Error running FreeSurferPipeline: no recon-all.v6 hires, conf2hires, longmc
Sujeevini Sujanthan
I am currently working with version 4.3.0 of the HCP pipeline and freesurfer 6.0. I ran the PreFreeSurfer step successfully and am currently having issues running FreeSurferPipeline. I get the following error:
no recon-all.v6 hires
no conf2hires
no longmc
I’ve tested the freesurfer installation (the -autorecon1 stage) and it finished without any errors.
I’d greatly appreciate it if you can let me know how to resolve this issue.
Regards,
Sujeevini
Harms, Michael
This is odd. $HCPPIPEDIR/FreeSurfer/custom needs to be in your $PATH, but FreeSurferPipeline.sh is set up prepend it to your $PATH if it doesn't find it. Please attach the actual log file from your attempted run.
--
Michael Harms, Ph.D.
-----------------------------------------------------------
Associate Professor of Psychiatry
Washington University School of Medicine
Department of Psychiatry, Box 8134
660 South Euclid Ave. Tel: 314-747-6173
St. Louis, MO 63110 Email: mha...@wustl.edu
On 6/22/22, 11:25 AM, "Sujeevini Sujanthan" <sujee...@gmail.com> wrote:
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Glasser, Matt
We need the whole logfile. What issue are you having attaching?
Matt.
From: GSAN McGill <gsan....@gmail.com>
Reply-To: "hcp-...@humanconnectome.org" <hcp-...@humanconnectome.org>
Date: Wednesday, June 22, 2022 at 1:06 PM
To: HCP-Users <hcp-...@humanconnectome.org>
Cc: "Harms, Michael" <mha...@wustl.edu>
Subject: Re: [hcp-users] Error running FreeSurferPipeline: no recon-all.v6 hires, conf2hires, longmc
I'm having issues attaching the file to this thread so I decided to copy/paste the warning and error messages I received:
******************************
Tue Jun 21 11:59:17 PDT 2022:FreeSurferPipeline.sh: WARNING: We were not able to locate one of the following required tools:
Tue Jun 21 11:59:17 PDT 2022:FreeSurferPipeline.sh: WARNING: recon-all.v6.hires, conf2hires, or longmc
ERROR: You are trying to re-run an existing subject with (possibly)
new input data (-i). If this is truly new input data, you should delete
the subject folder and re-run, or specify a different subject name.
If you are just continuing an analysis of an existing subject, then
omit all -i flags.
Tue Jun 21 11:59:27 PDT 2022:FreeSurferPipeline.sh: ERROR: recon-all command failed with return_code: 1
Tue Jun 21 11:59:27 PDT 2022:FreeSurferPipeline.sh: ABORTING
******************************
It looks like I may need to delete files/folders to run the FreeSurferPipeline. Could you please advise what files these are and where I can find them?
Thank you for your help,
Sujeevini
To view this discussion on the web visit https://groups.google.com/a/humanconnectome.org/d/msgid/hcp-users/5e51b0d8-dd6e-47c4-9f19-f23805b2b803n%40humanconnectome.org.
Sujeevini Sujanthan
Attached is the .sh.e file produced from my attempted run.
It looks like I may need to delete files/folders to run the FreeSurferPipeline. Could you please advise what files these are and where I can find them?
Thank you for your help,
Sujeevini
Glasser, Matt
Post the .o too.
Matt.
From: Sujeevini Sujanthan <sujee...@gmail.com>
Reply-To: "hcp-...@humanconnectome.org" <hcp-...@humanconnectome.org>
Date: Wednesday, June 22, 2022 at 1:12 PM
To: HCP-Users <hcp-...@humanconnectome.org>
Cc: "Harms, Michael" <mha...@wustl.edu>
Subject: Re: [hcp-users] Error running FreeSurferPipeline: no recon-all.v6 hires, conf2hires, longmc
Attached is the .sh.e file produced from my attempted run.
To view this discussion on the web visit https://groups.google.com/a/humanconnectome.org/d/msgid/hcp-users/964e7cec-a707-491a-ade3-d7fb66f029cbn%40humanconnectome.org.
Glasser, Matt
You can delete
${StudyFolder}/${Subject}/T1w/${Subject} and try again.
Harms, Michael
Those “WARNING” messages about recon-all.v6.hires, conf2hires, or longmc are not an ERROR, and the text after that (which wasn’t included) should say something about how they were being added to your PATH.
The real ERROR is that you are trying to run on top of an existing session. Unless you are attempting to apply FreeSurfer edits, delete the entire FS folder ($StudyFolder/$Session/T1w/$Session) and try again.
Cheers,
-MH
--
Michael Harms, Ph.D.
-----------------------------------------------------------
Associate Professor of Psychiatry
Washington University School of Medicine
Department of Psychiatry, Box 8134
660 South Euclid Ave. Tel: 314-747-6173
St. Louis, MO 63110 Email: mha...@wustl.edu