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
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
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
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.
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 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 > >
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.
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 fischl@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 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 > >
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@nmr.mgh.harvard.edu
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