Okay cool!
Is there a way to load the .dot file in with Python?
> On Oct 3, 2017, at 3:15 PM, Matt Glasser <[log in to unmask]> wrote:
>
> Need to decide whether you want to use matrix1 or matrix3 seeding strategy
> and then you set the appropriate probtrackx flags. You can load the .dot
> into matlab, convert to full, average within the vertices for the parcels
> and you have your parcellated conenctome.
>
> Peace,
>
> Matt.
>
> On 10/3/17, 1:40 PM, "FSL - FMRIB's Software Library on behalf of Maxwell
> Bertolero" <[log in to unmask] on behalf of [log in to unmask]> wrote:
>
>> 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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