There is only one file in the series. Is that right? It's trying to compute the slice direction cosine, which it cannot do from one file.
On 07/03/2012 12:36 PM, Chen, Xiaoyan wrote: > Hi, > I have the data from one of our collaborators. They are dicom files, > and they are collected from GE. I try to use mri_convert to convert the files > from dicom to nifti. However, the following error shows up. > > > mri_convert 1.2.840.113619.2.135.2025.3762570.5144.1309404440.95.dcm > 1.2.840.113619.2.135.2025.3762570.5144.1309404440.95.nii.gz > mri_convert 1.2.840.113619.2.135.2025.3762570.5144.1309404440.95.dcm > 1.2.840.113619.2.135.2025.3762570.5144.1309404440.95.nii.gz > $Id: mri_convert.c,v 1.179.2.2 2011/05/16 20:53:47 greve Exp $ > reading from 1.2.840.113619.2.135.2025.3762570.5144.1309404440.95.dcm... > Starting DICOMRead2() > dcmfile = > /autofs/cluster/randy/5/helen/resting_jiliang/1.2.840.113619.2.135.2025.3762570.5144.1309404440.95.dcm > dcmdir = /autofs/cluster/randy/5/helen/resting_jiliang > Ref Series No = 2 > Found 15 files, checking for dicoms > Found 1 dicom files in series. > First Sorting > Computing Slice Direction > Vs: 0 0 0 > Vs: nan nan nan > Second Sorting > Counting frames > nframes = 1 > nslices = 1 > ndcmfiles = 1 > PE Dir = COL (dicom read) > TransferSyntaxUID: --1.2.840.10008.1.2-- > jpegUID: --1.2.840.10008.1.2.4-- > Loading pixel data > TR=2500.00, TE=30.00, TI=0.00, flip angle=90.00 > i_ras = (-1, 0, 0) > j_ras = (0, -0.974123, -0.226021) > k_ras = (nan, nan, nan) > Reslicing using trilinear interpolation > MRIresample(): error inverting matrix; determinant is nan, matrix is: > -3.750 0.000 nan nan; > 0.000 -3.653 nan nan; > 0.000 -0.848 nan nan; > 0.000 0.000 0.000 1.000; > > Please suggest the possible reason for the error. Thanks a lot! > > Helen > > > On Jul 3, 2012, at 11:55 AM, Bruce Fischl wrote: > >> Hi Brianna >> >> If the white surface is correct and you can't get watershed/graph cuts to do >> any better, it may be that erasing voxels from the brainmask or >> brain.finalsurfs is your only option. If you had multi-echo MPRAGE you might >> be able to get rid of it also. >> >> sorry, >> Bruce >> On Tue, 3 Jul 2012, Kolody, Brianna wrote: >> >>> Hi, >>> We are having problems with some of our pial surfaces extending into the >>> sagittal sinus. We are interested in cortical thickness around the >>> precuneus, etc. I attached a couple screen shots to describe. The error is >>> not repaired by adjusting watershed parameters. How do you suggest we >>> proceed? Should we erase voxels from brainmask? We are concerned since these >>> errors extend for a significant number of slices, in many subjects, and >>> include such a large amount of the sinus. >>> As a second part to this question, I am unclear on how cortical thickness is >>> calculated and whether the statistics are directly derived from the visible >>> surfaces. For instance, when there is an error with the cortical surface >>> image including the sagittal sinus, it also visibly appears as an error in >>> aseg and aparc. However, the mistaken area doesn't have an associated region >>> label in aseg or aparc when we move the cursor over it. Are the cortical >>> thickness statistics reflected by the parcellation, which possibly does not >>> include the sinus, or the surfaces, which do seem to include the sinus? >>> Brianna >>> >>> ____________________________________________________________________________ >>> The materials in this message are private and may contain Protected >>> Healthcare Information or other information of a sensitive nature. If you >>> are not the intended recipient, be advised that any unauthorized use, >>> disclosure, copying or the taking of any action in reliance on the contents >>> of this information is strictly prohibited. If you have received this email >>> in error, please immediately notify the sender via telephone or return mail. >> _______________________________________________ >> Freesurfer mailing list >> [email protected] >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > _______________________________________________ > Freesurfer mailing list > [email protected] > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > -- Douglas N. Greve, Ph.D. MGH-NMR Center [email protected] Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html _______________________________________________ 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.
