Hi FS users,
I've tested the newer Tracula FS 5.2 on Snow Leopard and ran into
errors. The 5.2 recon-all of T1 was finished ok.
Here is the final part of log file.
#@# Priors Tue Mar 26 14:39:36 EDT 2013
/apps/freesurfer/bin/dmri_train --outdir
/Volumes/Access_Point_Backup/freesurfer/NCNC2348/d
ard build without a problem?
>
> a.y
>
>
> On Tue, 26 Mar 2013, Ping-Hong Yeh wrote:
>
>> Hi FS users,
>>
>> I've tested the newer Tracula FS 5.2 on Snow Leopard and ran into
>> errors. The 5.2 recon-all of T1 was finished ok.
>>
>> Here is
Hi Anastasia,
Just follow up on this thread..
If 5000 samples were used for each voxel, how can I normalize the
intensity of path.pd volumes to a sum of 1 ?
Also what thresholding value was chosen to calculate the tract volume,
shown in the pathstats.overall.txt ?
Thanks.
ping
On Fri, Nov 9, 2
e total samples to converge than
> the center of the distribution anyway). You can of course find your own
> averages at a different threshold from path.pd.nii.gz if you wish.
>
> Hope this helps,
> a.y
>
>
> On Fri, 14 Dec 2012, Ping-Hong Yeh wrote:
>
>> Hi Anastasia
a.y
>
>
> On Fri, 21 Dec 2012, Ping-Hong Yeh wrote:
>
>> Hi Anastasia,
>>
>> Thank you the answers.
>> One more question, if I'd like to use the scalar images created by
>> other methods, e.g. non-linear fitting, how can I feed this images to
>>
average: you average only over the voxels in path.map.nii.gz.
>
>
> On Fri, 21 Dec 2012, Ping-Hong Yeh wrote:
>
>> Sorry for not being clear. I meant how to calculate path length based
>> on path.pd.nii.gz, and the Center and Weight Average of the scalar
>> images
Hi,
I got the error running "trac-all -path -c configure.txt"
ERROR: Could not open
${SUBJECTS_DIR}/$Subject/dlabel/diff/lh.cst_AS_avg33_mni_flt_cpts_5.txt
I can only find only image files in the "dlabel/diff" directory, but
not text files.
Which step(s) create the lh.cst_AS_avg33_mni_flt_cpts
Hi Priti,
Adjusting the threshold does not help. Indeed, the voxel number, only
about 50 or so, is much less compared to right cst, which has couple
thousands. In addition, the segmented image is a binary image, i.e.
only intensity 0 and 1000, while other tracts have gray scale ranging
from 0 to
You can change the pathlist in dmrirc to do only the path that failed.
>
> We jump through various hoops to make sure this sort of thing doesn't happen
> but in a few cases it can't be prevented, unfortunately.
>
> Let me know if this has helped or if you have any other q
entire brain well, after the aparc+aseg fixes?
>
> a.y
>
> On Tue, 18 Oct 2011, Ping-Hong Yeh wrote:
>
>> Hi Anastasia,
>>
>> I got fixed of the aparc+aseg (see aparc+aseg.png) in one of
>> problematic data and re-ran the trac-all following your suggestions.
&
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