Thank you Anastasia,
ah, yes, that might have been easier [I wonder though if I might have
had some issues with different tract lengths etc.?]. I wanted to make
sure that my coordinates relate to the tract, so I decided just to flip
the x-coordinate, change the directory name and all the indication in
the byvoxel.txt files pertaining to e.g. 'lh.unc' to 'rh.unc'. And I did
all of this just for patients with right TLE. Then I ran trac-all stat
-c ... and looked at 'lh' as those ipsilateral tracts and 'rh' as
contralateral ones. Has worked as well.
All the best wishes,
Barbara
On 27/07/2016 06:32, Anastasia Yendiki wrote:
> Hi Barbara - Your hack sounds like the right idea. One option would be to
> switch the FA values between the pathstats.byvoxel.txt files in the lh.*
> and rh.* output directories, by editing the text files without renaming
> the directories.
>
> Hope this helps,
>
> a.y
>
> On Mon, 25 Jul 2016, Barbara Kreilkamp wrote:
>
>> Dear Freesurfers,
>>
>> I've got data pertaining to patients with left and right-sided temporal
>> lobe epilepsy (TLE).
>> My aim is to group those tracts according to side of epilepsy for
>> waypoint comparisons.
>>
>> Basically for patients with right TLE I'd like to look at right tracts
>> and at the same time for patients with left TLE I'd like to look at left
>> tracts (ipsilateral tracts), I need to do the same for the contralateral
>> tracts.
>> Is there a straightforward way of doing this?
>>
>> I've already copied the tracts to respective ipsi and contralateral
>> byvoxel.txt files. Like so: for i in R*/dpath/rh*/pathstats.byvoxel.txt;
>> do cp $i ${i/byvoxel./byvoxel_ipsiRTLE.}; done ; for i in
>> R*/dpath/lh*/pathstats.byvoxel.txt; do cp $i
>> ${i/byvoxel./byvoxel_contraRTLE.}; done
>> Now I have to flip the x-coordinates in the patients with right TLE (to
>> make them more comparable to the tracts of the patients with left TLE).
>> That will not be a problem, but I wonder if I am missing something?
>> Can I then just go ahead and run trac-all -stats -c dmrircfile to
>> generate the mean waypoint tracts etc.?
>>
>> Thank you very much,
>> Best wishes,
>>
>> Barbara
>>
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>>
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