Yes, you need to set —opd.
Cheers
Stam
On 12 Feb 2014, at 21:39, Jeff Waugh <[log in to unmask]> wrote:
> Thanks Stam! I've just started using the classification targets mode and
> proj_thresh and they look promising. I tried your first suggestion, using
> fdt_paths, but my probtrackx runs don't create this file. I have all other
> expected output files, just not this one.
> I use only command-line version of probtrackx2, not the gui - could
> this be why I don't get a fdt_paths file?
>
> Thank you,
> Jeff
>
>
>> Hi Jeff
>>
>> The numbers you are after are probably the ones contained in fdt_paths.
>> The "waytotal" is just a normalisation factor and its absolute value
>> mostly reflects your choices for different algorithmic options in
>> probtrackx. Depending on how you run tractography this can be very similar
>> across subjects for a given seed or quite different. It makes more sense
>> to normalise the fdt_paths of every subject with the respective waytotal
>> to get directly path probabilities (now normalised from 0 to 1).
>>
>> Another way to compare connectivity for given tracts is to use
>> classification targets. Have a look at the online documentation and
>> proj_thresh. Seed_to_target results are more easily comparable across
>> subjects rather than fdt_paths, because they have some anatomical priors
>> on. These values can be further transformed to proportions (using
>> proj_thresh) that further reduces undesired variability across subjects
>> (e.g. due to noise, partial volume effects).
>>
>> Cheers
>> Stam
>>
>>
>>
>>
>>
>> On 11 Feb 2014, at 21:01, Jeff Waugh <[log in to unmask]> wrote:
>>
>>> Hello experts,
>>> I am interested in assessing the absolute number of tracts generated
>>> from a given seed ROI, and comparing that number between my patient and
>>> control groups. Why? I want to know whether my tractography results
>>> represent an anatomically-isolated change in tract number, or merely
>>> the area of largest change in tract number. Probtrackx generates a file
>>> that might be used in this manner, the waytotal. From the FSL page for
>>> probtrackx: "waytotal - a text file containing a single number
>>> corresponding to the total number of generated tracts that have not
>>> been rejected by inclusion/exclusion mask criteria."
>>>
>>> Have any of you tried to use the waytotal in this manner?
>>>
>>> One interesting/confounding thing I've found so far: when I correct the
>>> waytotal number by the volume of the native-space ROI used to seed
>>> probtrackx, all subjects correct to almost exactly the same number (625
>>> +/- 0.1). This would lead me to believe that the total number of tracts
>>> generated by a voxel is always the same, regardless of subject
>>> characteristics. Is this right? I have done the same waytotal and ROI
>>> correction for over 40 regions and always come up with this same number,
>>> 625.
>>>
>>> Thank you for any insight you can provide.
>>>
>>> - Jeff
>>>
>>>
>>> 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
>>> but does not contain patient information, please contact the sender and
>>> properly
>>> dispose of the e-mail.
>>
>>
>>
|