The volume would have to be normalized to a total sum of 1 for the voxel values to represent an actual distribution.
________________________________ From: freesurfer-boun...@nmr.mgh.harvard.edu <freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Krieger, Donald N. <krieg...@upmc.edu> Sent: Wednesday, April 11, 2018 10:43:11 AM To: Freesurfer support list Subject: Re: [Freesurfer] newbie trac-all -bedp question Great – thanks – that’s what I need. I can use the probability for each pixel as a weight for the neuroelectric current count for that pixel to quantify the activity for the tract. I assume that each voxel value maps directly to its probability, i.e. 0-255 --> 0.0 – 1.0 Thanks again – best – Don From: freesurfer-boun...@nmr.mgh.harvard.edu [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Yendiki, Anastasia Sent: Wednesday, April 11, 2018 10:26 AM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] newbie trac-all -bedp question 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 ________________________________ From: freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu> <freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>> on behalf of Krieger, Donald N. <krieg...@upmc.edu<mailto:krieg...@upmc.edu>> Sent: Wednesday, April 11, 2018 8:06:01 AM To: Freesurfer support list Subject: Re: [Freesurfer] newbie trac-all -bedp question 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. 1. Are these the files that I’m looking for? 2. If so, where can I find documentation? 3. What is the shortest path to generate them? 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-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu> [mailto:freesurfer-boun...@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<mailto: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-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu> <freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>> on behalf of Krieger, Donald N. <krieg...@upmc.edu<mailto:krieg...@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-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu> [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Yendiki, Anastasia Sent: Tuesday, April 10, 2018 4:24 PM To: freesurfer <freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>> Subject: Re: [Freesurfer] newbie trac-all -bedp question Hi Don - See: https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg38004.html Best, a.y ________________________________ From: freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu> <freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>> on behalf of Krieger, Donald N. <krieg...@upmc.edu<mailto:krieg...@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
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