(sorry if you got this multiple times this morning I had some server issues)
I had not seen a post based on this email, so I am resending it. It is my understanding that I can use freesurfer and FSfast to get activation levels after data has been smoothed across the surface instead of 3D volume. Is the mir_segstats only able to use the 3D volume and not the surface data stored within vertices? Sorry if this questions is obvious to everyone. I want to basically get the average activation for a set of vertices at each time point included in a label from the surface mapped functional data. See below for additional details of the parameters I entered.
Thanks Erik Jahner
On Sep 9, 2016, at 8:20 AM, ERIK JAHNER <erik.jahner@icloud.com mailto:erik.jahner@icloud.com> wrote:
Dear Freesurfer experts,
I am attempting to get the waveform from a subject (401)using the preprocessed data (fmcpr.siemens.sm5.fsaverage.lh.nii.gz) by means of a label I created from the icosahedron 3 (lh.ic3.tri_vertex_638). This label was created from the subjects “sphere.reg" file.
I am using the following command:
mri_segstats --slabel 401 lh /Applications/freesurfer/subjects/fsaverage/label/ic3/lh.ic3.tri_vertex_638.label --avgwf out.dat --id 1 --i /Applications/freesurfer/LagStructure/401/rest/007/fmcpr.siemens.sm5.fsaverage.lh.nii.gz
However I am getting the following error:
ERROR: dimension mismatch between input volume and seg input 163842 1 1 seg 140104 1 1
Obviously there is something wrong with my file dimensions. But, I am unsure of how to fix this. I checked some of the files in my subject anatomical folder like the thickness file and they also have 140104 1 1 as the dimensions. But, as would be predicted the "fmcpr.siemens.sm5.fsaverage.lh.nii.gz” file has the dimensions 163842 1 1 210. Is there an easy way to fix this problem? I am unsure what I did to create this discrepancy.
Thanks for your continued support, Erik Jahner
you need to transfer the label into the space of subject 401 using mri_label2label. Currently, the label is in fsaverage space which is why you get the mismatch
On 09/12/2016 12:53 PM, ERIK JAHNER wrote:
(sorry if you got this multiple times this morning I had some server issues)
I had not seen a post based on this email, so I am resending it. It is my understanding that I can use freesurfer and FSfast to get activation levels after data has been smoothed across the surface instead of 3D volume. Is the mir_segstats only able to use the 3D volume and not the surface data stored within vertices? Sorry if this questions is obvious to everyone. I want to basically get the average activation for a set of vertices at each time point included in a label from the surface mapped functional data. See below for additional details of the parameters I entered.
Thanks Erik Jahner
On Sep 9, 2016, at 8:20 AM, ERIK JAHNER <erik.jahner@icloud.com mailto:erik.jahner@icloud.com> wrote:
Dear Freesurfer experts,
I am attempting to get the waveform from a subject (401)using the preprocessed data (fmcpr.siemens.sm5.fsaverage.lh.nii.gz) by means of a label I created from the icosahedron 3 (lh.ic3.tri_vertex_638). This label was created from the subjects “sphere.reg" file.
I am using the following command:
mri_segstats --slabel 401 lh /Applications/freesurfer/subjects/fsaverage/label/ic3/lh.ic3.tri_vertex_638.label
--avgwf out.dat --id 1 --i /Applications/freesurfer/LagStructure/401/rest/007/fmcpr.siemens.sm5.fsaverage.lh.nii.gz
However I am getting the following error:
ERROR: dimension mismatch between input volume and seg input 163842 1 1 seg 140104 1 1
Obviously there is something wrong with my file dimensions. But, I am unsure of how to fix this. I checked some of the files in my subject anatomical folder like the thickness file and they also have 140104 1 1 as the dimensions. But, as would be predicted the "fmcpr.siemens.sm5.fsaverage.lh.nii.gz” file has the dimensions 163842 1 1 210. Is there an easy way to fix this problem? I am unsure what I did to create this discrepancy.
Thanks for your continued support, Erik Jahner
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Douglas N Greve -
ERIK JAHNER