External Email - Use Caution Hi all, I was wondering if anyone had a chance to look at the log to shed some light on this mystery error, or if more info or a different log are needed.
Thank you, Michele On Fri, 12 Feb 2021 at 10:05, Michele Valotti <michele.valo...@gmail.com> wrote: > Hi Andrew, > thank you for your help, I have attached the mri_nu_correct log from the > base freesurfer directory, let me know if this helps > > Michele > > On Thu, 11 Feb 2021 at 17:16, Hoopes, Andrew <ahoo...@mgh.harvard.edu> > wrote: > >> If you send the mri_nu_correct.mni.log we can figure it out for sure. >> >> Andrew >> >> >> >> *From: *freesurfer-boun...@nmr.mgh.harvard.edu < >> freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Michele Valotti < >> michele.valo...@gmail.com> >> *Date: *Thursday, February 11, 2021 at 12:07 PM >> *To: *Freesurfer support list <freesurfer@nmr.mgh.harvard.edu> >> *Subject: *Re: [Freesurfer] mincRead error >> >> * External Email - Use Caution * >> >> Hi Andrew, >> >> I do think the problem is in the MINC but the minc paths point to the >> freesurfer installation, so I think it should be running using that >> >> >> >> thank you, >> >> Michele >> >> >> >> On Thu, 11 Feb 2021 at 16:29, Hoopes, Andrew <ahoo...@mgh.harvard.edu> >> wrote: >> >> Hi Michele, >> >> I think that’s the problem then. The freesurfer code is written to work >> with the specific version of minc that we distribute with the release. If >> possible, you should run freesurfer without setting any MINC paths to your >> local install to see if that fixes things. >> >> Andrew >> >> >> >> *From: *freesurfer-boun...@nmr.mgh.harvard.edu < >> freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Michele Valotti < >> michele.valo...@gmail.com> >> *Date: *Thursday, February 11, 2021 at 11:02 AM >> *To: *Freesurfer support list <freesurfer@nmr.mgh.harvard.edu> >> *Subject: *Re: [Freesurfer] mincRead error >> >> * External Email - Use Caution * >> >> Hi Trisanna, >> >> thank you for your reply, I am using minc2 (version 1.9.16) but this is >> the same version I use on my local machine and it does not give any errors >> there, and SetUpFreesurfer is sourced before exporting MINC paths and >> variables. >> >> >> >> Michele >> >> >> >> On Wed, 10 Feb 2021 at 14:57, Trisanna Sprung-Much < >> trisanna.sprung-m...@mail.mcgill.ca> wrote: >> >> * External Email - Use Caution * >> >> Hi All >> >> >> >> As a frequent user of minctools, I know I’ve had problems in the past if >> I source minctools before sourcing freesurfer in the same terminal, because >> freesurfer uses an older version of minctools. >> >> Also, freesurfer uses minc1 format not minc2. >> >> >> >> Best, >> >> >> >> Trisanna Sprung-Much >> >> Research Associate >> >> McGill University >> >> MD Anderson Cancer Centre >> >> -- >> >> >> >> >> >> *From: *<freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of "Hoopes, >> Andrew" <ahoo...@mgh.harvard.edu> >> *Reply-To: *Freesurfer support list <freesurfer@nmr.mgh.harvard.edu> >> *Date: *Wednesday, February 10, 2021 at 9:54 AM >> *To: *Freesurfer support list <freesurfer@nmr.mgh.harvard.edu> >> *Subject: *Re: [Freesurfer] mincRead error >> >> >> >> Can you send the `mri/mri_nu_correct.mni.log` file as well? Have you >> installed minc tools separately on your local machine and do you have any >> of these variables set in your default environment? >> >> >> >> MNI_DIR >> >> MINC_BIN_DIR >> >> MINC_LIB_DIR >> >> >> >> It’s possible there’s another install of MNI that’s interfering with the >> freesurfer one. >> >> Andrew >> >> >> >> *From: *freesurfer-boun...@nmr.mgh.harvard.edu < >> freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Michele Valotti < >> michele.valo...@gmail.com> >> *Date: *Monday, February 8, 2021 at 9:53 AM >> *To: *Freesurfer support list <freesurfer@nmr.mgh.harvard.edu> >> *Subject: *Re: [Freesurfer] mincRead error >> >> * External Email - Use Caution * >> >> attached is the log for the run, the version of mri_convert is the same >> version on my local machine (where the command runs) and in the cloud >> instance >> >> >> >> On Fri, 5 Feb 2021 at 18:02, Michele Valotti <michele.valo...@gmail.com> >> wrote: >> >> Hi all, >> >> I am running long FreeSurfer and after successfully testing it on my >> local machine I tried to run it on a server (which should however have the >> same FreeSurfer version and setup), but I am getting this error >> >> >> >> mri_convert ./tmp.mri_nu_correct.mni.533/nu1.mnc orig_nu.mgz --like >> orig.mgz --conform >> mri_convert.bin ./tmp.mri_nu_correct.mni.533/nu1.mnc orig_nu.mgz --like >> orig.mgz --conform >> ncopen: filename "./tmp.mri_nu_correct.mni.533/nu1.mnc": Not a netCDF file >> miopen: MINC package entry point >> Error opening ./tmp.mri_nu_correct.mni.533/nu1.mnc >> mincRead(): error reading volume from file >> ./tmp.mri_nu_correct.mni.533/nu1.mnc >> $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ >> reading from ./tmp.mri_nu_correct.mni.533/nu1.mnc... >> Linux 18e36413df0c 5.4.0-1030-aws #31~18.04.1-Ubuntu SMP Tue Nov 17 >> 10:48:34 UTC 2020 x86_64 GNU/Linux >> >> recon-all -s base_freesurfer exited with ERRORS at Fri Feb 5 17:45:34 >> UTC 2021 >> >> >> >> >> >> Any idea what the cause of this might be? >> >> Thank you! >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu >> *MailScanner has detected a possible fraud attempt from >> "secure-web.cisco.com" claiming to be* >> https://secure-web.cisco.com/1YiRbDWbfoHMWcoEyhd1M0GEGo15ivihUza-ApiYxwAplTWrs2xwWC5seFnZQVm99FwtMgNCulRtaoKUg8-2WWlPz2Gr6nopvrazdBKEyhCSP-5Q92wwxKxp9wgCRULgW244lOMGWwkoZxWJx40-QwWNWzg8Ydm1Ghylsw0shxgg2Z7RGAnN2HAmcCoEvJpcnCpBOBbO0AKbuGthI7WE5t1LC4zM8X0A_CTIF-Pw8NVIbwks3Bu1pOY9tsJ2onO_Hj0qqITsGKY5s9k6Gem3QgQ/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer >> <https://secure-web.cisco.com/1JGrZCpBCSuPapkm_HHIatoVooBbQLB65QiBaa7gloZuDTas3F7Jm5NUb0Jh70_kAxkiyAieOo4vj5KWnmyBckkZfLu5nV0KX3Mgw7SIvo89FMuleCURamxNMyNKLld0AulzlbFQN38jsbEpwGx9wGmFPQS4gS9S-eUBjNstDxOMweGNSdRBNhB41QYIdh7qgt-XD01A9MibR5VGK_Izj3WoT1yzm6BsCYIFiFRg95tYg3xA3NqMoGwukf1F2NvrYpc-xnrg8KIrVPxavMFasuA/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer> >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu >> *MailScanner has detected a possible fraud attempt from >> "secure-web.cisco.com" claiming to be* >> https://secure-web.cisco.com/1YiRbDWbfoHMWcoEyhd1M0GEGo15ivihUza-ApiYxwAplTWrs2xwWC5seFnZQVm99FwtMgNCulRtaoKUg8-2WWlPz2Gr6nopvrazdBKEyhCSP-5Q92wwxKxp9wgCRULgW244lOMGWwkoZxWJx40-QwWNWzg8Ydm1Ghylsw0shxgg2Z7RGAnN2HAmcCoEvJpcnCpBOBbO0AKbuGthI7WE5t1LC4zM8X0A_CTIF-Pw8NVIbwks3Bu1pOY9tsJ2onO_Hj0qqITsGKY5s9k6Gem3QgQ/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer >> <https://secure-web.cisco.com/1xs9PzPP9V2FuqxvdDUNBOJ4r4_8Psp1WNP2tVrDYnPLg4T1blP_wTgTNOvBQV4oNdMuIsD2N6iC5HUD1XgKtYuwymDzV_-gfo9Q1vPTy6x0DDdZWi1jfUJlMYtYb2mF1QNQlQZxa1_onIQnw9nrcvd4R2-Y7geTHa4C4IqiOSrQN9jkUXkvGupjRMcqImISZVGktvoiNSnuW8dj7Rn7G79C_d0NzthXmQwu62rTFU6fuQHd5ayefYvgAIPmiQ0PZ-QNRVjGeavlqRXeLvXks8Q/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer> >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu >> https://secure-web.cisco.com/1YiRbDWbfoHMWcoEyhd1M0GEGo15ivihUza-ApiYxwAplTWrs2xwWC5seFnZQVm99FwtMgNCulRtaoKUg8-2WWlPz2Gr6nopvrazdBKEyhCSP-5Q92wwxKxp9wgCRULgW244lOMGWwkoZxWJx40-QwWNWzg8Ydm1Ghylsw0shxgg2Z7RGAnN2HAmcCoEvJpcnCpBOBbO0AKbuGthI7WE5t1LC4zM8X0A_CTIF-Pw8NVIbwks3Bu1pOY9tsJ2onO_Hj0qqITsGKY5s9k6Gem3QgQ/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer > >
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