Hello Freesurfer Experts, Long story short--I would like to extract BOLD values from each TR across all vertices for one subjects flattened surface Following is a brief overview of my steps and at the end you can see where I am stuck. First, after *recon-all I* followed the steps to cut the lh inflated surface, saved as a patch, ran *mris_flatten, *converted patch into asc file. Second, I used read_patch.m to extract all spatial information and a net loss of approximately 10k vertices (127k to 116k)
We had all functional images processed in FSL, the 4D file has 64x64x36x240 dimensions (voxels are 3.4x3.4x3.0). Next, co-registered the functional and anatomicals together via the following cmd: * bbregister --s cbp001_v1 --mov filtered_func_data.nii.gz --bold --init-fsl --reg dummy1.da*t. Afterwards, converted the volume to a surface using the following cmd*: mri_vol2surf --mov filtered_func_data.nii.gz --reg dummy1.dat --projfrac 0.5 --interp trilinear --hemi lh --o ./lh.func.vol2surf.mgh. *THe dimensions are 127027 x 1 x 1 x 240. Visually no problem when using* tksurfer cbp001_v1 lh inflated -patch /path to flattened patch/ -overlay /lh.func.vol2surf.mgh/ -timecourse lh.func.vol2surf.mgh;* click on the patch and shows the timecourse for that selected vertex. Using the View>Configure>overlay I can shuffle through the TRs to inspect the change in raw BOLD signal per vertex. I have been perusing the email web server searching for how to extract the hemodynamic waveform for each vertex across the flattened surface and ultimately will be using matlab to understand how the spatial transformation is happening. As well I have all the matlab files that seemed relevant to my query (read_surf.m, read_patch.m, and readMRI.m). I was hoping that I would be able to have a text file with all the vertices (127K not the flattened 116k) in rows and each column would have the TRs; I ran this command;* mri_segstats --slabel cbp001_v1 lh /home/share/freesurfer/subjects/cbp001_v1/label/lh.cortex.label --avgwf mri_seg_stats.dat --i lh.func.vol2surf.mgh*, output was the 240 TRs as rows and seems like the average global BOLD signal in the single column corresponding with each TR. Excuse my naiveness, I just recently (1 month ago) started using freesurfer and I feel like I have exhausted as much of the information available on the FS wiki and email server. Any information or advice would be great! I put the commands just to give an idea of my workflow (most of the command lines are from the email server or the FS Wiki) and if there are any issues with my steps please let me know so I can correct them before starting the group analysis. Best, Taha -- Taha Abdullah Department of Physiology Northwestern University Masters of Science Physiology and Biophysics, Georgetown University 2015
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