Re: [Freesurfer] Fwd: recon-all error: ERROR! FOV=272.000 > 256

Douglas Greve Sun, 03 Sep 2017 15:37:25 -0700

Currently recon-all requires that the FOV be 256 or less. This was anoversight on our part as I think it should work if it is > 256. Can youexperiment for us? The easy thing to do is to simply disable the checkfor this. To do this, create a version of recon-all that you can edit.Find the line that says:


 if ($FOV_gt_256) then


and change it to

 if (0 && $FOV_gt_256) then

and re-run with the hires flag.

Alternatively, you can reduce the FOV to 256 or less with mri_convert--crop and --crop-size.



On 8/28/17 9:50 PM, Juhyoung Ryu wrote:

Hi FS team,

I encountered recon-all error and I want to solve the problem or findalternative method.As you can see forwarded mail thread, I asked about the problem beforebut i couldn’t any clear answer..


Would you suggest someone to advice me how to deal with the problem?

Thanks,
Juhyoung

Begin forwarded message:

*From: *juhyoung Ryu <jh67753...@gmail.com <mailto:jh67753...@gmail.com>>
*Subject: **Re: [Freesurfer] recon-all error: ERROR! FOV=272.000 > 256*
*Date: *August 8, 2017 at 8:27:33 AM GMT+9

*To: *Freesurfer support list <freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>>


===============================================================================================

server2:20170214_JEL JuhyoungRyu$ recon-all -subject JEL_v6 -iT1_bfc.nii -T2 T2_bfc.nii -T2pial -all -hires

INFO: hi-res volumes are conformed to the min voxel size
Subject Stamp: freesurfer-Darwin-OSX-stable-pub-v6.0.0-2beb96c
Current Stamp: freesurfer-Darwin-OSX-stable-pub-v6.0.0-2beb96c
INFO: SUBJECTS_DIR is /Applications/freesurfer/subjects
Actual FREESURFER_HOME /Applications/freesurfer

Darwin server2.local 16.6.0 Darwin Kernel Version 16.6.0: Fri Apr 1416:21:16 PDT 2017; root:xnu-3789.60.24~6/RELEASE_X86_64 x86_64

/Applications/freesurfer/subjects/JEL_v6

\n mri_convert/Users/JuhyoungRyu/Desktop/subjects/20170214_JEL/T1_bfc.nii/Applications/freesurfer/subjects/JEL_v6/mri/orig/001.mgz \nmri_convert.bin/Users/JuhyoungRyu/Desktop/subjects/20170214_JEL/T1_bfc.nii/Applications/freesurfer/subjects/JEL_v6/mri/orig/001.mgz

$Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $

reading from/Users/JuhyoungRyu/Desktop/subjects/20170214_JEL/T1_bfc.nii...

TR=2400.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (0.998342, 0, -0.057564)
j_ras = (0, 1, 0)
k_ras = (0.057564, 0, 0.998342)
writing to /Applications/freesurfer/subjects/JEL_v6/mri/orig/001.mgz...
#--------------------------------------------
#@# T2/FLAIR Input Mon Aug  7 11:54:55 KST 2017
/Applications/freesurfer/subjects/JEL_v6

\n mri_convert --no_scale 1/Users/JuhyoungRyu/Desktop/subjects/20170214_JEL/T2_bfc.nii/Applications/freesurfer/subjects/JEL_v6/mri/orig/T2raw.mgz \nmri_convert.bin --no_scale 1/Users/JuhyoungRyu/Desktop/subjects/20170214_JEL/T2_bfc.nii/Applications/freesurfer/subjects/JEL_v6/mri/orig/T2raw.mgz

$Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $

reading from/Users/JuhyoungRyu/Desktop/subjects/20170214_JEL/T2_bfc.nii...

TR=1000.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (0.998342, 0, -0.057564)
j_ras = (0, 1, 0)
k_ras = (0.057564, 0, 0.998342)
writing to /Applications/freesurfer/subjects/JEL_v6/mri/orig/T2raw.mgz...
#--------------------------------------------
#@# MotionCor Mon Aug  7 11:55:00 KST 2017
Found 1 runs
/Applications/freesurfer/subjects/JEL_v6/mri/orig/001.mgz
Checking for (invalid) multi-frame inputs...
WARNING: only one run found. This is OK, but motion
correction cannot be performed on one run, so I'll
copy the run to rawavg and continue.

\n cp /Applications/freesurfer/subjects/JEL_v6/mri/orig/001.mgz/Applications/freesurfer/subjects/JEL_v6/mri/rawavg.mgz \n

/Applications/freesurfer/subjects/JEL_v6

\n mri_convert/Applications/freesurfer/subjects/JEL_v6/mri/rawavg.mgz/Applications/freesurfer/subjects/JEL_v6/mri/orig.mgz --conform_min \nmri_convert.bin/Applications/freesurfer/subjects/JEL_v6/mri/rawavg.mgz/Applications/freesurfer/subjects/JEL_v6/mri/orig.mgz --conform_min

$Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $
reading from /Applications/freesurfer/subjects/JEL_v6/mri/rawavg.mgz...
TR=2400.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (0.998342, 0, -0.057564)
j_ras = (0, 1, 0)
k_ras = (0.057564, 0, 0.998342)
changing data type from float to uchar (noscale = 0)...
MRIchangeType: Building histogram
Reslicing using trilinear interpolation
writing to /Applications/freesurfer/subjects/JEL_v6/mri/orig.mgz...
\n****************************************
ERROR! FOV=272.000 > 256
Include the flag -cw256 with recon-all!
Inspect orig.mgz to ensure the head is fully visible.
****************************************\n

Darwin server2.local 16.6.0 Darwin Kernel Version 16.6.0: Fri Apr 1416:21:16 PDT 2017; root:xnu-3789.60.24~6/RELEASE_X86_64 x86_64


recon-all -s JEL_v6 exited with ERRORS at Mon Aug  7 11:55:17 KST 2017

===============================================================================================

Here it is!

Thank you so much,
Juhyoung

On Mon, Aug 7, 2017 at 11:18 PM, Bruce Fischl<fis...@nmr.mgh.harvard.edu <mailto:fis...@nmr.mgh.harvard.edu>> wrote:


    Hi Juhyoung

    can you just cut and paste the text into the email instead of a
    screen shot?

    thanks
    Bruce
    On Mon, 7 Aug 2017, Juhyoung Ryu wrote:

        Sure, screenshot image is below with commands.





            On Aug 7, 2017, at 11:14 AM, Bruce Fischl
            <fis...@nmr.mgh.harvard.edu
            <mailto:fis...@nmr.mgh.harvard.edu>> wrote:

            can you send us the entire screeen output of that command?

            On Mon, 7 Aug 2017, Juhyoung Ryu wrote:

                Thank you for the response.

                Then what do you suggest i use? Because same error is
                occurred when i typed like this; [recon-all -subject
                ${subjName} -i T1_bfc.nii -hires -T2 T2_bfc.nii
                -T2pial -all]

                Thanks!
                Juhyoung

                    On Aug 6, 2017, at 3:04 AM, Bruce Fischl
                    <fis...@nmr.mgh.harvard.edu
                    <mailto:fis...@nmr.mgh.harvard.edu>> wrote:

                    Hi Juhyoung

                    I think it's because you have -cw256. Since it
                    comes after -hires it overrides it and tells
                    recon-all to crop to a 256 volume size

                    cheers
                    Bruce
                    On Fri, 4 Aug 2017, Juhyoung Ryu wrote:

                        Dear FS experts,
                        I want to reconstruct white and pial surface
                        using both -hires and -T2pial
                        options.
                        My T1 and T2 image resolution is .85mm^3.
                        But [recon-all -subject ${subjName} -i
                        T1_bfc.nii -hires -T2 T2_bfc.nii -T2pial
                        -all -cw256] command is not working as I
                        emailed below..
                        Is there any suggestions to run freesurfer?
                        Thank you in advance!
                        Juhyoung

                            On Jul 28, 2017, at 8:45 AM, Juhyoung Ryu
                        <jh67753...@gmail.com
                        <mailto:jh67753...@gmail.com>>
                            wrote:
                        Hi Bruce,
                        Yes I’m using v6.0.
                        I found that there is -hires flag in version 6
                        (https://surfer.nmr.mgh.harvard.edu/fswiki/HiResRecon
                        <https://surfer.nmr.mgh.harvard.edu/fswiki/HiResRecon>)
                        and i included that;  recon-all -subject
                        ${subjName} -i T1_bfc.nii -hires
                        -T2 T2_bfc.nii -T2pial -all -cw256
                        Thanks,
                        Juhyoung

                            On Jul 28, 2017, at 2:19 AM, Bruce Fischl
                            <fis...@nmr.mgh.harvard.edu
                        <mailto:fis...@nmr.mgh.harvard.edu>> wrote:
                        Hi  Juhyoung
                        what FS version are you running with? If 6.0
                        you want to include
                        the -highres flag
                        cheers
                        Bruce
                        On Thu, 27 Jul 2017, juhyoung Ryu wrote:

                            Hi experts,
                            I'm trying to surface reconstruction using
                            high-resolution T1 and T2 data
                            using freesurfer version 6
                            So I typed like this:
                            recon-all -subject ${subjName} -i
                        T1_bfc.nii -hires -T2
                            T2_bfc.nii -T2pial
                            -all
                            and that excited with errors like this;
                            \n****************************************
                            ERROR! FOV=272.000 > 256
                            Include the flag -cw256 with recon-all!
                            Inspect orig.mgz to ensure the head is
                        fully visible.
                            ****************************************\n
                            So I added -cw256 flag and run the
                        command line again
                            (recon-all -subject
                            ${subjName} -i T1_bfc.nii -hires -T2
                        T2_bfc.nii -T2pial
                            -all -cw256). But
                            the result is same.
                            I'd appreciate any suggestion.
                            Thank you,
                            Juhyoung
                        _______________________________________________
                        Freesurfer mailing list
                        Freesurfer@nmr.mgh.harvard.edu
                        <mailto:Freesurfer@nmr.mgh.harvard.edu>
                        
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
                        
<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
                        <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.

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



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


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



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




_______________________________________________
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


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.

Re: [Freesurfer] Fwd: recon-all error: ERROR! FOV=272.000 > 256

Reply via email to