Hi,
I am hoping do a surface-based functional ROI analysis on subject-specific ROIs that are both defined structurally and are masked by an all/nothing functional contrast. func2roi-sess seems perfect for this except that my data are not in an FS-FAST data/analysis structure, but are instead pre-processed and preliminarily analyzed using FSL and mapped to the surface using reg-feat2anat.
Is there any way to pass my original analysis into func2roi-sess? I tried using:
func2roi-sess -roidef LH_ant_STG_soundthresh2 -analysis 1012_Run4_featFULLrev.feat/stats/zstat4.nii.gz -anatlabel lh_ant_STG -maskcontrast 1012_Run4_featFULLrev/stats/zstat16.nii.gz -maskthreshold 2 -s 1012 -d
but get "ERROR: cannot find any sessions."
Or is there another tool more appropriate for what I am trying to do? I am looking at mri_segstats, but my hand-drawn ROIs (drawn on fsaverage in tksurfer and morphed to each subject using label_2_label) are in .label format and are on the surface.
Thanks in advance for and advice or suggestions.
Susan McLaughlin Doctoral Candidate SPACE Lab (Stimulus-Parametric Imaging of Auditory Cortex) Dept. of Speech and Hearing Sciences University of Washington
Hi Susan, you can't use func2roi-sess. You'll have to put together some commands, but it should not be too hard, something like
mri_segstats --i lh.cope2.nii --slabel subjectname lh your.label --mask lh.zstat1.nii --maskthresh 2 --masksign abs --o sum.dat
where zstat1 is your all/nothing contrast sampled onto the surface and cope2 is some other contrast sampled on the surface. You can do this for each subject, then run asegstats2table giving it paths to all of your sum.dat files
doug
On 11/26/2012 07:01 PM, Susan Alice McLaughlin wrote:
Hi,
I am hoping do a surface-based functional ROI analysis on subject-specific ROIs that are both defined structurally and are masked by an all/nothing functional contrast. func2roi-sess seems perfect for this except that my data are not in an FS-FAST data/analysis structure, but are instead pre-processed and preliminarily analyzed using FSL and mapped to the surface using reg-feat2anat.
Is there any way to pass my original analysis into func2roi-sess? I tried using:
func2roi-sess -roidef LH_ant_STG_soundthresh2 -analysis 1012_Run4_featFULLrev.feat/stats/zstat4.nii.gz -anatlabel lh_ant_STG -maskcontrast 1012_Run4_featFULLrev/stats/zstat16.nii.gz -maskthreshold 2 -s 1012 -d
but get "ERROR: cannot find any sessions."
Or is there another tool more appropriate for what I am trying to do? I am looking at mri_segstats, but my hand-drawn ROIs (drawn on fsaverage in tksurfer and morphed to each subject using label_2_label) are in .label format and are on the surface.
Thanks in advance for and advice or suggestions.
Susan McLaughlin Doctoral Candidate SPACE Lab (Stimulus-Parametric Imaging of Auditory Cortex) Dept. of Speech and Hearing Sciences University of Washington
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Hi all,
I would need some information about the local gyrification index. I run the analyses and found which are the average indices for subject and hemisphere.
1. Is there a method to perform vertex-wise group statistics? that is may I compare maps of gyrification across groups?
2. Is there a method to obtain average gyrification for a single label of the atlas? For example gyrification of superior frontal gyrus. I understand that sulci are often used to find the delimitation of a gyrus or a brain area, and probably this is a problem.
3. Are there any other method to measure the presence or the depth of a sulcus. We are analysing a group of subjects with a genetic illness. They often lack a sulcus in the orbitofrontal area. Is there a method to quantify this using freesurfer?
thank you for your help
best wishes
Angela
Hi all, I found answers to ponts 1 and 2 in the webpage. Sorry for my question....
Angela
Hi all,
I would need some information about the local gyrification index. I run the analyses and found which are the average indices for subject and hemisphere.
- Is there a method to perform vertex-wise group statistics? that is may
I compare maps of gyrification across groups?
- Is there a method to obtain average gyrification for a single label of
the atlas? For example gyrification of superior frontal gyrus. I understand that sulci are often used to find the delimitation of a gyrus or a brain area, and probably this is a problem.
- Are there any other method to measure the presence or the depth of a
sulcus. We are analysing a group of subjects with a genetic illness. They often lack a sulcus in the orbitofrontal area. Is there a method to quantify this using freesurfer?
thank you for your help
best wishes
Angela
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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Hi Angela, Marie is the best one to answer the questions about gyrification, but I've tried below doug
On 11/28/2012 11:30 AM, angela.favaro@unipd.it wrote:
Hi all,
I would need some information about the local gyrification index. I run the analyses and found which are the average indices for subject and hemisphere.
- Is there a method to perform vertex-wise group statistics? that is may
I compare maps of gyrification across groups?
You should be able to use mris_preproc and mri_glmfit similar to doing a thickness analysis.
- Is there a method to obtain average gyrification for a single label of
the atlas? For example gyrification of superior frontal gyrus. I understand that sulci are often used to find the delimitation of a gyrus or a brain area, and probably this is a problem.
You should be able to run mris_anatomical_stats or mri_segstats to give you summaries over the annotation ROIs.
- Are there any other method to measure the presence or the depth of a
sulcus. We are analysing a group of subjects with a genetic illness. They often lack a sulcus in the orbitofrontal area. Is there a method to quantify this using freesurfer?
You can try doing a group analysis using ?h.curv or ?h.sulc (instead of ?h.thickness). doug
thank you for your help
best wishes
Angela
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
freesurfer@nmr.mgh.harvard.edu
-
angela.favaro＠unipd.it -
Douglas N Greve -
Susan Alice McLaughlin