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.
_______________________________________________
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.
