Hi Elisabetta

it looks like you only ran autorecon1, which is just the first few steps of the processing. Was that your intent? If not, you might try -all instead (or -autorecon2 -autorecon3 after what you have already run).

cheers Bruce On Wed, 30 Apr 2014, Del Re, Elisabetta wrote:

Hi Bruce, thank you. No, the stats have only 2 files and aparc and aseg are missing.

Elisabetta C. del Re, Ph.D. Instructor, Department of Psychiatry Harvard Medical School phone 617 9675569 mail elisabetta_delre@hms.harvard.edu ________________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] On Behalf Of Bruce Fischl [fischl@nmr.mgh.harvard.edu] Sent: Wednesday, April 30, 2014 3:39 PM To: Freesurfer support list Subject: Re: [Freesurfer] FS F.5 error

Hi Elisabetta

that is a warning that you can ignore, not an error. Did the output look ok?

cheers Bruce On Wed, 30 Apr 2014, Elisabetta del Re wrote:

...

I ran a few cases through freesurfer5.3 last night and

...

        found that they all
        exited with the same error. This is the input that I
        used:

recon-all -s 01100.t1-realign-masked -i /tmp/01100.t1-realign-masked.nii.gz -autorecon1 && cp /projects/pnl/software/freesurfer5.3b/subjects/01100.t1-realign-masked/mri/T1.mgz /projects/pnl/software/freesurfer5.3b/subjects/01122.t1-realign-masked/mri/brainmask.mgz && recon-all -autorecon2 -subjid 01100.t1-realign-masked && recon-all -autorecon3 -subjid 01100.t1-realign-masked && mv /projects/pnl/software/freesurfer5.3b/subjects/01100.t1-realign-masked 01100.freesurfer

...

        I've attached the recon-all.log file which shows the
        following error:

         IFLAG= -1  LINE SEARCH FAILED. SEE DOCUMENTATION OF
        ROUTINE MCSRCH ERROR
        RETURN OF LINE SEARCH: INFO= 3 POSSIBLE CAUSES:
        FUNCTION OR GRADIENT ARE
        INCORRECT OR INCORRECT TOLERANCESoutof
        QuasiNewtonEMA: 007: -log(p) =
        -0.0  tol 0.000010

   Thank you so much for any help,

best,

...

     Elisabetta del Re

        --

Elisabetta del Re, instructor, psychiatry, Harvard Medical School

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then you need to specify additional targets to recon-all, like -all or -autorecon2 -autorecon3

cheers Bruce On Wed, 30 Apr 2014, Del Re, Elisabetta wrote:

Bruce, thank you so much. No, I wanted to run recon-all. Is the input only working for autorecon1 you think?

recon-all -s 01100.t1-realign-masked -i /tmp/01100.t1-realign-masked.nii.gz -autorecon1 && cp

...

...

/projects/pnl/software/freesurfer5.3b/subjects/01100.t1-realign-masked/mri/T1.mgz /projects/pnl/software/freesurfer5.3b/subjects/01122.t1-realign-masked/mri/brainmask.mgz && recon-all -autorecon2 -subjid 01100.t1-realign-masked && recon-all -autorecon3 -subjid 01100.t1-realign-masked && mv /projects/pnl/software/freesurfer5.3b/subjects/01100.t1-realign-masked 01100.freesurfer

Thank you again, Elisabetta

Elisabetta C. del Re, Ph.D. Instructor, Department of Psychiatry Harvard Medical School phone 617 9675569 mail elisabetta_delre@hms.harvard.edu ________________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] On Behalf Of Bruce Fischl [fischl@nmr.mgh.harvard.edu] Sent: Wednesday, April 30, 2014 3:53 PM To: Freesurfer support list Subject: Re: [Freesurfer] FS F.5 error

Hi Elisabetta

it looks like you only ran autorecon1, which is just the first few steps of the processing. Was that your intent? If not, you might try -all instead (or -autorecon2 -autorecon3 after what you have already run).

cheers Bruce On Wed, 30 Apr 2014, Del Re, Elisabetta wrote:

...

Hi Bruce, thank you. No, the stats have only 2 files and aparc and aseg are missing.

Elisabetta C. del Re, Ph.D. Instructor, Department of Psychiatry Harvard Medical School phone 617 9675569 mail elisabetta_delre@hms.harvard.edu ________________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] On Behalf Of Bruce Fischl [fischl@nmr.mgh.harvard.edu] Sent: Wednesday, April 30, 2014 3:39 PM To: Freesurfer support list Subject: Re: [Freesurfer] FS F.5 error

Hi Elisabetta

that is a warning that you can ignore, not an error. Did the output look ok?

cheers Bruce On Wed, 30 Apr 2014, Elisabetta del Re wrote:

...

I ran a few cases through freesurfer5.3 last night and

...

        found that they all
        exited with the same error. This is the input that I
        used:

recon-all -s 01100.t1-realign-masked -i /tmp/01100.t1-realign-masked.nii.gz -autorecon1 && cp /projects/pnl/software/freesurfer5.3b/subjects/01100.t1-realign-masked/mri/T1.mgz /projects/pnl/software/freesurfer5.3b/subjects/01122.t1-realign-masked/mri/brainmask.mgz && recon-all -autorecon2 -subjid 01100.t1-realign-masked && recon-all -autorecon3 -subjid 01100.t1-realign-masked && mv /projects/pnl/software/freesurfer5.3b/subjects/01100.t1-realign-masked 01100.freesurfer

...

        I've attached the recon-all.log file which shows the
        following error:

         IFLAG= -1  LINE SEARCH FAILED. SEE DOCUMENTATION OF
        ROUTINE MCSRCH ERROR
        RETURN OF LINE SEARCH: INFO= 3 POSSIBLE CAUSES:
        FUNCTION OR GRADIENT ARE
        INCORRECT OR INCORRECT TOLERANCESoutof
        QuasiNewtonEMA: 007: -log(p) =
        -0.0  tol 0.000010

   Thank you so much for any help,

best,

...

     Elisabetta del Re

        --

Elisabetta del Re, instructor, psychiatry, Harvard Medical School

---

Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.

---

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---

Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer