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.jah...@icloud.com >> <mailto:erik.jah...@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 > > > _______________________________________________ > 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 gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
