Re: [Freesurfer] Tracula_critical issue
Hi Mohamad - What you did with your binarization was that you lowered the threshold all the way to zero, i.e., included all the voxels that had any probability 0 to be in the tract. This means that you included more voxels than the default, which is to threshold at 20% of the max probability. Changing the threshold to get a broader ROI would be an alternative to running more iterations to get a more realiable distribution. How either of those approaches would behave depends on the noise level in the data. Also, you averaged the FA/MD/etc over those voxels without multiplying with their probability, which corresponds to the unweigthed average that trac-all gives you. Note that trac-all calls the dmri_pathstats command to compute the stats, and you can run that command with a different threshold to get the same behavior as what you did. You can find an example of the dmri_pathstats command line in the trac-all.log file of any of your subjects. Best, a.y On Mon, 24 Nov 2014, Alshikho, Mohamad J. wrote: Dear Anastasia, Thank you very much for your answer. In my analysis I have two groups 23 patients and 27 controls. My problem right now is that this change in the results (from the output of trac-all -path -c) gave me different P values between the groups, sometimes the results are significant and sometimes it is not! Till today I repeated this analysis many times and I collected the results after 5 consecutive runs (all the tracts for all the subjects) Recently and In order to find a solution for this problem I used the following command line to generate the mean metrics and the tracts volume: fslstats - dti_FA.nii.gz -k path.pd_bin.nii.gz -M -V [ I binarized path.pd.nii.gz (the output of trac-all -path -c for every tract) using fslmaths path.pd.nii.gz -thr 0.999 path.pd_bin.nii.gz and I used this treashold to make my mask conservative as possible] In this case I got stable numbers. i.e when I run this command line again the results are the same. Kindly is this valid? can I use fslstats instead of the third step in Tracula trac-all -path -c to calculate the mean metrics and the tract's volume? Also what is the difference between fslstats and trac-all -path -c (technically) I highly appreciate your support Mohamad From: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Anastasia Yendiki [ayend...@nmr.mgh.harvard.edu] Sent: Friday, November 21, 2014 5:10 PM To: Freesurfer support list Subject: Re: [Freesurfer] Tracula_critical issue Hi Mohamad - As it's a probabilistic method that's sampling from a distribution, there is a bit of randomness built in (which should decrease as you increase the number of samples that you collect). You'll find that the the weighted average measures are the most reliable, as they are less affected by the tails of the distribution. a.y On Wed, 5 Nov 2014, Alshikho, Mohamad J. wrote: Hi Anastasia, I started recently using Tracula to do tractography for my DTI data. I did the analysis exactly as mentioned in wiki. The problem is that when I am repeating the third step (trac-all -path -c ) for the same subjects to generate the statistics; Tracula is updating all the information mentioned in the file pathstats.overal.txt regarding the tract's volume and the tract's metrics values. Every time the output is different. I think we have a problem in the scripts or something like this? Attached are three pathstats.overal.txt files for the same subject after three consecutive runs for the trac-all -path -c (the same subject) Looking forward for your support Thanks ___ 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.
Re: [Freesurfer] Tracula_critical issue
Dear Anastasia, Thank you very much for your answer. In my analysis I have two groups 23 patients and 27 controls. My problem right now is that this change in the results (from the output of trac-all -path -c) gave me different P values between the groups, sometimes the results are significant and sometimes it is not! Till today I repeated this analysis many times and I collected the results after 5 consecutive runs (all the tracts for all the subjects) Recently and In order to find a solution for this problem I used the following command line to generate the mean metrics and the tracts volume: fslstats - dti_FA.nii.gz -k path.pd_bin.nii.gz -M -V [ I binarized path.pd.nii.gz (the output of trac-all -path -c for every tract) using fslmaths path.pd.nii.gz -thr 0.999 path.pd_bin.nii.gz and I used this treashold to make my mask conservative as possible] In this case I got stable numbers. i.e when I run this command line again the results are the same. Kindly is this valid? can I use fslstats instead of the third step in Tracula trac-all -path -c to calculate the mean metrics and the tract's volume? Also what is the difference between fslstats and trac-all -path -c (technically) I highly appreciate your support Mohamad From: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Anastasia Yendiki [ayend...@nmr.mgh.harvard.edu] Sent: Friday, November 21, 2014 5:10 PM To: Freesurfer support list Subject: Re: [Freesurfer] Tracula_critical issue Hi Mohamad - As it's a probabilistic method that's sampling from a distribution, there is a bit of randomness built in (which should decrease as you increase the number of samples that you collect). You'll find that the the weighted average measures are the most reliable, as they are less affected by the tails of the distribution. a.y On Wed, 5 Nov 2014, Alshikho, Mohamad J. wrote: Hi Anastasia, I started recently using Tracula to do tractography for my DTI data. I did the analysis exactly as mentioned in wiki. The problem is that when I am repeating the third step (trac-all -path -c ) for the same subjects to generate the statistics; Tracula is updating all the information mentioned in the file pathstats.overal.txt regarding the tract's volume and the tract's metrics values. Every time the output is different. I think we have a problem in the scripts or something like this? Attached are three pathstats.overal.txt files for the same subject after three consecutive runs for the trac-all -path -c (the same subject) Looking forward for your support Thanks ___ 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_critical issue
Hi Mohamad - As it's a probabilistic method that's sampling from a distribution, there is a bit of randomness built in (which should decrease as you increase the number of samples that you collect). You'll find that the the weighted average measures are the most reliable, as they are less affected by the tails of the distribution. a.y On Wed, 5 Nov 2014, Alshikho, Mohamad J. wrote: Hi Anastasia, I started recently using Tracula to do tractography for my DTI data. I did the analysis exactly as mentioned in wiki. The problem is that when I am repeating the third step (trac-all -path -c ) for the same subjects to generate the statistics; Tracula is updating all the information mentioned in the file pathstats.overal.txt regarding the tract's volume and the tract's metrics values. Every time the output is different. I think we have a problem in the scripts or something like this? Attached are three pathstats.overal.txt files for the same subject after three consecutive runs for the trac-all -path -c (the same subject) Looking forward for your support Thanks ___ 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_critical issue
Hi Anastasia, I started recently using Tracula to do tractography for my DTI data. I did the analysis exactly as mentioned in wiki. The problem is that when I am repeating the third step (trac-all -path -c ) for the same subjects to generate the statistics; Tracula is updating all the information mentioned in the file pathstats.overal.txt regarding the tract's volume and the tract's metrics values. Every time the output is different. I think we have a problem in the scripts or something like this? Attached are three pathstats.overal.txt files for the same subject after three consecutive runs for the trac-all -path -c (the same subject) Looking forward for your support Thanks # Title Pathway Statistics # # generating_program /usr/local/freesurfer/stable5_3_0/bin/dmri_pathstats # cvs_version # cmdline /usr/local/freesurfer/stable5_3_0/bin/dmri_pathstats --intrc /autofs/cluster/transcend/malshikho/tractography/tracula_1/002201/dpath/fmajor_PP_avg33_mni_bbr --dtbase /autofs/cluster/transcend/malshikho/tractography/tracula_1/002201/dmri/dtifit --path fmajor --subj 002201 --out /autofs/cluster/transcend/malshikho/tractography/tracula_1/002201/dpath/fmajor_PP_avg33_mni_bbr/pathstats.overall.txt --outvox /autofs/cluster/transcend/malshikho/tractography/tracula_1/002201/dpath/fmajor_PP_avg33_mni_bbr/pathstats.byvoxel.txt # sysname Linux # hostname icepuff2 # machine x86_64 # user malshikh # anatomy_type pathway # # subjectname 002201 # pathwayname fmajor # Count 1500 Volume 1151 Len_Min 54 Len_Max 91 Len_Avg 71.1467 Len_Center 70 AD_Avg 0.00143148 AD_Avg_Weight 0.00148653 AD_Avg_Center 0.00146087 RD_Avg 0.000475763 RD_Avg_Weight 0.000414811 RD_Avg_Center 0.000390255 MD_Avg 0.000794336 MD_Avg_Weight 0.000772051 MD_Avg_Center 0.000747128 FA_Avg 0.593211 FA_Avg_Weight 0.653136 FA_Avg_Center 0.664371 # Title Pathway Statistics # # generating_program /usr/local/freesurfer/stable5_3_0/bin/dmri_pathstats # cvs_version # cmdline /usr/local/freesurfer/stable5_3_0/bin/dmri_pathstats --intrc /autofs/cluster/transcend/malshikho/tractography/tracula_1/002201/dpath/fmajor_PP_avg33_mni_bbr --dtbase /autofs/cluster/transcend/malshikho/tractography/tracula_1/002201/dmri/dtifit --path fmajor --subj 002201 --out /autofs/cluster/transcend/malshikho/tractography/tracula_1/002201/dpath/fmajor_PP_avg33_mni_bbr/pathstats.overall.txt --outvox /autofs/cluster/transcend/malshikho/tractography/tracula_1/002201/dpath/fmajor_PP_avg33_mni_bbr/pathstats.byvoxel.txt # sysname Linux # hostname icepuff2 # machine x86_64 # user malshikh # anatomy_type pathway # # subjectname 002201 # pathwayname fmajor # Count 1500 Volume 998 Len_Min 55 Len_Max 105 Len_Avg 70.452 Len_Center 70 AD_Avg 0.00144797 AD_Avg_Weight 0.00148739 AD_Avg_Center 0.00147972 RD_Avg 0.000450739 RD_Avg_Weight 0.000414348 RD_Avg_Center 0.000411816 MD_Avg 0.00078315 MD_Avg_Weight 0.000772027 MD_Avg_Center 0.000767783 FA_Avg 0.614367 FA_Avg_Weight 0.654019 FA_Avg_Center 0.648396 # Title Pathway Statistics # # generating_program /usr/local/freesurfer/stable5_3_0/bin/dmri_pathstats # cvs_version # cmdline /usr/local/freesurfer/stable5_3_0/bin/dmri_pathstats --intrc /autofs/cluster/transcend/malshikho/tractography/tracula_1/002201/dpath/fmajor_PP_avg33_mni_bbr --dtbase /autofs/cluster/transcend/malshikho/tractography/tracula_1/002201/dmri/dtifit --path fmajor --subj 002201 --out /autofs/cluster/transcend/malshikho/tractography/tracula_1/002201/dpath/fmajor_PP_avg33_mni_bbr/pathstats.overall.txt --outvox /autofs/cluster/transcend/malshikho/tractography/tracula_1/002201/dpath/fmajor_PP_avg33_mni_bbr/pathstats.byvoxel.txt # sysname Linux # hostname icepuff2 # machine x86_64 # user malshikh # anatomy_type pathway # # subjectname 002201 # pathwayname fmajor # Count 1500 Volume 693 Len_Min 56 Len_Max 97 Len_Avg 72.1413 Len_Center 29 AD_Avg 0.00150666 AD_Avg_Weight 0.00151482 AD_Avg_Center 0.00130182 RD_Avg 0.000431594 RD_Avg_Weight 0.000428958 RD_Avg_Center 0.000632432 MD_Avg 0.000789951 MD_Avg_Weight 0.000790911 MD_Avg_Center 0.000855561 FA_Avg 0.648118 FA_Avg_Weight 0.653595 FA_Avg_Center 0.457097 ___ 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.
