[Freesurfer] Inflation of one hemi only
Hi, I am trying to inflate right hemisphere only using the commands: recon-all -autorecon2 -hemi rh -subjid 160526 recon-all -autorecon3 -hemi rh -subjid 160526 The inflation stopped at the step: mris_volmask --label_left_white 2 --label_left_ribbon 3 --label_right_white 41 --label_right_ribbon 42 --save_ribbon 160526 SUBJECTS_DIR is /home/sata3/FreeSurfer/Subjects MRISread(/home/sata3/FreeSurfer/Subjects/160526/surf/lh.white): could not open file The program "mris_volmask" needs to read "lh.white", which is not generated. Any expert has any suggestions? Maybe I didn't use the commands correctly? 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] Inflation of one hemi only
Thank you for your reply. The image "wmparc.mgz" does not have the correct values. I am not sure if that because of the interruption of the procedures or not. Also I need to use some other files. Thank you for your explanations. I will wait for the future corrections on the problem. On 7/7/2016 11:11 AM, Bruce Fischl wrote: Hi XJ this is a known problem but we haven't gotten to fixing it yet. Do you need it to complete that step? It is pretty close to the end so it may be that the error doesn't effect you cheers Bruce On Thu, 7 Jul 2016, Kang, XJ wrote: Hi, I am trying to inflate right hemisphere only using the commands: recon-all -autorecon2 -hemi rh -subjid 160526 recon-all -autorecon3 -hemi rh -subjid 160526 The inflation stopped at the step: mris_volmask --label_left_white 2 --label_left_ribbon 3 --label_right_white 41 --label_right_ribbon 42 --save_ribbon 160526 SUBJECTS_DIR is /home/sata3/FreeSurfer/Subjects MRISread(/home/sata3/FreeSurfer/Subjects/160526/surf/lh.white): could not open file The program "mris_volmask" needs to read "lh.white", which is not generated. Any expert has any suggestions? Maybe I didn't use the commands correctly? 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] Inflation of one hemi only
For the normal inflated brain, wmparc.mgz has values: 0~85, 251~255, 1000~1035, 2000~2035, 3000~3035, 4000~4035, and 5001, 5002. I have two unfinished one hemi inflation brains, one wmparc.mgz has values 0 ~176, and the other has 0~156. No other values found. On 7/7/2016 11:25 AM, Bruce Fischl wrote: what values does the wmparc have? On Thu, 7 Jul 2016, Kang, XJ wrote: Thank you for your reply. The image "wmparc.mgz" does not have the correct values. I am not sure if that because of the interruption of the procedures or not. Also I need to use some other files. Thank you for your explanations. I will wait for the future corrections on the problem. On 7/7/2016 11:11 AM, Bruce Fischl wrote: Hi XJ this is a known problem but we haven't gotten to fixing it yet. Do you need it to complete that step? It is pretty close to the end so it may be that the error doesn't effect you cheers Bruce On Thu, 7 Jul 2016, Kang, XJ wrote: Hi, I am trying to inflate right hemisphere only using the commands: recon-all -autorecon2 -hemi rh -subjid 160526 recon-all -autorecon3 -hemi rh -subjid 160526 The inflation stopped at the step: mris_volmask --label_left_white 2 --label_left_ribbon 3 --label_right_white 41 --label_right_ribbon 42 --save_ribbon 160526 SUBJECTS_DIR is /home/sata3/FreeSurfer/Subjects MRISread(/home/sata3/FreeSurfer/Subjects/160526/surf/lh.white): could not open file The program "mris_volmask" needs to read "lh.white", which is not generated. Any expert has any suggestions? Maybe I didn't use the commands correctly? 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-mai l contains patient information, please contact the Partners Compliance HelpLin e at http://www.partners.org/complianceline . If the e-mail was sent to you in er ror but does not contain patient information, please contact the sender and prop erly 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. ___ 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 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.
[Freesurfer] TRACULA results
Hi, I downloaded FreeSurfer development version built on Sep 20. Then I ran the "trac-all" for the same set of DWI data four times. The volume and averaged DTI parameters of the fiber pathways, which found in the file ~/sub/dpath/*_PP_avg33_mni_flt/pathstats.overall.txt, are different for each run. The maximum differences can be upto +-90% for volume, +-10% for FA_avg. Any ideas for the inconsistency? Thanks. 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.
