Missing:
--target3='seeds'
Moises
On 10 July 2015 at 14:48, Maarten Vaessen <[email protected]> wrote:
> I tried this and here I get the error:
>
> Done loading samples.
> does not exist
>
> Using the command:
> probtrackx2 -x L.STS.fsl.gii --onewaycondition --omatrix3
> --lrtarget3=../fsaverage_LR32k/102816.L.white.32k_fs_LR.surf.gii -P 50
> --forcedir --dir=./test_surf_track_STS_Lwhite -s
> ../Diffusion.bedpostX/merged -m nodif_brain_mask.nii.gz
> --seedref=nodif_brain_mask.nii.gz
>
> Any idea what this means?
>
> -M
>
>
>
>
> On Fri, Jul 10, 2015 at 3:34 PM, Moises Hernandez Fernandez <
> [email protected]> wrote:
>
>> Hi Maarten,
>>
>> you can use Matrix3:
>>
>> --omatrix3 --target3='seeds' --lrtarget3='wholebrain'
>>
>> Best,
>> Moises.
>>
>> On 10 July 2015 at 11:12, Maarten Vaessen <[email protected]> wrote:
>>
>>> Thanks for the reply. I am using FSL v5.0.8, but have also tried with
>>> 5.0.6.
>>>
>>> Does that mean that there is no way to do seed-to-wholebrain
>>> connectivity based on surfaces right now? Or is it possible to do a similar
>>> thing using one of the other --omatrix options?
>>>
>>> -M
>>>
>>>
>>> On Thu, Jul 9, 2015 at 5:49 PM, Glasser, Matthew <
>>> [email protected]> wrote:
>>>
>>>> That error suggests that that particular flag is not ready for
>>>> surfaces yet and is looking for a NIFTI volume. Do you have the latest
>>>> version of FSL? Perhaps Stam can comment on whether --target2 will be able
>>>> to handle surfaces in the future.
>>>>
>>>> Peace,
>>>>
>>>> Matt.
>>>>
>>>> From: <[email protected]> on behalf of Maarten
>>>> Vaessen <[email protected]>
>>>> Date: Thursday, July 9, 2015 at 9:43 AM
>>>> To: "[email protected]" <[email protected]>
>>>> Subject: [HCP-Users] probtrackx2 surface tracking in matrix2 mode
>>>>
>>>> Hello experts,
>>>>
>>>> I am trying track from a seed surface roi to all WM surface vertices
>>>> using matrix2 mode in probtackx2 using data from the HCP. I have followed
>>>> the guide on how to convert surfaces using the surf2surf command where
>>>> necessary. However I get this error when running probtrackx2
>>>>
>>>> Done loading samples.
>>>> Image Exception : #22 :: ERROR: Could not open image
>>>> ../fsaverage_LR32k/102816.L.white.32k_fs_LR.surf.gii
>>>> terminate called after throwing an instance of
>>>> 'RBD_COMMON::BaseException'
>>>> Aborted
>>>>
>>>> I am not sure what is wrong, the file is definitely there. Moreover
>>>> when I take this file as the seed (-x
>>>> ../fsaverage_LR32k/102816.L.white.32k_fs_LR.surf.gii), there is no error
>>>> when loading the seeds:
>>>>
>>>> Running in seedmask mode
>>>> load seeds
>>>> read gifti
>>>> done.
>>>>
>>>> Here is the full command:
>>>>
>>>> probtrackx2 -x L.STS.fsl.gii --onewaycondition --omatrix2
>>>> --target2=../fsaverage_LR32k/102816.L.white.32k_fs_LR.surf.gii -P 50
>>>> --forcedir --dir=./test_surf_track_STS_Lwhite -s
>>>> ../Diffusion.bedpostX/merged -m nodif_brain_mask.nii.gz
>>>> --seedref=nodif_brain_mask.nii.gz
>>>>
>>>>
>>>> Thanks for the help!
>>>>
>>>> -Maarten
>>>>
>>>> _______________________________________________
>>>> HCP-Users mailing list
>>>> [email protected]
>>>> http://lists.humanconnectome.org/mailman/listinfo/hcp-users
>>>>
>>>>
>>>> ------------------------------
>>>>
>>>> The materials in this message are private and may contain Protected
>>>> Healthcare Information or other information of a sensitive nature. If you
>>>> are not the intended recipient, be advised that any unauthorized use,
>>>> disclosure, copying or the taking of any action in reliance on the contents
>>>> of this information is strictly prohibited. If you have received this email
>>>> in error, please immediately notify the sender via telephone or return
>>>> mail.
>>>>
>>>
>>> _______________________________________________
>>> HCP-Users mailing list
>>> [email protected]
>>> http://lists.humanconnectome.org/mailman/listinfo/hcp-users
>>>
>>
>>
>
_______________________________________________
HCP-Users mailing list
[email protected]
http://lists.humanconnectome.org/mailman/listinfo/hcp-users
