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> > 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> > > =============================================================================================== > 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. > >
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