Hi Anastasia and list,

sorry, I just now got around to testing out the new build of dmri_paths you sent me. Sadly, the results look about the same:




Here the path stats file for the left SLFt:



What could be the problem?! I think I did what you suggested:

- install the new version of dmri_paths (https://www.dropbox.com/s/g6i7rcnbegwj5pm/dmri_paths?dl=0) and make it executable
- rerun trac-all -path for the subjects with only one time point
- rerun trac-all -stat for all subjects

Also: Is that problem only a visualization problem, or does it also mean that the values I get for a participant at a specific part of a tract are not aligned and I cannot analyze the data in that way?

Thanks for your help!!

Best,

Janosch


> On 20 Aug 2015, at 21:35, Anastasia Yendiki <ayendiki@nmr.mgh.harvard.edu> wrote:
>
>
> Hi Janosch - Indeed, someone has to be first. I'll send you a fresh build of dmri_paths tomorrow. You'll have to replace your copy of $FREESURFER_HOME/bin/dmri_paths with it and then rerun "trac-all -path" only for the subjects that have 1 time point. Then rerun "trac-all -stat" with all subjects together. And then tell us what other problem you find :)
>
> Best,
> a.y
>
> On Thu, 20 Aug 2015, Janosch Linkersdörfer wrote:
>
>> Hey Anastasia,
>>
>>> Am 19.08.2015 um 14:03 schrieb Anastasia Yendiki <ayendiki@nmr.mgh.harvard.edu>:
>>>
>>>
>>> Hi Janosch - There is a bug in how the output paths are saved when longitudinal TRACULA is run with one time point only. I'm working on a fix.
>>
>> OK, then I'm relieved that it isn't an error on my side. Thank you very much for looking into it!
>>
>>> In the meantime, you can try your analysis with the subjects that have multiple time points and you won't be affected by this problem. I can see that the subjects with a single time point are about 1/3 of your sample, and so you may not want to drop them completely.
>>
>> Yeah, it's children's data, so I'm happy about every measurement we got. I'll be waiting for the fixed script to be able to include all subjects in the analysis...
>>
>>>
>>> Thank you for trying things that nobody else has tried and finding these bugs!
>>
>> Somebody has to be the first, eh? :)
>>
>> Thank you very much,
>>
>> Janosch
>>
>>>
>>> More soon,
>>> a.y
>>>
>>> On Mon, 17 Aug 2015, Janosch Linkersdörfer wrote:
>>>
>>>> Hey Anastasia,
>>>>
>>>> thanks for looking into this.
>>>>
>>>>> Am 17.08.2015 um 20:33 schrieb Anastasia Yendiki <ayendiki@nmr.mgh.harvard.edu>:
>>>>>
>>>>>
>>>>> Hi Janosch - Looking at the stats files of your subjects, just by a quick count of the number of lines, I see that there are some subjects that have only 1 time point and some that have multiple time points, and that the pathstats.byvoxel.txt files have different lengths between those two types of subjects.
>>>>>
>>>>> I suspect that the strange average path that you get has to do with how this mixing of subjects was done. Did you run the subjects with a single time point through the longitudinal stream as well?
>>>>
>>>> Yes, I ran the longitudinal stream for all subjects, also for the ones with only one time point.
>>>>
>>>> Thanks,
>>>>
>>>> Janosch
>>>>
>>>>>
>>>>> Best,
>>>>> a.y
>>>>>
>>>>> On Sun, 9 Aug 2015, Janosch Linkersdörfer wrote:
>>>>>
>>>>>> Hi Anastasia,
>>>>>>
>>>>>> yes, I am. But it looks similar in the distributed version :(
>>>>>>
>>>>>> Thanks,
>>>>>>
>>>>>> Janosch
>>>>>>
>>>>>>> Am 08.08.2015 um 00:48 schrieb Anastasia Yendiki <ayendiki@nmr.mgh.harvard.edu>:
>>>>>>>
>>>>>>>
>>>>>>> Hi Janosch - Are you by any chance using the dev version of freeview?
>>>>>>>
>>>>>>> a.y
>>>>>>>
>>>>>>> On Fri, 7 Aug 2015, Janosch Linkersdörfer wrote:
>>>>>>>
>>>>>>>> Hi Anastasia and list,
>>>>>>>>
>>>>>>>> I'm trying to do analyses along the tract with the path_stats_byvoxel files.
>>>>>>>>
>>>>>>>> When I am visualizing the points using the waypoint functionality of Freeview, it looks a little strange, i.e., the points are not equally spaces on the tract, but clumped together at some parts and spread out on others, see:
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>> this looks different to your slides:
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>> Also, the most posterior points seem to be strangely located (in the other hemisphere). What could be the reason for this strange behavior?
>>>>>>>>
>>>>>>>> Thanks,
>>>>>>>>
>>>>>>>> Janosch
>>>>>>>
>>>>>>>
>>>>>>> The information in this e-mail is intended only for the person to whom it is
>>>>>>> addressed. If you believe this e-mail was sent to you in error and the e-mail
>>>>>>> contains patient information, please contact the Partners Compliance HelpLine at
>>>>>>> http://www.partners.org/complianceline . If the e-mail was sent to you in error
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>>>>>>
>>>>>>
>>>>>>
>>>>
>>>>
>>>>
>>
>>
>>


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