I was thinking that for a single voxel, the total of the values assigned to the voxel over all the tracts would have a maximum of 255 and that 255 would correspond to a probability of 1.0. I can see is likely wrong but for sure it's too simple since each voxel could contain crossing fibers from several tracts; hence the total probability assigned to the voxel over all the tracts might be greater than 1.0. ??
Surely there is some normalization applied to the values assigned to the voxels so they fall between 0 and 255. Does that normalization vary from one subject to the next and perhaps even from one tract to the next? And how is the normalization mapped to probability? Thanks - 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 10:48 AM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] newbie trac-all -bedp question 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<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 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> [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<mailto: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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