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
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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 Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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 Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
freesurfer@nmr.mgh.harvard.edu
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Bruce Fischl -
Chen, Xiaoyan -
Douglas N Greve -
Kolody, Brianna