[Freesurfer] how to edit the pial surface

2012-05-19 Thread 李盟 
Hi FreeSurfer Experts,

I had 2 question about the output troubleshooting.

 

1) when I used the mri_convert command, the format of the input image I 
choosed was 4D nii format, but not the original dicom format, which would 
affect the result of reconstruction?

2) When I checked the quality of output using tksurfer, I found the color 
line representing the surface (pial and white) were not along the folding 
pattern, and the distance between the two sufaces was rather short. Whether or 
not it was caused by the bad GM/WM contrast? What is the best way to deal with 
them?

 

Thanks.

 

Meng Li
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[Freesurfer] how to map the anatomical to the diffusion space

2012-05-19 Thread 李盟 
Hi FreeSurfer Experts,
Using the mri_surfcluster command, I got the labels of the significant regions 
from qdec comparisons of thickness between two groups.
The diffusion data was not processed using the dt_recon, but DTI-studio. So how 
can I map the significant regions to the individual diffusion space?
 
Thanks a lot.
Meng Li
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[Freesurfer] How to edit the pial surface

2012-05-19 Thread 李盟 
Hi professor,
The attachment is the subject after running the recon-all command. MR data were 
obtained on a 1.5T Philips Achieva Nova Dual MR  scanner. the sequence name is 
T1W.3D.FFE.SENSE and the voxel size is 0.90*0.90*1mm. how should I fix the poor 
quality surface reconstruction?
 
Thanks a lot for your help.
Meng Li


At 2012-05-19 23:10:31,Bruce Fischl fis...@nmr.mgh.harvard.edu wrote:
p.s. looks like an intensity normalization failure. Can you give us details 
of the acquisition? Sequence name, voxel resolution, etc? If you upload 
the subject I'll take a look

cheers
Bruce

On Sat, 19 May 2012, 
limengsecret wrote:

 Hi Professor,
 The image blow shows the problems which occur.
 color lines representing the surfaces (pial and white) were not along the
 folding pattern, and the distance between the two sufaces was rather short.
 How to deal with these problems?
  [IMAGE]
 Thanks.
  
 Meng Li
  
 
 
 limengsecret
  
 From: Bruce Fischl
 Date: 2012-05-19 22:08
 To: ??
 CC: freesurfer
 Subject: Re: [Freesurfer] how to edit the pial surface
 Hi Meng
  
 1. Not positive  I understand, but I don't think it should matter.
  
 2. we'll need to see some data to diagnose this.
  
 cheers
 Bruce
  
  
 On Sat, 19 May 2012, ?? wrote:
  
  
  Hi FreeSurfer Experts,
  
  I had 2 question about the output troubleshooting.
  
  ?
  
  1)?? when I used the mri_convert command, the format of the input image I
  choosed was 4D nii format, but not the original dicom format, which would
  affect the result of reconstruction?
  
  2)?? When I checked the quality of output using tksurfer, I found the
  color line representing the surface (pial and white) were not along the
  folding pattern, and the distance between the two sufaces was rather shor
 t.
  Whether or not it was caused by the bad GM/WM contrast? What is the best
?? ?way
  to deal with them?
  
  ?
  
  Thanks.
  
  ?
  
  Meng Li
  
  
  
  
 
  
  
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 rror
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 perly
 dispose of the e-mail.
  
 



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