Thanks Greve! Command with ‘-hires’ and ‘-hires -cw256’ flag both work without any error message.
Thank you again!! Juhyoung > On Sep 4, 2017, at 7:36 AM, Douglas Greve <gr...@nmr.mgh.harvard.edu> wrote: > > Currently recon-all requires that the FOV be 256 or less. This was an > oversight on our part as I think it should work if it is > 256. Can you > experiment for us? The easy thing to do is to simply disable the check for > 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 && $FOV_gt_256) then > > > > and re-run with the hires flag. > > Alternatively, you can reduce the FOV to 256 or less with mri_convert --crop > and --crop-size. > > On 8/28/17 9:50 PM, Juhyoung Ryu wrote: >> Hi FS team, >> >> I encountered recon-all error and I want to solve the problem or find >> alternative method. >> As you can see forwarded mail thread, I asked about the problem before but i >> couldn’t any clear answer.. >> >> Would you suggest someone to advice me how to deal with the problem? >> >> Thanks, >> Juhyoung >> >>> Begin forwarded message: >>> >>> From: juhyoung Ryu <jh67753...@gmail.com <mailto:jh67753...@gmail.com>> >>> Subject: Re: [Freesurfer] recon-all error: ERROR! FOV=272.000 > 256 >>> Date: August 8, 2017 at 8:27:33 AM GMT+9 >>> To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu >>> <mailto:freesurfer@nmr.mgh.harvard.edu>> >>> >>> =============================================================================================== >>> server2:20170214_JEL JuhyoungRyu$ recon-all -subject JEL_v6 -i T1_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 14 >>> 16:21:16 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 \n >>> mri_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 \n >>> mri_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 \n >>> mri_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 14 >>> 16:21:16 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 <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 > 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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