Re: [Freesurfer] Hippocampal Subfield Segmentation Error
t; Reply-To: FS Help Date: Wednesday, April 8, 2020 at 11:26 PM To: FS Help Subject: Re: [Freesurfer] Hippocampal Subfield Segmentation Error External Email - Use Caution Hello! So I have installed the latest Java, reinstalled the Runtime following the instructions on the Freesurf
Re: [Freesurfer] Hippocampal Subfield Segmentation Error
2020-04-08
Thread
Lab of Autism and Developmental Neuroscience, Lab of Autism and Developmental Neuroscience
> > /Eugenio > > > > > > Juan Eugenio Iglesias > > Senior research fellow > > CMIC (UCL), MGH (HMS) and CSAIL (MIT) > > http://www.jeiglesias.com > > > > > > > > *From: * on behalf of "Lab of > Autism and Developmental Neuroscience, Lab of
Re: [Freesurfer] Hippocampal Subfield Segmentation Error
S Help Cc: "Hoopes, Andrew" Subject: Re: [Freesurfer] Hippocampal Subfield Segmentation Error Uuuummm this is a tough one. Any ideas, Andrew? Maybe updating java? Juan Eugenio Iglesias Senior research fellow CMIC (UCL), MGH (HMS) and CSAIL (MIT) http://www.jeiglesias.com From
Re: [Freesurfer] Hippocampal Subfield Segmentation Error
ience" Reply-To: Freesurfer support list Date: Tuesday, March 31, 2020 at 17:59 To: Freesurfer support list Subject: Re: [Freesurfer] Hippocampal Subfield Segmentation Error External Email - Use Caution Hello Eugenio, No I wasn't! When I first tried to run the subfields I wasn
Re: [Freesurfer] Hippocampal Subfield Segmentation Error
2020-03-31
Thread
Lab of Autism and Developmental Neuroscience, Lab of Autism and Developmental Neuroscience
"Lab of > Autism and Developmental Neuroscience, Lab of Autism and Developmental > Neuroscience" > *Reply-To: *Freesurfer support list > *Date: *Saturday, March 28, 2020 at 02:07 > *To: *Freesurfer support list > *Subject: *Re: [Freesurfer] Hippocampal Subfield Seg
Re: [Freesurfer] Hippocampal Subfield Segmentation Error
t;Lab of Autism and Developmental Neuroscience, Lab of Autism and Developmental Neuroscience" Reply-To: Freesurfer support list Date: Saturday, March 28, 2020 at 02:07 To: Freesurfer support list Subject: Re: [Freesurfer] Hippocampal Subfield Segmentation Error External Email - U
Re: [Freesurfer] Hippocampal Subfield Segmentation Error
2020-03-28
Thread
Lab of Autism and Developmental Neuroscience, Lab of Autism and Developmental Neuroscience
MIC (UCL), MGH (HMS) and CSAIL (MIT) > > http://www.jeiglesias.com > > > > > > > > *From: * on behalf of "Lab of > Autism and Developmental Neuroscience, Lab of Autism and Developmental > Neuroscience" > *Reply-To: *Freesurfer support list > *Da
Re: [Freesurfer] Hippocampal Subfield Segmentation Error
://www.jeiglesias.com From: on behalf of "Lab of Autism and Developmental Neuroscience, Lab of Autism and Developmental Neuroscience" Reply-To: Freesurfer support list Date: Saturday, March 21, 2020 at 23:33 To: Freesurfer support list Subject: [Freesurfer] Hippocampal Subfield Segmenta
[Freesurfer] Hippocampal Subfield Segmentation Error
2020-03-21
Thread
Lab of Autism and Developmental Neuroscience, Lab of Autism and Developmental Neuroscience
External Email - Use Caution Dear Freesurfer experts, I am having a problem with hippocampal subfield segmentation. The issue appears to be related to JavaVM - after I run the code: recon-all -s (subject ID) -hippocampal-subfields-T1 This is the error: JavaVM: Failed to load
Re: [Freesurfer] hippocampal subfield segmentation error (fsv6.0)
, 2018 8:37:44 PM To: Freesurfer support list Subject: Re: [Freesurfer] hippocampal subfield segmentation error (fsv6.0) External Email - Use Caution My freesurfer home is /opt/freesurfer-6.0.0 which contains all the necessary freesurfer binaries, .sh files etc in order for freesurfer
Re: [Freesurfer] hippocampal subfield segmentation error (fsv6.0)
mr.mgh.harvard.edu < >> freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of miracle ozzoude < >> miracoo...@gmail.com> >> *Sent:* Wednesday, May 30, 2018 9:21:19 PM >> *To:* Freesurfer support list >> >> *Subject:* Re: [Freesurfer] hippocampal subfie
Re: [Freesurfer] hippocampal subfield segmentation error (fsv6.0)
://cmictig.cs.ucl.ac.uk/ > > > -- > *From:* freesurfer-boun...@nmr.mgh.harvard.edu < > freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of miracle ozzoude < > miracoo...@gmail.com> > *Sent:* Wednesday, May 30, 2018 9:21:19 PM > *To:*
Re: [Freesurfer] hippocampal subfield segmentation error (fsv6.0)
: [Freesurfer] hippocampal subfield segmentation error (fsv6.0) External Email - Use Caution Thanks. So I changed it to " export FREESURFER_HOME=/opt/freesurfer-6.0.0; source $FREESURFER_HOME/freesurfer/SetUpFreeSurfer.sh" (based on printenv). However, when i tried to run m
Re: [Freesurfer] hippocampal subfield segmentation error (fsv6.0)
k/ > > > > > > *From: * on behalf of miracle > ozzoude > *Reply-To: *Freesurfer support list > *Date: *Wednesday, 30 May 2018 at 18:57 > > *To: *Freesurfer support list > *Subject: *Re: [Freesurfer] hippocampal subfield segmentation error > (fsv6.0) > > >
Re: [Freesurfer] hippocampal subfield segmentation error (fsv6.0)
list Date: Wednesday, 30 May 2018 at 18:57 To: Freesurfer support list Subject: Re: [Freesurfer] hippocampal subfield segmentation error (fsv6.0) External Email - Use Caution Yes, because I processed all my subjects with v6.0 without any issue. When i type "printenv FREESURFER_HOME&
Re: [Freesurfer] hippocampal subfield segmentation error (fsv6.0)
; > > -- > > Juan Eugenio Iglesias > > ERC Senior Research Fellow > > Centre for Medical Image Computing (CMIC) > > University College London > > http://www.jeiglesias.com > > http://cmictig.cs.ucl.ac.uk/ > > > > > > *From: * on behalf of mira
Re: [Freesurfer] hippocampal subfield segmentation error (fsv6.0)
support list Subject: Re: [Freesurfer] hippocampal subfield segmentation error (fsv6.0) External Email - Use Caution Hello, I checked and my sources.sh is located in /opt/freesurfer-6.0.0/freesurfer/sources.sh not /opt/freesurfer-6.0.0/sources.sh. I opened the kvlAutoCropt file
Re: [Freesurfer] hippocampal subfield segmentation error (fsv6.0)
ing versions. > > What exact version are you using? > > Cheers, > > /Eugenio > > > > -- > > Juan Eugenio Iglesias > > ERC Senior Research Fellow > > Centre for Medical Image Computing (CMIC) > > University College London > > http://www.
Re: [Freesurfer] hippocampal subfield segmentation error (fsv6.0)
:46 To: Freesurfer support list Subject: Re: [Freesurfer] hippocampal subfield segmentation error (fsv6.0) External Email - Use Caution Hello Eugenio, Thanks for the response. All my processing was done with FreeSurfer v6.0 although, we have version 5.3 installed on the server too. I
Re: [Freesurfer] hippocampal subfield segmentation error (fsv6.0)
> > > > > > *From: * on behalf of miracle > ozzoude > *Reply-To: *Freesurfer support list > *Date: *Wednesday, 30 May 2018 at 16:11 > *To: *Douglas N Greve > *Subject: *[Freesurfer] hippocampal subfield segmentation error (fsv6.0) > > > > *Ex
Re: [Freesurfer] hippocampal subfield segmentation error (fsv6.0)
Image Computing (CMIC) University College London http://www.jeiglesias.com http://cmictig.cs.ucl.ac.uk/ From: on behalf of miracle ozzoude Reply-To: Freesurfer support list Date: Wednesday, 30 May 2018 at 16:11 To: Douglas N Greve Subject: [Freesurfer] hippocampal subfield segmentation error
[Freesurfer] hippocampal subfield segmentation error (fsv6.0)
External Email - Use Caution Hello, I am using v6.0 installed on a linux server (via PUTTY) to segment hippocampal subfields. I downloaded the runtime from this link ( https://surfer.nmr.mgh.harvard.edu/fswiki/MatlabRuntime) and followed the instructions on how to install it ( it
[Freesurfer] Hippocampal subfield segmentation error: kvlAutoCrop.bin: command not found
External Email - Use Caution Hello FreeSurfer users, I am trying to run hippocampal subfield segmentation on our subjects on FreeSurfer version 6.0. Unfortunately, I was not able to get very far. I got an error relatively early:
Re: [Freesurfer] Hippocampal subfield segmentation error: kvlAutoCrop.bin: command not found
External Email - Use Caution Hi Ryan, This is weird! I am safely assuming that you sourced FreeSurfer, etc? What was the command you ran? Cheers, /Eugenio -- Juan Eugenio Iglesias ERC Senior Research Fellow Translational Imaging Group University College London
[Freesurfer] Hippocampal subfield segmentation error: kvlAutoCrop.bin: command not found
External Email - Use Caution Hello FreeSurfer users, I am trying to run hippocampal subfield segmentation on our subjects on FreeSurfer version 6.0. Unfortunately, I was not able to get very far. I got an error relatively early:
Re: [Freesurfer] Hippocampal subfield segmentation error
> > http://cmictig.cs.ucl.ac.uk/ > > > > > > *From: *<freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of "Md. Mamun > Al-Amin" <mdalaminba...@gmail.com> > *Reply-To: *Freesurfer support list <freesurfer@nmr.mgh.harvard.edu> > *Date: *Sunday
Re: [Freesurfer] Hippocampal subfield segmentation error
"Md. Mamun Al-Amin" <mdalaminba...@gmail.com> Reply-To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu> Date: Sunday, 17 September 2017 at 03:46 To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] Hippocampal subfield segmentatio
Re: [Freesurfer] Hippocampal subfield segmentation error
st <freesurfer@nmr.mgh.harvard.edu> > *Date: *Friday, 15 September 2017 at 00:54 > *To: *Freesurfer support list <freesurfer@nmr.mgh.harvard.edu> > *Subject: *[Freesurfer] Hippocampal subfield segmentation error > > > > Dear Experts > > I have been experien
Re: [Freesurfer] Hippocampal subfield segmentation error
oun...@nmr.mgh.harvard.edu> on behalf of "Md. Mamun Al-Amin" <mdalaminba...@gmail.com> Reply-To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu> Date: Friday, 15 September 2017 at 00:54 To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu> Subject:
[Freesurfer] Hippocampal subfield segmentation error
Dear Experts I have been experiencing a problem while running the following command *segmentHA_T1.sh subject_name* The program exits with the following error "MATLAB is exiting because of fatal error /Applications/freesurfer-dev/bin/run_segmentSubjectT1_autoEstimateAlveusML.sh: line 39: 660
Re: [Freesurfer] Hippocampal subfield segmentation "error" with T1 image
Hi, Perfect, thank you for the quick response! Best, Gustav On 2017-02-10 14:37, Iglesias Gonzalez, Eugenio wrote: Hi Gustav, No problem at all (ingen fara!). The idea is that, when our new joint atlas of the hippocampal subfields and amygdala nuclei is ready to be released, we’ll just need
Re: [Freesurfer] Hippocampal subfield segmentation "error" with T1 image
Hi Gustav, No problem at all (ingen fara!). The idea is that, when our new joint atlas of the hippocampal subfields and amygdala nuclei is ready to be released, we’ll just need to replace the atlas files, without having to touch the code. It was my fault not to wrap that move command inside an
[Freesurfer] Hippocampal subfield segmentation error
Hello,I got the following error in one of my subjects when running hippocampal subfields segmentation (only for the left hemisphere). Could you help me to solve this problem?maximalDeformation: 75.1793 Transforming mesh Done transforming mesh Rasterizing Levenberg-Marquardt...
