External Email - Use Caution
Dear experts,
I would like to show the across-subject overlap of voxels by creating a map with color coding indicating the number of subjects activating corresponding voxels. For each subject I have run the first level model in spss and saved the 1000 most activated voxels for a given contrast as an roi (binary file). Now with freesurfer I am trying to : 1) display the saved roi on the subject's surface (which has been obtained with recon all) - this step worked 2) align each subject's surface to fsaverage - this step gave me the problem 3) add all subjects together and create the map showing how many subjects activated each location
To do so I have done the following:
1) this first step worked fine and I could display the roi on my subject's surface mri_vol2surf --mov ${DATA_DIR}/sub01/vois/1000vox_IPS.nii \ --reg ${DATA_DIR}/sub01/fmri/register.dat \ --hemi rh \ --o ${DATA_DIR}/sub01/probmap/testIPS.rh.mgh \ --projfrac ${thisprojfrac}
2) this step crashed mri_surf2surf --hemi rh --s fsaverage --fwhm 3 --cortex \ --sval ${DATA_DIR}/sub01/probmap/testIPS.rh.mgh --tval ${DATA_DIR}/sub01/probmap/testIPSfs.mgh
The error is: Loading source data ERROR: dimension inconsistency in source data Number of surface vertices = 163842 Number of value vertices = 133030
Do you have any idea why?
3)Then I was planning to use fscalc and add all subjects together, is this correct?
If there is another/easier way to do the same thing, please let me know Thanks in advance for your help, Best Elisa
Hi Elisa
if you only use --s fsaverage, then mri_surf2surf assumes you are mapping within subject. If you want to map from one subject to another you need to use --srcsubject sub01 --trgsubject fsaverage
And yes, if you get that working I think fscalc should do the trick (or it would be easy to do in matlab).
cheers Bruce On Fri, 13 Jul 2018, Elisa Castaldi wrote:
External Email - Use Caution
Dear experts,
I would like to show the across-subject overlap of voxels by creating a map with color coding indicating the number of subjects activating corresponding voxels. For each subject I have run the first level model in spss and saved the 1000 most activated voxels for a given contrast as an roi (binary file). Now with freesurfer I am trying to :
- display the saved roi on the subject's surface (which has been obtained with recon all) - this
step worked 2) align each subject's surface to fsaverage - this step gave me the problem 3) add all subjects together and create the map showing how many subjects activated each location
To do so I have done the following:
- this first step worked fine and I could display the roi on my subject's surface
mri_vol2surf --mov ${DATA_DIR}/sub01/vois/1000vox_IPS.nii \ --reg ${DATA_DIR}/sub01/fmri/register.dat \ --hemi rh \ --o ${DATA_DIR}/sub01/probmap/testIPS.rh.mgh \ --projfrac ${thisprojfrac}
- this step crashed
mri_surf2surf --hemi rh --s fsaverage --fwhm 3 --cortex \ --sval ${DATA_DIR}/sub01/probmap/testIPS.rh.mgh --tval ${DATA_DIR}/sub01/probmap/testIPSfs.mgh
The error is: Loading source data ERROR: dimension inconsistency in source data Number of surface vertices = 163842 Number of value vertices = 133030
Do you have any idea why?
3)Then I was planning to use fscalc and add all subjects together, is this correct?
If there is another/easier way to do the same thing, please let me know Thanks in advance for your help, Best Elisa
You can also use mri_concat to compute the mean, eg, mri_concat file1.mgh file2.mgh ... fileN.mgh --mean --o average.mgh
On 07/13/2018 11:17 AM, Bruce Fischl wrote:
Hi Elisa
if you only use --s fsaverage, then mri_surf2surf assumes you are mapping within subject. If you want to map from one subject to another you need to use --srcsubject sub01 --trgsubject fsaverage
And yes, if you get that working I think fscalc should do the trick (or it would be easy to do in matlab).
cheers Bruce On Fri, 13 Jul 2018, Elisa Castaldi wrote:
External Email - Use Caution
Dear experts,
I would like to show the across-subject overlap of voxels by creating a map with color coding indicating the number of subjects activating corresponding voxels. For each subject I have run the first level model in spss and saved the 1000 most activated voxels for a given contrast as an roi (binary file). Now with freesurfer I am trying to :
- display the saved roi on the subject's surface (which has been
obtained with recon all) - this step worked 2) align each subject's surface to fsaverage - this step gave me the problem 3) add all subjects together and create the map showing how many subjects activated each location
To do so I have done the following:
- this first step worked fine and I could display the roi on my
subject's surface mri_vol2surf --mov ${DATA_DIR}/sub01/vois/1000vox_IPS.nii \ --reg ${DATA_DIR}/sub01/fmri/register.dat \ --hemi rh \ --o ${DATA_DIR}/sub01/probmap/testIPS.rh.mgh \ --projfrac ${thisprojfrac}
- this step crashed
mri_surf2surf --hemi rh --s fsaverage --fwhm 3 --cortex \ --sval ${DATA_DIR}/sub01/probmap/testIPS.rh.mgh --tval ${DATA_DIR}/sub01/probmap/testIPSfs.mgh
The error is: Loading source data ERROR: dimension inconsistency in source data Number of surface vertices = 163842 Number of value vertices = 133030
Do you have any idea why?
3)Then I was planning to use fscalc and add all subjects together, is this correct?
If there is another/easier way to do the same thing, please let me know Thanks in advance for your help, Best Elisa
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
External Email - Use Caution
Thanks a lot!
On 16 July 2018 at 18:47, Douglas N. Greve dgreve@mgh.harvard.edu wrote:
You can also use mri_concat to compute the mean, eg, mri_concat file1.mgh file2.mgh ... fileN.mgh --mean --o average.mgh
On 07/13/2018 11:17 AM, Bruce Fischl wrote:
Hi Elisa
if you only use --s fsaverage, then mri_surf2surf assumes you are mapping within subject. If you want to map from one subject to another you need to use --srcsubject sub01 --trgsubject fsaverage
And yes, if you get that working I think fscalc should do the trick (or it would be easy to do in matlab).
cheers Bruce On Fri, 13 Jul 2018, Elisa Castaldi wrote:
External Email - Use CautionDear experts,
I would like to show the across-subject overlap of voxels by creating a map with color coding indicating the number of subjects activating corresponding voxels. For each subject I have run the first level model in spss and saved the 1000 most activated voxels for a given contrast as an roi (binary file). Now with freesurfer I am trying to :
- display the saved roi on the subject's surface (which has been
obtained with recon all) - this step worked 2) align each subject's surface to fsaverage - this step gave me the problem 3) add all subjects together and create the map showing how many subjects activated each location
To do so I have done the following:
- this first step worked fine and I could display the roi on my
subject's surface mri_vol2surf --mov ${DATA_DIR}/sub01/vois/1000vox_IPS.nii \ --reg ${DATA_DIR}/sub01/fmri/register.dat \ --hemi rh \ --o ${DATA_DIR}/sub01/probmap/testIPS.rh.mgh \ --projfrac ${thisprojfrac}
- this step crashed
mri_surf2surf --hemi rh --s fsaverage --fwhm 3 --cortex \ --sval ${DATA_DIR}/sub01/probmap/testIPS.rh.mgh --tval ${DATA_DIR}/sub01/probmap/testIPSfs.mgh
The error is: Loading source data ERROR: dimension inconsistency in source data Number of surface vertices = 163842 Number of value vertices = 133030
Do you have any idea why?
3)Then I was planning to use fscalc and add all subjects together, is this correct?
If there is another/easier way to do the same thing, please let me know Thanks in advance for your help, Best Elisa
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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Elisa Castaldi