[Freesurfer] conjunction analysis stats

[Maria Czarnecka]

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Dear Sisters and Brothers in neuroscience,

I have a problem with conjunction analysis. I do my analysis using:
*mri_concat --i con1/sig.nii.gz --i con2/sig.nii.gz --min --o con.nii.gz*

I get a nice map, there are clusters. What about the multiple comparison
correction? Maybe I should do the conjunction on the already corrected maps?

I would also like to get the cluster table for this conjunction. I
tried: mri_surfcluster
and it gives me Found 0 clusters and does not save anything.

I will be grateful if you help me find the problem.
Kind regards,
Maria Czarnecka
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[Freesurfer] Cluster summary table

[Maria Czarnecka]

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Dear Experts,

I calculated a conjunction using "mri_concat". I have a beautiful map but I
need a cluster summary table for it. How can I get that?

Best,
Maria Czarnecka
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Re: [Freesurfer] mris_label2annot

[Maria Czarnecka]

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Dear Yujing,

Thank you so much for your answer. Everything works now.

Best,
Maria Czarnecka

pt., 30 cze 2023 o 16:59 Maria Czarnecka  napisał(a):

> Dear Yujing,
>
> Thank you so much for your answer.
> My ctab looks like this:
>
> 11100  Unknown   0   0   00
> 11102  G_and_S_occipital_inf 0   0   00
> 1  G_cuneus  0   0   00
> 9  G_occipital_middle  221  60  600
> 11120  G_occipital_sup   0   0   00
> 11121  G_oc-temp_lat-fusifor 0   0   00
> 11122  G_oc-temp_med-Lingual 0   0   00
> 11130  G_precuneus   0   0   00
> 11143  Pole_occipital  221  60  600
> 11145  S_calcarine 221  60  600
> 11158  S_oc_middle_and_Lunatus   0   0   00
> 11160  S_occipital_ant   0   0   00
> 11161  S_oc-temp_lat20 180 1400
> 11162  S_oc-temp_med_and_Lingual 0   0   00
> 11166  S_parieto_occipital 221  60  600
>
> a sample of one of my label files:
>
> #!ascii label  , from subject fsaverage vox2ras=TkReg
> 1630
> 139  -4.532  -75.888  20.953 0.00
> 300  -15.423  -72.840  16.348 0.00
> 301  -15.452  -76.689  23.049 0.00
> 571  -15.631  -67.683  9.887 0.00
> 573  -4.258  -84.880  12.147 0.00
>
> version of FreeSurfer:
> freesurfer-linux-centos7_x86_64-7.3.2-20220804-6354275
>
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Re: [Freesurfer] mris_label2annot

[Maria Czarnecka]

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Dear Yujing,

Thank you so much for your answer.
My ctab looks like this:

11100  Unknown   0   0   00
11102  G_and_S_occipital_inf 0   0   00
1  G_cuneus  0   0   00
9  G_occipital_middle  221  60  600
11120  G_occipital_sup   0   0   00
11121  G_oc-temp_lat-fusifor 0   0   00
11122  G_oc-temp_med-Lingual 0   0   00
11130  G_precuneus   0   0   00
11143  Pole_occipital  221  60  600
11145  S_calcarine 221  60  600
11158  S_oc_middle_and_Lunatus   0   0   00
11160  S_occipital_ant   0   0   00
11161  S_oc-temp_lat20 180 1400
11162  S_oc-temp_med_and_Lingual 0   0   00
11166  S_parieto_occipital 221  60  600

a sample of one of my label files:

#!ascii label  , from subject fsaverage vox2ras=TkReg
1630
139  -4.532  -75.888  20.953 0.00
300  -15.423  -72.840  16.348 0.00
301  -15.452  -76.689  23.049 0.00
571  -15.631  -67.683  9.887 0.00
573  -4.258  -84.880  12.147 0.00

version of FreeSurfer:
freesurfer-linux-centos7_x86_64-7.3.2-20220804-6354275
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 .
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[Freesurfer] mris_label2annot

[Maria Czarnecka]

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Dear Sisters and Brothers in neuroscience,

I am trying to make my own annotation file that will include only occipital
cortex labels from the a2009s atlas. Is it possible?

I am trying to do that with:

mris_label2annot
--ctab lh.my-color-table.txt
--a my-annot-name
--h lh
--s fsaverage
--l lh.S_calcarine.label
--l lh.S_parieto_occipita.label
--l lh.G_cuneus.label
--l lh.G_oc-temp_med-Lingual.label
--l lh.S_collat_transv_post.label
--l lh.G_and_S_occipital_inf.label
--l lh.Pole_occipital.label
--l lh.G_occipital_middle.label
--l lh.S_oc_middle_and_Lunatus.label
--l lh.S_oc_sup_and_transversal.label
--l lh.G_occipital_sup.label
--l lh.S_oc-temp_med_and_Lingual.label
--l lh.G_oc-temp_lat-fusifor.label
--l lh.S_oc-temp_lat.label

If i run it i get:

0  0
 1 -1 NOT_FOUND
 2 -1 NOT_FOUND
 3 -1 NOT_FOUND
 4 -1 NOT_FOUND
 5 -1 NOT_FOUND
 6 -1 NOT_FOUND
 7 -1 NOT_FOUND
 8 -1 NOT_FOUND
 9 -1 NOT_FOUND
10 -1 NOT_FOUND
11 -1 NOT_FOUND
12 -1 NOT_FOUND
13 -1 NOT_FOUND
Writing annot to...

The file is saved and it is empty. Where is my mistake?

I will be grateful for your help,
Best,
Maria Czarnecka
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[Freesurfer] conjunction

[Maria Czarnecka]

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Dear experts,

Another question: How do I do conjunction analysis? I have my contrasts on
1lvl, I have the second level, I need a conjunction of two contrasts.

I would guess "mergecontrasts-sess", unfortunately, it doesn't seem to
work.
[image: image.png]

Could you help me with that issue?
Kind regards,
Maria Czarnecka
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[Freesurfer] fsfast percent signal change

[Maria Czarnecka]

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Dear experts,

I struggle with the functional analysis in Freesurfer. How can I calculate
the percent signal change in a specific contrast in an ROI?

I will be grateful for your suggestions (especially if you point toward a
specific function).

Kind regards,
Maria Czarnecka
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[Freesurfer] covariates in 2nd level anaysis

[Maria Czarnecka]

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Dear Sisters and Brothers in neuroscience

I am analyzing functional data in FSfast in Freesurfer. I define my
conditions in an osgm file, then I create contrasts. On the second level, I
would like to add two covariates (scanning facility and handedness). I
don't need contrasts, I just need the model to account for the variance.
Can I define both osgm and fsgd files? How do I construct the fsgd?

I will be grateful for your suggestions.

Best,

Maria Czarnecka
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[Freesurfer] cortical thickness and z-scores correlation

[Maria Czarnecka]

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Dear Sisters and Brothers in neuroscience

I am a huge fan but a very new user of the freesurfer, please treat me as
such when answering this email.

I have successfully performed anatomical and functional data analysis using
fmriprep, freesurfer and fsfast. I have all the files needed, everything
looks perfect. As a next step of my analysis I would like to perform a
correlation of Cortical thickness and the functional activation in one of
my contrasts (I would like to correlate the CT with the z-scores). I would
like to do that separately for each subject and in ROIs (ideally,
self-defined Rois, but if there is an easy way to do it in anatomical ones
I will be very happy as well). What I need is for the program to take the
z-score from each vertex in an ROI and the value of cortical thickness for
each vertex and do the correlation on those values. I can also do the
statistics in another tool (R), so simply extracting those values for
vertices in an ROIs would be great.

Do you have any suggestions how to do that?

Best,

Maria Czarnecka
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