Hi Bruce, I Have sent the raw data to you and I find if it is the problem of tksurfer Installing? Can it result in the problem? How can I Fix it?
Thanks, Xiaojun.
-------- 原始消息 -------- 主题: Re: [Freesurfer] Fwd: Re: Fwd: Some problems of the brain image after recon-all 日期: Tue, 10 Dec 2013 08:22:36 -0500 (EST) 发件人: Bruce Fischl fischl@nmr.mgh.harvard.edu 收件人: Xiaojun.Huang lvdosha@gmail.com
yes, or the whole subject dir so I can diagnose what went wrong
cheers Bruce On Tue, 10 Dec 2013, Xiaojun.Huang wrote:
Hi Bruce, I wonder if I need to upload the 3d raw data to you, If you need them. Best, Huang. 于 2013/12/7 0:12, Bruce Fischl 写道:
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 >
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.
sorry, I don't think I got it. How did you send it? On Fri, 13 Dec 2013, Xiaojun.Huang wrote:
Hi Bruce, I Have sent the raw data to you and I find if it is the problem of tksurfer Installing? Can it result in the problem? How can I Fix it?
Thanks, Xiaojun.
-------- 原始消息 -------- 主题: Re: [Freesurfer] Fwd: Re: Fwd: Some problems of the brain image after recon-all 日期: Tue, 10 Dec 2013 08:22:36 -0500 (EST) 发件人: Bruce Fischl fischl@nmr.mgh.harvard.edu 收件人: Xiaojun.Huang lvdosha@gmail.com
yes, or the whole subject dir so I can diagnose what went wrong
cheers Bruce On Tue, 10 Dec 2013, Xiaojun.Huang wrote:
Hi Bruce, I wonder if I need to upload the 3d raw data to you, If you need them. Best, Huang. 于 2013/12/7 0:12, Bruce Fischl 写道:
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 3
D
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 a
s
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
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