Re: [Freesurfer] Question about volume matrix in hippocampus
quantifyHAsubregions.sh hippoSf T1 results.txt /home/weishao/At_risk Cheers, /E Juan Eugenio Iglesias Senior research fellow CMIC (UCL), MGH (HMS) and CSAIL (MIT) http://www.jeiglesias.com From: on behalf of Wei Shao Reply-To: Freesurfer support list Date: Thursday, April 22, 2021 at 17:12 To: Freesurfer support list Subject: Re: [Freesurfer] Question about volume matrix in hippocampus External Email - Use Caution Hi. Dear Eugenio Thanks for your reply, could you be more specific? I have tried many times with this command but with the same problem happened. For example, I use the one subject quantifyHAsubregions.sh hippoSf T1-AVP6176 At_risk/volume And the feedback Gathering results from subjects in: /home/weishao/At_risk Using the prefix name: hippoSf Using the suffix name: T1-AVP6176 And writing them to: home/weishao/At_risk/volume However, there is no result text file in the output directory. [weishao@gra-login1 ~]$ cd At_risk/volume/ [weishao@gra-login1 volume]$ ls -ltr total 0 The attachment is the original script of quantifyHAsubregions.sh Best, Wei On Thu, Apr 22, 2021 at 3:21 PM Iglesias Gonzalez, Juan E. mailto:jiglesiasgonza...@mgh.harvard.edu>> wrote: Dear Wei, The syntax of the command is: quantifyHAsubregions.sh hippoSf - Juan Eugenio Iglesias Senior research fellow CMIC (UCL), MGH (HMS) and CSAIL (MIT) MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be http://www.jeiglesias.com<http://secure-web.cisco.com/1JMQZFodc2ZeKRIdC2wNQ0ofo-HaHdAORal7oOrAUz7-tO2Db6jV2MPQlWKnNLpvTrElx5paBPy1YOLk30wxeHcCllCk3q5WOD4BnvbPHdgEhA6cvcruA5SVQ2qDFypia0sqAoSxitVKwVD5WPcVZbZ_1EaSdxIgIcxRhGawHn0jEe4JWpIl7gqXA1LRXVl43wYcE-ht-QPEKXwmx4MdvE5vE8Rkm_nXchVsr6tvSvnaW1Z8RtnHlfKKEFGQFHXemMfXSGkYwZucCJJ8aVMipyw/http%3A%2F%2Fwww.jeiglesias.com> From: mailto:freesurfer-boun...@nmr.mgh.harvard.edu>> on behalf of Wei Shao mailto:ws...@research.baycrest.org>> Reply-To: Freesurfer support list mailto:freesurfer@nmr.mgh.harvard.edu>> Date: Thursday, April 22, 2021 at 15:10 To: Freesurfer support list mailto:freesurfer@nmr.mgh.harvard.edu>> Subject: Re: [Freesurfer] Question about volume matrix in hippocampus External Email - Use Caution Hi, Eugenio Thanks for your kind reply. I have tried this command with a dataset and it wasn't function. For example, Here is my script #!/bin/bash module load freesurfer/7.1.0 source $EBROOTFREESURFER/FreeSurferEnv.sh export SUBJECTS_DIR=/home/weishao/At_risk quantifyHAsubregions.sh hippoSf sub-AVP8580 sub-AVP6176 sub-BAY10224 /home/weishao/At_risk And there is the feedback Gathering results from subjects in: sub-BAY10224 Using the prefix name: hippoSf Using the suffix name: sub-AVP8580 And writing them to: sub-AVP6176 /project/6019291/shared/software/2017/Core/freesurfer/7.1.0/bin/quantifyHAsubregions.sh: line 8: cd: sub-BAY10224: No such file or directory failed to do cd sub-BAY10224 I also tried this with one subject, And I don't find the text file at /home/weishao/At_risk, I also tried this with one subject, couldn't find the text file neither. Would you mind tell me where I did wrong? Thanks Best, Wei On Wed, Apr 21, 2021 at 5:26 PM Iglesias Gonzalez, Juan E. mailto:jiglesiasgonza...@mgh.harvard.edu>> wrote: Dear Wei, All the volume measurements use the underlying probabilities with the maximum level of granularity. Kind regards, Eugenio Juan Eugenio Iglesias Senior research fellow CMIC (UCL), MGH (HMS) and CSAIL (MIT) MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be http://www.jeiglesias.com<http://secure-web.cisco.com/1bK9Xmm7cNRBWH73XeUE3ROyYVFC0VU8bFAuK6d5WSElLPFE2zDlSEpKsgjrFb1ckAVriuarMf8sfizjd-Jxqz0Z_7NkO1ndGSwPXmMj7979KyP1iHCiaTdPkN869_aFAGbUN4ZLUsqbJjwIXhzhty2QQp4GqBy1FXa5ws4z6kQxH4k-DGASyP0cXn1OYAvtGNGD1ijRcivM59q-wKnNALtSFPWo50p9qmikNWzoeYfPt9n6qvFUzRNqe6IpfhpzgtArpyYdRc_Yiz0T6Kfy8xg/http%3A%2F%2Fwww.jeiglesias.com> From: mailto:freesurfer-boun...@nmr.mgh.harvard.edu>> on behalf of Wei Shao mailto:ws...@research.baycrest.org>> Reply-To: Freesurfer support list mailto:freesurfer@nmr.mgh.harvard.edu>> Date: Wednesday, April 21, 2021 at 17:20 To: Freesurfer support list mailto:freesurfer@nmr.mgh.harvard.edu>> Subject: [Freesurfer] Question about volume matrix in hippocampus External Email - Use Caution Hi, Freesurfer experts. I have used "quantifyHAsubregions.sh hippoSf" to gather the volume information from the hippocampus. A quick question about the volume matrix, would you tell me which label system ("HBT" "FS60" or "CA") this code used to extract the volume information? or there is no difference? Thanks Best, Wei ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvar
Re: [Freesurfer] Question about volume matrix in hippocampus
External Email - Use Caution Hi. Dear Eugenio Thanks for your reply, could you be more specific? I have tried many times with this command but with the same problem happened. For example, I use the one subject quantifyHAsubregions.sh hippoSf T1-AVP6176 At_risk/volume And the feedback Gathering results from subjects in: /home/weishao/At_risk Using the prefix name: hippoSf Using the suffix name: T1-AVP6176 And writing them to: home/weishao/At_risk/volume However, there is no result text file in the output directory. [weishao@gra-login1 ~]$ cd At_risk/volume/ [weishao@gra-login1 volume]$ ls -ltr total 0 The attachment is the original script of quantifyHAsubregions.sh Best, Wei On Thu, Apr 22, 2021 at 3:21 PM Iglesias Gonzalez, Juan E. < jiglesiasgonza...@mgh.harvard.edu> wrote: > Dear Wei, > > The syntax of the command is: > > quantifyHAsubregions.sh hippoSf - > > > > > > > > > Juan Eugenio Iglesias > > Senior research fellow > > CMIC (UCL), MGH (HMS) and CSAIL (MIT) > > http://secure-web.cisco.com/1JMQZFodc2ZeKRIdC2wNQ0ofo-HaHdAORal7oOrAUz7-tO2Db6jV2MPQlWKnNLpvTrElx5paBPy1YOLk30wxeHcCllCk3q5WOD4BnvbPHdgEhA6cvcruA5SVQ2qDFypia0sqAoSxitVKwVD5WPcVZbZ_1EaSdxIgIcxRhGawHn0jEe4JWpIl7gqXA1LRXVl43wYcE-ht-QPEKXwmx4MdvE5vE8Rkm_nXchVsr6tvSvnaW1Z8RtnHlfKKEFGQFHXemMfXSGkYwZucCJJ8aVMipyw/http%3A%2F%2Fwww.jeiglesias.com > > > > > > > > *From: * on behalf of Wei Shao < > ws...@research.baycrest.org> > *Reply-To: *Freesurfer support list > *Date: *Thursday, April 22, 2021 at 15:10 > *To: *Freesurfer support list > *Subject: *Re: [Freesurfer] Question about volume matrix in hippocampus > > > > *External Email - Use Caution* > > Hi, Eugenio > > > > Thanks for your kind reply. I have tried this command with a dataset and > it wasn't function. > > > > For example, Here is my script > > > > #!/bin/bash > > module load freesurfer/7.1.0 > source $EBROOTFREESURFER/FreeSurferEnv.sh > export SUBJECTS_DIR=/home/weishao/At_risk > > quantifyHAsubregions.sh hippoSf sub-AVP8580 sub-AVP6176 sub-BAY10224 > /home/weishao/At_risk > > *And there is the feedback * > > > > Gathering results from subjects in: >sub-BAY10224 > Using the prefix name: >hippoSf > Using the suffix name: >sub-AVP8580 > And writing them to: >sub-AVP6176 > /project/6019291/shared/software/2017/Core/freesurfer/7.1.0/bin/quantifyHAsubregions.sh: > line 8: cd: sub-BAY10224: No such file or directory > failed to do cd sub-BAY10224 > > > > I also tried this with one subject, > > > > And I don't find the text file at /home/weishao/At_risk, I also tried > this with one subject, couldn't find the text file neither. > > > > Would you mind tell me where I did wrong? Thanks > > > > Best, > > Wei > > > > On Wed, Apr 21, 2021 at 5:26 PM Iglesias Gonzalez, Juan E. < > jiglesiasgonza...@mgh.harvard.edu> wrote: > > Dear Wei, > > All the volume measurements use the underlying probabilities with the > maximum level of granularity. > > Kind regards, > > Eugenio > > > > > > Juan Eugenio Iglesias > > Senior research fellow > > CMIC (UCL), MGH (HMS) and CSAIL (MIT) > > *MailScanner has detected a possible fraud attempt from > "secure-web.cisco.com" claiming to be* > http://secure-web.cisco.com/1JMQZFodc2ZeKRIdC2wNQ0ofo-HaHdAORal7oOrAUz7-tO2Db6jV2MPQlWKnNLpvTrElx5paBPy1YOLk30wxeHcCllCk3q5WOD4BnvbPHdgEhA6cvcruA5SVQ2qDFypia0sqAoSxitVKwVD5WPcVZbZ_1EaSdxIgIcxRhGawHn0jEe4JWpIl7gqXA1LRXVl43wYcE-ht-QPEKXwmx4MdvE5vE8Rkm_nXchVsr6tvSvnaW1Z8RtnHlfKKEFGQFHXemMfXSGkYwZucCJJ8aVMipyw/http%3A%2F%2Fwww.jeiglesias.com > <http://secure-web.cisco.com/1bK9Xmm7cNRBWH73XeUE3ROyYVFC0VU8bFAuK6d5WSElLPFE2zDlSEpKsgjrFb1ckAVriuarMf8sfizjd-Jxqz0Z_7NkO1ndGSwPXmMj7979KyP1iHCiaTdPkN869_aFAGbUN4ZLUsqbJjwIXhzhty2QQp4GqBy1FXa5ws4z6kQxH4k-DGASyP0cXn1OYAvtGNGD1ijRcivM59q-wKnNALtSFPWo50p9qmikNWzoeYfPt9n6qvFUzRNqe6IpfhpzgtArpyYdRc_Yiz0T6Kfy8xg/http%3A%2F%2Fwww.jeiglesias.com> > > > > > > > > > *From: * on behalf of Wei Shao < > ws...@research.baycrest.org> > *Reply-To: *Freesurfer support list > *Date: *Wednesday, April 21, 2021 at 17:20 > *To: *Freesurfer support list > *Subject: *[Freesurfer] Question about volume matrix in hippocampus > > > > *External Email - Use Caution* > > Hi, Freesurfer experts. > > > > I have used "quantifyHAsubregions.sh hippoSf" to gather the volume > information from the hippocampus
Re: [Freesurfer] Question about volume matrix in hippocampus
Dear Wei, The syntax of the command is: quantifyHAsubregions.sh hippoSf - Juan Eugenio Iglesias Senior research fellow CMIC (UCL), MGH (HMS) and CSAIL (MIT) http://www.jeiglesias.com From: on behalf of Wei Shao Reply-To: Freesurfer support list Date: Thursday, April 22, 2021 at 15:10 To: Freesurfer support list Subject: Re: [Freesurfer] Question about volume matrix in hippocampus External Email - Use Caution Hi, Eugenio Thanks for your kind reply. I have tried this command with a dataset and it wasn't function. For example, Here is my script #!/bin/bash module load freesurfer/7.1.0 source $EBROOTFREESURFER/FreeSurferEnv.sh export SUBJECTS_DIR=/home/weishao/At_risk quantifyHAsubregions.sh hippoSf sub-AVP8580 sub-AVP6176 sub-BAY10224 /home/weishao/At_risk And there is the feedback Gathering results from subjects in: sub-BAY10224 Using the prefix name: hippoSf Using the suffix name: sub-AVP8580 And writing them to: sub-AVP6176 /project/6019291/shared/software/2017/Core/freesurfer/7.1.0/bin/quantifyHAsubregions.sh: line 8: cd: sub-BAY10224: No such file or directory failed to do cd sub-BAY10224 I also tried this with one subject, And I don't find the text file at /home/weishao/At_risk, I also tried this with one subject, couldn't find the text file neither. Would you mind tell me where I did wrong? Thanks Best, Wei On Wed, Apr 21, 2021 at 5:26 PM Iglesias Gonzalez, Juan E. mailto:jiglesiasgonza...@mgh.harvard.edu>> wrote: Dear Wei, All the volume measurements use the underlying probabilities with the maximum level of granularity. Kind regards, Eugenio Juan Eugenio Iglesias Senior research fellow CMIC (UCL), MGH (HMS) and CSAIL (MIT) MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be http://www.jeiglesias.com<http://secure-web.cisco.com/1bK9Xmm7cNRBWH73XeUE3ROyYVFC0VU8bFAuK6d5WSElLPFE2zDlSEpKsgjrFb1ckAVriuarMf8sfizjd-Jxqz0Z_7NkO1ndGSwPXmMj7979KyP1iHCiaTdPkN869_aFAGbUN4ZLUsqbJjwIXhzhty2QQp4GqBy1FXa5ws4z6kQxH4k-DGASyP0cXn1OYAvtGNGD1ijRcivM59q-wKnNALtSFPWo50p9qmikNWzoeYfPt9n6qvFUzRNqe6IpfhpzgtArpyYdRc_Yiz0T6Kfy8xg/http%3A%2F%2Fwww.jeiglesias.com> From: mailto:freesurfer-boun...@nmr.mgh.harvard.edu>> on behalf of Wei Shao mailto:ws...@research.baycrest.org>> Reply-To: Freesurfer support list mailto:freesurfer@nmr.mgh.harvard.edu>> Date: Wednesday, April 21, 2021 at 17:20 To: Freesurfer support list mailto:freesurfer@nmr.mgh.harvard.edu>> Subject: [Freesurfer] Question about volume matrix in hippocampus External Email - Use Caution Hi, Freesurfer experts. I have used "quantifyHAsubregions.sh hippoSf" to gather the volume information from the hippocampus. A quick question about the volume matrix, would you tell me which label system ("HBT" "FS60" or "CA") this code used to extract the volume information? or there is no difference? Thanks Best, Wei ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu> MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer<https://secure-web.cisco.com/1bQET30Fd0RkuxVIyhifmZHJ3AlO4xEABPW1K8Bvre1kGrSRcUyKdtKjdls2IuomAJH0iNCJZ2_eQwvRWJBzBISplYRjFd8HjHoAyNs8Ys1RK0M-B4P_fa61AnpXcle-ywuhZxB6m4xq1_XMhXnf65iT64b52KGVVV1UGlRkboRnfbkLrioI1B1xrIJATAumn0KJMKkw8dcfoLQarDrUMAkrLVmy3Va0sEEJnpkCXKiuKtFD9aYTWil-Y5JAumMa52gBiPnyzqpRS_g-8-ujtWQ/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer> 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 Mass General Brigham Compliance HelpLine at MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be http://www.massgeneralbrigham.org/complianceline<http://secure-web.cisco.com/1gzeDXQNgVL-J-dSTU8cX3uw7PjDlmyFpQuy24BIEEjmKnkexbBn8i1UW-3eSV0ulGKBuFTb1G5iPnvbKZkEcJKg6YMJaI4WA5kD9gFJOQ3r_p3htvczAHvsr92wM3DORhzOPCZw8BoZ_CEue1UYWa_WYwVczPaw6hlTFPVar2jWNOkvog_P8xDbq-6WsGONKqRnyOoXa4hz37MRJqfKYR8AMglppnARk30DSC8o4-RRPkld24v9ZVYI1kd8MK441KFkEDeG6c92CwB6oGgIQaA/http%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline> . 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. Please note that this e-mail is not secure (encrypted). If you do not wish to continue communication over unencrypted e-mail, please notify the sender of this message immediately. Continuing to send or respond to e-mail after receiving this message means you understand and accept this risk and wish to continue to communicate over unencrypted e-mail. ___
Re: [Freesurfer] Question about volume matrix in hippocampus
External Email - Use Caution Hi, Eugenio Thanks for your kind reply. I have tried this command with a dataset and it wasn't function. For example, Here is my script #!/bin/bash module load freesurfer/7.1.0 source $EBROOTFREESURFER/FreeSurferEnv.sh export SUBJECTS_DIR=/home/weishao/At_risk quantifyHAsubregions.sh hippoSf sub-AVP8580 sub-AVP6176 sub-BAY10224 /home/weishao/At_risk *And there is the feedback * Gathering results from subjects in: sub-BAY10224 Using the prefix name: hippoSf Using the suffix name: sub-AVP8580 And writing them to: sub-AVP6176 /project/6019291/shared/software/2017/Core/freesurfer/7.1.0/bin/quantifyHAsubregions.sh: line 8: cd: sub-BAY10224: No such file or directory failed to do cd sub-BAY10224 I also tried this with one subject, And I don't find the text file at /home/weishao/At_risk, I also tried this with one subject, couldn't find the text file neither. Would you mind tell me where I did wrong? Thanks Best, Wei On Wed, Apr 21, 2021 at 5:26 PM Iglesias Gonzalez, Juan E. < jiglesiasgonza...@mgh.harvard.edu> wrote: > Dear Wei, > > All the volume measurements use the underlying probabilities with the > maximum level of granularity. > > Kind regards, > > Eugenio > > > > > > Juan Eugenio Iglesias > > Senior research fellow > > CMIC (UCL), MGH (HMS) and CSAIL (MIT) > > http://secure-web.cisco.com/1bK9Xmm7cNRBWH73XeUE3ROyYVFC0VU8bFAuK6d5WSElLPFE2zDlSEpKsgjrFb1ckAVriuarMf8sfizjd-Jxqz0Z_7NkO1ndGSwPXmMj7979KyP1iHCiaTdPkN869_aFAGbUN4ZLUsqbJjwIXhzhty2QQp4GqBy1FXa5ws4z6kQxH4k-DGASyP0cXn1OYAvtGNGD1ijRcivM59q-wKnNALtSFPWo50p9qmikNWzoeYfPt9n6qvFUzRNqe6IpfhpzgtArpyYdRc_Yiz0T6Kfy8xg/http%3A%2F%2Fwww.jeiglesias.com > > > > > > > > *From: * on behalf of Wei Shao < > ws...@research.baycrest.org> > *Reply-To: *Freesurfer support list > *Date: *Wednesday, April 21, 2021 at 17:20 > *To: *Freesurfer support list > *Subject: *[Freesurfer] Question about volume matrix in hippocampus > > > > *External Email - Use Caution* > > Hi, Freesurfer experts. > > > > I have used "quantifyHAsubregions.sh hippoSf" to gather the volume > information from the hippocampus. A quick question about the volume matrix, > would you tell me which label system ("HBT" "FS60" or "CA") this code used > to extract the volume information? or there is no difference? Thanks > > > > Best, > > Wei > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://secure-web.cisco.com/1bQET30Fd0RkuxVIyhifmZHJ3AlO4xEABPW1K8Bvre1kGrSRcUyKdtKjdls2IuomAJH0iNCJZ2_eQwvRWJBzBISplYRjFd8HjHoAyNs8Ys1RK0M-B4P_fa61AnpXcle-ywuhZxB6m4xq1_XMhXnf65iT64b52KGVVV1UGlRkboRnfbkLrioI1B1xrIJATAumn0KJMKkw8dcfoLQarDrUMAkrLVmy3Va0sEEJnpkCXKiuKtFD9aYTWil-Y5JAumMa52gBiPnyzqpRS_g-8-ujtWQ/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer > 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 Mass General > Brigham Compliance HelpLine at > http://secure-web.cisco.com/1gzeDXQNgVL-J-dSTU8cX3uw7PjDlmyFpQuy24BIEEjmKnkexbBn8i1UW-3eSV0ulGKBuFTb1G5iPnvbKZkEcJKg6YMJaI4WA5kD9gFJOQ3r_p3htvczAHvsr92wM3DORhzOPCZw8BoZ_CEue1UYWa_WYwVczPaw6hlTFPVar2jWNOkvog_P8xDbq-6WsGONKqRnyOoXa4hz37MRJqfKYR8AMglppnARk30DSC8o4-RRPkld24v9ZVYI1kd8MK441KFkEDeG6c92CwB6oGgIQaA/http%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline > . 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. > Please note that this e-mail is not secure (encrypted). If you do not > wish to continue communication over unencrypted e-mail, please notify the > sender of this message immediately. Continuing to send or respond to > e-mail after receiving this message means you understand and accept this > risk and wish to continue to communicate over unencrypted e-mail. > ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Question about volume matrix in hippocampus
Dear Wei, All the volume measurements use the underlying probabilities with the maximum level of granularity. Kind regards, Eugenio Juan Eugenio Iglesias Senior research fellow CMIC (UCL), MGH (HMS) and CSAIL (MIT) http://www.jeiglesias.com From: on behalf of Wei Shao Reply-To: Freesurfer support list Date: Wednesday, April 21, 2021 at 17:20 To: Freesurfer support list Subject: [Freesurfer] Question about volume matrix in hippocampus External Email - Use Caution Hi, Freesurfer experts. I have used "quantifyHAsubregions.sh hippoSf" to gather the volume information from the hippocampus. A quick question about the volume matrix, would you tell me which label system ("HBT" "FS60" or "CA") this code used to extract the volume information? or there is no difference? Thanks Best, Wei ___ 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 Mass General Brigham Compliance HelpLine at http://www.massgeneralbrigham.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. Please note that this e-mail is not secure (encrypted). If you do not wish to continue communication over unencrypted e-mail, please notify the sender of this message immediately. Continuing to send or respond to e-mail after receiving this message means you understand and accept this risk and wish to continue to communicate over unencrypted e-mail.
[Freesurfer] Question about volume matrix in hippocampus
External Email - Use Caution Hi, Freesurfer experts. I have used "quantifyHAsubregions.sh hippoSf" to gather the volume information from the hippocampus. A quick question about the volume matrix, would you tell me which label system ("HBT" "FS60" or "CA") this code used to extract the volume information? or there is no difference? Thanks Best, Wei ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] question about volume of the hippocampus
Dear Douglas N Greve Following your comments, I could open aseg.stats, and obtain the hippocampus volume. Thank you for your grateful advise. Yours sincerely, Junji Komatsu 2016-07-08 02:50 に Douglas N Greve さんは書きました: > aseg.stats is just a text file, so you can view it with any text viewer > (eg, the unix more or less commands, vi, emacs) > > On 07/07/2016 06:41 AM, kju...@med.kanazawa-u.ac.jp wrote: >> Dear freesurfer developers. >> >> I am working at department of neurology in university Hospital, Japan. >> I am beginner of freesurfer, please forgive me to ask you a basic >> question. >> >> I want to measure the volume of the hippocampus in my patients. >> I was able to segment the MRI successfully and display the image in >> freeviewer. >> However, I could not recognize the way to obtain the volume of the >> hippocampus. >> >> *I saw the "mail acheive" >> (http://www.mail-archive.com/freesurfer%40nmr.mgh.harvard.edu/msg14679.html), >> however, I could not understand the way to look at the the aseg.stats. >> >> Could you teach me the way for obtaining the volume of the >> hippocampus? >> I and very looking forward to hearing from you. >> >> Yours sincerely, >> Junji Komatsu >> ___ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> > > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > gr...@nmr.mgh.harvard.edu > Phone Number: 617-724-2358 > Fax: 617-726-7422 > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 > www.nmr.mgh.harvard.edu/facility/filedrop/index.html > Outgoing: > ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ > > ___ > 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
Re: [Freesurfer] question about volume of the hippocampus
aseg.stats is just a text file, so you can view it with any text viewer (eg, the unix more or less commands, vi, emacs) On 07/07/2016 06:41 AM, kju...@med.kanazawa-u.ac.jp wrote: > Dear freesurfer developers. > > I am working at department of neurology in university Hospital, Japan. > I am beginner of freesurfer, please forgive me to ask you a basic > question. > > I want to measure the volume of the hippocampus in my patients. > I was able to segment the MRI successfully and display the image in > freeviewer. > However, I could not recognize the way to obtain the volume of the > hippocampus. > > *I saw the "mail acheive" > (http://www.mail-archive.com/freesurfer%40nmr.mgh.harvard.edu/msg14679.html), > however, I could not understand the way to look at the the aseg.stats. > > Could you teach me the way for obtaining the volume of the hippocampus? > I and very looking forward to hearing from you. > > Yours sincerely, > Junji Komatsu > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ ___ 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] question about volume of the hippocampus
Dear freesurfer developers. I am working at department of neurology in university Hospital, Japan. I am beginner of freesurfer, please forgive me to ask you a basic question. I want to measure the volume of the hippocampus in my patients. I was able to segment the MRI successfully and display the image in freeviewer. However, I could not recognize the way to obtain the volume of the hippocampus. *I saw the "mail acheive" (http://www.mail-archive.com/freesurfer%40nmr.mgh.harvard.edu/msg14679.html), however, I could not understand the way to look at the the aseg.stats. Could you teach me the way for obtaining the volume of the hippocampus? I and very looking forward to hearing from you. Yours sincerely, Junji Komatsu ___ 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.