>>> I wonder if your writing to the fmri_mapping_files that are intended to be
>>> read-only might cause trouble.
>>>
>>> Also, I would not expect to find a SPHERE or CMW configuration in that
>>> fmri_mapping_files spec.
>>>
>>> Will look more at this later, but here are some hints as to what looks
>>> amiss.
>>>
>>> Donna
>>>
>>>
>>> On May 5, 2014, at 10:28 AM, Audrey-Anne Dubé <[email protected]>
>>> wrote:
>>>
>>>> Here the attached image
>>>>
>>>> Audrey-Anne Dubé
>>>> Candidate au PhD R/I neuropsychologie
>>>> Université de Montréal
>>>>
>>>>
>>>> On Mon, May 5, 2014 at 11:23 AM, Audrey-Anne Dubé
>>>> <[email protected]> wrote:
>>>> Dear Donna,
>>>>
>>>> It is not a read-only issue since the spec files are modified when I do
>>>> the mapping. Here is exactly what I did:
>>>>
>>>> 1. open CARET v5.65
>>>> 2. Attributes > Map volume(s) to surface(s)
>>>> 3. chose Metric for Data mapping type
>>>> 4. Enable entry of volume threshold
>>>> 5. Add volumes from disk --> selected my ALE map, which is a nifti image,
>>>> in Talairach format
>>>> 6. Entered the volume thresholding in the pop-up window (positive: 0.028;
>>>> negative: 0.00)
>>>> 7. Map to spec file with Atlas
>>>> 8. select in fmri_mapping_files >
>>>> Human.Conte69.midthickness_FNIRT_fMRI-MAPPER.LEFT.164k_fs_LR.spec as you
>>>> suggested
>>>> 9. Space : FNIRT; Atlas: Conte69 Map LEFT midthickness (164k_LR nodes)
>>>> 10. idem 8 and 9, but with RIGHT
>>>> 11. renamed by data files (L and R)
>>>> 12. Mapping algorith: METRIC_ENCLOSING_VOXEL
>>>> 13. ok (or next), heard a "bip" like there was an error, but the summary
>>>> shows
>>>> 14. Close
>>>> 15. Open spec file >
>>>> Human.Conte69.midthickness_FNIRT_fMRI-MAPPER.LEFT.164k_fs_LR.spec
>>>> 16. check my metric file (please see joint image) > load
>>>> 17. Got this error message
>>>>
>>>> Error
>>>> PDHCEM_Conte69_LEFT_midthickness_164k_fs_LR_5_May_2014_11_13_13.metric:
>>>> Error
>>>> PDHCEM_Conte69_LEFT_midthickness_164k_fs_LR_5_May_2014_11_13_13.metric:
>>>> contains a different number of nodes than
>>>> Conte69.L.midthickness.164k_fs_LR.coord.gii
>>>>
>>>> Pressed ok
>>>>
>>>> 18. The brain image is displayed, but without my data on it
>>>>
>>>> Can you see if I did something wrong?
>>>>
>>>> Thanks very much
>>>>
>>>>
>>>> Audrey-Anne Dubé
>>>> Candidate au PhD R/I neuropsychologie
>>>> Université de Montréal
>>>>
>>>>
>>>> On Wed, Apr 30, 2014 at 3:22 PM, Donna Dierker <[email protected]>
>>>> wrote:
>>>> Hi Audrey,
>>>>
>>>> Hmmm. I wonder if this might be because the spec file you name below is
>>>> part of the Caret distribution, and it might be read-only. In fact, it's
>>>> a good idea for it to be read-only. The files under data_files are
>>>> intended to be used by Caret without risk of users writing their analysis
>>>> files there. Is this spec file under $CARET_HOME/data_files or has it
>>>> been copied from there? And is the directory and spec file writeable?
>>>>
>>>> There are better choices for other visualization specs, e.g., like those
>>>> in this tutorial spec:
>>>>
>>>> http://brainmap.wustl.edu/pub/donna/ATLASES/HUMAN/CARET_TUTORIAL_SEPT06.zip
>>>> login pub
>>>> password download
>>>>
>>>> Also, depending on the constraints of your meta-analysis, you might
>>>> consider moving from the PALS atlas to the Conte69 atlas:
>>>>
>>>> http://brainvis.wustl.edu/wiki/index.php/Caret:Atlases:Conte69_Atlas
>>>>
>>>>
>>>> Donna
>>>>
>>>>
>>>> On Apr 30, 2014, at 1:19 PM, Audrey-Anne Dubé <[email protected]>
>>>> wrote:
>>>>
>>>>> Dear Caret users,
>>>>>
>>>>> I want to map my meta-analysis results on an PALS surface. So I tried to
>>>>> map my ALE map (nifti format) to a surface atlas using this spec file
>>>>> Human.PALS_B12.LR.MULTI-FIDUCIAL_711-2C_fMRI-MAPPER.B1-12.RIGHT.align2.73730.spec
>>>>>
>>>>> I got this error message:
>>>>> Error PDHCEM_Mapped_to_PALS.RIGHT.73730.metric: Error
>>>>> PDHCEM_Mapped_to_PALS.RIGHT.73730.metric: contains a different number of
>>>>> nodes than
>>>>> Human_Buck_Case12.R.M.RegToPALS_B12.LR.FIDUCIAL_711-2C.align2.73730.coord
>>>>>
>>>>> I cannot figure how to resolve this problem. Help would be greatly
>>>>> appreciated!
>>>>>
>>>>> Thank!
>>>>>
>>>>> Audrey-Anne Dubé
>>>>> Candidate au PhD R/I neuropsychologie
>>>>> Université de Montréal
>>>>> _______________________________________________
>>>>> 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
>>>>
>>>>
>>>> <Screen Shot 2014-05-05 at
>>>> 11.18.18.jpg>_______________________________________________
>>>> 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
>
>
>_______________________________________________
>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
