Yes, I modified the pathway a little bit. The folder contains one diffusion
folder and one T1w folder, I use the
${StudyFolder}/${SubjectID}/Diffusion/data.nii.gz
as my diffusion data. I ran bedpostX on the data and the results looks
quite convincing. So I want to move on to tractography. However, the same
mistake message keep shows up and I am not sure what matrix it refers to?
Do you have any clue where might be the wrong part?
Thank you,
Su
2013/7/17 Glasser, Matthew <[email protected]>
> If it's Q2 data, shouldn't you be in
> ${StudyFolder}/${SubjectID}/T1w/Diffusion? The Q1+Q2 release that we
> recently put out has the diffusion data in 1.25mm native volume
> (structural) space.
>
> Peace,
>
> Matt.
>
> From: Huang Su-Chun <[email protected]>
> Date: Wednesday, July 17, 2013 6:03 PM
>
> To: Matt Glasser <[email protected]>
> Cc: "[email protected]" <[email protected]>
> Subject: Re: [HCP-Users] A question about FDT 3.0
>
> The data is a Q2 data, this is the waypoint txt:
> ---------
>
> /NAS_II/Public-Data/Parcellation/100307/Diffusion/Masks/MNI2DTI_shadowreg_L_Cortex.nii.gz
> ----------
> and this is the fdt_log
> -----------------
> set tool probtrackx
> set probtrack(bedpost_dir)
> /NAS_II/Public-Data/Parcellation/100307/Diffusion/data.bedpostX
> set probtrack(xfm)
> set probtrack(mode) seedmask
> set probtrack(exclude_yn) 0
> set probtrack(usereference_yn) 0
> set probtrack(verbose_yn) 0
> set probtrack(loopcheck_yn) 1
> set probtrack(modeuler_yn) 0
> set probtrack(curvature) 0.2
> set probtrack(nsteps) 2000
> set probtrack(steplength) 0.5
> set probtrack(nparticles) 5000
> set probtrack(fibthresh) 0.01
> set probtrack(distthresh) 0.0
> set probtrack(sampvox) 0.0
> set probtrack(oneway_yn) 1
> set probtrack(wayorder_yn) 0
> set probtrack(waycond) AND
> set probtrack(reference)
> /NAS_II/Public-Data/Parcellation/100307/Diffusion/Masks/MNI2DTI_shadowreg_L_Thalamus.nii.gz
> set probtrack(output)
> /NAS_II/Public-Data/Parcellation/100307/Diffusion/L_Thalamocortico_connection
> set probtrack(waypoint_yn) 1
> .fdt.data.targets.wf.tf.targets insert end
> /NAS_II/Public-Data/Parcellation/100307/Diffusion/Masks/MNI2DTI_shadowreg_L_Cortex.nii.gz
> ----------------------
>
> Thank you very much!
>
> Su
>
>
>
> 2013/7/17 Glasser, Matthew <[email protected]>
>
>> Is this Q1 or Q2 data. Can you also post the contents of waypoints.txt.
>>
>> Peace,
>>
>> Matt.
>>
>> From: Huang Su-Chun <[email protected]>
>> Date: Wednesday, July 17, 2013 5:59 PM
>> To: Matt Glasser <[email protected]>
>> Cc: "[email protected]" <[email protected]>
>> Subject: Re: [HCP-Users] A question about FDT 3.0
>>
>> Just this:
>> --------------------------------------------
>> /usr/share/fsl/5.0/bin/probtrackx2 -x
>> /NAS_II/Public-Data/Parcellation/100307/Diffusion/Masks/MNI2DTI_shadowreg_L_Thalamus.nii.gz
>> -l --onewaycondition -c 0.2 -S 2000 --steplength=0.5 -P 5000
>> --fibthresh=0.01 --distthresh=0.0 --sampvox=0.0 --forcedir --opd -s
>> /NAS_II/Public-Data/Parcellation/100307/Diffusion/data.bedpostX/merged -m
>> /NAS_II/Public-Data/Parcellation/100307/Diffusion/data.bedpostX/nodif_brain_mask
>> --dir=/NAS_II/Public-Data/Parcellation/100307/Diffusion/L_Thalamocortico_connection
>> --waypoints=/NAS_II/Public-Data/Parcellation/100307/Diffusion/L_Thalamocortico_connection/waypoints.txt
>> --waycond=AND
>> ---------------------------------------------
>>
>>
>>
>>
>> 2013/7/17 Glasser, Matthew <[email protected]>
>>
>>> What is your probtrackx.log file say?
>>>
>>> Peace,
>>>
>>> Matt.
>>>
>>> From: Huang Su-Chun <[email protected]>
>>> Date: Wednesday, July 17, 2013 5:45 PM
>>> To: "[email protected]" <[email protected]>
>>> Subject: [HCP-Users] A question about FDT 3.0
>>>
>>> Hello all,
>>>
>>> I want to run probabilistic tracking on one of the HCP data, all the
>>> setting I put in is the same as usual (seed mask, waypoint masks, and
>>> output directory), however, the error message as follow keep shows up :
>>>
>>> Errors: Image Exception : #3 :: Mask of different size used in matrix
>>> ()
>>> terminate called after throwing an instance of
>>> 'RBD_COMMOM :: BaseException'
>>>
>>>
>>> Anyone has any idea what's going on here? Did I miss something?
>>>
>>> Thank you very much,
>>>
>>> Su
>>> --
>>> Su-Chun Huang
>>> Research Scientist
>>> Integrated Brain Imaging Center
>>> Department of Radiology
>>> Seattle, WA 98105
>>> 206-687-0113
>>>
>>> _______________________________________________
>>> 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.
>>>
>>
>>
>>
>> --
>> Su-Chun Huang
>> Research Scientist
>> Integrated Brain Imaging Center
>> Department of Radiology
>> Seattle, WA 98105
>> 206-687-0113
>>
>>
>> ------------------------------
>>
>> 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.
>>
>
>
>
> --
> Su-Chun Huang
> Research Scientist
> Integrated Brain Imaging Center
> Department of Radiology
> Seattle, WA 98105
> 206-687-0113
>
>
> ------------------------------
>
> 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.
>
--
Su-Chun Huang
Research Scientist
Integrated Brain Imaging Center
Department of Radiology
Seattle, WA 98195
phone: 206-687-0113
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