Dear All,
I was trying to find an explanation of the color map: min, Mid, MAx and Offset values in Freeview. Can someone please explain me if I have the color map set it up as HEAT what is the meaning of this values if for example I am viewing the existing clusters after multiple comparison for the DTI data.Also can I load my FA group data registered on TAL: group-fa-tal.nii with tkmedit?
Many thanks. Antonella
They are standard parameters to linearly map a voxel value (val) into heat-scale color (c), something like this:
first apply offset: val = val + offset then:
if val <= min, c = black if min < val < mid, c = between black and red if val = mid, c = red if mid < val < max, c = between red and yellow if val >= max, c = yellow
Ruopeng
On 12/05/2011 03:05 PM, Antonella Kis wrote:
Dear All,
I was trying to find an explanation of the color map: min, Mid, MAx and Offset values in Freeview. Can someone please explain me if I have the color map set it up as HEAT what is the meaning of this values if for example I am viewing the existing clusters after multiple comparison for the DTI data.Also can I load my FA group data registered on TAL: group-fa-tal.nii with tkmedit?
Many thanks. Antonella
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Dear All,
1) On the FS Diffusion Tutorial webpage I found for the Group Analysis the following scrip: GroupAnalysis.csh with the following instruction:
# Assemble input for group analysis set type = CVS-to-avg35 # alternatively could be 'TAL-to-avg35' or 'MNI-to-avg35' Can you please explain what means TAL-to-avg35 if my DTI data (FA) is by default registered on the TAL space and I got the file fa-tal.nii? How I can get the TAL-to-avg35 template? Is this different than the one on which my data was registered by default?
2) I was trying to find an explanation for the color map: Min, Mid, Max and Offset values in Free View. Can someone please explain me if I have the color map set it up as HEAT what is the meaning of the above values if for example I am viewing the existing clusters after multiple comparison for the DTI data.
3) Can I load my FA group data registered on TAL: group-fa-tal.nii with tkmedit?
Many thanks. Antonella
Hi Antonella,
- On the FS Diffusion Tutorial webpage I found for the Group Analysis the following scrip: GroupAnalysis.csh with the following instruction:
# Assemble input for group analysis set type = CVS-to-avg35 # alternatively could be 'TAL-to-avg35' or 'MNI-to-avg35' Can you please explain what means TAL-to-avg35 if my DTI data (FA) is by default registered on the TAL space and I got the file fa-tal.nii? How I can get the TAL-to-avg35 template? Is this different than the one on which my data was registered by default?
There is probably a typo in the tutorial. It should read # alternatively could be 'TAL' or 'MNI'
You can replace the mri_cvs_registered files with any other tools output that you want to use for your final comparison.
- Can I load my FA group data registered on TAL: group-fa-tal.nii with tkmedit?
Yes, you shoud and also with Freeview.
Lilla
Dear Lilla,
Thank you very much for your directions. Sorry I have so many questions but I am new to this type of research.
I will appreciated a lot if you confirm my understanding regarding some outputs from dtrecon:
1) Is the mask.nii a mask, a binary image of the anatomical to diffusion image of the same subject?
2) Is the mask-tal.niia mask, a binary image of the diffusion image to TAL space of one subject?
3) Is the fa-tal.nii.reg the transformation from diffusion space to TAL while register.dat is the transformation from diffusion space to anatomical space?
4) If I want to check my DTI data's registration on the anatomical structure for one of my subjects I need first to get the re-sampled image of the DTI registration data so is correct if I run: mri_vol2vol --mov /media/1Tra/Antonella_2011/DTI_FS/dtrecon/C51_dti.nii.gz \ --targ /media/1Tra/Antonella_2011/DTI_FS/dtrecon/C51.nii.gz \ --reg /media/1Tra/Antonella_2011/DTI_FS/dtrecon/C51_dti/register.dat --no-save-reg \ --o /media/1Tra/Antonella_2011/DTI_FS/dtrecon/C51_dti/C51_dti-to-C51.nii.gz \ --interp trilin
such that my resampled registered image for my DTI data to the anatomical image is C51_dti_to C51.nii.gz so in order to check if the registration is good or not I can comapre the original anatomical data C51.nii.gz with the DTI data C51_dti.nii.gz and with my registered and resampled image C51_dti-to-C51.nii.gz?
Thank you very much! Antonella
________________________________ From: Lilla Zollei lzollei@nmr.mgh.harvard.edu To: Antonella Kis atorok9@yahoo.com Cc: "freesurfer@nmr.mgh.harvard.edu" freesurfer@nmr.mgh.harvard.edu Sent: Tuesday, December 6, 2011 5:01 PM Subject: Re: [Freesurfer] Diffusion Tutorial and GroupAnalysis.csh
Hi Antonella,
- On the FS Diffusion Tutorial webpage I found for the Group Analysis the following scrip: GroupAnalysis.csh with the following instruction:
# Assemble input for group analysis set type = CVS-to-avg35 # alternatively could be 'TAL-to-avg35' or 'MNI-to-avg35' Can you please explain what means TAL-to-avg35 if my DTI data (FA) is by default registered on the TAL space and I got the file fa-tal.nii? How I can get the TAL-to-avg35 template? Is this different than the one on which my data was registered by default?
There is probably a typo in the tutorial. It should read # alternatively could be 'TAL' or 'MNI'
You can replace the mri_cvs_registered files with any other tools output that you want to use for your final comparison.
- Can I load my FA group data registered on TAL: group-fa-tal.nii with tkmedit?
Yes, you shoud and also with Freeview.
Lilla
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Antonella Kis -
Lilla Zollei -
Ruopeng Wang