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 <greve@nmr.mgh.harvard.edu mailto:greve@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 <mailto:Freesurfer@nmr.mgh.harvard.edu> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> Phone Number: 617-724-2358 <tel:617-724-2358> Fax: 617-726-7422 <tel:617-726-7422> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html <http://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 <mailto: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.-- Taha Abdullah Department of Physiology Northwestern University Masters of Science Physiology and Biophysics, Georgetown University 2015
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