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: <freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Wei Shao <ws...@research.baycrest.org> Reply-To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu> Date: Thursday, April 22, 2021 at 17:12 To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu> 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. <jiglesiasgonza...@mgh.harvard.edu<mailto:jiglesiasgonza...@mgh.harvard.edu>> wrote: Dear Wei, The syntax of the command is: quantifyHAsubregions.sh hippoSf <T1>-<analysisID> <output_file> <OPTIONAL_SUBJECTS_DIR> 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: <freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>> on behalf of Wei Shao <ws...@research.baycrest.org<mailto:ws...@research.baycrest.org>> Reply-To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>> Date: Thursday, April 22, 2021 at 15:10 To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu<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. <jiglesiasgonza...@mgh.harvard.edu<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: <freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>> on behalf of Wei Shao <ws...@research.baycrest.org<mailto:ws...@research.baycrest.org>> Reply-To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>> Date: Wednesday, April 21, 2021 at 17:20 To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu<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? 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