That is probably a better idea. Would that be pretty easy? What outputs would I want to generate?
> On Oct 3, 2017, at 1:15 PM, Matt Glasser <[log in to unmask]> wrote:
>
> I wonder if it would be better to just compute the dense connectome and
> then parcellate afterwards?
>
> Peace,
>
> Matt.
>
> On 10/3/17, 12:02 PM, "FSL - FMRIB's Software Library on behalf of Maxwell
> Bertolero" <[log in to unmask] on behalf of [log in to unmask]> wrote:
>
>> Yes, that’s what I figured.
>>
>> Given that, one thing I am trying to avoid is loading all of the target
>> surface parcels for every seed parcel. If I don’t include targets and
>> instead pass all of the surface parcels as seeds, what options do I need
>> to flag to generate the seed to seed matrix? I know I can reconstruct it
>> in MATLAB from the coords and matrix1 files, but I haven’t figured out a
>> python solution, and I don’t know MATLAB that well.
>>
>> Also, can I suppress the seeds_to* files from saving somehow? Saving
>> these out takes a significant amount of time.
>>
>> Thanks!
>>
>>> On Oct 3, 2017, at 11:54 AM, Matt Glasser <[log in to unmask]> wrote:
>>>
>>> Thanks Bruce. On a plane in the middle of the ocean so not able to
>>> check
>>> so easy.
>>>
>>> Sounds like it is just a function of a large number of ROIs+Surfaces
>>> being
>>> loaded. Ideally probtrackx would function such that only a single
>>> surface
>>> was needed and then the much smaller ROIs could be specified separately
>>> rather than the current behavior of having to have a combined
>>> surface+ROI
>>> for each ROI. Also the combined surface+ROI isn¹t really an official
>>> GIFTI file type so other GIFTI software may not be able to understand it
>>> (like Connectome Workbench).
>>>
>>> Matt.
>>>
>>> On 10/3/17, 11:34 AM, "FSL - FMRIB's Software Library on behalf of Bruce
>>> Fischl" <[log in to unmask] on behalf of [log in to unmask]>
>>> wrote:
>>>
>>>> p.s. so 10242 vertices in fsaverage5 (v=vertices, e=edges, f=faces)
>>>>
>>>> cheers
>>>> Bruce
>>>>
>>>> On Tue, 3 Oct 2017,
>>>> Bruce Fischl wrote:
>>>>
>>>>> mris_euler_number $FREESURFER_HOME/lib/bem/ic5.tri
>>>>> euler # = v-e+f = 2g-2: 10242 - 30720 + 20480 = 2 --> 0 holes
>>>>> F =2V-4: 20480 = 20484-4 (0)
>>>>> 2E=3F: 61440 = 61440 (0)
>>>>>
>>>>> total defect index = 0
>>>>>
>>>>>> On Tue, 3 Oct 2017, Matt Glasser wrote:
>>>>>>
>>>>>> How many vertices is that?
>>>>>>
>>>>>> Matt.
>>>>>>
>>>>>> On 10/3/17, 8:54 AM, "FSL - FMRIB's Software Library on behalf of Max
>>>>>> Bertolero" <[log in to unmask] on behalf of [log in to unmask]>
>>>>>> wrote:
>>>>>>
>>>>>>> It is fsaverage5 resolution.
>>>>>>
>>>>>>
>>>>>>
>>>>>
>>>>>
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