[Freesurfer] subcortical segmentation only
Hi FS-folks! I would like to perform a subcortical segmentation only and I am not sure which preprocessing steps I would have to perform to achieve this goal. So far I did always the full monty using reconall -all. Which reconall stages are needed if only the subcortical segmentation is of interest? Best wishes and many thanks for you help! Luke___ 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] use of high res T1 for subcortical segmentation
Hi folks! Is there any way to convince FS to make use of a high spatial resolution (better than 1 x 1 x 1 mm3) for subcortical segmentation? Best wishes, Luke___ 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] use of high res T1 for subcortical segmentation
Yup. http://surfer.nmr.mgh.harvard.edu/fswiki/HiResRecon Depending how far you intend to push it, you might need a different version of the mri_tesselate function. Best Remi Gau On 10/12/14 08:44, lukas.sch...@ukb.uni-bonn.de wrote: Hi folks! Is there any way to convince FS to make use of a high spatial resolution (better than 1 x 1 x 1 mm3) for subcortical segmentation? Best wishes, Luke ___ 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 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] use of high res T1 for subcortical segmentation
Dear Remi! Thanks a lot for the fast response. Could comment further on your point that I might need a different version of mri_tesselate ... The spatial resolution I am talking about is 0.5x0.5x0.8 mm3. Best wihes, Luke Yup. http://surfer.nmr.mgh.harvard.edu/fswiki/HiResRecon Depending how far you intend to push it, you might need a different version of the mri_tesselate function. Best Remi Gau On 10/12/14 08:44, lukas.sch...@ukb.uni-bonn.de wrote: Hi folks! Is there any way to convince FS to make use of a high spatial resolution (better than 1 x 1 x 1 mm3) for subcortical segmentation? Best wishes,___ 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] Probabilities in the Brodmann area labels
It is in fsaverage. On Tue, 9 Dec 2014 14:37:43 +0100 pfannmo...@uni-greifswald.de wrote: Dear FreeSurfer Experts, I am puzzeled about the probabilities in the Brodmann area labels. If I take the Brodmann areas 1, 2, 3a and 3b and add their probabilities at a certain vertex a probability sum 1 should arise. This is due to the fact that 10 brains where analyzed in order to compute the probabilities and in each brain only one Brodmann area was found at each location. In my current test I recognized that values 1 occur as often as values 1. How is this possible? Respectfully pfannmoe ___ 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. -- Joerg Pfannmoeller pfannmo...@uni-greifswald.de ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Getting voxel values from aseg.mgz
Hi Pradeep you can use mri_extract_label to copy just the hippocampal labels out of the segmentation if that is what you mean. The values for left and right hippocampus (17 and 53) can be found in $FREESURFER_HOME/FreeSurferColorLUT.txt cheers Bruce On Wed, 10 Dec 2014, pradeep mahato wrote: After the recon-all process I want to access all the voxels in the left hippocampus ( any subcortical region ) . Please tell me is there any method to extract this voxel values from an segmented image. Thanking you Pradeep Kumar Mahato ___ 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] subcortical segmentation only
Hi Luke you can run -autorecon1 and -autorecon2 if all you care about is the aseg (although we have tools for editing the cortical aseg labels with the surfaces that you will not be able to use in this case) cheers Bruce On Wed, 10 Dec 2014, lukas.sch...@ukb.uni-bonn.de wrote: Hi FS-folks! I would like to perform a subcortical segmentation only and I am not sure which preprocessing steps I would have to perform to achieve this goal. So far I did always the full monty using reconall -all. Which reconall stages are needed if only the subcortical segmentation is of interest? Best wishes and many thanks for you help! Luke ___ 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] Probabilities in the Brodmann area labels
hmmm, is it on the boundaries of the labels? And only a bit 1? That can certainly happen due to resampling and small registration inaccuracies On Wed, 10 Dec 2014, pfannmo...@uni-greifswald.de wrote: It is in fsaverage. On Tue, 9 Dec 2014 14:37:43 +0100 pfannmo...@uni-greifswald.de wrote: Dear FreeSurfer Experts, I am puzzeled about the probabilities in the Brodmann area labels. If I take the Brodmann areas 1, 2, 3a and 3b and add their probabilities at a certain vertex a probability sum 1 should arise. This is due to the fact that 10 brains where analyzed in order to compute the probabilities and in each brain only one Brodmann area was found at each location. In my current test I recognized that values 1 occur as often as values 1. How is this possible? Respectfully pfannmoe ___ 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
Re: [Freesurfer] use of high res T1 for subcortical segmentation
Hey, Someone corrects me if I am wrong, but it seems that the number of vertices currently allowed with freesurfer cannot accomodate more than a certain number of vertices. I suspect that the new version of Freesurfer should allow for more vertices. On high res you might get such error message: mri_tessellate: max vertices 100 exceeded recon-all -s Subject_12 exited with ERRORS at Thu Apr 10 11:16:42 BST 2014 Seems the issue has been raised before in this thread: http://www.mail-archive.com/freesurfer%40nmr.mgh.harvard.edu/msg31331.html Zeke sent me a file of the new mri_tessellate: I can forward it to you if you want. Best Remi Gau On 10/12/14 10:24, lukas.sch...@ukb.uni-bonn.de wrote: Dear Remi! Thanks a lot for the fast response. Could comment further on your point that I might need a different version of mri_tesselate ... The spatial resolution I am talking about is 0.5x0.5x0.8 mm3. Best wihes, Luke Yup. http://surfer.nmr.mgh.harvard.edu/fswiki/HiResRecon Depending how far you intend to push it, you might need a different version of the mri_tesselate function. Best Remi Gau On 10/12/14 08:44, lukas.sch...@ukb.uni-bonn.de wrote: Hi folks! Is there any way to convince FS to make use of a high spatial resolution (better than 1 x 1 x 1 mm3) for subcortical segmentation? Best wishes, ___ 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 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] use of high res T1 for subcortical segmentation
Hi Remi yes, that's true. The limit is pretty arbitrary and supposed to be bigger than we would ever want, but if it is limiting we can bump it up Bruce On Wed, 10 Dec 2014, Remi Gau wrote: Hey, Someone corrects me if I am wrong, but it seems that the number of vertices currently allowed with freesurfer cannot accomodate more than a certain numb er of vertices. I suspect that the new version of Freesurfer should allow for more vertices. On high res you might get such error message: mri_tessellate: max vertices 100 exceeded recon-all -s Subject_12 exited with ERRORS at Thu Apr 10 11:16:42 BST 2014 Seems the issue has been raised before in this thread: http://www.mail-archive.com/freesurfer%40nmr.mgh.harvard.edu/msg31331.html Zeke sent me a file of the new mri_tessellate: I can forward it to you if yo u want. Best Remi Gau On 10/12/14 10:24, lukas.sch...@ukb.uni-bonn.de wrote: Dear Remi! Thanks a lot for the fast response. Could comment further on your point that I might need a different version of mri_tesselate ... The spatial resolution I am talking about is 0.5x0.5x0.8 mm3. Best wihes, Luke Yup. http://surfer.nmr.mgh.harvard.edu/fswiki/HiResRecon Depending how far you intend to push it, you might need a different version of the mri_tesselate function. Best Remi Gau On 10/12/14 08:44, lukas.sch...@ukb.uni-bonn.de wrote: Hi folks! Is there any way to convince FS to make use of a high spatial resolution (better than 1 x 1 x 1 mm3) for subcortical segmentation? Best wishes, ___ 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-mai l contains patient information, please contact the Partners Compliance HelpLin e at http://www.partners.org/complianceline . If the e-mail was sent to you in er ror but does not contain patient information, please contact the sender and prop erly dispose of the e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] thickness from pial and white
Hi Bruce, the mris_thickness was looking for ?h.gray file to run correctly. But no such file exists. The freesurfer used is 5.3. Any ideas? The command line is: mris_thickness test_DB48 lh lh.thicknessThe error: reading gray matter surface /misc/data41/yuex/recon_test/test_DB48/surf/lh.gray MRISread(/misc/data41/yuex/recon_test/test_DB48/surf/lh.gray): could not open file. Thanks,Xiaomin From: yu...@hotmail.com To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] thickness from pial and white Date: Wed, 10 Dec 2014 02:47:02 + Thanks. I will try mris_fill. Xiaomin From: Bruce Fischl Sent: Tuesday, December 9, 2014 4:31 PM To: Freesurfer support list it creates a file in curvature format, yes. Did you try mris_fill for the wm.mgz? It won't be exactly the same as the one we would generate. You could use mris_fill to generate the interior of the ?h.white surface, then use the aseg to remove non-wm voxels I guess On Tue, 9 Dec 2014, Xiaomin Yue wrote: Thanks very much. Does this create curvature file? Again, is it possible to generate wm.mgz from those files? Thanks, Xiaomin On Dec 9, 2014, at 4:19 PM, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote: I think just the ?h.white and ?h.pial cheers Bruce On Tue, 9 Dec 2014, Xiaomin Yue wrote: What I mean by inputs is the default files the mris_thickness will be looking for to run correctly Xiaomin On Dec 9, 2014, at 1:08 PM, Xiaomin Yue yu...@hotmail.com wrote: Hi Bruce, Thanks for your response. What's the inputs to the mris_thickness? I need the wm.mgz to generate the ratio of gray vs. white matter. Xiaomin Date: Tue, 9 Dec 2014 09:55:21 -0500 From: fis...@nmr.mgh.harvard.edu To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] thickness from pial and white the thickness you can generate using mris_thikness. Why do you want to generate a wm.mgz? I guess you could from the wmparc On Mon, 8 Dec 2014, Xiaomin Yue wrote: Hi All, Cortical surface reconstructed using caret from a high resolution MRI data (0.25 mm) has been converted to freesurfer format, and viewed correctly using freeview. My questions are whether it is possible to generate 1) a ?h.thickness from the ?h.pial and ?h.white; 2) wm.mgz file using ?h.pial a nd ?h.white Thanks very much for your inputs. Xiaomin ___ 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 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 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 mailing list Freesurfer@nmr.mgh.harvard.edu https://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
Re: [Freesurfer] thickness from pial and white
it only looks for that if it can't find lh.pial. Does that exist? On Wed, 10 Dec 2014, Xiaomin Yue wrote: Hi Bruce, the mris_thickness was looking for ?h.gray file to run correctly. But no such file exists. The freesurfer used is 5.3. Any ideas? The command line is: mris_thickness test_DB48 lh lh.thickness The error: reading gray matter surface /misc/data41/yuex/recon_test/test_DB48/surf/lh.gray MRISread(/misc/data41/yuex/recon_test/test_DB48/surf/lh.gray): could not open file. Thanks, Xiaomin From: yu...@hotmail.com To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] thickness from pial and white Date: Wed, 10 Dec 2014 02:47:02 + Thanks. I will try mris_fill. Xiaomin From: Bruce Fischl Sent: Tuesday, December 9, 2014 4:31 PM To: Freesurfer support list it creates a file in curvature format, yes. Did you try mris_fill for the wm.mgz? It won't be exactly the same as the one we would generate. You could use mris_fill to generate the interior of the ?h.white surface, then use the aseg to remove non-wm voxels I guess On Tue, 9 Dec 2014, Xiaomin Yue wrote: Thanks very much. Does this create curvature file? Again, is it possible to generate wm.mgz from those files? Thanks, Xiaomin On Dec 9, 2014, at 4:19 PM, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote: I think just the ?h.white and ?h.pial cheers Bruce On Tue, 9 Dec 2014, Xiaomin Yue wrote: What I mean by inputs is the default files the mris_thickness will be looking for to run correctly Xiaomin On Dec 9, 2014, at 1:08 PM, Xiaomin Yue yu...@hotmail.com wrote: Hi Bruce, Thanks for your response. What's the inputs to the mris_thickness? I need the wm.mgz to generate the ratio of gray vs. white matter. Xiaomin Date: Tue, 9 Dec 2014 09:55:21 -0500 From: fis...@nmr.mgh.harvard.edu To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] thickness from pial and white the thickness you can generate using mris_thikness. Why do you want to generate a wm.mgz? I guess you could from the wmparc On Mon, 8 Dec 2014, Xiaomin Yue wrote: Hi All, Cortical surface reconstructed using caret from a high resolution MRI data (0.25 mm) has been converted to freesurfer format, and viewed correctly using freeview. My questions are whether it is possible to generate 1) a ?h.thickness from the ?h.pial and ?h.white; 2) wm.mgz file using ?h.pial a nd ?h.white Thanks very much for your inputs. Xiaomin ___ 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 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 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 mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu
Re: [Freesurfer] Probabilities in the Brodmann area labels
Dear Bruce, if I take BA1, BA2, BA3a and BA3b and sum the probabilities at each vertex there are 17 % of the vertices which show probabilities 1. The largest probability is 1.7778. There is a histogramm of the values attached to this mail. Is there a possibility to correct those values? Respectfully pfannmoe On Wed, 10 Dec 2014 08:28:34 -0500 (EST) Bruce Fischl fis...@nmr.mgh.harvard.edu wrote: hmmm, is it on the boundaries of the labels? And only a bit 1? That can certainly happen due to resampling and small registration inaccuracies On Wed, 10 Dec 2014, pfannmo...@uni-greifswald.de wrote: It is in fsaverage. On Tue, 9 Dec 2014 14:37:43 +0100 pfannmo...@uni-greifswald.de wrote: Dear FreeSurfer Experts, I am puzzeled about the probabilities in the Brodmann area labels. If I take the Brodmann areas 1, 2, 3a and 3b and add their probabilities at a certain vertex a probability sum 1 should arise. This is due to the fact that 10 brains where analyzed in order to compute the probabilities and in each brain only one Brodmann area was found at each location. In my current test I recognized that values 1 occur as often as values 1. How is this possible? Respectfully pfannmoe ___ 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 -- Joerg Pfannmoeller pfannmo...@uni-greifswald.de ___ 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] Probabilities in the Brodmann area labels
Hi pfannmoe that seems reasonable given small registration inaccuracies and resampling issues cheers Bruce On Wed, 10 Dec 2014, pfannmo...@uni-greifswald.de wrote: Dear Bruce, if I take BA1, BA2, BA3a and BA3b and sum the probabilities at each vertex there are 17 % of the vertices which show probabilities 1. The largest probability is 1.7778. There is a histogramm of the values attached to this mail. Is there a possibility to correct those values? Respectfully pfannmoe On Wed, 10 Dec 2014 08:28:34 -0500 (EST) Bruce Fischl fis...@nmr.mgh.harvard.edu wrote: hmmm, is it on the boundaries of the labels? And only a bit 1? That can certainly happen due to resampling and small registration inaccuracies On Wed, 10 Dec 2014, pfannmo...@uni-greifswald.de wrote: It is in fsaverage. On Tue, 9 Dec 2014 14:37:43 +0100 pfannmo...@uni-greifswald.de wrote: Dear FreeSurfer Experts, I am puzzeled about the probabilities in the Brodmann area labels. If I take the Brodmann areas 1, 2, 3a and 3b and add their probabilities at a certain vertex a probability sum 1 should arise. This is due to the fact that 10 brains where analyzed in order to compute the probabilities and in each brain only one Brodmann area was found at each location. In my current test I recognized that values 1 occur as often as values 1. How is this possible? Respectfully pfannmoe ___ 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 mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] retinotopy analysis viewing problem in Freesurfer 5
On 12/08/2014 09:19 PM, zhang mingxia wrote: Hi Doug, I followed this guide: https://surfer.nmr.mgh.harvard.edu/fswiki/FsFastIndividualRetinotopyAnalysis. I used tksurfer-sess to view. Does significant activation in the visual cortex mean the map fromtksurfer-sess -a rtopy.self.?h -s sessid? If so, yes. My question is (1) What do the maps from tksurfer-sess -a rtopy.self.?h -s sessid -- this shows you the significance map (-log10(p)) with eccen and polar in different frames in the tksurfer overaly. , tksurfer-sess -a rtopy.self.?h -s sessid -map angle This shows you the angle with eccen and polar in different frames in the tksurfer overlay , tksurfer-sess -a rtopy.self.?h -s sessid -map angle.masked This shows you the angle with eccen and polar in different frames in the tksurfer overlay with the angle masked to only those voxels that are significant (p.01). and tksurfer-sess -a rtopy.self.?h -s sessid -fieldsign represent? This shows you the field sign map. (2)I expected to get a red, green and blue map, but none of them is. The first three are heat (yellow and red) and the fourth is red-blue. This is the first time for me to do retinotopic analysis. The data is from an experienced group for doing retinotopic research. I analyzed four runs with two for eccen and two for polar. Do other people also get this kind of color by using the script in the website above? tksurfer-sess will not generate a RGB colorwheel map. This functionality has been hard to continue to support. You can try rtview. You would use the RGB map to show the angle maps. (3)Which map is for delineating the boarder of visual area? field sign (4)Again, I expect to get a red, green and blue map as this people asked :https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg21512.html. How can I get a standard color? Thanks again! Mingxia On Tue, Dec 9, 2014 at 12:07 AM, Douglas N Greve gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu wrote: I'm not sure what you are asking for. Do you see significant activation in the visual cortex? What command are you running to view? On 12/08/2014 09:48 AM, zhang mingxia wrote: Dear freesurfer experts, I used Freesurfer 5 to do the retinotopic analysis followed by https://surfer.nmr.mgh.harvard.edu/fswiki/FsFastIndividualRetinotopyAnalysis. However, finally I didn't get a red, green and blue map as I expected. This is the first time for me to analyze retinotopic data. I have not quite understood what the raw angle map, the angle map masked by sig and field sign map meant. My purpose was to delineate the boarder of visual area. To my knowledge from previous study, I should get a colorful map. It seems I didn't get a right one (However, I exactly follow the guide and didn't get any error). Some other people seems having the same viewing problem: (He/She didn't have eccen data. I have both eccen and polar data. I also only got a heat map instead of a red, green and blue one) https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg21512.html (1)Is it due to the threshold? How can I get a red, green and blue map? (2) What does the three maps represent? Thanks a lot! Mingxia ___ 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 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 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.
Re: [Freesurfer] (no subject)
No, not for surfaces. Alphasim has to smooth the data which requires knowledge of the underlying geometry. Alphasim assumes a volume-based geometry and has no knowledge of surface-based geometry (unless it has been updated in the last 5 years). We have the ability to do simulations like alphasim on surface-based geometry. doug On 12/08/2014 09:36 PM, Xinfa Shi wrote: Hello,everyone Your reply said I can't use alphasim with qdec.By the way ,Could I use alphasim in other ways in FreeSurfer,for example command line ? Best regards. Xin-Fa Shi. ___ 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 gr...@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.
Re: [Freesurfer] multiple comparisons correction for individual hemispheres (native space)
Are you using 1.3 or 1,3 ? On 12/09/2014 03:10 AM, Milde, Christopher wrote: Dear Doug, I tried to run MCC with cluster-sess but unfortunately I got the same error message like when I'm using mri_glmfit-sim. It does not recognize the thresh (cluster-forming thresh) Here is the terminal output: Setting up environment for FreeSurfer/FS-FAST (and FSL) FREESURFER_HOME /home/christopher/Desktop/freesurfer FSFAST_HOME /home/christopher/Desktop/freesurfer/fsfast FSF_OUTPUT_FORMAT nii.gz SUBJECTS_DIR /home/christopher/Desktop/freesurfer/subjects MNI_DIR /home/christopher/Desktop/freesurfer/mni FSL_DIR /usr/local/fsl [christopher@fu20a S1]$ proj_dir=/home/christopher/Desktop/freesurfer/S1 [christopher@fu20a S1]$ cd $proj_dir [christopher@fu20a S1]$ [christopher@fu20a S1]$ cluster-sess -s PM_02540 -c stim_DL -analysis DL.sm5.rh -thresh 1.3 -cwp .05 -sign pos ERROR: thresh = 1,3, must be 1.3, 2.0, 2.3, 3.0, 3.3, 4.0 Sincerely yours, Christopher -Ursprüngliche Nachricht- Von: freesurfer-boun...@nmr.mgh.harvard.edu [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] Im Auftrag von Douglas N Greve Gesendet: Montag, 24. November 2014 20:34 An: freesurfer@nmr.mgh.harvard.edu Betreff: Re: [Freesurfer] multiple comparisons correction for individual hemispheres (native space) Hi Christopher, sorry for the delay. I had a write a new program. You can download it from here ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/cluster-sess Let me know how it goes doug On 11/14/2014 06:05 AM, Milde, Christopher wrote: Dear Freesurfer experts, I performed fMRI analysis using FSFast resulting in uncorrected significance maps (fsig.nii.gz). For selxavg3-sess I did not use the -fwhm flag (I rerun selxavg3-sess with -fwhm at moment). How can I use simulations for native space hemispheres?. I tried to adapt mri_glmfit-sim but unfortunately it failed... Sincerely yours, Christopher ___ 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 gr...@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. ___ 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 gr...@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
Re: [Freesurfer] thickness from pial and white
Yes, lh.pial exists Xiaomin On Dec 10, 2014, at 10:33 AM, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote: it only looks for that if it can't find lh.pial. Does that exist? On Wed, 10 Dec 2014, Xiaomin Yue wrote: Hi Bruce, the mris_thickness was looking for ?h.gray file to run correctly. But no such file exists. The freesurfer used is 5.3. Any ideas? The command line is: mris_thickness test_DB48 lh lh.thickness The error: reading gray matter surface /misc/data41/yuex/recon_test/test_DB48/surf/lh.gray MRISread(/misc/data41/yuex/recon_test/test_DB48/surf/lh.gray): could not open file. Thanks, Xiaomin From: yu...@hotmail.com To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] thickness from pial and white Date: Wed, 10 Dec 2014 02:47:02 + Thanks. I will try mris_fill. Xiaomin From: Bruce Fischl Sent: Tuesday, December 9, 2014 4:31 PM To: Freesurfer support list it creates a file in curvature format, yes. Did you try mris_fill for the wm.mgz? It won't be exactly the same as the one we would generate. You could use mris_fill to generate the interior of the ?h.white surface, then use the aseg to remove non-wm voxels I guess On Tue, 9 Dec 2014, Xiaomin Yue wrote: Thanks very much. Does this create curvature file? Again, is it possible to generate wm.mgz from those files? Thanks, Xiaomin On Dec 9, 2014, at 4:19 PM, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote: I think just the ?h.white and ?h.pial cheers Bruce On Tue, 9 Dec 2014, Xiaomin Yue wrote: What I mean by inputs is the default files the mris_thickness will be looking for to run correctly Xiaomin On Dec 9, 2014, at 1:08 PM, Xiaomin Yue yu...@hotmail.com wrote: Hi Bruce, Thanks for your response. What's the inputs to the mris_thickness? I need the wm.mgz to generate the ratio of gray vs. white matter. Xiaomin Date: Tue, 9 Dec 2014 09:55:21 -0500 From: fis...@nmr.mgh.harvard.edu To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] thickness from pial and white the thickness you can generate using mris_thikness. Why do you want to generate a wm.mgz? I guess you could from the wmparc On Mon, 8 Dec 2014, Xiaomin Yue wrote: Hi All, Cortical surface reconstructed using caret from a high resolution MRI data (0.25 mm) has been converted to freesurfer format, and viewed correctly using freeview. My questions are whether it is possible to generate 1) a ?h.thickness from the ?h.pial and ?h.white; 2) wm.mgz file using ?h.pial a nd ?h.white Thanks very much for your inputs. Xiaomin ___ 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 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 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 mailing list
Re: [Freesurfer] thickness from pial and white
Yes, lh.pial exists Xiaomin On Dec 10, 2014, at 10:33 AM, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote: it only looks for that if it can't find lh.pial. Does that exist? On Wed, 10 Dec 2014, Xiaomin Yue wrote: Hi Bruce, the mris_thickness was looking for ?h.gray file to run correctly. But no such file exists. The freesurfer used is 5.3. Any ideas? The command line is: mris_thickness test_DB48 lh lh.thickness The error: reading gray matter surface /misc/data41/yuex/recon_test/test_DB48/surf/lh.gray MRISread(/misc/data41/yuex/recon_test/test_DB48/surf/lh.gray): could not open file. Thanks, Xiaomin From: yu...@hotmail.com To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] thickness from pial and white Date: Wed, 10 Dec 2014 02:47:02 + Thanks. I will try mris_fill. Xiaomin From: Bruce Fischl Sent: Tuesday, December 9, 2014 4:31 PM To: Freesurfer support list it creates a file in curvature format, yes. Did you try mris_fill for the wm.mgz? It won't be exactly the same as the one we would generate. You could use mris_fill to generate the interior of the ?h.white surface, then use the aseg to remove non-wm voxels I guess On Tue, 9 Dec 2014, Xiaomin Yue wrote: Thanks very much. Does this create curvature file? Again, is it possible to generate wm.mgz from those files? Thanks, Xiaomin On Dec 9, 2014, at 4:19 PM, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote: I think just the ?h.white and ?h.pial cheers Bruce On Tue, 9 Dec 2014, Xiaomin Yue wrote: What I mean by inputs is the default files the mris_thickness will be looking for to run correctly Xiaomin On Dec 9, 2014, at 1:08 PM, Xiaomin Yue yu...@hotmail.com wrote: Hi Bruce, Thanks for your response. What's the inputs to the mris_thickness? I need the wm.mgz to generate the ratio of gray vs. white matter. Xiaomin Date: Tue, 9 Dec 2014 09:55:21 -0500 From: fis...@nmr.mgh.harvard.edu To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] thickness from pial and white the thickness you can generate using mris_thikness. Why do you want to generate a wm.mgz? I guess you could from the wmparc On Mon, 8 Dec 2014, Xiaomin Yue wrote: Hi All, Cortical surface reconstructed using caret from a high resolution MRI data (0.25 mm) has been converted to freesurfer format, and viewed correctly using freeview. My questions are whether it is possible to generate 1) a ?h.thickness from the ?h.pial and ?h.white; 2) wm.mgz file using ?h.pial a nd ?h.white Thanks very much for your inputs. Xiaomin ___ 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 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 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 mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] thickness from pial and white
what version of FS do you have? You can try runing it with -pial pial but I wouldn't think that is needed. Is the lh.pial in /misc/data41/yuex/recon_test/test_DB48/surf/ and is it readable? On Wed, 10 Dec 2014, Xiaomin Yue wrote: Yes, lh.pial exists Xiaomin On Dec 10, 2014, at 10:33 AM, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote: it only looks for that if it can't find lh.pial. Does that exist? On Wed, 10 Dec 2014, Xiaomin Yue wrote: Hi Bruce, the mris_thickness was looking for ?h.gray file to run correctly. But no such file exists. The freesurfer used is 5.3. Any ideas? The command line is: mris_thickness test_DB48 lh lh.thickness The error: reading gray matter surface /misc/data41/yuex/recon_test/test_DB48/surf/lh.gray MRISread(/misc/data41/yuex/recon_test/test_DB48/surf/lh.gray): could not open file. Thanks, Xiaomin From: yu...@hotmail.com To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] thickness from pial and white Date: Wed, 10 Dec 2014 02:47:02 + Thanks. I will try mris_fill. Xiaomin From: Bruce Fischl Sent: Tuesday, December 9, 2014 4:31 PM To: Freesurfer support list it creates a file in curvature format, yes. Did you try mris_fill for the wm.mgz? It won't be exactly the same as the one we would generate. You could use mris_fill to generate the interior of the ?h.white surface, then use the aseg to remove non-wm voxels I guess On Tue, 9 Dec 2014, Xiaomin Yue wrote: Thanks very much. Does this create curvature file? Again, is it possible to generate wm.mgz from those files? Thanks, Xiaomin On Dec 9, 2014, at 4:19 PM, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote: I think just the ?h.white and ?h.pial cheers Bruce On Tue, 9 Dec 2014, Xiaomin Yue wrote: What I mean by inputs is the default files the mris_thickness will be looking for to run correctly Xiaomin On Dec 9, 2014, at 1:08 PM, Xiaomin Yue yu...@hotmail.com wrote: Hi Bruce, Thanks for your response. What's the inputs to the mris_thickness? I need the wm.mgz to generate the ratio of gray vs. white matter. Xiaomin Date: Tue, 9 Dec 2014 09:55:21 -0500 From: fis...@nmr.mgh.harvard.edu To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] thickness from pial and white the thickness you can generate using mris_thikness. Why do you want to generate a wm.mgz? I guess you could from the wmparc On Mon, 8 Dec 2014, Xiaomin Yue wrote: Hi All, Cortical surface reconstructed using caret from a high resolution MRI data (0.25 mm) has been converted to freesurfer format, and viewed correctly using freeview. My questions are whether it is possible to generate 1) a ?h.thickness from the ?h.pial and ?h.white; 2) wm.mgz file using ?h.pial a nd ?h.white Thanks very much for your inputs. Xiaomin ___ 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 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 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] --reg in mri_vol2surf
Converting that matrix will not be easy. If you want to try, look at our wiki page on coordinate systems and see how your coordinate systems match up. It won't be easy. Your bbregister command is not going to work for sure, you cannot use --init-header (which should only be used for two MRIs acquired in the same session). Try --init-fsl or --init-spm. Most PET tracers have an effective T2 weighting On 12/08/2014 04:52 PM, Liang Wang wrote: Hi Bruce, Thanks a lot for the suggestions! Here are some followup questions. 1) The functional volume was PET data and anatomical data have been processed with Freesurfer. I run the bbregister as: bbregister --mov PET.nii --s subject_name --reg register.dat --t1 --init-header It does not register the PET to anatomical images well. Since PET contrast does not like the typical t1/t2, I am not sure how to set the --contrast argument (already tried to both t1 and t2). Also, as PET and anatomical are both in native space, not sure how to set the --init- 2) Actually, the PET image has been aligned with orig.mgz well (in the native space) using a in-house method. The registration matrix likes below: 0.992629 0.109294 0.052358 10.4812 -0.102034 0.986829 -0.125525 16.5118 -0.065387 0.119257 0.990708 -23.4735 0.00 0.00 0.001. I wonder if there is a way that can convert this matrix to a readable format for mri_vol2surf. 3) I tried to run mri_vol2surf (using a --regheader option as pet.nii and orig.mgz already aligning well) as: mri_vol2surf --mov PET.nii --hemi lh --regheader subject_name --o lh.pet.mgh. But the results does not look right. Any suggestions for these questions would be very appreciated! -Liang On Fri, Dec 5, 2014 at 5:40 PM, Bruce Fischl fis...@nmr.mgh.harvard.edu mailto:fis...@nmr.mgh.harvard.edu wrote: Hi Liang try bbregister. cheers Bruce On Fri, 5 Dec 2014, Liang Wang wrote: Hi Experts, At subject level, I want to convert a functional volume (in a subject's native space) to this subject's native surface. The functional volume has been registered to this subject T1 images in native space. I know mri_vol2surf' would do the job but unsure how to generate the registration matrix for --reg option. I appreciate any suggestions. Thanks -Liang ___ 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. ___ 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 gr...@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
[Freesurfer] [Fwd: Re: Modeling cortical thickness question]
Hi Doug, Thanks for your response! Please see Josh's follow-up question below. Thanks again for your help! Best, Alex Original Message Subject: Re: [Fwd: Re: [Freesurfer] Modeling cortical thickness question] From:Roffman, Joshua L.,M.D. jroff...@partners.org Date:Wed, December 10, 2014 11:52 am To: Alexandra Tanner atan...@nmr.mgh.harvard.edu -- Maybe...if we take this approach I guess we would want the cube root of age, not age cubed? The relationship we are testing is whether y=x^3 (where x is age and y is cortical thickness). So if we took the cube root of both sides, that might be closer to what we want? (Alex: could you forward this to the list) Thx Josh Sent from my iPhone On Dec 10, 2014, at 9:32 AM, Alexandra Tanner atan...@nmr.mgh.harvard.edu wrote: Hi Josh, Below is Doug's response...does this answer your question? Thanks, Alex Original Message Subject: Re: [Freesurfer] Modeling cortical thickness question From:Douglas N Greve gr...@nmr.mgh.harvard.edu Date:Tue, December 9, 2014 4:48 pm To: freesurfer@nmr.mgh.harvard.edu -- Do you mean a polynomial of age? If so, just add age age^2 and age^3 as variables in the FSGD file doug On 12/09/2014 02:04 PM, Alexandra Tanner wrote: Hello Freesurfers, Our group is wondering if any of you know whether it is possible to model cortical thickness as a third order polynomial? The specific question is: we are looking at whether there is a hyperbolic relationship between cortical thickness and date of birth among a cohort of individuals born over a 6 year period. Any insights would be greatly appreciated! Thanks, Alex ___ 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 gr...@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 ___ 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] QDEC cluster stats
Hi All, I am using QDEC to run a correlation analysis and I have a lot of large significant clusters that encompass various different cortical regions. I am hoping to extract mean thickness' from the significant clusters in order to create a plot to display the correlations. Can anyone tell me where to find or how to generate stats (e.g. mean thickness/SD) for each significant cluster? At the moment I am only able to visualise the regions or plot correlations for regional thickness' but this doesn't reflect the significant clusters. Do I need to draw an ROI around the cluster and generate the stats? Best wishes, Amanda ___ 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] thickness from pial and white
The problem was solved. I typed the wrong name. mris_fill had generated wm.mgz correctly, with the problem that a significant portion of white matter was cutted off. The problem I believe is that the resolution or the matrix size of wm.mgz is limited to 256 X 256 X 256, but the high resolution data has dimension larger than that. Is it possible to have a wm.mgz larger than 256^3? Or some kind of trick to make it happen? Thanks,Xiaomin Date: Wed, 10 Dec 2014 11:37:29 -0500 From: fis...@nmr.mgh.harvard.edu To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] thickness from pial and white what version of FS do you have? You can try runing it with -pial pial but I wouldn't think that is needed. Is the lh.pial in /misc/data41/yuex/recon_test/test_DB48/surf/ and is it readable? On Wed, 10 Dec 2014, Xiaomin Yue wrote: Yes, lh.pial exists Xiaomin On Dec 10, 2014, at 10:33 AM, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote: it only looks for that if it can't find lh.pial. Does that exist? On Wed, 10 Dec 2014, Xiaomin Yue wrote: Hi Bruce, the mris_thickness was looking for ?h.gray file to run correctly. But no such file exists. The freesurfer used is 5.3. Any ideas? The command line is: mris_thickness test_DB48 lh lh.thickness The error: reading gray matter surface /misc/data41/yuex/recon_test/test_DB48/surf/lh.gray MRISread(/misc/data41/yuex/recon_test/test_DB48/surf/lh.gray): could not open file. Thanks, Xiaomin From: yu...@hotmail.com To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] thickness from pial and white Date: Wed, 10 Dec 2014 02:47:02 + Thanks. I will try mris_fill. Xiaomin From: Bruce Fischl Sent: Tuesday, December 9, 2014 4:31 PM To: Freesurfer support list it creates a file in curvature format, yes. Did you try mris_fill for the wm.mgz? It won't be exactly the same as the one we would generate. You could use mris_fill to generate the interior of the ?h.white surface, then use the aseg to remove non-wm voxels I guess On Tue, 9 Dec 2014, Xiaomin Yue wrote: Thanks very much. Does this create curvature file? Again, is it possible to generate wm.mgz from those files? Thanks, Xiaomin On Dec 9, 2014, at 4:19 PM, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote: I think just the ?h.white and ?h.pial cheers Bruce On Tue, 9 Dec 2014, Xiaomin Yue wrote: What I mean by inputs is the default files the mris_thickness will be looking for to run correctly Xiaomin On Dec 9, 2014, at 1:08 PM, Xiaomin Yue yu...@hotmail.com wrote: Hi Bruce, Thanks for your response. What's the inputs to the mris_thickness? I need the wm.mgz to generate the ratio of gray vs. white matter. Xiaomin Date: Tue, 9 Dec 2014 09:55:21 -0500 From: fis...@nmr.mgh.harvard.edu To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] thickness from pial and white the thickness you can generate using mris_thikness. Why do you want to generate a wm.mgz? I guess you could from the wmparc On Mon, 8 Dec 2014, Xiaomin Yue wrote: Hi All, Cortical surface reconstructed using caret from a high resolution MRI data (0.25 mm) has been converted to freesurfer format, and viewed correctly using freeview. My questions are whether it is possible to generate 1) a ?h.thickness from the ?h.pial and ?h.white; 2) wm.mgz file using ?h.pial a nd ?h.white Thanks very much for your inputs. Xiaomin ___ 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 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
[Freesurfer] GI and CT relationship
Dear FreeSurfer users, I have a question regarding the link between cortical thickness and gyrification index: suppose I have a general decrease of cortical thickness in a lobe of the brain. Is it correct to suppose that consiquentely the gyrification index will decrease in the sulci (because of the decreased curvature) and that it will increase in the gyri (because of the increased curvature)? So that probably I would not be able to measure any difference in the gyrification index of that lobe? Thank you. Best, elisa ___ 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] coordinates in label-file?
Hello all! I saved clusters as labelfiles with mri_surfcluster (fMRI-Data, surface = self). The labels seem to hold the following data in each row: Vertex-No., x-, y-, z-coordinates of some kind (not so sure about that), and a t-value. The Label-Vertex-No. and t-value match the output (VtxMax and Max) in the sumfile of mri_surfcluster, while the coordinates don't match those in the sumfile. They seem to be neither in Talairach nor in MNI space, at least I don't get matching coordinates with the transforms described here: http://imaging.mrc-cbu.cam.ac.uk/imaging/MniTalairach I hope you could shed some light on whether these columns really hold some kind of coordinates, and if you know of a way to transform them into Talairach space! Best regards, Philipp This message was sent through https://webmail.uni-jena.de ___ 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] [Fwd: Re: Modeling cortical thickness question]
No, just include age^3, if the mean function is E(thickness | X) = B_0 + B_1 * age^3 It's similar to taking the logarithm of one of your predictors. Just remember that the units for the parameter estimate will be different than if you were just including age. On 12/10/2014 12:12 PM, Alexandra Tanner wrote: Hi Doug, Thanks for your response! Please see Josh's follow-up question below. Thanks again for your help! Best, Alex Original Message Subject: Re: [Fwd: Re: [Freesurfer] Modeling cortical thickness question] From:Roffman, Joshua L.,M.D. jroff...@partners.org Date:Wed, December 10, 2014 11:52 am To: Alexandra Tanner atan...@nmr.mgh.harvard.edu -- Maybe...if we take this approach I guess we would want the cube root of age, not age cubed? The relationship we are testing is whether y=x^3 (where x is age and y is cortical thickness). So if we took the cube root of both sides, that might be closer to what we want? (Alex: could you forward this to the list) Thx Josh Sent from my iPhone On Dec 10, 2014, at 9:32 AM, Alexandra Tanner atan...@nmr.mgh.harvard.edu wrote: Hi Josh, Below is Doug's response...does this answer your question? Thanks, Alex Original Message Subject: Re: [Freesurfer] Modeling cortical thickness question From:Douglas N Greve gr...@nmr.mgh.harvard.edu Date:Tue, December 9, 2014 4:48 pm To: freesurfer@nmr.mgh.harvard.edu -- Do you mean a polynomial of age? If so, just add age age^2 and age^3 as variables in the FSGD file doug On 12/09/2014 02:04 PM, Alexandra Tanner wrote: Hello Freesurfers, Our group is wondering if any of you know whether it is possible to model cortical thickness as a third order polynomial? The specific question is: we are looking at whether there is a hyperbolic relationship between cortical thickness and date of birth among a cohort of individuals born over a 6 year period. Any insights would be greatly appreciated! Thanks, Alex ___ 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 gr...@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 ___ 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 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] --reg in mri_vol2surf
Thanks Doug! Will try the --init-fsl or --init-spm for bbregister. -Liang On Wed, Dec 10, 2014 at 10:50 AM, Douglas N Greve gr...@nmr.mgh.harvard.edu wrote: Converting that matrix will not be easy. If you want to try, look at our wiki page on coordinate systems and see how your coordinate systems match up. It won't be easy. Your bbregister command is not going to work for sure, you cannot use --init-header (which should only be used for two MRIs acquired in the same session). Try --init-fsl or --init-spm. Most PET tracers have an effective T2 weighting On 12/08/2014 04:52 PM, Liang Wang wrote: Hi Bruce, Thanks a lot for the suggestions! Here are some followup questions. 1) The functional volume was PET data and anatomical data have been processed with Freesurfer. I run the bbregister as: bbregister --mov PET.nii --s subject_name --reg register.dat --t1 --init-header It does not register the PET to anatomical images well. Since PET contrast does not like the typical t1/t2, I am not sure how to set the --contrast argument (already tried to both t1 and t2). Also, as PET and anatomical are both in native space, not sure how to set the --init- 2) Actually, the PET image has been aligned with orig.mgz well (in the native space) using a in-house method. The registration matrix likes below: 0.992629 0.109294 0.052358 10.4812 -0.102034 0.986829 -0.125525 16.5118 -0.065387 0.119257 0.990708 -23.4735 0.00 0.00 0.001. I wonder if there is a way that can convert this matrix to a readable format for mri_vol2surf. 3) I tried to run mri_vol2surf (using a --regheader option as pet.nii and orig.mgz already aligning well) as: mri_vol2surf --mov PET.nii --hemi lh --regheader subject_name --o lh.pet.mgh. But the results does not look right. Any suggestions for these questions would be very appreciated! -Liang On Fri, Dec 5, 2014 at 5:40 PM, Bruce Fischl fis...@nmr.mgh.harvard.edu mailto:fis...@nmr.mgh.harvard.edu wrote: Hi Liang try bbregister. cheers Bruce On Fri, 5 Dec 2014, Liang Wang wrote: Hi Experts, At subject level, I want to convert a functional volume (in a subject's native space) to this subject's native surface. The functional volume has been registered to this subject T1 images in native space. I know mri_vol2surf' would do the job but unsure how to generate the registration matrix for --reg option. I appreciate any suggestions. Thanks -Liang ___ 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. ___ 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 gr...@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 ___ 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] mris_calc or other calculators
Hi experts, I have cortical thickness on fsaverage surfaces (?h.thickness_on_fsaverage.mgh) from a group of individuals. I'd like to create a volume (.mgh) that represents group mean or sd or other descriptive statistics. I know mris_calc can do similar job but wonder if there is more straightforward way for this? Or I have to convert this (mgh) to other format and then use image calculator (e.g., fslmath etc) to do this? Thanks -Liang ___ 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] mris_calc or other calculators
You can use mri_concat, something like mri_concat file1.mgh file2.mgh --mean --o mean.mgh On 12/10/2014 04:00 PM, Liang Wang wrote: Hi experts, I have cortical thickness on fsaverage surfaces (?h.thickness_on_fsaverage.mgh) from a group of individuals. I'd like to create a volume (.mgh) that represents group mean or sd or other descriptive statistics. I know mris_calc can do similar job but wonder if there is more straightforward way for this? Or I have to convert this (mgh) to other format and then use image calculator (e.g., fslmath etc) to do this? Thanks -Liang ___ 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 gr...@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.
Re: [Freesurfer] mris_calc or other calculators
Cool! Thanks Doug! -Liang On Wed, Dec 10, 2014 at 3:05 PM, Douglas N Greve gr...@nmr.mgh.harvard.edu wrote: You can use mri_concat, something like mri_concat file1.mgh file2.mgh --mean --o mean.mgh On 12/10/2014 04:00 PM, Liang Wang wrote: Hi experts, I have cortical thickness on fsaverage surfaces (?h.thickness_on_fsaverage.mgh) from a group of individuals. I'd like to create a volume (.mgh) that represents group mean or sd or other descriptive statistics. I know mris_calc can do similar job but wonder if there is more straightforward way for this? Or I have to convert this (mgh) to other format and then use image calculator (e.g., fslmath etc) to do this? Thanks -Liang ___ 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 gr...@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. ___ 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] Question re. Tracula motion measures
Hi, I ran our pipeline script that contains DTI_prep and Tracula, and when I extracted the individual motion data, they are mostly zeros (see below) Is this normal? If this is a problem, can anyone please let me know if there any way to fix this (e.g. re-run the motion script..)? Your help would be greatly appreciated! ps: I just need to examine the motions between 2 groups (below are all data from the 2 groups). AvgTranslation AvgRotation PercentBadSlices AvgDropoutScore 0 0 0 1 0 0 0 1 0 0 0 1 0 0 0 1 0 0 0 1 0 0 0 1 0 0 0 1 0 0 0 1 0 0 0 1 0 0 0 1 0 0 0 1 0 0 0 1 0 0 0 1 0 0 0.0419463 1.02647 0 0 0 1 0 0 0 1 0 0 0 1 0 0 0 1 0 0 0 1 0 0 0 1 0 0 0 1 0 0 0 1 0 0 0 1 0 0 0 1 0 0 0 1 0 0 0 1 0 0 0 1 0 0 0.370763 1.23369 0 0 0 1 0 0 0 1 0 0 0 1 0 0 0 1 0 0 0 1 0 0 0 1 0 0 0 1 0 0 0.414365 1.13071 0 0 0 1 0 0 0 1 0 0 0 1 0 0 0 1 0 0 0 1 0 0 0 1 0 0 0 1 0 0 0 1 0 0 0 1 0 0 0 1 Thanks so much for helping! ___ 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] Discrete video card: ATI/AMD success stories?
ATI/AMD cards with up to date drivers should be fine. -Zeke On 12/05/2014 10:00 PM, Chris McNorgan wrote: Hi Freesurfers, I am spec'ing a couple of Linux workstations to run Freesurfer, among other software. Complicating matters, our preferred vendor's configurations include ATI/AMD video cards, but the FSWiki recommends nVidia cards. I was wondering if I am likely to run into problems if I go with the standard configurations, or if I should press to get an nVidia card certified for the system. Thanks ___ 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] Extracting hippocampus
the ribbon.mgz isn't part of autorecon2 (or autorecon1) I don't think. What are you trying to run? On Thu, 11 Dec 2014, pradeep mahato wrote: Hi Bruce, After running autorecon1 and autorecon2, I am getting an error saying ribbon.mgz file is missing. Is it that autorecon2 the 23rd function didn't execute. Attaching the recon log also. On Tue, Dec 9, 2014 at 6:48 PM, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote: Hi Pradeep sorry, I meant autorecon1 and autorecon2 (but not autorecon3) cheers Bruce On Tue, 9 Dec 2014, pradeep mahato wrote: Hi Bruce, I am using Intel Core 2 Quad core processor 2.2 GHz with 4 GB ram. The version i am using is freesurfer-i686-redhat-linux-gnu-stable5-20130513 Using autorecon2 process , I got error saying nu.mgz file is missing. Error : mghRead(/home/nsb/oasis/OAS2_RAW_PART1/OAS1_2/mri/nu.mgz, -1): could not open file Should I include nuintensitycor. Thanks Pradeep On Mon, Dec 8, 2014 at 7:01 PM, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote: Hi Pradeep you could only run recon-all -autorecon2 instead of -all which should save you some time. 30 hours is pretty long though. What hardware are you using? If you have a modern Linux box with say 4-8 cores it should take less than 10. Or with 2 cores and 4G of ram you could run 2 recons at the same time. What version of FS are you using? The newer ones use openmp, although only the dev version has a bunch of things that take advantage of it. If you want to use more than one core try using -openmmp 4 (to use 4 cores). cheers Bruce On Mon, 8 Dec 2014, pradeep mahato wrote: Hello, I need to extract Hippocampus from brain mri image. The recon-all process takes more than 30 hours to reconstruct from an single image. I am having an dataset of 200 subjects, it is not feasible to run the recon process for all individual brain mri images. Is there any method to possibly get the hippocampus segmented and get the statistical values faster and efficient way. Thanking You Pradeep Kumar Mahato ___ 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. -- Pradeep Kumar Mahato ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Pradeep Kumar Mahato ___ 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] Extracting hippocampus
I am running the recon method for oasis recon-all -autorecon1 -autorecon2 -i ./OAS2_0001_MR1/RAW/mpr-1.nifti.img -i ./OAS2_0001_MR1/RAW/mpr-2.nifti.img -i ./OAS2_0001_MR1/RAW/mpr-3.nifti.img -s OAS12_1 The program exited saying ribbon.mgz file is missing. Thus I am unable to get aseg.stats data. Pls help On Thu, Dec 11, 2014 at 8:54 AM, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote: the ribbon.mgz isn't part of autorecon2 (or autorecon1) I don't think. What are you trying to run? On Thu, 11 Dec 2014, pradeep mahato wrote: Hi Bruce, After running autorecon1 and autorecon2, I am getting an error saying ribbon.mgz file is missing. Is it that autorecon2 the 23rd function didn't execute. Attaching the recon log also. On Tue, Dec 9, 2014 at 6:48 PM, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote: Hi Pradeep sorry, I meant autorecon1 and autorecon2 (but not autorecon3) cheers Bruce On Tue, 9 Dec 2014, pradeep mahato wrote: Hi Bruce, I am using Intel Core 2 Quad core processor 2.2 GHz with 4 GB ram. The version i am using is freesurfer-i686-redhat-linux-gnu-stable5-20130513 Using autorecon2 process , I got error saying nu.mgz file is missing. Error : mghRead(/home/nsb/oasis/OAS2_RAW_PART1/OAS1_2/mri/nu.mgz, -1): could not open file Should I include nuintensitycor. Thanks Pradeep On Mon, Dec 8, 2014 at 7:01 PM, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote: Hi Pradeep you could only run recon-all -autorecon2 instead of -all which should save you some time. 30 hours is pretty long though. What hardware are you using? If you have a modern Linux box with say 4-8 cores it should take less than 10. Or with 2 cores and 4G of ram you could run 2 recons at the same time. What version of FS are you using? The newer ones use openmp, although only the dev version has a bunch of things that take advantage of it. If you want to use more than one core try using -openmmp 4 (to use 4 cores). cheers Bruce On Mon, 8 Dec 2014, pradeep mahato wrote: Hello, I need to extract Hippocampus from brain mri image. The recon-all process takes more than 30 hours to reconstruct from an single image. I am having an dataset of 200 subjects, it is not feasible to run the recon process for all individual brain mri images. Is there any method to possibly get the hippocampus segmented and get the statistical values faster and efficient way. Thanking You Pradeep Kumar Mahato ___ 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. -- Pradeep Kumar Mahato ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Pradeep Kumar Mahato ___ 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. -- Pradeep Kumar Mahato ___ Freesurfer mailing
Re: [Freesurfer] Getting voxel values from aseg.mgz
There is no documentation or example for mri_extract_label. What should be the syntax for it. What kernel and xform file should be used. On Wed, Dec 10, 2014 at 6:50 PM, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote: Hi Pradeep you can use mri_extract_label to copy just the hippocampal labels out of the segmentation if that is what you mean. The values for left and right hippocampus (17 and 53) can be found in $FREESURFER_HOME/FreeSurferColorLUT.txt cheers Bruce On Wed, 10 Dec 2014, pradeep mahato wrote: After the recon-all process I want to access all the voxels in the left hippocampus ( any subcortical region ) . Please tell me is there any method to extract this voxel values from an segmented image. Thanking you Pradeep Kumar Mahato ___ 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. -- Pradeep Kumar Mahato ___ 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.
