Hello Doug,
Sorry for the confusing and long email, I am interested in extracting the
raw BOLD signal from a processed 4D nifit file. After registering the
functional to ${subject}/mri/orig.mgz and generating the registration file,
I proceeded to convert the functional image to the same dimensions as
the lh.inflated surface via mri_vol2surf so the functional data image now
has 127000 x 1 x 1 x 240. So I ran mri_segstats command to extract the bold
signal, but I ended up having 240 rows and 1 column in the text file...the
ultimate goal is to quantify the wave propagation of the BOLD time series
across a flattened patch. Any advice would be greatly appreciated.
Thanks!
On Wed, May 4, 2016 at 2:26 PM, Douglas N Greve <gr...@nmr.mgh.harvard.edu>
wrote:
>
> Sorry, can you tell me what you are trying to do? You just want a number
> of time points -by- number of vertices file? Then mri_vol2surf should do
> that for you. Flattening is irrelevant for this as it only changes the
> xyz coordinate of the vertex and not the vertex identity.
> doug
>
>
> On 04/29/2016 11:24 AM, Taha Abdullah wrote:
> > 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
> >
> >
> > _______________________________________________
> > 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
>
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>
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--
Taha Abdullah
Department of Physiology
Northwestern University
Masters of Science Physiology and Biophysics, Georgetown University 2015
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