Re: [Freesurfer] multiple comparisons correction for individual hemispheres (native space)
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
Re: [Freesurfer] Extracting hippocampus
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
[Freesurfer] Probabilities in the Brodmann area labels
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.
Re: [Freesurfer] Probabilities in the Brodmann area labels
is this in your individual subject space or in fsaverage? On Tue, 9 Dec 2014, 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 ___ 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 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 and ?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.
Re: [Freesurfer] thickness from pial and white
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 and ?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] Modeling cortical thickness question
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 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] Problem with mris_register: face not in vertex face list
Dear Freesurfer support community, I am having a recurring issue with re-running a participant after making manual white matter edits (i.e., filling in holes in the wm.mgz file). I saved the new wm.mgz file and then reran using -make all (twice). For some reason, Freesurfer stops at the Surf Reg step, but only for the right hemisphere. When I check the surfaces, I have lh white and pial, but only rh white (no pial). Here is the error message I received both times (bold added for emphasis). Tue Dec 9 12:21:39 EST 2014 /gpfs/data/ddickstein/MRI_REVISED_STRUCTURE/Projects/Freesurfer_Analyses/data/s4504 /gpfs/runtime/opt/freesurfer/5.3.0/bin/recon-all -s /gpfs/data/ddickstein/MRI_REVISED_STRUCTURE/Projects/Freesurfer_Analyses/data/s4504 -hemi rh -surfreg # #@# Surf Reg rh Tue Dec 9 12:21:40 EST 2014 /gpfs/data/ddickstein/MRI_REVISED_STRUCTURE/Projects/Freesurfer_Analyses/data/s4504/scripts *mris_register -curv ../surf/rh.sphere /gpfs/runtime/opt/freesurfer/5.3.0/average/rh.average.curvature.filled.buckner40.tif ../surf/rh.sphere.reg * using smoothwm curvature for final alignment $Id: mris_register.c,v 1.59 2011/03/02 00:04:33 nicks Exp $ $Id: mrisurf.c,v 1.693.2.7 2013/05/12 22:28:01 nicks Exp $ reading surface from ../surf/rh.sphere... *mrisFindNeighbors: ../surf/rh.sphere: face[205364].v[0] = 103504, but face 205364 not in vertex 103504 face list* No such file or directory Linux node426 2.6.32-358.23.2.el6.x86_64 #1 SMP Wed Oct 16 18:37:12 UTC 2013 x86_64 x86_64 x86_64 GNU/Linux I think my error is related to the following error that someone else reported recently ( http://www.mail-archive.com/freesurfer%40nmr.mgh.harvard.edu/msg36707.html) though the function with the error (mris_euler_number) was different than the one I have. Dr. Fischl's response was to suggest a re-run (which I did) and to suggest that the surfaces ended up too big and that this bug could be fixed in the future. Could I have added too many WM voxels, making the resulting surface too big? I tried to be as conservative as possible, while still filling white matter holes in the anterior temporal lobes. I'm running Freesurfer v. 5.3.0 on a Linux system. Thanks in advance for answers! Ezra *___* *Ezra Wegbreit, PhD* NIMH T32 Post-doctoral Research Fellow in Child Mental Health Pedi-MIND Program at Bradley Hospital Department of Psychiatry and Human Behavior Brown University Warren Alpert Medical School (401) 432-1615 ezra_wegbr...@brown.edu *___* ___ 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
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 and ?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.
Re: [Freesurfer] thickness from pial and white
mris_thickness usage: mris_thickness [options] subject name hemi thickness file This program measures the thickness of the cortical surface and writes the resulting scalar field into a 'curvature' file thickness file. valid options are: -max max use max to threshold thickness (default=5mm) -fill_holes cortex label fsaverage cortex label fill in thickness in holes in the cortex label On Tue, 9 Dec 2014, Xiaomin Yue 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.
Re: [Freesurfer] Problem with mris_register: face not in vertex face list
seems like the rh.sphere file is corrupted. Maybe you ran out of disk space? I would try deleting it and reruning with -make all cheers Bruce On Tue, 9 Dec 2014, Wegbreit, Ezra wrote: Dear Freesurfer support community, I am having a recurring issue with re-running a participant after making manual white matter edits (i.e., filling in holes in the wm.mgz file). I saved the new wm.mgz file and then reran using -make all (twice). For some reason, Freesurfer stops at the Surf Reg step, but only for the right hemisphere. When I check the surfaces, I have lh white and pial, but only rh white (no pial). Here is the error message I received both times (bold added for emphasis). Tue Dec 9 12:21:39 EST 2014 /gpfs/data/ddickstein/MRI_REVISED_STRUCTURE/Projects/Freesurfer_Analyses/da ta/s4504 /gpfs/runtime/opt/freesurfer/5.3.0/bin/recon-all -s/gpfs/data/ddickstein/MRI_REVISED_STRUCTURE/Projects/Freesurfer_Analyses/da ta/s4504 -hemi rh -surfreg # #@# Surf Reg rh Tue Dec 9 12:21:40 EST 2014 /gpfs/data/ddickstein/MRI_REVISED_STRUCTURE/Projects/Freesurfer_Analyses/da ta/s4504/scripts mris_register -curv ../surf/rh.sphere/gpfs/runtime/opt/freesurfer/5.3.0/average/rh.average.curvature.filled.buck ner40.tif ../surf/rh.sphere.reg using smoothwm curvature for final alignment $Id: mris_register.c,v 1.59 2011/03/02 00:04:33 nicks Exp $ $Id: mrisurf.c,v 1.693.2.7 2013/05/12 22:28:01 nicks Exp $ reading surface from ../surf/rh.sphere... mrisFindNeighbors: ../surf/rh.sphere: face[205364].v[0] = 103504, but face 205364 not in vertex 103504 face list No such file or directory Linux node426 2.6.32-358.23.2.el6.x86_64 #1 SMP Wed Oct 16 18:37:12 UTC 2013 x86_64 x86_64 x86_64 GNU/Linux I think my error is related to the following error that someone else reported recently(http://www.mail-archive.com/freesurfer%40nmr.mgh.harvard.edu/msg36707.html ) though the function with the error (mris_euler_number) was different than the one I have. Dr. Fischl's response was to suggest a re-run (which I did) and to suggest that the surfaces ended up too big and that this bug could be fixed in the future. Could I have added too many WM voxels, making the resulting surface too big? I tried to be as conservative as possible, while still filling white matter holes in the anterior temporal lobes. I'm running Freesurfer v. 5.3.0 on a Linux system. Thanks in advance for answers! Ezra ___ Ezra Wegbreit, PhD NIMH T32 Post-doctoral Research Fellow in Child Mental Health Pedi-MIND Program at Bradley Hospital Department of Psychiatry and Human Behavior Brown University Warren Alpert Medical School (401) 432-1615 ezra_wegbr...@brown.edu ___ ___ 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
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.
Re: [Freesurfer] thickness from pial and white
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] thickness from pial and white
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] Modeling cortical thickness question
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 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
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 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] Getting voxel values from aseg.mgz
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.
