Thank you! Hopefully, I can either figure it out myself or be helped by someone.
Thanks! Best, Peng On Wednesday, December 9, 2015, Bruce Fischl <fis...@nmr.mgh.harvard.edu> wrote: > Hi Peng > > nifti should be fine as input, but definitely don't use analyze. It > doesn't preserve the direction cosines so once you convert to it you will > never be sure which side of the image is the left hemim and which is the > right. > > I can't help with the 'can't locate MNI/Startup.pm ' error. Hopefully > someone else can. > > You will need some T1-weighted image with reasonably high res as input > htough. > > cheers > Bruce > > On Wed, 9 Dec 2015, Peng Zan wrote: > > Hi Bruce, >> Thank you for your email! These dicom files are transferred from nifti >> files, '.nii.gz' by xmedcon, and I think for this subject(R2261_S0283), >> they >> are not mprage or flash scans and so far I do not have mprage or flash >> scans >> for this subject. >> >> However, I do have mprage dicom files for other subjects in .img format, >> which freesurfer cannot read(I attached two screenshots of my folder in >> case >> you know by their names which files can work). Since I have most of my MRI >> data in nifti and .img formats, it is worth the efforts to make these >> files >> work in freesurfer. Do the input files have to be distributed into many >> dicom slices or they can be in one file in .nii or .dcm? >> >> On the other hand, I also tested the my dicom files of subject R2105 (in >> flash scans), and here comes the errors 'can't locate MNI/Startup.pm in >> @INC...', and the 'log' file warns the input volume axes are not >> orthogonal. >> (see 'recon-all.log' file attached). I think the input dicoms should not >> have coordinates themselves, they are aligned and then assigned >> coordinates >> by freesurfer, am I right? >> >> I am sorry for my verbose problems at this very beginning of using >> freesurfer. >> >> Thank you very much! >> >> Sincerely, >> Peng >> >> >> >> >> >> On Wed, Dec 9, 2015 at 3:08 PM, Bruce Fischl <fis...@nmr.mgh.harvard.edu> >> wrote: >> Hi Peng >> >> it looks like we can't read your input dicom. For example, the >> log says: >> reading from >> >> /Users/Peng/Documents/MNE/MNE_analysis/MRI/R2261_S0283/m000-gm_A0136_N12518 >> _S0283_20120817_P5716_averageCBF_normalized.dcm... >> Starting DICOMRead2() >> dcmfile = >> >> /Users/Peng/Documents/MNE/MNE_analysis/MRI/R2261_S0283/m000-gm_A0136_N12518 >> _S0283_20120817_P5716_averageCBF_normalized.dcm >> dcmdir = /Users/Peng/Documents/MNE/MNE_analysis/MRI/R2261_S0283 >> WARNING: tag ImageNumber not found in >> >> /Users/Peng/Documents/MNE/MNE_analysis/MRI/R2261_S0283/m000-gm_A0136_N12518 >> _S0283_20120817_P5716_averageCBF_normalized.dcm >> WARNING: tag SeriesNumber not found in >> >> /Users/Peng/Documents/MNE/MNE_analysis/MRI/R2261_S0283/m000-gm_A0136_N12518 >> _S0283_20120817_P5716_averageCBF_normalized.dcm >> WARNING: tag image orientation not found in >> >> /Users/Peng/Documents/MNE/MNE_analysis/MRI/R2261_S0283/m000-gm_A0136_N12518 >> _S0283_20120817_P5716_averageCBF_normalized.dcm >> Ref Series No = 0 >> Found 5 files, checking for dicoms >> WARNING: tag ImageNumber not found in >> >> /Users/Peng/Documents/MNE/MNE_analysis/MRI/R2261_S0283/m000-gm_A0136_N12518 >> _S0283_20120817_P5716_averageCBF_normalized.dcm >> >> where did that dicom file come from? And is it supposed to be a >> T1-weighted volume like an mprage or FLASH scan? >> >> cheers >> Bruce >> >> >> >> On Wed, 9 Dec 2015, Peng Zan >> wrote: >> >> > Dear freesurfer expert, >> > I am a student from University of Maryland, learning >> freesurfer for MNE >> > analysis recently. I have a perhaps silly problem and could >> not solve by >> > myself. The problem occurred as 'recon-all -s R2261_S0283 >> exited with >> > errors...' when I was running 'recon-all -autorecon-all >> -subjid >> > R2261_S0283'. I tried several subjects and got the same error. >> I am >> > wondering whether you can look at the 'recon-all.log' file and >> > 'recon-all.error' file and help me figure out what the problem >> is and how to >> > solve it? >> > >> > Thank you very much! Looking forward to your reply! >> > >> > Sincerely, >> > Peng >> > >> > >> _______________________________________________ >> 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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