Doug,

thank you very much. I tried with --ctab-out my timecourse data and annot has different dimention and I got this message.

ERROR: dimension mismatch between input volume and seg input 96 32 96 seg 119778 1 1

Then I tried this to get the same dimension, mri_label2vol --label ./ROI.label --temp ./filtered_func_data.nii --reg reg.dat --fillthresh 0.5 --o ./ROI_func.mgz

mri_segstats --i ./filtered_func_data.nii --seg ROI_func.mgz --avgwf output

I got the output which contains 2 columns. the second one seems to be timecourese but I am not quite sure it is correct or not. and also I dont know what is the first column.

will you tell me about the output ? thank you very much.

YUMI

You have specified two segmentations (an annotation and a segmentation). Just use one (probably the annot). There will be a column for each label in the annot. Use the --ctab-out to get a color table that indicates which column belongs to which region. doug

YUMI MAEDA wrote:

...

HI, I am trying to get timecourse from each subject within a ROI with GUI as follows, in tksurfer GUI, Tools > timecourse > Write summary of marked vetices/label,

I would like to do it command line, would you tell me what line I can use?

I tried to use mri_segstats --i ./filtered_func_data.nii --subject subj1 --sum ./test_summary --avgwf test_output --annot subj1 aparc lh --seg ./testaseg-in-func.img

the output has 7 columns and does not seems to be timecourse and also it is different from the one that I get when I use GUI as I described above.

thank you very much. YUMI _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html

when I want to get the timecourse from vertex number, what is the option name can I use?

YUMI

Yes, that is correct. You can have it produce one time course with --id

1

doug

YUMI MAEDA wrote:

...

Doug, thank you very much. I tried with --ctab-out my timecourse data and annot has different dimention and I got this

message.

...

ERROR: dimension mismatch between input volume and seg input 96 32 96 seg 119778 1 1 Then I tried this to get the same dimension, mri_label2vol --label ./ROI.label --temp ./filtered_func_data.nii --reg

reg.dat --fillthresh 0.5 --o ./ROI_func.mgz

...

mri_segstats --i ./filtered_func_data.nii --seg ROI_func.mgz --avgwf

output

...

I got the output which contains 2 columns. the second one seems to be

timecourese but I am not quite sure it is correct or not. and also I dont

...

know what is the first column. will you tell me about the output ? thank you very much. YUMI

...

You have specified two segmentations (an annotation and a segmentation). Just use one (probably the annot). There will be a column for each label in the annot. Use the --ctab-out to get a color table that indicates

which column belongs to which region.

...

...

doug YUMI MAEDA wrote:

...

HI, I am trying to get timecourse from each subject within a ROI with GUI as follows, in tksurfer GUI, Tools > timecourse > Write summary of marked vetices/label, I would like to do it command line, would you tell me what line I can

use?

...

...

...

I tried to use mri_segstats --i ./filtered_func_data.nii --subject subj1 --sum ./test_summary --avgwf test_output --annot subj1 aparc lh --seg ./testaseg-in-func.img the

output has 7 columns and does not seems to be timecourse and also it

...

...

...

is different from the one that I get when I use GUI as I described

above.

...

...

...

thank you very much. YUMI _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html

---

Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html

Dear All,

When I designed the  matrix consisted of two discrete groups, (patients vs. controls), I choose age as a covariate so during my analysis I was  lookingif there is a difference in the  cortical thickness within patients versus controls while accounting for age. Should I change my FSGD in order to be able to compare between patients and controls accounting for age (I want to make sure that the age does not confound my results). Please see attached my FSGD file.

Also, my question is how the clusters are created: the clusters formation is due to a  similar value within cortical thickness(cortical thickness with similar values from patients and controls are grouped together in a cluster (e.g. cluster no.1) while other cortical thickness values are forming different clusters) or the clusters are formed based on age -age grouping (each subject belong to an age cluster)?

Thank you, AK

Dear All,

What should be my contrast vector if I want to do a direct comparison between groups (patients vs. controls) after eliminating gender and age? Should this be [1 -1]?

Should I change my FSGD in order to be able to compare between patients and controls accounting for age (I want to make sure that the age does not confound my results). Please see attached my FSGD file.

Also, my question is how the clusters are created: the clusters formation is due to a  similar value within cortical thickness(cortical thickness with similar values from patients and controls are grouped together in a cluster (e.g. cluster no.1) while other cortical thickness values are forming different clusters) or the clusters are formed based on age -age grouping (each subject belong to an age cluster)?

Thank you, AK

you're fsgd includes age, so it should account for differences in age in your groups

The cluster formation does not use any information about the thickness or age directly. It strictly uses the voxel-wise p-values. doug

Antonella Kis wrote:

Dear All,

When I designed the matrix consisted of two discrete groups, (patients vs. controls), I choose age as a covariate so during my analysis I was lookingif there is a difference in the cortical thickness within patients versus controls while accounting for age. Should I change my FSGD in order to be able to compare between patients and controls accounting for age (I want to make sure that the age does not confound my results). Please see attached my FSGD file.

Also, my question is how the clusters are created: the clusters formation is due to a similar value within cortical thickness(cortical thickness with similar values from patients and controls are grouped together in a cluster (e.g. cluster no.1) while other cortical thickness values are forming different clusters) or the clusters are formed based on age -age grouping (each subject belong to an age cluster)?

Thank you, AK