So you have 1 column, but you want 1 column for each vertex? We don't
have anything to do that, but you can do it in matlab, eg,
M = fast_vol2mat(MRIread('lh.yourdata.mgh'));
M will be a 240x127000 matrix
On 5/4/16 8:36 PM, Taha Abdullah wrote:
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 <mailto: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
>
>
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--
Douglas N. Greve, Ph.D.
MGH-NMR Center
gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu>
Phone Number: 617-724-2358 <tel:617-724-2358>
Fax: 617-726-7422 <tel:617-726-7422>
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The information in this e-mail is intended only for the person to
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--
Taha Abdullah
Department of Physiology
Northwestern University
Masters of Science Physiology and Biophysics, Georgetown University 2015
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