[Freesurfer] applying Yeo atlas to individual brains
Our lab has a need to apply the Yeo atlas to individual brains. As I understand it, Yeo atlas is only currently available for the FSAverage brain. Any plans to incorporate Yeo on to the default FS segmentation, or have it available as an option? -Jeff Eriksen ___ 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] integrating another atlas into Freesurfer
I have the Yeo resting-state fMRI atlases which I downloaded from http://www.freesurfer.net/fswiki/CorticalParcellation_Yeo2011 They consist of 3 versions, fsaverage being of interest here. The fsaverage folder provided includes the typical FS folders corresponding a recon-all for the average brain for this atlas. I wish to use this high resolution atlas to parcellate my individual subjects. I am unclear how to go about this. I have perused wiki pages on Annotation files FS labels Automatic surface labeling process Surface registration process but still do not find a clear path to my goal. Specifically I would like to end up with a matching set of surface and annot files, as high of resolution as possible, for each of my subjects. Using some specific numbers, the Yeo atlas has around 300,000 vertices when combining the lh.pial and rh.pial surfaces. The matching annot files I believe are lrh.Yeo2011_17Networks_N1000.annot, which together should also have 300,000 vertices. I suppose what I need to do is align each of my subjects to this atlas and project the atlas onto each subject to get a new surface and annot file for that subject, which will have some unique number of vertices for each subject. Please point me to the right set of documentation that will tell me how to do this. Thanks, -Jeff ___ 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] combining lh.annot and rh.annot files
Is it possible to combine the lh and rh annotation files into a single annotation file? How? -Jeff ___ 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] sub-parcellation
I just attended the pre-OHBM FSL/FS course, and spoke to David Salat there about possibilities to create more detailed sub-parcellationsfrom the two major structural atlases. Could someone please let me know if David was right that such tools exist, and/or point me to them? My goal is essentially to create relatively equal-area parcellations with say 100, 200, 500, 1000, 2000, 5000, etc. ROIs per hemisphere, retaining some type of labeling to indicate where each ROI came from. Thanks, -Jeff PS I am at the HBM meeting through mid-day Thursday if someone here is able to talk to me in person (maybe even David!). My cell is 971-533-3942 if someone in Seattle wants to call or text. ___ 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] re-posting: reversing recon-all resampling
I am reposting this since I did not get any response. Can I clarify my problem/request in any way? Can anyone point me to some avenues for further exploration? Thanks, -Jeff From: Jeff Eriksen eriks...@ohsu.edumailto:eriks...@ohsu.edu Date: Thursday, January 10, 2013 3:24 PM To: freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu Subject: reversing recon-all resampling I have been asked to use FreeSurfer to create a good brain mask for use in another analysis stream (DTI and other things). I have chosen to do this by running recon-all on the structural scan, then taking the (aseg+aparc) and using FSL to dilate and erode to fill holes. This I binarize and rotate back into the same orientation as the original structural volume, and finally strip the padding added by recon-all, thus making the mask match the original T1 so it can be overlaid properly. The only problem is that, besides rotating and padding, recon-all also resamples to exactly 1.0 isovoxel, whereas the original T1 was 1.0 x 1.0 x 1.1 mm. Thus, I need to find a way to undo this resampling. Best I can determine this happens in the recon-all stream near the beginning where is seems to create some Talariach transform. Any ideas how to undo this xform, or can you suggest a better way to accomplish my goal. -Jeff Eriksen ___ 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] reversing recon-all resampling
I have been asked to use FreeSurfer to create a good brain mask for use in another analysis stream (DTI and other things). I have chosen to do this by running recon-all on the structural scan, then taking the (aseg+aparc) and using FSL to dilate and erode to fill holes. This I binarize and rotate back into the same orientation as the original structural volume, and finally strip the padding added by recon-all, thus making the mask match the original T1 so it can be overlaid properly. The only problem is that, besides rotating and padding, recon-all also resamples to exactly 1.0 isovoxel, whereas the original T1 was 1.0 x 1.0 x 1.1 mm. Thus, I need to find a way to undo this resampling. Best I can determine this happens in the recon-all stream near the beginning where is seems to create some Talariach transform. Any ideas how to undo this xform, or can you suggest a better way to accomplish my goal. -Jeff Eriksen ___ 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.
Re: [Freesurfer] FW: how to obtain MRI coordinates of scalp surface points marked in tksurfer
Hi Ruopeng, Do you know if freeview has a way to show the selected point on the 3D surface? Double-ckicking in the 3D window seems to choose the point I want on the 3D surface (projecting perpenducularly from the 2D screen to the underlying scalp surface point) and displays a red cross in the 3 2D views, but it show nothing in the 3D window. Thanks, -Jeff On 1/5/13 11:43 AM, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote: Hi Jeff I'm not sure you can, but Ruopeng would know. If not, we can add it to the FreeView feature request list. cheers Bruce On Sat, 5 Jan 2013, Jeff Eriksen wrote: Doug, Freeview looks like the best way to get what I want. Still trying to figure out how to mark a point in the 3D viewing window, but at least when I mark them in the 2D windows I get all the coordinates I need. Thanks, -Jeff Message: 5 Date: Fri, 04 Jan 2013 13:36:59 -0500 From: Douglas N Greve gr...@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] FW: FW: how to obtain MRI coordinates of scalp surface points marked in tksurfer To: freesurfer@nmr.mgh.harvard.edu Message-ID: 50e7214b.6010...@nmr.mgh.harvard.edu Content-Type: text/plain; charset=ISO-8859-1; format=flowed tksurfer may be putting all 0s in the RAS field because the head surface does not match the cortical surface (tksurfer is very inflexible in this way). One way around it is to find the vertex number, then find the RAS for that vertex by converting the surface to ascii. freeview might do a better job than tksurfer. doug On 01/03/2013 10:38 PM, Jeff Eriksen wrote: FreeSurfer experts, I am trying to mark points on a surface in tksurfer, then obtain their original voxel coordinates. These are some of the problems I have encountered, and some of the instructions and examples I do not yet understand. -Jeff From: Bruce Fischl fis...@nmr.mgh.harvard.edu mailto:fis...@nmr.mgh.harvard.edu Date: Thursday, January 3, 2013 6:27 PM To: Jeff Eriksen eriks...@ohsu.edu mailto:eriks...@ohsu.edu Subject: Re: [Freesurfer] FW: how to obtain MRI coordinates of scalp surface points marked in tksurfer Can you cc the list so others can answer? Freeview can rotate 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 mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] FW: how to obtain MRI coordinates of scalp surface points marked in tksurfer
Doug, Freeview looks like the best way to get what I want. Still trying to figure out how to mark a point in the 3D viewing window, but at least when I mark them in the 2D windows I get all the coordinates I need. Thanks, -Jeff Message: 5 Date: Fri, 04 Jan 2013 13:36:59 -0500 From: Douglas N Greve gr...@nmr.mgh.harvard.edumailto:gr...@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] FW: FW: how to obtain MRI coordinates of scalp surface points marked in tksurfer To: freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu Message-ID: 50e7214b.6010...@nmr.mgh.harvard.edumailto:50e7214b.6010...@nmr.mgh.harvard.edu Content-Type: text/plain; charset=ISO-8859-1; format=flowed tksurfer may be putting all 0s in the RAS field because the head surface does not match the cortical surface (tksurfer is very inflexible in this way). One way around it is to find the vertex number, then find the RAS for that vertex by converting the surface to ascii. freeview might do a better job than tksurfer. doug On 01/03/2013 10:38 PM, Jeff Eriksen wrote: FreeSurfer experts, I am trying to mark points on a surface in tksurfer, then obtain their original voxel coordinates. These are some of the problems I have encountered, and some of the instructions and examples I do not yet understand. -Jeff From: Bruce Fischl fis...@nmr.mgh.harvard.edumailto:fis...@nmr.mgh.harvard.edu mailto:fis...@nmr.mgh.harvard.edumailto:fis...@nmr.mgh.harvard.edu%3E Date: Thursday, January 3, 2013 6:27 PM To: Jeff Eriksen eriks...@ohsu.edumailto:eriks...@ohsu.edu mailto:eriks...@ohsu.edumailto:eriks...@ohsu.edu%3E Subject: Re: [Freesurfer] FW: how to obtain MRI coordinates of scalp surface points marked in tksurfer Can you cc the list so others can answer? Freeview can rotate ___ 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] FW: how to obtain MRI coordinates of scalp surface points marked in tksurfer
HI, I created a scalp surface mesh with mkheadsurf. I need to mark or select some scalp surface points and obtain their MRI coordinates. That is, if my MRI is 256-cubed I need the (ix,iy,iz) MRI voxel coordinates closest to the scalp mesh point I mark, where these run from 1 to 256 (or 0-255 if you must). The tksurfer display shows several types of floating point coordinates, but they assume an origin in the center of the head somewhere. If I knew the MRI coordinates of this origin I could calculate the original MRI. Thanks, -Jeff ___ 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] FW: misalignment of aseg GM/WM and surface midway between pial and white
I am wondering about how the pial and white surfaces are supposed to match up with the aseg file. I was expecting that when I created a new surface, usinfg mri_surf2surf, halfway between the pial and white surfaces (which I call the cortical ribbon), it would run right down the center of the GM. After creating that surface I converted it to voxel representation with mri_surf2vol. I found that it doesn't match everywhere. Are the pial and white surfaces not based on the aseg segmentation of GWM? If they are, why the discrepancy? Thanks, -Jeff ___ 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] pial surface file format
I wish to extract the pial and GW surfaces from their surface files to manipulate in Matlab. As far as I can determine, these are the files lRh.white and lrh.pial. Can someone please confirm this, and also confirm that these are in the triangle surface file binary format? If this is all true, I can proceed to opening and reading the meshes. Thanks, -Jeff Eriksen ___ 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.
Re: [Freesurfer] pial surface file format
Super! Please tell me how to obtain the m-files. -Jeff On 9/14/11 6:49 PM, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote: Yes, and we provide m files for reading them Cheers Bruce On Sep 14, 2011, at 9:46 PM, Jeff Eriksen eriks...@ohsu.edu wrote: I wish to extract the pial and GW surfaces from their surface files to manipulate in Matlab. As far as I can determine, these are the files lRh.white and lrh.pial. Can someone please confirm this, and also confirm that these are in the triangle surface file binary format? If this is all true, I can proceed to opening and reading the meshes. Thanks, -Jeff Eriksen ___ 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 mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] pial surface documentation
Where may I find the documentation explaining the content and format of the pial and gray-white surface files? Thanks, -Jeff ___ 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] recon-all steps necessary to get aseg.nii
I would like to run FreeSurfer just up to the point it creates the aseg file, and no further. I believe this would be steps 1 through 11. Is there any way other than making a copy of the recon-all script and removing everything after step 11. Not sure I know exactly where this is. -Jeff ___ 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.
