I tried to change ct., but when I change the extension to ctf,
It also give errors as below.
Error:CTF file '/usr/local/freesurfer/bin/segmentSubjectT1_autoEstimateAlveusML.ctf' failed to open for 'Read' access. Error message: 'Open a zip file for read/modify failed.'
Ubuntu 14.04, nightly dev. version of freesurfer.
I also use several mac on 10.9~10.10.5, but they all works well with new hippocampal subfields segmentation function in latest dev. version.
June.
On Jun 17, 2016, at 2:01 AM, Greenberg, Jonathan <JGREENBERG5@mgh.harvard.edu> wrote:
Thanks.
Has anyone else encountered this error message or knows how it can be solved?
Thank you
Jonathan
________________________________________
From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Hibert, Matthew Louis [MHIBERT@mgh.harvard.edu]
Sent: Thursday, June 16, 2016 12:44 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] Hippocampal subfields error
No, I just wanted to mention that in case it helps with troubleshooting what went wrong with the new dev version build.
Matt
________________________________________
From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Greenberg, Jonathan [JGREENBERG5@mgh.harvard.edu]
Sent: Thursday, June 16, 2016 11:24 AM
To: Freesurfer support list
Subject: Re: [Freesurfer] Hippocampal subfields error
Thanks Matt. Did you somehow get it to work or recognize the file without the ctf extension?
Thanks
Jonathan
________________________________________
From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Hibert, Matthew Louis [MHIBERT@mgh.harvard.edu]
Sent: Thursday, June 16, 2016 11:10 AM
To: Freesurfer support list
Subject: Re: [Freesurfer] Hippocampal subfields error
I've also gotten this error recently, with T1, T2, and combined T1+T2 hippocampal segmentations. It looks like the files exist at /autofs/cluster/freesurfer/centos6_x86_64/dev/bin/segmentSubjectT1_autoEstimateAlveusML.ctf exist, they just don't have the ".ctf" file extension.
Matt
________________________________________
From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Greenberg, Jonathan [JGREENBERG5@mgh.harvard.edu]
Sent: Thursday, June 16, 2016 10:29 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] Hippocampal subfields error
Hi all
I ran recon-all on data from about 60 participants pre and post an intervention, with the hippocampal subfields flag
(e.g. "recon-all -all -subjid SPS01-1910_pre_lazar -hippocampal-subfields-T1"). The recon-all.log file states that the process finished without errors. However, the hippocampal-subfieldsT1.log indicated the following:
"Error:Cannot find CTF archive /autofs/cluster/freesurfer/centos6_x86_64/dev/bin/segmentSubjectT1_autoEstimateAlveusML.ctf" (see below for the full content of hippocampal-subfieldsT1.log).
I tried to run only the hippocampal subfield recon-all again (e.g. "recon-all -s recon-all -all -subjid SPS01-1910_pre_lazar hippocampal-subfields-T1") and received the same error message.
I tried to look in the indicated folder ("/autofs/cluster/freesurfer/centos6_x86_64/dev/bin") and found a file named segmentSubjectT1_autoEstimateAlveusML (without the ctf extension). I do not know if this is the source of the problem.
My FREESURFER_HOME directory is /autofs/cluster/freesurfer/centos6_x86_64/stable6/. My SUBJECTS_DIR is /autofs/cluster/lazar/Projects/jonathan-miracle/unpacking-dicoms/SUBJECTS_DIR/.
Any suggestions? (full hippocampal-subfieldsT1.log below)
Thank you!
Jonathan
hippocampal-subfieldsT1.log content:
#--------------------------------------------
#@# Hippocampal Subfields processing (T1 only) left Thu Jun 16 09:58:23 EDT 2016
------------------------------------------
Setting up environment variables
---
LD_LIBRARY_PATH is .:/usr/local/freesurfer/stable6/MCRv80/runtime/glnxa64:/usr/local/freesurfer/stable6/MCRv80/bin/glnxa64:/usr/local/freesurfer/stable6/MCRv80/sys/os/glnxa64:/usr/local/freesurfer/stable6/MCRv80/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/usr/local/freesurfer/stable6/MCRv80/sys/java/jre/glnxa64/jre/lib/amd64/server:/usr/local/freesurfer/stable6/MCRv80/sys/java/jre/glnxa64/jre/lib/amd64/client:/usr/local/freesurfer/stable6/MCRv80/sys/java/jre/glnxa64/jre/lib/amd64:
Error:Cannot find CTF archive /autofs/cluster/freesurfer/centos6_x86_64/dev/bin/segmentSubjectT1_autoEstimateAlveusML.ctf
#--------------------------------------------
#@# Hippocampal Subfields processing (T1 only) right Thu Jun 16 09:58:26 EDT 2016
------------------------------------------
Setting up environment variables
---
LD_LIBRARY_PATH is .:/usr/local/freesurfer/stable6/MCRv80/runtime/glnxa64:/usr/local/freesurfer/stable6/MCRv80/bin/glnxa64:/usr/local/freesurfer/stable6/MCRv80/sys/os/glnxa64:/usr/local/freesurfer/stable6/MCRv80/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/usr/local/freesurfer/stable6/MCRv80/sys/java/jre/glnxa64/jre/lib/amd64/server:/usr/local/freesurfer/stable6/MCRv80/sys/java/jre/glnxa64/jre/lib/amd64/client:/usr/local/freesurfer/stable6/MCRv80/sys/java/jre/glnxa64/jre/lib/amd64:
Error:Cannot find CTF archive /autofs/cluster/freesurfer/centos6_x86_64/dev/bin/segmentSubjectT1_autoEstimateAlveusML.ctf
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