Re: [Freesurfer] About TRACULA results
Thank you for your reply. I will wait for the new version, hopefully in months. On 8/31/2016 1:54 PM, Anastasia Yendiki wrote: Hi there - If you upload the tracula directories for me, I'm happy to try to figure out what's going on. Although honestly at this point it's worth waiting for the new version. Thanks! a.y On Tue, 30 Aug 2016, Kang, XJ wrote: Hi, I am trying to computer the changes of cortical parcellations and fiber pathways using FreeSurfer v5.3 and Tracula (2014/05/26 update) . I copied the anatomical and DWI images from the same scan session into five directories. Run recon-all and trac-all on the 5 same data sets, in order to check the reproducibility of the analysis. Here are what I got: the Desikan-Killiany parcellations in both GM and WM, and the subcortical structures, repeat well. No difference found in volume or size of those structures. However, the volume and averaged DTI parameters of the fiber pathways, which found in the file ~/sub/dpath/*_PP_avg33_mni_flt/pathstats.overall.txt, varies for the 5 sets. tracula.conf files were copied from ~/freesurfer/bin/dmrirc.example. The changes are calculated in percentage by (S1-S0)/((S1+S0)/2)*100%. For example, the changes of averaged FA between the 5 data sets are : ?? ? S1-S0, S2-S0, S3-S0, S4-S0 Corpus Callosum - Forceps Major , -1.1 ,6.0 ,0.5 ,1.3 , Corpus Callosum - Forceps Minor ,0.1 ,0.0 , -1.6 ,0.0 , Right Anterior Thalamic Radiations ,0.1 , -1.0 ,0.5 ,0.9 , Right Cingulum - Angular Bundle , -4.8 , -2.0 , -1.5 ,3.8 , Right Cingulum - Cingulate Gyrus Endings, 0.5 , -0.9 ,0.4 , -2.3 , Right Corticospinal Tract ,1.9 ,0.6 , -2.2 ,1.4 , Right Inferior Longitudinal Fasciculus , -2.2 , -0.8 , -1.3 ,3.0 , Right Superior Longitudinal Fasciculus - Parietal Endings , 0.8 , -0.4 , -1.2 ,0.2 , Right Superior Longitudinal Fasciculus - Temporal Endings , -4.9 , -0.6 , -2.6 , -1.3 , Right Uncinate Fasciculus , 0.5 ,1.6 , -0.9 ,3.5 , Even larger changes for the volume of the pathways: ?? ? S1-S0, S2-S0, S3-S0, S4-S0 Corpus Callosum - Forceps Major ,2.2 , -33.7 , -12.3 ,1.1 , Corpus Callosum - Forceps Minor , 11.9 ,4.8 ,0.6 ,7.2 , Right Anterior Thalamic Radiations , -8.9 ,2.2 , -12.5 ,7.5 , Right Cingulum - Angular Bundle , -38.1 , 41.6 , 34.8 ,8.6 , Right Cingulum - Cingulate Gyrus Endings , 24.4 , 33.1 , 21.3 , 17.5 , Right Corticospinal Tract , 9.8 , -3.0 ,2.2 , 19.5 , Right Inferior Longitudinal Fasciculus ,7.2 , 24.1 , -7.3 , 23.8 , Right Superior Longitudinal Fasciculus - Parietal Endings , 17.2 , 10.2 , 25.1 ,9.9 , Right Superior Longitudinal Fasciculus - Temporal Endings , 15.4 , 3.4 , -3.1 , -11.5 , Right Uncinate Fasciculus , 13.3 , -1.2 , 16.4 , -3.4 , Any expert has the experience on these? Thank you for your help. XJ Kang ___ 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 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] About TRACULA results
Hi there - If you upload the tracula directories for me, I'm happy to try to figure out what's going on. Although honestly at this point it's worth waiting for the new version. Thanks! a.y On Tue, 30 Aug 2016, Kang, XJ wrote: Hi, I am trying to computer the changes of cortical parcellations and fiber pathways using FreeSurfer v5.3 and Tracula (2014/05/26 update) . I copied the anatomical and DWI images from the same scan session into five directories. Run recon-all and trac-all on the 5 same data sets, in order to check the reproducibility of the analysis. Here are what I got: the Desikan-Killiany parcellations in both GM and WM, and the subcortical structures, repeat well. No difference found in volume or size of those structures. However, the volume and averaged DTI parameters of the fiber pathways, which found in the file ~/sub/dpath/*_PP_avg33_mni_flt/pathstats.overall.txt, varies for the 5 sets. tracula.conf files were copied from ~/freesurfer/bin/dmrirc.example. The changes are calculated in percentage by (S1-S0)/((S1+S0)/2)*100%. For example, the changes of averaged FA between the 5 data sets are : ?? ? S1-S0, S2-S0, S3-S0, S4-S0 Corpus Callosum - Forceps Major , -1.1 , 6.0 , 0.5 , 1.3 , Corpus Callosum - Forceps Minor , 0.1 , 0.0 , -1.6 , 0.0 , Right Anterior Thalamic Radiations , 0.1 , -1.0 , 0.5 , 0.9 , Right Cingulum - Angular Bundle , -4.8 , -2.0 , -1.5 , 3.8 , Right Cingulum - Cingulate Gyrus Endings , 0.5 , -0.9 , 0.4 , -2.3 , Right Corticospinal Tract , 1.9 , 0.6 , -2.2 , 1.4 , Right Inferior Longitudinal Fasciculus , -2.2 , -0.8 , -1.3 , 3.0 , Right Superior Longitudinal Fasciculus - Parietal Endings , 0.8 , -0.4 , -1.2 , 0.2 , Right Superior Longitudinal Fasciculus - Temporal Endings , -4.9 , -0.6 , -2.6 , -1.3 , Right Uncinate Fasciculus , 0.5 , 1.6 , -0.9 , 3.5 , Even larger changes for the volume of the pathways: ?? ? S1-S0, S2-S0, S3-S0, S4-S0 Corpus Callosum - Forceps Major , 2.2 , -33.7 , -12.3 , 1.1 , Corpus Callosum - Forceps Minor , 11.9 , 4.8 , 0.6 , 7.2 , Right Anterior Thalamic Radiations , -8.9 , 2.2 , -12.5 , 7.5 , Right Cingulum - Angular Bundle , -38.1 , 41.6 , 34.8 , 8.6 , Right Cingulum - Cingulate Gyrus Endings , 24.4 , 33.1 , 21.3 , 17.5 , Right Corticospinal Tract , 9.8 , -3.0 , 2.2 , 19.5 , Right Inferior Longitudinal Fasciculus , 7.2 , 24.1 , -7.3 , 23.8 , Right Superior Longitudinal Fasciculus - Parietal Endings , 17.2 , 10.2 , 25.1 , 9.9 , Right Superior Longitudinal Fasciculus - Temporal Endings , 15.4 , 3.4 , -3.1 , -11.5 , Right Uncinate Fasciculus , 13.3 , -1.2 , 16.4 , -3.4 , Any expert has the experience on these? Thank you for your help. XJ Kang ___ 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] About TRACULA results
Hi, I am trying to computer the changes of cortical parcellations and fiber pathways using FreeSurfer v5.3 and Tracula (2014/05/26 update) . I copied the anatomical and DWI images from the same scan session into five directories. Run recon-all and trac-all on the 5 same data sets, in order to check thereproducibility of the analysis. Here are what I got: the /Desikan/-Killiany parcellations in both GM and WM, and the subcortical structures, repeat well. No difference found in volume or size of those structures. However, the volume and averaged DTI parameters of the fiber pathways, which found in the file ~/sub/dpath/*_PP_avg33_mni_flt/pathstats.overall.txt, varies for the 5 sets. tracula.conf files were copied from ~/freesurfer/bin/dmrirc.example. The changes are calculated in percentage by (S1-S0)/((S1+S0)/2)*100%. For example, the changes of averaged FA between the 5 data sets are : S1-S0, S2-S0, S3-S0, S4-S0 Corpus Callosum - Forceps Major , -1.1 ,6.0 ,0.5 ,1.3 , Corpus Callosum - Forceps Minor ,0.1 ,0.0 , -1.6 ,0.0 , Right Anterior Thalamic Radiations ,0.1 , -1.0 , 0.5 ,0.9 , Right Cingulum - Angular Bundle , -4.8 , -2.0 , -1.5 ,3.8 , Right Cingulum - Cingulate Gyrus Endings, 0.5 , -0.9 , 0.4 , -2.3 , Right Corticospinal Tract ,1.9 ,0.6 , -2.2 ,1.4 , Right Inferior Longitudinal Fasciculus , -2.2 , -0.8 , -1.3 ,3.0 , Right Superior Longitudinal Fasciculus - Parietal Endings , 0.8 , -0.4 , -1.2 ,0.2 , Right Superior Longitudinal Fasciculus - Temporal Endings , -4.9 , -0.6 , -2.6 , -1.3 , Right Uncinate Fasciculus ,0.5 ,1.6 , -0.9 ,3.5 , Even larger changes for the volume of the pathways: S1-S0, S2-S0, S3-S0, S4-S0 Corpus Callosum - Forceps Major ,2.2 , -33.7 , -12.3 ,1.1 , Corpus Callosum - Forceps Minor, 11.9 , 4.8 , 0.6 ,7.2 , Right Anterior Thalamic Radiations , -8.9 ,2.2 , -12.5 ,7.5 , Right Cingulum - Angular Bundle , -38.1 , 41.6 , 34.8 ,8.6 , Right Cingulum - Cingulate Gyrus Endings , 24.4 , 33.1 , 21.3 , 17.5 , Right Corticospinal Tract ,9.8 , -3.0 ,2.2 , 19.5 , Right Inferior Longitudinal Fasciculus ,7.2 , 24.1 , -7.3 , 23.8 , Right Superior Longitudinal Fasciculus - Parietal Endings , 17.2 , 10.2 , 25.1 ,9.9 , Right Superior Longitudinal Fasciculus - Temporal Endings , 15.4 , 3.4 , -3.1 , -11.5 , Right Uncinate Fasciculus , 13.3 , -1.2 , 16.4 , -3.4 , Any expert has the experience on these? Thank you for your help. XJ Kang ___ 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] About TRACULA
Hi Yang - TRACULA does not assume that the shape, size, or integrity of the tracts is the same in the study subjects as in the atlas subjects. It just assumes that the relative position of the tracts with respect to the cortical and subcortical segmentation labels from freesurfer. For example, does tract X go lateral to the thalamus or superior to the thalamus, and does this happen in the beginning, end, or 2/3 along the length of tract X? If these general relationships are preserved, and if the cortical and subcortical segmentation can be reconstructed in the study subjects, then TRACULA should work. Again, the best way to know if TRACULA will work is to run it on a couple of representative subjects. I may have written every line of code in it, I can explain how it works, but even I can't predict how it'll do on every single data set out there that I haven't even seen :) Best, a.y On Thu, 2 Jun 2016, ?? wrote: Hi, To be specific, I'm trying to reconstruct arcuate fasciculus (refer to SLFT according to your paper 2011) in patients who suffered from frontal or temporal or parietal gliomas. I noticed that TRACULA was used to study neuropsychiatry and neurodegeneration diseases, such as schizophrenia, autism etc. When it comes to organic diseases, like brain tumor, white matter structures may be pushed or deformed due to mass effect. So my question is should I involve the patients in the training set? What can I do to succeed in reconstruction of arcuate fasciculus using TRACULA in my research? Thanks for your time. BW, yang -- Original -- From: "ayendiki";<ayend...@nmr.mgh.harvard.edu>; Date: Jun 2, 2016 To: "Freesurfer support list"<freesurfer@nmr.mgh.harvard.edu>; Subject: Re: [Freesurfer] About TRACULA Hi - It's hard to predict in advance what will happen without trying it out. A lot will depend on the size/position/nature of the tumor. Some tumor patients will go through just fine, other will have issues. If the freesurfer segmentation works, then tracula will work too. Best, a.y On Thu, 2 Jun 2016, yangfuxing wrote: > Dear professor, > I'm a postgraduate of neurosurgery. Recently, I'm interested in cortical > parcellation and subcortical segmentation using freesurfer. In my study, all > patients have brain tumors. So I begin to wonder if "recon-all" can still be > applied to these subjects, or in other word, is it possible that > freesurfer's automated brain segmentation could be applied to brain tumor > patients because their normal structures were changed? If I just run it > regularly according to fswiki, would the outcome be accurate? > Second question is about automatic tractography using TRACULA. > Similarly, I'd like to use "trac-all" to reconstruct arcuate fasciculus in > patients with brain tumor, is it possible? How can I set up the > configuration? Hope to hear from you soon. Best wishes! > Sincerely > > ___ 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 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] About TRACULA
Hi, To be specific, I'm trying to reconstruct arcuate fasciculus (refer to SLFT according to your paper 2011) in patients who suffered from frontal or temporal or parietal gliomas. I noticed that TRACULA was used to study neuropsychiatry and neurodegeneration diseases, such as schizophrenia, autism etc. When it comes to organic diseases, like brain tumor, white matter structures may be pushed or deformed due to mass effect. So my question is should I involve the patients in the training set? What can I do to succeed in reconstruction of arcuate fasciculus using TRACULA in my research? Thanks for your time. BW, yang -- Original -- From: "ayendiki";<ayend...@nmr.mgh.harvard.edu>; Date: Jun 2, 2016 To: "Freesurfer support list"<freesurfer@nmr.mgh.harvard.edu>; Subject: Re: [Freesurfer] About TRACULA Hi - It's hard to predict in advance what will happen without trying it out. A lot will depend on the size/position/nature of the tumor. Some tumor patients will go through just fine, other will have issues. If the freesurfer segmentation works, then tracula will work too. Best, a.y On Thu, 2 Jun 2016, yangfuxing wrote: > Dear professor, > I'm a postgraduate of neurosurgery. Recently, I'm interested in cortical > parcellation and subcortical segmentation using freesurfer. In my study, all > patients have brain tumors. So I begin to wonder if "recon-all" can still be > applied to these subjects, or in other word, is it possible that > freesurfer's automated brain segmentation could be applied to brain tumor > patients because their normal structures were changed? If I just run it > regularly according to fswiki, would the outcome be accurate? > Second question is about automatic tractography using TRACULA. > Similarly, I'd like to use "trac-all" to reconstruct arcuate fasciculus in > patients with brain tumor, is it possible? How can I set up the > configuration? Hope to hear from you soon. Best wishes! > Sincerely > > ___ 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 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] About TRACULA
Hi - It's hard to predict in advance what will happen without trying it out. A lot will depend on the size/position/nature of the tumor. Some tumor patients will go through just fine, other will have issues. If the freesurfer segmentation works, then tracula will work too. Best, a.y On Thu, 2 Jun 2016, yangfuxing wrote: Dear professor, I'm a postgraduate of neurosurgery. Recently, I'm interested in cortical parcellation and subcortical segmentation using freesurfer. In my study, all patients have brain tumors. So I begin to wonder if "recon-all" can still be applied to these subjects, or in other word, is it possible that freesurfer's automated brain segmentation could be applied to brain tumor patients because their normal structures were changed? If I just run it regularly according to fswiki, would the outcome be accurate? Second question is about automatic tractography using TRACULA. Similarly, I'd like to use "trac-all" to reconstruct arcuate fasciculus in patients with brain tumor, is it possible? How can I set up the configuration? Hope to hear from you soon. Best wishes! Sincerely ___ 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.
