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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> 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> >>> 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> >>>>> 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> >>>>>> 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) >>>>>> 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> 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 >>>>>> 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. >>>>>> >>>>> _______________________________________________ >>>>> 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. >>>>> >>>> >>>> >>>> _______________________________________________ >>>> 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. >>> >> >> > _______________________________________________ > 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. > >
_______________________________________________ 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.