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 fischl@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
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