Hi Freesurfers,
I have tried to obtain a flat surface as described by the upper part (full cortex) of the following page:
http://freesurfer.net/fswiki/FreeSurferOccipitalFlattenedPatch
However, I failed to load the results in freeview (it took forever), nor can I read in matlab with read_surf. The error in matlab is as following ====== Error using reshape To RESHAPE the number of elements must not change.
Error in read_surf (line 77) vertex_coords = reshape(vertex_coords, 3, vnum)' ; ====== Thus I suspect in the newly generated surface, the number of vertices in the header does not meet that indicated by the data. I did sth wrong.
Questions: 1 Is this webpage still up-to-date or I shall try something new to flatten the surface? 2 Probably there are "frequently made mistakes" during my manual process, would you please give me a hint? I my case afterwards mris_flatten took 2-3 hours.
btw: the inflated surface is OK either checked by freeview or matlab.
best Peng
More information, error from tksurfer is as following:
======================== MRISalloc(16711682, 480): could not allocate vertices Cannot allocate memory ============
---------- Forwarded message ---------- From: peng prion.w@gmail.com Date: Fri, May 9, 2014 at 1:01 PM Subject: a question on flat surface To: "Freesurfer@nmr.mgh.harvard.edu" freesurfer@nmr.mgh.harvard.edu
Hi Freesurfers,
I have tried to obtain a flat surface as described by the upper part (full cortex) of the following page:
http://freesurfer.net/fswiki/FreeSurferOccipitalFlattenedPatch
However, I failed to load the results in freeview (it took forever), nor can I read in matlab with read_surf. The error in matlab is as following ====== Error using reshape To RESHAPE the number of elements must not change.
Error in read_surf (line 77) vertex_coords = reshape(vertex_coords, 3, vnum)' ; ====== Thus I suspect in the newly generated surface, the number of vertices in the header does not meet that indicated by the data. I did sth wrong.
Questions: 1 Is this webpage still up-to-date or I shall try something new to flatten the surface? 2 Probably there are "frequently made mistakes" during my manual process, would you please give me a hint? I my case afterwards mris_flatten took 2-3 hours.
btw: the inflated surface is OK either checked by freeview or matlab.
best Peng
Hi Peng
the flat maps are stored in a different format than the surfaces, called a "patch" format (since they are only a piece of the whole surface - not the entire thing). You can load them with file->load patch in tksurfer. Not sure about freeview, perhaps Ruopeng can comment?
cheers Bruce
On Fri, 9 May 2014, peng wrote:
More information, error from tksurfer is as following:
======================== MRISalloc(16711682, 480): could not allocate vertices Cannot allocate memory ============
---------- Forwarded message ----------
From: peng prion.w@gmail.com Date: Fri, May 9, 2014 at 1:01 PM Subject: a question on flat surface To: "Freesurfer@nmr.mgh.harvard.edu" freesurfer@nmr.mgh.harvard.edu
Hi Freesurfers, I have tried to obtain a flat surface as described by the upper part (full cortex) of the following page:
http://freesurfer.net/fswiki/FreeSurferOccipitalFlattenedPatch
However, I failed to load the results in freeview (it took forever), nor can I read in matlab with read_surf. The error in matlab is as following ====== Error using reshape To RESHAPE the number of elements must not change.
Error in read_surf (line 77) vertex_coords = reshape(vertex_coords, 3, vnum)' ; ====== Thus I suspect in the newly generated surface, the number of vertices in the header does not meet that indicated by the data. I did sth wrong.
Questions: 1 Is this webpage still up-to-date or I shall try something new to flatten the surface? 2 Probably there are "frequently made mistakes" during my manual process, would you please give me a hint? I my case afterwards mris_flatten took 2-3 hours.
btw: the inflated surface is OK either checked by freeview or matlab.
best Peng
Thank you Bruce. I can load it as patch as you suggested. I can also load the curvatures to color it. Thus I imagine in the data, there would be 2D locations of the vertices, and their indices respect to the full surface. Is it true? How can I read this information (e.g. into matlab) ? Thanks again! Also thanks to anyone who would like to comment!
best Peng
On Fri, May 9, 2014 at 5:12 PM, Bruce Fischl fischl@nmr.mgh.harvard.eduwrote:
Hi Peng
the flat maps are stored in a different format than the surfaces, called a "patch" format (since they are only a piece of the whole surface - not the entire thing). You can load them with file->load patch in tksurfer. Not sure about freeview, perhaps Ruopeng can comment?
cheers Bruce
On Fri, 9 May 2014, peng wrote:
More information, error from tksurfer is as following:
======================== MRISalloc(16711682, 480): could not allocate vertices Cannot allocate memory ============
---------- Forwarded message ----------
From: peng prion.w@gmail.com Date: Fri, May 9, 2014 at 1:01 PM Subject: a question on flat surface To: "Freesurfer@nmr.mgh.harvard.edu" freesurfer@nmr.mgh.harvard.edu
Hi Freesurfers, I have tried to obtain a flat surface as described by the upper part (full cortex) of the following page:
http://freesurfer.net/fswiki/FreeSurferOccipitalFlattenedPatch
However, I failed to load the results in freeview (it took forever), nor can I read in matlab with read_surf. The error in matlab is as following ====== Error using reshape To RESHAPE the number of elements must not change.
Error in read_surf (line 77) vertex_coords = reshape(vertex_coords, 3, vnum)' ; ====== Thus I suspect in the newly generated surface, the number of vertices in the header does not meet that indicated by the data. I did sth wrong.
Questions: 1 Is this webpage still up-to-date or I shall try something new to flatten the surface? 2 Probably there are "frequently made mistakes" during my manual process, would you please give me a hint? I my case afterwards mris_flatten took 2-3 hours.
btw: the inflated surface is OK either checked by freeview or matlab.
best Peng
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.
Hi Peng
we provide matlab code (read_patch.m) for reading patches and for reading patches converted to ascii format (read_patch_asc.m). You can use mri_convert to generate the ascii format
cheers Bruce On Sat, 10 May 2014, peng wrote:
Thank you Bruce. I can load it as patch as you suggested. I can also load the curvatures to color it. Thus I imagine in the data, there would be 2D locations of the vertices, and their indices respect to the full surface. Is it true? How can I read this information (e.g. into matlab) ? Thanks again! Also thanks to anyone who would like to comment! best Peng
On Fri, May 9, 2014 at 5:12 PM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote: Hi Peng
the flat maps are stored in a different format than the surfaces, called a "patch" format (since they are only a piece of the whole surface - not the entire thing). You can load them with file->load patch in tksurfer. Not sure about freeview, perhaps Ruopeng can comment? cheers Bruce On Fri, 9 May 2014, peng wrote: More information, error from tksurfer is as following: ======================== MRISalloc(16711682, 480): could not allocate vertices Cannot allocate memory ============ ---------- Forwarded message ---------- From: peng <prion.w@gmail.com> Date: Fri, May 9, 2014 at 1:01 PM Subject: a question on flat surface To: "Freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu> Hi Freesurfers, I have tried to obtain a flat surface as described by the upper part (full cortex) of the following page: http://freesurfer.net/fswiki/FreeSurferOccipitalFlattenedPatch However, I failed to load the results in freeview (it took forever), nor can I read in matlab with read_surf. The error in matlab is as following ====== Error using reshape To RESHAPE the number of elements must not change. Error in read_surf (line 77) vertex_coords = reshape(vertex_coords, 3, vnum)' ; ====== Thus I suspect in the newly generated surface, the number of vertices in the header does not meet that indicated by the data. I did sth wrong. Questions: 1 Is this webpage still up-to-date or I shall try something new to flatten the surface? 2 Probably there are "frequently made mistakes" during my manual process, would you please give me a hint? I my case afterwards mris_flatten took 2-3 hours. btw: the inflated surface is OK either checked by freeview or matlab. best Peng _______________________________________________ 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.
Great, Thank you Bruce!
On Sat, May 10, 2014 at 3:09 PM, Bruce Fischl fischl@nmr.mgh.harvard.eduwrote:
Hi Peng
we provide matlab code (read_patch.m) for reading patches and for reading patches converted to ascii format (read_patch_asc.m). You can use mri_convert to generate the ascii format
cheers Bruce On Sat, 10 May 2014, peng wrote:
Thank you Bruce. I can load it as patch as you suggested. I can also load
the curvatures to color it. Thus I imagine in the data, there would be 2D locations of the vertices, and their indices respect to the full surface. Is it true? How can I read this information (e.g. into matlab) ? Thanks again! Also thanks to anyone who would like to comment! best Peng
On Fri, May 9, 2014 at 5:12 PM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote: Hi Peng
the flat maps are stored in a different format than the surfaces,called a "patch" format (since they are only a piece of the whole surface - not the entire thing). You can load them with file->load patch in tksurfer. Not sure about freeview, perhaps Ruopeng can comment?
cheers Bruce On Fri, 9 May 2014, peng wrote: More information, error from tksurfer is as following: ======================== MRISalloc(16711682, 480): could not allocate vertices Cannot allocate memory ============ ---------- Forwarded message ---------- From: peng <prion.w@gmail.com> Date: Fri, May 9, 2014 at 1:01 PM Subject: a question on flat surface To: "Freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu> Hi Freesurfers, I have tried to obtain a flat surface as described by theupper part (full cortex) of the following page:
http://freesurfer.net/fswiki/FreeSurferOccipitalFlattenedPatch
However, I failed to load the results in freeview (it took forever), nor can I read in matlab with read_surf. The error in matlab is as following ====== Error using reshape To RESHAPE the number of elements must not change. Error in read_surf (line 77) vertex_coords = reshape(vertex_coords, 3, vnum)' ; ====== Thus I suspect in the newly generated surface, the numberof vertices in the header does not meet that indicated by the data. I did sth wrong.
Questions: 1 Is this webpage still up-to-date or I shall try somethingnew to flatten the surface? 2 Probably there are "frequently made mistakes" during my manual process, would you please give me a hint? I my case afterwards mris_flatten took 2-3 hours.
btw: the inflated surface is OK either checked by freeview or matlab. best Peng _______________________________________________ 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 towhom 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 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
-
Bruce Fischl -
peng