hi all,
I am processing the 3D PD patients brain now . After recon-all running, the segmentations of the GM and WM is not accurate although the original data is normal. additionally, when I use the TKSurfer Tools to review the 3D brain,it is reverse.
More informations and images as follows:
-------- 原始消息 -------- 主题: Re: [Freesurfer] Fwd: Some problems of the brain image after recon-all 日期: Thu, 05 Dec 2013 12:45:10 +0800 发件人: Xiaojun.Huang lvdosha@gmail.com 收件人: Bruce Fischl fischl@nmr.mgh.harvard.edu
Hi Bruce, Sorry for reply late. The data were provided by a hospital and the input data were 3D images.Some image informations as followed(eg.PDSub_02):
0008,103E,Series Description=Ax 3D VBM 0008,1090,Manufacturer's Model Name=SIGNA EXCITE 0018,0000,Acquisition Group Length=484 0018,0020,Scanning Sequence=GR 0018,0021,Sequence Variant=SS\SP\SK 0018,0022,Scan Options=FAST.GEMS\EDR.GEMS\FILTERED.GEMS 0018,0023,MR Acquisition Type=3D 0018,0025,Angio Flag=N 0018,0050,Slice Thickness=1 0018,0080,Repetition Time [TR, ms]=7.652 0018,0081,Echo Time [TE, ms]=3.312 0018,0082,Inversion Time=0 0018,0083,Number of Averages=1 0018,0084,Imaging Frequency=127.755675 0018,0085,Imaged Nucleus=1H 0018,0086,Echo Number= 0018,0087,Magnetic Field Strength=3 0018,0088,Spacing Between Slices=1 0018,0091,Echo Train Length=1 0018,0093,Percent Sampling=100 0018,0094,Percent Phase Field View=100 0018,0095,Pixel Bandwidth=97.6562 0018,1020,Software Version=12\LX\MR Software release.12.0.M5A.0819.a 0018,1030,Protocol Name=PDD-YANGWANQUN/4 0018,1310,Acquisition Matrix=0, 256, 228, 0 0018,1312,Phase Encoding Direction=ROW 0018,1314,Flip Angle=13 0018,1315,Variable Flip Angle Flag=N 0028,0010,Rows=512 0028,0011,Columns=512
It comes up in the proper orientation in tkmedit in three orientations as attachment(eg.coromaland saggital view).
Tanks, Xiaojun.
于 2013/12/4 22:45, Bruce Fischl 写道:
Hi Xiaojun
we need more details in order to help you. What was your input data? What format was it in? Does it come up in the proper orientation in tkmedit? What kind of acquisition (resolution, type, etc...) did you use?
cheers Bruce On Wed, 4 Dec 2013, Xiaojun.Huang wrote:
-------- 原始消息 -------- 主题: Some problems of the brain image after recon-all 日期: Tue, 03 Dec 2013 21:33:41 +0800 发件人: Xiaojun.Huang lvdosha@gmail.com 收件人: Freesurfer@nmr.mgh.harvard.edu
Hi,
I am processing the 3D PD patients brain now . After recon-all running, the segmentations of the GM and WM is not accurate although the original data is normal. additionally, when I use the TKSurfer Tools to review the 3D brain,it is reverse. (eg. PDSub_02 in the attach files)
It is the first time for me to use Freesurfer.I'm sorry for the trouble I'm giving you.And looking forward your reply.
Thanks, Xiaojun
2013.12.3
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.
it comes up upside down in tksurfer without pressing any buttons or anything? Never seen that before - if you upload the subject I'll take a look
cheers Bruce On Fri, 6 Dec 2013, Xiaojun.Huang wrote:
hi all,
I am processing the 3D PD patients brain now . After recon-all running, the segmentations of the GM and WM is not accurate although the original dat a is normal. additionally, when I use the TKSurfer Tools to review the 3D brain,it is rev erse. More informations and images as follows:
-------- 原始消息 -------- 主题: Re: [Freesurfer] Fwd: Some problems of the brain image after recon-all 日期: Thu, 05 Dec 2013 12:45:10 +0800 发件人: Xiaojun.Huang lvdosha@gmail.com 收件人: Bruce Fischl fischl@nmr.mgh.harvard.edu
Hi Bruce, Sorry for reply late. The data were provided by a hospital and the input data were 3D images.Some image informations as followed(eg.PDSub_02):
0008,103E,Series Description=Ax 3D VBM 0008,1090,Manufacturer's Model Name=SIGNA EXCITE 0018,0000,Acquisition Group Length=484 0018,0020,Scanning Sequence=GR 0018,0021,Sequence Variant=SS\SP\SK 0018,0022,Scan Options=FAST.GEMS\EDR.GEMS\FILTERED.GEMS 0018,0023,MR Acquisition Type=3D 0018,0025,Angio Flag=N 0018,0050,Slice Thickness=1 0018,0080,Repetition Time [TR, ms]=7.652 0018,0081,Echo Time [TE, ms]=3.312 0018,0082,Inversion Time=0 0018,0083,Number of Averages=1 0018,0084,Imaging Frequency=127.755675 0018,0085,Imaged Nucleus=1H 0018,0086,Echo Number= 0018,0087,Magnetic Field Strength=3 0018,0088,Spacing Between Slices=1 0018,0091,Echo Train Length=1 0018,0093,Percent Sampling=100 0018,0094,Percent Phase Field View=100 0018,0095,Pixel Bandwidth=97.6562 0018,1020,Software Version=12\LX\MR Software release.12.0.M5A.0819.a 0018,1030,Protocol Name=PDD-YANGWANQUN/4 0018,1310,Acquisition Matrix=0, 256, 228, 0 0018,1312,Phase Encoding Direction=ROW 0018,1314,Flip Angle=13 0018,1315,Variable Flip Angle Flag=N 0028,0010,Rows=512 0028,0011,Columns=512
It comes up in the proper orientation in tkmedit in three orientations as attachment(eg.coromaland saggital view).
Tanks, Xiaojun.
于 2013/12/4 22:45, Bruce Fischl 写道:
Hi Xiaojun
we need more details in order to help you. What was your input data? What format was it in? Does it come up in the proper orientation in tkmedit? What kind of acquisition (resolution, type, etc...) did you use?
cheers Bruce On Wed, 4 Dec 2013, Xiaojun.Huang wrote:
-------- 原始消息 -------- 主题: Some problems of the brain image after recon-all 日期: Tue, 03 Dec 2013 21:33:41 +0800 发件人: Xiaojun.Huang lvdosha@gmail.com 收件人: Freesurfer@nmr.mgh.harvard.edu
Hi,
I am processing the 3D PD patients brain now . After recon-all running, the segmentations of the GM and WM is not accurate although the original data is normal. additionally, when I use the TKSurfer Tools to review the 3D brain,it is reverse. (eg. PDSub_02 in the attach files)
It is the first time for me to use Freesurfer.I'm sorry for the trouble I'm giving you.And looking forward your reply.
Thanks, Xiaojun
2013.12.3
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
-
Bruce Fischl -
Xiaojun.Huang