[color=#000000]me?
[/color][i]Originally posted by Mohammad Iyas Kawas:[/i][quote]Thank you Alfonso,
I am using the Mayo clinic adult life span template and atlas.
I use the default preprocessing pipeline and when I am prompted with the (Segment/normalize/resample settings) window I specify the the TPM file for the mayo clinic template.
And in setup>ROI I use the corresponding atlas too (an 122 ROI modified AAL atlas that is coregistered the template.)
In Setup>Options I also Use the (GM+WM) Brain mask created from and provided with the template as my explicit analysis mask.
And when I reach the 2nd level analysis display I specify the reference T1 for this template also and then I specify the Atlas too.
All the files (TPM, T1, Atlas, and mask are co-registered) and I download them as such.
NOTE: I did one thing that seems to have corrected the labeling issue in the GUI's display, which is I modified the .txt file associated with my atlas as it started the first line with a 0_unknown and then started listing the ROI's starting from the second line 1_precentral,....... (as you can see in the attached image). I changed the .txt file for the atlas to be very similar to the .txt file of the default conn atlas. (this fixed the display, but I didn't rerun the Setup or rerun the analysis as the for ROI to ROI analysis CONN seems to have generated the seeds correctly from the Atlas file. Do you think I need to rerun the Setup and analysis?)
Also, I understand from you that if the analysis Mask has different dimensions but is properly co-registered to the TPM file CONN will handle it correctly ?
Hope this is correct and that the analysis is not affected by these issues.
Many thanks,
Mohammad Kawas[/quote][quote]Hello Mohammad Kawas[/quote][quote]I have the same problem. I am using the pediatric template.[/quote][quote]I used the default preprocessing pipeline and in the (Segment/normalize/resample settings) window I specified the the TPM.nii file for the pediatric template. I have noticed that dimensions of the functional Nifti files after pre-processing are (91,109,91) but the dimensions of my template are (197,233,189), Also the dimensions of the warped structural images (wWM,wCSF,wGM) are different with my template.[/quote][quote]I didn't understand is it a problem or not? What should I do?[/quote][quote]Would you please advise me?[/quote][quote]Thanks in advance,[/quote][quote]Hengameh
[/quote]
[/color][i]Originally posted by Mohammad Iyas Kawas:[/i][quote]Thank you Alfonso,
I am using the Mayo clinic adult life span template and atlas.
I use the default preprocessing pipeline and when I am prompted with the (Segment/normalize/resample settings) window I specify the the TPM file for the mayo clinic template.
And in setup>ROI I use the corresponding atlas too (an 122 ROI modified AAL atlas that is coregistered the template.)
In Setup>Options I also Use the (GM+WM) Brain mask created from and provided with the template as my explicit analysis mask.
And when I reach the 2nd level analysis display I specify the reference T1 for this template also and then I specify the Atlas too.
All the files (TPM, T1, Atlas, and mask are co-registered) and I download them as such.
NOTE: I did one thing that seems to have corrected the labeling issue in the GUI's display, which is I modified the .txt file associated with my atlas as it started the first line with a 0_unknown and then started listing the ROI's starting from the second line 1_precentral,....... (as you can see in the attached image). I changed the .txt file for the atlas to be very similar to the .txt file of the default conn atlas. (this fixed the display, but I didn't rerun the Setup or rerun the analysis as the for ROI to ROI analysis CONN seems to have generated the seeds correctly from the Atlas file. Do you think I need to rerun the Setup and analysis?)
Also, I understand from you that if the analysis Mask has different dimensions but is properly co-registered to the TPM file CONN will handle it correctly ?
Hope this is correct and that the analysis is not affected by these issues.
Many thanks,
Mohammad Kawas[/quote][quote]Hello Mohammad Kawas[/quote][quote]I have the same problem. I am using the pediatric template.[/quote][quote]I used the default preprocessing pipeline and in the (Segment/normalize/resample settings) window I specified the the TPM.nii file for the pediatric template. I have noticed that dimensions of the functional Nifti files after pre-processing are (91,109,91) but the dimensions of my template are (197,233,189), Also the dimensions of the warped structural images (wWM,wCSF,wGM) are different with my template.[/quote][quote]I didn't understand is it a problem or not? What should I do?[/quote][quote]Would you please advise me?[/quote][quote]Thanks in advance,[/quote][quote]Hengameh
[/quote]