I would suggest running 7.4.1 ‘recon-all’ with those manual setup to first make sure 7.4.1 works for your system. If that works, the issue is in the makefile.

 

From: Noah Reardon <nreardon@umich.edu>
Sent: Monday, November 11, 2024 1:43 PM
To: Huang, Yujing <YHUANG43@mgh.harvard.edu>
Cc: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>; Jeffrey Neal <jsneal@umich.edu>
Subject: Re: [Freesurfer] [WARNING: ATTACHMENT UNSCANNED]Re: mri_convert: Command terminated by signal 9

 

        External Email - Use Caution        

Hi Yujing,

 

I'm the lab manager for this lab. I appreciate your help and wanted to provide some background information. We use a makefile that helps us run all of our preprocessing steps for a large number of subjects. Here is the code we use in the makefile:

 

.PHONY: recon-all cleanfreesurfer

 

recon-all: /nfs/tpolk/mind/freesurfer/$(subject)/scripts/recon-all.done

 

/nfs/tpolk/mind/freesurfer/$(subject)/scripts/recon-all.done: $(mrsstruct) $(placstruct)

    export SUBJECTS_DIR=/nfs/tpolk/mind/freesurfer ;\

    recon-all -all -s $(subject) -i $(mrsdicom) -i $(placdicom)

 

#/nfs/tpolk/mind/freesurfer/$(subject)/scripts/recon-all.done: $(drugstruct) $(mrsstruct) $(placstruct)

#    export SUBJECTS_DIR=/nfs/tpolk/mind/freesurfer ;\

#    recon-all -all -s $(subject) -i $(drugdicom) -i $(mrsdicom) -i $(placdicom)

 

cleanfreesurfer:

    rm -r /nfs/tpolk/mind/freesurfer/$(subject)

 

We have never encountered this issue with freesurfer, but now that we're trying to use the updated version (7.4.1), it is giving us the errors Jeffrey attached.

 

Please advise.

 

Noah Reardon, B.S. 

Lab Coordinator

Department of Psychology 

University of Michigan

Phone: (734) 763-0343

 

 

On Mon, Nov 11, 2024 at 1:08 PM Huang, Yujing <YHUANG43@mgh.harvard.edu> wrote:

‘recon-all’ is a shell script that is ready to be run. I don’t understand why they need to have makefile to make recon-all.

 

Here are the steps to setup Freesurfer environment and run ‘recon-all’:

  1. Source the correct Freesurfer environment needs to be sourced before running recon-all - MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://surfer.nmr.mgh.harvard.edu/fswiki/SetupConfiguration_Linux
  2. Set ‘SUBJECTS_DIR’ to point to directory outside the Freesurfer installation tree, and make sure you have write permission
  3. Run recon-all MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://surfer.nmr.mgh.harvard.edu/fswiki/recon-all

(ex. recon-all -all -s <> -i <>)

 

Yujing

 

 

 

From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> On Behalf Of Jeffrey Neal
Sent: Monday, November 11, 2024 10:47 AM
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Cc: Noah Reardon <nreardon@umich.edu>
Subject: Re: [Freesurfer] [WARNING: ATTACHMENT UNSCANNED]Re: mri_convert: Command terminated by signal 9

 

Hello,

 

Thanks for the helpful links. I did double check through everything and it all looks correct; Sorry about the log file I needed to change permissions on it. Here is the log file from the first email and here is an additional one from today as well as some screenshots:

After running it once and getting the “terminated by signal 9” error when I try to run it again packages have disappeared out of the freesurfer/bin causing more issues. 

The command they are running is make recon-all -k. If you need to see the makefile or other things let me know and I will get them for you.

 

Best Regards,
Jeffrey Neal
jsneal@umich.edu
LSA EHTS Desktop Support Specialist Senior
University of Michigan

 

On Nov 6, 2024, at 4:27 PM, Huang, Yujing <YHUANG43@mgh.harvard.edu> wrote:

 

 

 

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