Dear Bruce:
1).I am planning to do a GLM group comparison of FA/DTI data, using dtrecon. I checked all the recon-all results and I found that there is a small amount of scalp left for one subject (it appears only on 3 slices). I wonder if this small amount will affect my subject registration and if I should remove it or if I can continue my data analysis with this small amount of scalp left only for this subject (it shows only on few slices). Please see the attached image.
2). Is there a way to download the cvs template? Why this is called cvs_avg35? Does this mean that the age avg is 35 or what exactly means 35?
Many thanks, Antonella
1) As long as the remaining skull/scalp is not distorting the surfaces then it should not cause any problems with your analysis. Based on the snapshot you sent it looks fine, although be sure to check the entire volume of that subject.
2)The cvs_avg35 template should be located here: $FREESURFER_HOME/subjects/cvs_avg35 Not sure about the name.
-Louis
On Fri, 25 Nov 2011, Antonella Kis wrote:
Dear Bruce:
1).I am planning to do a GLM group comparison of FA/DTI data, using dtrecon. I checked all the recon-all results and I found that there is a small amount of scalp left for one subject (it appears only on 3 slices). I wonder if this small amount will affect my subject registration and if I should remove it or if I can continue my data analysis with this small amount of scalp left only for this subject (it shows only on few slices). Please see the attached image.
2). Is there a way to download the cvs template? Why this is called cvs_avg35? Does this mean that the age avg is 35 or what exactly means 35?
Many thanks, Antonella
2) The name suggests that the avg was created from 35 subjects.
Lilla
On Fri, 25 Nov 2011, Louis Nicholas Vinke wrote:
- As long as the remaining skull/scalp is not distorting the surfaces then
it should not cause any problems with your analysis. Based on the snapshot you sent it looks fine, although be sure to check the entire volume of that subject.
2)The cvs_avg35 template should be located here: $FREESURFER_HOME/subjects/cvs_avg35 Not sure about the name.
-Louis
On Fri, 25 Nov 2011, Antonella Kis wrote:
Dear Bruce:
1).I am planning to do a GLM group comparison of FA/DTI data, using dtrecon. I checked all the recon-all results and I found that there is a small amount of scalp left for one subject (it appears only on 3 slices). I wonder if this small amount will affect my subject registration and if I should remove it or if I can continue my data analysis with this small amount of scalp left only for this subject (it shows only on few slices). Please see the attached image.
2). Is there a way to download the cvs template? Why this is called cvs_avg35? Does this mean that the age avg is 35 or what exactly means 35?
Many thanks, Antonella
Dear Lilla,
1) I will be very grateful if you let me know what data I should use for my fsgd when I run the GLM group analysis: the dti data after running the dtrecon (for example for my first control I called this directory C01_dti or the FS data after running recon-all on the structural data in this case called C01?
2) When I concatenate fa from individuals into one file using: mri_concat */fa-tal.nii --o group-fa-tal.nii how I can check if the order agrees with my fsgd?
3) When I concatenate fa from individuals into one file do I need to move all the fa-tal.nii into one directory or I can have each of the fa-tal files under different subject's directory? Aas example: C01_dti will contain the corresponding fa-tal.nii for the control 1, C02_dti will contain his corresponding fa-tal.nii, etc and all the subjects C01_dti, C02_dti,...P01_dti, P02_dti... are located into one directory called dtrecon.
I attached my fsgd file and I will appreciate if you can take a look to see if I need to change my inputs from C01,...,P01 to C01_dti,...P01_dti...
Thank you very much. Antonella
Hi Antonella,
- I will be very grateful if you let me know what data I should use for my fsgd when I run the GLM group analysis: the dti data after running the dtrecon (for example for my first control I called this directory C01_dti or the FS data after running recon-all on the
structural data in this case called C01?
Given that you are preparing your fa data for the analysis, indicated below, you will need to use the dti directories, eg.: C01_dti.
- When I concatenate fa from individuals into one file using: mri_concat */fa-tal.nii --o group-fa-tal.nii
how I can check if the order agrees with my fsgd?
You can list the files using "ls -l */fa-tal.nii" and the order that you see is the order in which they get concatenated in your output file. You need to make sure that that order agrees with the contents of your fsgd file.
- When I concatenate fa from individuals into one file do I need to move all the fa-tal.nii into one directory or I can have each of the fa-tal files under different subject's directory?
Aas example: C01_dti will contain the corresponding fa-tal.nii for the control 1, C02_dti will contain his corresponding fa-tal.nii, etc and all the subjects C01_dti, C02_dti,...P01_dti, P02_dti... are located into one directory called dtrecon.
You can have them under different subdirectories, but then your mri_concat command needs to reflect that, for example, mri_concat */dtrecon/fa-tal.nii --o group-fa-tal.nii
--Lilla
freesurfer@nmr.mgh.harvard.edu
-
Antonella Kis -
Lilla Zollei -
Louis Nicholas Vinke