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
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
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 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 greve@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.
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
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Hello Freesurfer Team,
Sorry for being so late with this message I was trying different things to accomplish extracting BOLD values from a flattened surface. I followed the overall instructions on this website http://web.mit.edu/fsl_v5.0.8/fsl/doc/wiki/FreeSurfer.html. I have the flattened patch from tksurfer and I want to conduct a rsfMRI analysis on a flattened patch from a feat directory. Do you have any recommendations on the proper workflow? I believe that I need to run
mri_label2vol --annot /path to subj/label/lh.aparc.annot --temp func4d.nii.gz --reg (output from reg-feat2anat) --o myoutput --hemi lh --subject --proj 0 1 .1
The output has similar dimensions as functional and it is only cortical areas but the time dimensions are no longer there. Not sure how to actually extract the bold signal, maybe something with mri_segstats? And I think it will be straightforward to understand the spatial changes occurring during flattening since vertex identity stays the same and can be read in MATLAB, correct? Please let me know at your earliest convenience.
Best, Taha
On Thu, May 5, 2016 at 9:21 AM, Douglas Greve greve@nmr.mgh.harvard.edu wrote:
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
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 greve@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.
-- Taha Abdullah Department of Physiology Northwestern University Masters of Science Physiology and Biophysics, Georgetown University 2015
Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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.
freesurfer@nmr.mgh.harvard.edu
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Taha Abdullah