Hi Don - No, dlabel/ contains files that are used in the pathway reconstruction, but the output of the reconstruction is saved in dpath/. There's a subdirectory in there for each pathway, and it contains a volume called path.pd.nii.gz. This is the probability that each voxel belongs to this pathway, in the subject's native diffusion space. As TRACULA is a probabilistic method, you get a probability associated with each voxel, rather than a set of voxel coordinates.
More info (potentially too much info) on TRACULA outputs:
https://surfer.nmr.mgh.harvard.edu/fswiki/trac-all#Outputdirectoriesandfiles
Best,
a.y
Thanks for the additional information, Anastasia.
I will look for those files.
What I am after is a list of xyz coordinates for each of the 18 tracts. I see masks in the trctrain/trc0xy/dlabel/mni directories which appear to be what I’m looking for. They have names like
<roi>_AS_<str1>.<str2>.nii.gz
where str1 = bbr or flt and
str2 = roi1 or roi2
I can extract the lists of coordinates from them with mri_cor2label although I haven’t checked these lists to make sure they are actually what we need.
I haven’t found documentation on these files nor do I see them in the tutorial directories for the three elmo’s.
I have bedbpostx running but do not expect it to produce them. I suppose it is trac-all -path which will do so but I thought I would ask my questions anyway.
It strikes me that maybe it is the streamlines which best define the tracts rather than these volumetric masks. I still do not thoroughly understand where in the processing sequence the streamlines get assigned to specific tracts. ??
Thanks - Don
From: freesurfer-bounces@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard.edu]
On Behalf Of Yendiki, Anastasia
Sent: Tuesday, April 10, 2018 9:23 PM
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] newbie trac-all -bedp question
Hi Don - If the output files described here show up in the end, all is well:
https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/FDT/UserGuide#BEDPOSTX
Best,
a.y
From:
freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Krieger, Donald N. <kriegerd@upmc.edu>
Sent: Tuesday, April 10, 2018 4:52:57 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] newbie trac-all -bedp question
Great – thanks.
It’s running.
I see several warnings which I presume can be ignored:
hostname: Name or service not known
Best - Don
From:
freesurfer-bounces@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard.edu]
On Behalf Of Yendiki, Anastasia
Sent: Tuesday, April 10, 2018 4:24 PM
To: freesurfer <freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] newbie trac-all -bedp question
From:
freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Krieger, Donald N. <kriegerd@upmc.edu>
Sent: Tuesday, April 10, 2018 1:15:05 PM
To: freesurfer
Subject: [Freesurfer] newbie trac-all -bedp question
I am getting the following output with error on this command:
trac-all -bedp -s HDFT1001 -i ep2d_diff_SliceAcc_b1k_64_768x768.23
INFO: SUBJECTS_DIR is /media/portable/home/kriegerd/Contrib/Freesurfer_6.0/subjects
INFO: Diffusion root is /media/portable/home/kriegerd/Contrib/Freesurfer_6.0/subjects
Actual FREESURFER_HOME /media/portable/home/kriegerd/Contrib/Freesurfer_6.0
WARN: Running bedbostx locally - this might take a while
WARN: It is recommended to run this step on a cluster
bedpostx_mgh -n 2 /media/portable/home/kriegerd/Contrib/Freesurfer_6.0/subjects/HDFT1001/dmri
/home/kriegerd/Contrib/Freesurfer/bin/bedpostx_mgh: 131: /home/kriegerd/Contrib/Freesurfer/bin/bedpostx_mgh: Syntax error: "(" unexpected
I apologize for not finding the answer in the list archive.
It's probably there.
I'm running under ubuntu 14.04.
bedpostx_mgh is a shell script which calls for /bin/sh.
On my machine, that is a symlink to /bin/bash
If I change it to be explicitly /bin/bash, it runs a bit further.
Here is the full output:
INFO: SUBJECTS_DIR is /media/portable/home/kriegerd/Contrib/Freesurfer_6.0/subjects
INFO: Diffusion root is /media/portable/home/kriegerd/Contrib/Freesurfer_6.0/subjects
Actual FREESURFER_HOME /media/portable/home/kriegerd/Contrib/Freesurfer_6.0
WARN: Running bedbostx locally - this might take a while
WARN: It is recommended to run this step on a cluster
bedpostx_mgh -n 2 /media/portable/home/kriegerd/Contrib/Freesurfer_6.0/subjects/HDFT1001/dmri
subjectdir is /media/portable/home/kriegerd/Contrib/Freesurfer_6.0/subjects/HDFT1001/dmri
Making bedpostx directory structure
Queuing preprocessing stages
/home/kriegerd/Contrib/Freesurfer/bin/fsl_sub_mgh: 470: /home/kriegerd/Contrib/Freesurfer/bin/fsl_sub_mgh: Syntax error: "(" unexpected (expecting ";;")
Queuing parallel processing stage
0 slices processed
/home/kriegerd/Contrib/Freesurfer/bin/fsl_sub_mgh: 470: /home/kriegerd/Contrib/Freesurfer/bin/fsl_sub_mgh: Syntax error: "(" unexpected (expecting ";;")
Queuing post processing stage
/home/kriegerd/Contrib/Freesurfer/bin/fsl_sub_mgh: 470: /home/kriegerd/Contrib/Freesurfer/bin/fsl_sub_mgh: Syntax error: "(" unexpected (expecting ";;")
/home/kriegerd/Contrib/Freesurfer/bin/bedpostx_mgh: line 439: 26461 Terminated ${subjdir}.bedpostX/monitor
Thanks - Don