External Email - Use Caution Dear Eugenio,
it works:) thanks for your help! it was really helpful! have a nice day~ Jinyoung 2018년 9월 11일 (화) 오전 2:07, Iglesias Gonzalez, Eugenio <e.igles...@ucl.ac.uk>님이 작성: > External Email - Use Caution > > Hi Jinyoung > Sorry for the slow response but I'm traveling these days > I believe this is a bug that was fixed in the dev version 2-3 weeks ago. > Would you mind trying the latest dev, and checking whether that solves the > problem? > Cheers > Eugenio > > Sent from my phone, please excuse brevity and typos > > ------------------------------ > *From:* freesurfer-boun...@nmr.mgh.harvard.edu < > freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of 오진영 < > jinyoung.oh...@gmail.com> > *Sent:* Wednesday, September 5, 2018 6:13:48 AM > *To:* Freesurfer support list > *Subject:* [Freesurfer] amygdala segmentation using additional scan error > > > External Email - Use Caution > > Hello, freesurfer experts > > I'm trying to run segmentation of hippocampal subfields and nuclei of > amygdala with additional scan. > I already ran segmentation of hippocampal subfields and nuclei of amygdala > with only T1 image, using segmentHA_T1.sh command and succeeded. > After success of segmentation of amygdala with T1 image, I tried to run > segmentation again with additional scan(T2 image) to get more reliable > results. > However, when I use command segmentHA_T2.sh, I got the following error: > > Error in segmentSubjectT1T2_autoEstimateAlveusML (line 2628) > > > And the last few lines before the error are below: > > *Fitting mesh to image data mask took 264.2808 seconds* > > *Transforming points* > > *Transforming points* > > *Wrote image to file image1.mgz* > > *Wrote image to file image2.mgz* > > *INFO: dst volume info differs from the one stored in lta. gets modified > now.* > > *volume geometry:* > > *extent : (232, 469, 208)* > > *voxel : ( 0.3333, 0.3333, 0.3333)* > > *x_(ras) : ( 0.0000, -1.0000, 0.0000)* > > *y_(ras) : ( 0.0000, 0.0000, -1.0000)* > > *z_(ras) : ( 1.0000, 0.0000, 0.0000)* > > *c_(ras) : (-21.1788, -1.8961, 3.8447)* > > *file : T2isotropic.mgz* > > *volume geometry:* > > *extent : (256, 256, 256)* > > *voxel : ( 1.0000, 1.0000, 1.0000)* > > *x_(ras) : ( 0.0000, -1.0000, 0.0000)* > > *y_(ras) : ( 0.0000, 0.0000, -1.0000)* > > *z_(ras) : ( 1.0000, 0.0000, 0.0000)* > > *c_(ras) : ( 2.3212, 8.6039, -21.1553)* > > *file : /Users/mnd_mac/Desktop/JY_surfer/sub_05_T2.nii* > > *Constructing image-to-world transform from header information (asmr1.mgz)* > > *Constructing image-to-world transform from header information > (/Users/mnd_mac/Desktop/JY_surfer//recon_sub_05/tmp/hippoSF_T1T2_v21_T2_left/imageDump.mgz)* > > *Wrote image to file asmr2.mgz* > > *This file does not contain MRI parameters* > > *This file does not contain MRI parameters* > > *This file does not contain MRI parameters* > > *In an assignment A(:) = B, the number of elements in A and B must be the > same.* > > > *Error in segmentSubjectT1T2_autoEstimateAlveusML (line 2628)* > > > > > *MATLAB:subsassignnumelmismatch* > > *Darwin MnD-macui-iMac.local 17.7.0 Darwin Kernel Version 17.7.0: Thu Jun > 21 22:53:14 PDT 2018; root:xnu-4570.71.2~1/RELEASE_X86_64 x86_64* > > and I have no idea how to solve this problem out. > > I use the dev version of freesurfer. > T1 scan image and T2 scan image of participant were taken on the same day. > > If you have any recommendations, please send me the email back. > > Thanks! > > Jinyoung > _______________________________________________ > 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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