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help > the necessary qualifications of conn v13
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Dec 4, 2011 01:12 PM | yan hongjie
the necessary qualifications of conn v13
Hello export,
i only got the images without structural ones but only functional kinds,is that necessary about using the connv13? many choices i was puzzled.my teacher asked me to use default T1.nii as standard of structural images.But i tried and feild.Also what is the system volume information? or i can not do the analysis by ROI-ROI or Seed-to-voxel or voxel-to-voxel?
thank you very much.
one basic question: the differences between “subject” and “session”？
waiting for your reply.
thanks again.
i only got the images without structural ones but only functional kinds,is that necessary about using the connv13? many choices i was puzzled.my teacher asked me to use default T1.nii as standard of structural images.But i tried and feild.Also what is the system volume information? or i can not do the analysis by ROI-ROI or Seed-to-voxel or voxel-to-voxel?
thank you very much.
one basic question: the differences between “subject” and “session”？
waiting for your reply.
thanks again.
Dec 6, 2011 01:12 AM | Alfonso Nieto-Castanon - Boston University
RE: the necessary qualifications of conn v13
Hello Yan Hongjie,
If you do not have structural images of your subjects that is fine, in this case you should simply:
a) enter the default T1.nii as 'structural' volumes for all of your subjects
and b) use SPM to segment the first EPI volume of each subject and enter the resulting gray/white/csf masks (files named c1/c2/c3*.img) in the 'ROIs' tab (as gray matter, white matter, and CSF ROIs, respectively)
The default structural volume will then only be used for display purposes (so your individual-subject results will be displayed on top of the default template, instead of each subject's anatomical volume). The gray/white/CSF areas are used to extract a basis of potential 'noise' effects on the BOLD timeseries. These masks are typically defined from the anatomical volumes of each subject (since they typically have better spatial resolution), but it is also perfectly fine to define these masks from the functional volumes instead. You should be able to perform all forms of functional connectivity analyses in the toolbox (seed-to-voxel, ROI-to-ROI, voxel-to-voxel), even if you do not have any structural volumes for your subjects.
And regarding your question about 'subjects' and 'sessions', I am not sure I understand correctly your question. Typically 'subjects' refers to each subject/person scanned in your experiment, where each subject might have been scanned in one or multiple ocassions (these are referred to as 'sessions' or 'runs', interchangably).
Hope this helps
Best
Alfonso
Originally posted by yan hongjie:
If you do not have structural images of your subjects that is fine, in this case you should simply:
a) enter the default T1.nii as 'structural' volumes for all of your subjects
and b) use SPM to segment the first EPI volume of each subject and enter the resulting gray/white/csf masks (files named c1/c2/c3*.img) in the 'ROIs' tab (as gray matter, white matter, and CSF ROIs, respectively)
The default structural volume will then only be used for display purposes (so your individual-subject results will be displayed on top of the default template, instead of each subject's anatomical volume). The gray/white/CSF areas are used to extract a basis of potential 'noise' effects on the BOLD timeseries. These masks are typically defined from the anatomical volumes of each subject (since they typically have better spatial resolution), but it is also perfectly fine to define these masks from the functional volumes instead. You should be able to perform all forms of functional connectivity analyses in the toolbox (seed-to-voxel, ROI-to-ROI, voxel-to-voxel), even if you do not have any structural volumes for your subjects.
And regarding your question about 'subjects' and 'sessions', I am not sure I understand correctly your question. Typically 'subjects' refers to each subject/person scanned in your experiment, where each subject might have been scanned in one or multiple ocassions (these are referred to as 'sessions' or 'runs', interchangably).
Hope this helps
Best
Alfonso
Originally posted by yan hongjie:
Hello export,
i only got the images without structural ones but only functional kinds,is that necessary about using the connv13? many choices i was puzzled.my teacher asked me to use default T1.nii as standard of structural images.But i tried and feild.Also what is the system volume information? or i can not do the analysis by ROI-ROI or Seed-to-voxel or voxel-to-voxel?
thank you very much.
one basic question: the differences between “subject” and “session”？
waiting for your reply.
thanks again.
i only got the images without structural ones but only functional kinds,is that necessary about using the connv13? many choices i was puzzled.my teacher asked me to use default T1.nii as standard of structural images.But i tried and feild.Also what is the system volume information? or i can not do the analysis by ROI-ROI or Seed-to-voxel or voxel-to-voxel?
thank you very much.
one basic question: the differences between “subject” and “session”？
waiting for your reply.
thanks again.
Dec 16, 2011 07:12 AM | yan hongjie
thank you very much ,but other new problems
Dear export Alfonso,
Thank you very much for the
excellent answers , which really solved my emergency problems.i did
operate as you said, finally step by step get through .But there
are someting appearing then :
the first-level analyses warning
CONN: RUNNING PREPROCESSING STEP
??? 警告: 構造体フィールドの割り当てはクラス "cell" の値を上書きします。
詳細については MATLAB 7.0.4 Release Notes, Assigning Nonstructure Variables As Structures Displays Warning を参照してください。
> In conn_process at 883
In conn_process at 13
In conn at 1283
In conn_menumanager at 116
CONN: RUNNING PREPROCESSING STEP
??? 警告: 構造体フィールドの割り当てはクラス "cell" の値を上書きします。
詳細については MATLAB 7.0.4 Release Notes, Assigning Nonstructure Variables As Structures Displays Warning を参照してください。
> In conn_process at 883
In conn_process at 13
In conn at 1283
In conn_menumanager at 116
i am very sorry that i am also puzzled
in JAPANESE , because my teacher only has japanese edition matlab.i
do not know how to change language.So this time the warning comes
out, maybe because of my lack of structural image and use the
default T1 instead? By the way , i did segment on EPI.nii of each
subject , then
CONN: RUNNING PREPROCESSING
STEP
??? 警告: 構造体フィールドの割り当てはクラス "cell" の値を上書きします。
詳細については MATLAB 7.0.4 Release Notes, Assigning Nonstructure Variables As Structures Displays Warning を参照してください。
> In conn_process at 883
In conn_process at 13
In conn at 1283
In conn_menumanager at 116
'gui_setup_save'
??? 警告: 構造体フィールドの割り当てはクラス "cell" の値を上書きします。
詳細については MATLAB 7.0.4 Release Notes, Assigning Nonstructure Variables As Structures Displays Warning を参照してください。
> In conn_process at 883
In conn_process at 13
In conn at 1283
In conn_menumanager at 116
'gui_setup_save'
'save' [1x52 char]
'gui_preproc'
'gui_setup_save'
'save' [1x52 char]
i
finished the basic preparing ,but my teacher here said that the EPI
image i chose is not standard.I chose very swa0011.nii of each
group, i am not sure it is right or not? then follow my teacher
advice , i use the default C1T1, C2T1,C3T1 .the images looked
different ,after that all the things goes well except the warning
.So does that will affect the result of my experiment? Thanks again
.waiting for your reply.
Best
wishes for you ,
Yours
sincerely,
Yan
Hongjie