Hi Douglas and Bruce, Thanks for your suggestions. I found the reason. The mistake begins from the compressing dcm to nii by using dcm2nii. In the first 3 dcm images, two of them have same index, then the dcm2nii could not keep the original information of voxel size. I omitted the first 3 dcm images then it worked during freesurfer analysis.
Cheers Yawu On Fri, Feb 6, 2015 at 6:26 PM, Bruce Fischl <[email protected]> wrote: > and what was the recon-all -i command line? Does the rawavg.mgz look > correct? You can send us whatever file you gave to recon-all -i and we'll > see why it is being converted incorrectly, or you can try the mri_convert > command line I gave below (check out mri_convert --help) to override the > voxel size info we read out of the header > > On Fri, 6 Feb 2015, Liu Y wrote: > > Hi Bruce,The full recon-all command line is "recon-all -cw256 >> -s T8_1 -all" >> >> and the input format is mgz. The mgz file is created by >> running recon-all -i. The 001.mgz under /mri/orig looks just normal, but >> when complete the "recon-all -cw256 -s T8_1 -all", the orig.mgz was >> re-scaled (stretched) in left-right direction, and could not see the left >> and right boundaries of the brain. >> Thanks, >> Yawu >> >> On Fri, Feb 6, 2015 at 3:18 PM, Bruce Fischl <[email protected]> >> wrote: >> Hi Yawu >> >> what was the full recon-all command line? What is your input >> format? If >> all else fails you can mri_convert your input volume nifti or >> mgz and >> override what is in the header (e.g. mri_convert -iks 1 ...) >> >> cheers >> Bruce >> On Fri, 6 Feb >> 2015, Liu Y wrote: >> >> > Dear Experts, >> > When I run recon-all -cw256 -s problemcase -all, the program >> seems not able >> > accurately to recognize the voxel size in this problematic >> case, in other >> > cases there is no problem. The program gave a warning like >> this: >> > >> >WARNING==================++++++++++++++++++++++++========== >> ================ >> ======= >> > ====== >> > The physical sizes are (240.00 mm, 240.00 mm, 338.00 mm), >> which cannot fit >> > in 256^3 mm^3 volume. >> > The resulting volume will have 338 slices. >> > If you find problems, please let us know >> ([email protected]). >> >==================================================+++++++++ >> +++++++++++++++= >> >> > ============== >> > >> > $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp >> $ >> > reading from >> /usr/local/src/freesurfer/subjects/T8_1/mri/rawavg.mgz... >> > TR=8.08, TE=0.00, TI=0.00, flip angle=0.00 >> > i_ras = (0, -1, 0) >> > j_ras = (0, 0, 1) >> > k_ras = (1, 0, 0) >> > Original Data has (1, 1, 2) mm size and (240, 240, 169) >> voxels. >> > Data is conformed to 1 mm size and 338 voxels for all >> directions >> > changing data type from float to uchar (noscale = 0)... >> > MRIchangeType: Building histogram >> > Reslicing using trilinear interpolation >> > writing to >> /usr/local/src/freesurfer/subjects/Turku8_1/mri/orig.mgz... >> > >> > **************************************** >> > ERROR! FOV=338.000 > 256 >> > Include the flag -cw256 with recon-all! >> > Inspect orig.mgz to ensure the head is fully visible. >> > **************************************** >> > >> > Then I checked the orig.mgz, the image was re-scaled >> (stretched) in >> > left-right direction, and could not see the left and right >> boundaries of the >> > brain. The program said that the Original Data has (1, 1, 2) >> mm size, but >> > actually the voxel size is 1*1*1 mm3. >> > >> > The freesurfer version 5.3, Ubuntu 12.04 >> > >> > Thanks, >> > >> > Yawu >> > >> > >> > >> > >> _______________________________________________ >> Freesurfer mailing list >> [email protected] >> 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 > [email protected] > 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 [email protected] 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.
