Re: [Freesurfer] Longitudinal Freesurfer TRACULA quality control
Hi Anastasia! I will go backwards with increasing difficulty for me to understand everything: 4. I see, yes this would not make sense. Thank you for the explanation! 3. With fslview I will have to run through 393,120 slices, then. (72 slices in z-direction for our 70 DWI scans for tp1 and tp2 for each of our 39 subjects) I will go dwi image by dwi image running through the 72 slices rather fast. Just to make sure I am not wasting a lot of time: is this what I should do? If I detect slices that are much darker than their neighbors, will I need to exclude this subject for the analysis or can I do something about it? 2. Yes, I use bbregister and I also use the anatomical T1 weighted scan to extract the brain mask (usemaskanat=1). To make sure that everything is alright, I would go slice by slice in tkmedit with tkmedit [subject] brainmask.mgz -surfs -aparc+aseg where [subject] would be the base AND both longitudinal runs. I understand that I need to check if white matter is where it should be, if the cortical and pial surfaces are where they should be and if the labeling is correct. Again, as this will take probably even longer than 3. I would like to make sure this is the right thing to do before starting the quality check. Thanks again! Vincent Hi Vincent - I'll take on the tracula-related parts: 2. For tracula, the part of the recon-all output that matters is the aparc+aseg. The surfaces will play a role only the DWI-to-T1 registration (assuming you opt to use bbregister). 3. It's important to check your DWI data for obvious motion artifacts, (slices that are much darker than their neighbors). Right now this has to be done visually, but it's on my list to produce some motion metrics as part of the preprocessing. 4. The ball-and-stick model (that bedpostx fits to your data) is used by the tractography algorithm in tracula, but there are no stats produced on the parameters of that model currently. That's something that can be added in the future as well. Note though that it wouldn't make sense to just average f1 or f2 over the pathway, because compartment 1 in one voxel may correspond to compartment 2 in some other voxel. Hope this helps, a.y On Fri, 11 Oct 2013, vbrun...@nmr.mgh.harvard.edu wrote: Dear Freesurfer experts, I want to do a quality check on our imaging data. I used the longitudinal stream for SBA and as the first step for the longitudinal white matter analysis with TRACULA. We had two time points in our study and thus, in the freesurfer output directory there are 5 folders per subject (2 cross-sectional runs, 2 long runs and the base). 1. Would you recommend to use (all of) the QA_TOOLS on all of these 5 folders per subject for the SBA? 2. Independent of the previous question, for the longitudinal version of TRACULA would you recommend to use (all of) the QA_TOOLS on the freesurfer base folder only / additional folders? 3. In addition to the late visual check for well reconstructed pathways with freeview, is there another automated possibility to check the quality of the diffusion weighted images beforehand/do you think this is necessary? 4. On another note: If I understand correctly, in TRACULA bedpostX is used to reconstruct the pathways but then the mean over the voxels that were hit (by the MCMC sampling of the paths) of measures from the tensor model are taken as outputs. I wonder, is there also the possibility of using the partial volumes f1, f2,.. as output measures? Best, Vincent ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] Longitudinal Freesurfer TRACULA quality control
Dear Freesurfer experts, I want to do a quality check on our imaging data. I used the longitudinal stream for SBA and as the first step for the longitudinal white matter analysis with TRACULA. We had two time points in our study and thus, in the freesurfer output directory there are 5 folders per subject (2 cross-sectional runs, 2 long runs and the base). 1. Would you recommend to use (all of) the QA_TOOLS on all of these 5 folders per subject for the SBA? 2. Independent of the previous question, for the longitudinal version of TRACULA would you recommend to use (all of) the QA_TOOLS on the freesurfer base folder only / additional folders? 3. In addition to the late visual check for well reconstructed pathways with freeview, is there another automated possibility to check the quality of the diffusion weighted images beforehand/do you think this is necessary? 4. On another note: If I understand correctly, in TRACULA bedpostX is used to reconstruct the pathways but then the mean over the voxels that were hit (by the MCMC sampling of the paths) of measures from the tensor model are taken as outputs. I wonder, is there also the possibility of using the partial volumes f1, f2,.. as output measures? Best, Vincent ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] long_mris_slopes sign of do-rate
Dear Freesurfer experts, I have followed the LongitudinalTutorial with two time points + two groups and now, after looking at the output of the qdec analysis, I just want to make sure I haven't made a sign error as for the control group the difference is as expected around 0 but for the experimental group I see negative values (= thinning?) all over the place which seems weird, just want to make sure I got this right: I set the time variable to 0 for the baseline scan and to 1 for the after-intervention-scan. Is it correct that for do-rate the calculation is then only thickness of tp2 - thickness of tp1 and not the other way around? I ask because in the long_mris_slopes -help it says that do-rate would yield the thinning in mm/time and if this means that a positive value stands for thinning then this would contradict what I understood from the Tutorial where it says for the rate thick2-thick1 is calculated, so a positive value should mean thickening. Also, how does long_mris_slopes know which one is tp1 and which one is tp2? I assume it takes the first entry in the fsid column of long.qdec.table.dat as tp1 and the second entry below as tp2? Hm, I see no other possibilities of making a sign error during the whole process, did anyone report a similar issue? Thanks for your help! Best, Vincent ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] Tracula longitudinal nan values for highest probability path
Hi Anastasia, the files are here: /autofs/cluster/lazar/projects/Templeton/dng/dtionly/Tracula/tracall/TC055FB.v2/dpathlong/lh.cst_AS_avg33_mni_bbr The base is here: /autofs/cluster/lazar/projects/Templeton/dng/dtionly/Tracula/tracall/longbaseTC055FB Freesurfer outputs: /autofs/cluster/lazar/projects/Templeton/dng/dtionly/Tracula/freesurfer/subjects/TC055FB.v2 and /autofs/cluster/lazar/projects/Templeton/dng/dtionly/Tracula/freesurfer/subjects/TC055FB.v2.long.longbaseTC055FB You should have permissions to see everything, if not, please tell me. Fyi: Maybe it's random, but the 4 errors occurred all in the first time point. Thanks, Vincent Hi Vincent - If you upload the tracula dirs for this particular time point, I'll take a look. a.y On Mon, 20 May 2013, Vincent Brunsch wrote: Hi Anastasia, Thanks for your help! I had this issue with 4 tracts in total. I just want to add that before rerunning dmri_pathstats not only pathstats.overall but also pathstats.byvoxel was affected (in the latter there were no matrix entries at all). I found some information in the trac-all.log but not explicitly the command line - this was found in pathstats.overall.txt, though. After rerunning dmri_pathstats everything looks great now for 3 out of the 4 tracts, YEAH! I am not sure what to do with the last one, though: Here, the same error occurs but in cpts.map.txt no two lines are identical: For lh.cst: 58 48 10 62 51 21 65 55 26 70 58 35 72 57 39 64 55 56 Would you suggest deleting randomly one time point for this tract of this subject? Thanks! Vincent Am 5/20/2013 10:31 AM, schrieb Anastasia Yendiki: Hi Vincent - Thanks for bringing this to my attention. I can see what might cause this glitch (only in the longitudinal case) and I'll fix it in the next version. In the meantime, if you delete one of the two identical lines from cpts.map.txt, and then rerun the dmri_pathstats command line that you'll find in the trac-all.log of your subject, it should regenerate the stats files correctly. Sorry for the inconvenience. a.y On Fri, 17 May 2013, vbrun...@nmr.mgh.harvard.edu wrote: Dear Anastasia, When running the longitudinal tracula version on our 39 subjects I found for some of them nan-values for the center_avg variables of some tracts. When I have a look at the tract distribution and the highest probability path, everything seems to be ok. However, when checking the control points of this path, two of them are the same. Do you know how this could have happened / what to do? E.g. control points of forceps major from a subject (cpts.map.txt), see 4th and 5th control point: 63 20 39 67 31 39 59 43 38 52 42 38 52 42 38 43 32 38 50 19 33 And the respective pathstats.overall.txt: Count 1500 Volume 370 Len_Min 62 Len_Max 99 Len_Avg 78.9307 Len_Center 0 AD_Avg 0.00155598 AD_Avg_Weight 0.00158424 AD_Avg_Center -nan RD_Avg 0.000438439 RD_Avg_Weight 0.000401328 RD_Avg_Center -nan MD_Avg 0.000810952 MD_Avg_Weight 0.000795633 MD_Avg_Center -nan FA_Avg 0.662419 FA_Avg_Weight 0.696257 FA_Avg_Center -nan Thanks for your help!! :) Best, Vincent ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] Tracula longitudinal nan values for highest probability path
Dear Anastasia, When running the longitudinal tracula version on our 39 subjects I found for some of them nan-values for the center_avg variables of some tracts. When I have a look at the tract distribution and the highest probability path, everything seems to be ok. However, when checking the control points of this path, two of them are the same. Do you know how this could have happened / what to do? E.g. control points of forceps major from a subject (cpts.map.txt), see 4th and 5th control point: 63 20 39 67 31 39 59 43 38 52 42 38 52 42 38 43 32 38 50 19 33 And the respective pathstats.overall.txt: Count 1500 Volume 370 Len_Min 62 Len_Max 99 Len_Avg 78.9307 Len_Center 0 AD_Avg 0.00155598 AD_Avg_Weight 0.00158424 AD_Avg_Center -nan RD_Avg 0.000438439 RD_Avg_Weight 0.000401328 RD_Avg_Center -nan MD_Avg 0.000810952 MD_Avg_Weight 0.000795633 MD_Avg_Center -nan FA_Avg 0.662419 FA_Avg_Weight 0.696257 FA_Avg_Center -nan Thanks for your help!! :) Best, Vincent ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] tracall longitudinal default options
Thank you so much for your help! :) - Field inhomogeneity: great, I'll stick with the default option then - Number of sticks: thank you..I had a look at Figures 8 and 9 in the mentioned paper..and this does not look good: we have 60 non b0 images with a b-value of 700 and the dwi_snr text file in the dmri folder states that our SNRs are around 5 or even lower..if I understand the figures correctly, this means that we are far from recovering 2 anisotropic compartments, not to mention more. :( Do you think that tracula is then even a good option for our data or do you suggest we just have a look at the output of dtifit? - Yes, I saw that you increased the number of iterations in the longitudinal example file from 5000 to 7500, but maybe it should be even more? I ran through all of the three trac-all steps with our data (nsample = 7500, sticks = 2) and I think I have a similar problem as was already mentioned in the list today: almost for every subject I have at least one out of the 18 paths that was not reconstructed and it seems to be random which path that is. For one subject no path was reconstructed at all. Maybe this is all due to the low b-value and SNR? Or should I just rerun the analysis? Best, Vincent Hi Vincent: - Field inhomogeneity correction: This is done using the FSL fugue utility, which uses a field map to mitigate the geometric distortions in the DWI due to field inhomogeneity. However, as you point out, DWI-to-T1 registration will be performed anyway, and this may mitigate this type of geometric distortions. - Number of sticks: How many you can fit to your data depends on the angular resolution in your data. You can keep adding parameters to the model, but if there's not enough data to estimate those parameters reliably, there's no point. You can get an idea from Behrens et al 2007 on what's feasible. - The one MCMC parameter that may be useful to play with is nsample, the total number of path samples collected. Particularly for longitudinal, you may want to increase it if the tracts look narrow, since it may take longer to sample the full tract with data from more than one time point. Hope this helps, a.y On Wed, 17 Apr 2013, vbrun...@nmr.mgh.harvard.edu wrote: Hi all! I am almost ready to do my first longitudinal run with Tracula. I guess that for the remaining insecurities it is probably best to stick with the default options but I'd like to be more confident with it and just wanted to ask which option to choose and why or why not: My config file contains information about two time points of 39 subjects. - Perform Registration-based B0-inhomogeneity compensation If I understand correctly, although I would have the fieldmap information this step (as well as BET) is not necessary as I can use the respective T1 weighted image (usemaskanat=1) for registration? - Number of sticks in the ball-stick model Since last month it is possible to change the default value of 2. Would you recommend a higher value? That would give me more information also about crossing fibers, right? But if so, which value would be reasonable and why? - MCMC burn-in iterations (default:200), iterations (default:7500) and frequency (default:5) (Why are we allowed to change these options at all?) Thank you! Best, Vincent ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] tracall longitudinal default options
Hi all! I am almost ready to do my first longitudinal run with Tracula. I guess that for the remaining insecurities it is probably best to stick with the default options but I'd like to be more confident with it and just wanted to ask which option to choose and why or why not: My config file contains information about two time points of 39 subjects. - Perform Registration-based B0-inhomogeneity compensation If I understand correctly, although I would have the fieldmap information this step (as well as BET) is not necessary as I can use the respective T1 weighted image (usemaskanat=1) for registration? - Number of sticks in the ball-stick model Since last month it is possible to change the default value of 2. Would you recommend a higher value? That would give me more information also about crossing fibers, right? But if so, which value would be reasonable and why? - MCMC burn-in iterations (default:200), iterations (default:7500) and frequency (default:5) (Why are we allowed to change these options at all?) Thank you! Best, Vincent ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
