Re: [Freesurfer] Xhemi results
Is lh.lh-rh.thickness.sm00.mgh the left hemisphere overlay or the stack of voxel-wise cortical thickness difference between left and right hemisphere of each subject? I need to see the difference map of left and right (lh-rh) overlaid on both hemispheres! On Thu, Jul 11, 2013 at 6:01 PM, Douglas N Greve gr...@nmr.mgh.harvard.eduwrote: The first command loads the left hemisphere overlay onto the right hemisphere. Why do you want to do this? doug On 07/11/2013 11:13 AM, amirhossein manzouri wrote: As I mentioned before in my second question : tksurfer fsaverage_sym rh inflated -aparc -overlay lh.lh-rh.thickness.sm00.mgh tksurfer fsaverage_sym lh inflated -aparc -overlay lh.lh-rh.thickness.sm00.mgh For Right and Left side! BR On Thu, Jul 11, 2013 at 4:38 PM, Douglas Greve gr...@nmr.mgh.harvard.edumailto: gr...@nmr.mgh.harvard.**edu gr...@nmr.mgh.harvard.edu wrote: I don't know what you mean by overlaying the results on L R. What is your command line? On 7/11/13 3:34 AM, amirhossein manzouri wrote: Thanks Doug, When I overlay the results on L R , I see different patterns on each hemisphere. Is it something that I don't understand correctly? BR On Wed, Jul 10, 2013 at 5:45 PM, Douglas N Greve gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.**edugr...@nmr.mgh.harvard.edu wrote: On 07/10/2013 01:26 AM, amirhossein manzouri wrote: Dear Doug and FS experts, I am trying to use Xhemi tool to study asymmetry in the brain. I have done the exact procedure you mentioned in WiKi for a group of 40 controls. 1) Is lh.lh-rh.thickness.sm00.mgh the stack of voxel-wise cortical thickness difference between left and right hemisphere of each subject? Yes. 2) If yes, shouldn't I see the similar mapping by overlaying this to lh and rh? (tksurfer fsaverage_sym rh inflated -aparc -overlay lh.lh-rh.thickness.sm00.mgh) I don't know what you mean. Can you elaborate/ 3) How do you interpret the result after analyzing within one group? ( tksurfer fsaverage_sym lh inflated -aparc -overlay glm.lh.lh-rh.thickness.sm05/**osgm/sig.mgh) It is the difference between left and right hemisphere at each vertex. 4) Is there any way to look at the results through the brain per slice and also the whole brain? Do you mean mapping the difference into the volume and then viewing it as a volume? If so, You can try mri_surf2vol doug -- Best regards, Amirhossein Manzouri __**_ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu mailto:freesur...@nmr.mgh.**harvard.eduFreesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.**edu/mailman/listinfo/** freesurferhttps://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.**edugr...@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/BugReportinghttp://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting http://surfer.nmr.mgh.**harvard.edu/fswiki/**BugReportinghttp://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.**edu/filedrop2https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/**facility/filedrop/index.htmlhttp://www.nmr.mgh.harvard.edu/facility/filedrop/index.html http://www.nmr.mgh.harvard.**edu/facility/filedrop/index.**htmlhttp://www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.**edu/transfer/outgoing/flat/** greve/ ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ __**_ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu mailto:freesur...@nmr.mgh.**harvard.eduFreesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.**edu/mailman/listinfo/**freesurferhttps://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/**compliancelinehttp://www.partners.org/complianceline. If the e-mail was sent to you in error
Re: [Freesurfer] Non-grey matter classified as grey matter
Dear Bruce, Would you please explain how and where to acquire FLAIR or T2 images to solve the problem? BR/Amir On Thu, Jul 11, 2013 at 9:47 PM, ye tian tianye...@gmail.com wrote: Dear Bruce and Doug, Thank you very much! PS: I searched through my data folder and didn't find T2 images. There goes all my afternoon! Ye On Thu, Jul 11, 2013 at 1:29 PM, Bruce Fischl fis...@nmr.mgh.harvard.eduwrote: the fix is to acquire a FLAIR or T2 image. What you are seing is the tentorium of the cerebellum which is very difficult to distinguish from cortical gray matter on a T1-weighted image. If you don't have either of those datasets you probably will need to do manual editing Bruce On Thu, 11 Jul 2013, ye tian wrote: Sorry! The attachments are really showing the same structure, but in different views. I have at least a hundred slices which include it. Since the pial surface is not extending into cerebellum, should I just edit brainmask.mgz? Is there a quicker fix to the problem than manual editing? Thank you very much! Sincerely, Ye On Thu, Jul 11, 2013 at 12:30 PM, Douglas N Greve gr...@nmr.mgh.harvard.edu wrote: what do you mean by the structure in the circle? The circles are pretty big and have a lot of WM and GM in them. On 07/11/2013 12:55 PM, ye tian wrote: Dear Doug, Thank you very much! Are you basically saying that the structure in the circle is not part of the cortex? Sincerely, Ye On Thu, Jul 11, 2013 at 11:01 AM, Douglas N Greve gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.**edugr...@nmr.mgh.harvard.edu wrote: yes On 07/11/2013 11:22 AM, ye tian wrote: Dear Freesurfers, Do you think I should delete the extra dura-like structure in the attached case? Thank you very much! Sincerely, Ye __**_ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu mailto:freesur...@nmr.mgh.**harvard.eduFreesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.**edu/mailman/listinfo/**freesurferhttps://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.**edugr...@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/BugReportinghttp://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting http://surfer.nmr.mgh.**harvard.edu/fswiki/**BugReportinghttp://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.**edu/filedrop2https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/**facility/filedrop/index.htmlhttp://www.nmr.mgh.harvard.edu/facility/filedrop/index.html http://www.nmr.mgh.harvard.**edu/facility/filedrop/index.**htmlhttp://www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.**edu/transfer/outgoing/flat/**greve/ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ __**_ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu mailto:freesur...@nmr.mgh.**harvard.eduFreesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.**edu/mailman/listinfo/**freesurferhttps://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/**compliancelinehttp://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. -- 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/BugReportinghttp://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.**edu/filedrop2https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/**facility/filedrop/index.htmlhttp://www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.**edu/transfer/outgoing/flat/**greve/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
Re: [Freesurfer] Pearsons r / adj. r squared
That helps! Great, thanks! On Thu, Jul 11, 2013 at 11:39 PM, Douglas N Greve gr...@nmr.mgh.harvard.edu wrote: I've attached a matlab script which should do it. doug On 07/11/2013 04:28 PM, Martijn Steenwijk wrote: Dear all, Is there a way in freesurfer to compute surface wise pearsons r (for simple correlations) or adjusted r square / the vertex-wise explained variance for a GLM? Best, Martijn __**_ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.**edu/mailman/listinfo/**freesurferhttps://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/BugReportinghttp://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.**edu/filedrop2https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/**facility/filedrop/index.htmlhttp://www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.**edu/transfer/outgoing/flat/** greve/ 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.
[Freesurfer] Adjust lighting in Freeview
Hi all, Is there a way to ajust the camera lighting / add lights in Freeview? Currently the lighthing is such that the surface with normal pointing upwards are illuminated well, but the surface with normal pointing downwards not that good. Thanks for replies in advance, Martijn ___ 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] Non-grey matter classified as grey matter
Hi Amir I'm not sure I understand the question. You need to acquire them on each subject them same way you acquire your MPRAGE/T1-weighted image. Andre van der Kouwe (ccd) has some sequences you can use on his website if you want guidance on parameters and such. cheers Bruce On Fri, 12 Jul 2013, amirhossein manzouri wrote: Dear Bruce, Would you please explain how and where to acquire FLAIR or T2 images to solve the problem? BR/Amir On Thu, Jul 11, 2013 at 9:47 PM, ye tian tianye...@gmail.com wrote: Dear Bruce and Doug, Thank you very much! PS: I searched through my data folder and didn't find T2 images. There goes all my afternoon! Ye On Thu, Jul 11, 2013 at 1:29 PM, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote: the fix is to acquire a FLAIR or T2 image. What you are seing is the tentorium of the cerebellum which is very difficult to distinguish from cortical gray matter on a T1-weighted image. If you don't have either of those datasets you probably will need to do manual editing Bruce On Thu, 11 Jul 2013, ye tian wrote: Sorry! The attachments are really showing the same structure, but in different views. I have at least a hundred slices which include it. Since the pial surface is not extending into cerebellum, should I just edit brainmask.mgz? Is there a quicker fix to the problem than manual editing? Thank you very much! Sincerely, Ye On Thu, Jul 11, 2013 at 12:30 PM, Douglas N Greve gr...@nmr.mgh.harvard.edu wrote: what do you mean by the structure in the circle? The circles are pretty big and have a lot of WM and GM in them. On 07/11/2013 12:55 PM, ye tian wrote: Dear Doug, Thank you very much! Are you basically saying that the structure in the circle is not part of the cortex? Sincerely, Ye On Thu, Jul 11, 2013 at 11:01 AM, Douglas N Greve gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu wrote: yes On 07/11/2013 11:22 AM, ye tian wrote: Dear Freesurfers, Do you think I should delete the extra dura-like structure in the attached case? Thank you very much! Sincerely, Ye ___ 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. -- Douglas N. Greve, Ph.D. MGH-NMR Center
[Freesurfer] Freesurfer faster with CUDA or I7 3770k ?
Dear list, We are buying a computer dedicated mostly to Freesurfer. Initially we thought an I7 3770k a bit overclocked (about 4.5ghz) should be a good choice. However, I noticed that Freesurfer seem better tuned to use CUDA. Many of the messages I read are from 2010 so I am not sure whether this is the case. In sum is it better to focus on CUDA gpu or on Intel I7? Second, does the CUDA speeds matter a lot? Third, is it true that I will not be able to run multiple instances of Freesurfer with CUDA, which is possible with I7? Will it still be faster using CUDA rather than running a Freesurfer instance on each I7 core? Fourth, is the OS important, for example can we just continue on Ubuntu or is it better Debian/CentOS etc.? Thank you for your help and apologies if the questions are too basic. Dorian TJU ___ 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] Non-grey matter classified as grey matter
Thanks a lot! On Fri, Jul 12, 2013 at 4:15 PM, Bruce Fischl fis...@nmr.mgh.harvard.eduwrote: Hi Amir I'm not sure I understand the question. You need to acquire them on each subject them same way you acquire your MPRAGE/T1-weighted image. Andre van der Kouwe (ccd) has some sequences you can use on his website if you want guidance on parameters and such. cheers Bruce On Fri, 12 Jul 2013, amirhossein manzouri wrote: Dear Bruce, Would you please explain how and where to acquire FLAIR or T2 images to solve the problem? BR/Amir On Thu, Jul 11, 2013 at 9:47 PM, ye tian tianye...@gmail.com wrote: Dear Bruce and Doug, Thank you very much! PS: I searched through my data folder and didn't find T2 images. There goes all my afternoon! Ye On Thu, Jul 11, 2013 at 1:29 PM, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote: the fix is to acquire a FLAIR or T2 image. What you are seing is the tentorium of the cerebellum which is very difficult to distinguish from cortical gray matter on a T1-weighted image. If you don't have either of those datasets you probably will need to do manual editing Bruce On Thu, 11 Jul 2013, ye tian wrote: Sorry! The attachments are really showing the same structure, but in different views. I have at least a hundred slices which include it. Since the pial surface is not extending into cerebellum, should I just edit brainmask.mgz? Is there a quicker fix to the problem than manual editing? Thank you very much! Sincerely, Ye On Thu, Jul 11, 2013 at 12:30 PM, Douglas N Greve gr...@nmr.mgh.harvard.edu wrote: what do you mean by the structure in the circle? The circles are pretty big and have a lot of WM and GM in them. On 07/11/2013 12:55 PM, ye tian wrote: Dear Doug, Thank you very much! Are you basically saying that the structure in the circle is not part of the cortex? Sincerely, Ye On Thu, Jul 11, 2013 at 11:01 AM, Douglas N Greve gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.**edugr...@nmr.mgh.harvard.edu wrote: yes On 07/11/2013 11:22 AM, ye tian wrote: Dear Freesurfers, Do you think I should delete the extra dura-like structure in the attached case? Thank you very much! Sincerely, Ye __**_ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu mailto:freesur...@nmr.mgh.**harvard.eduFreesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.**edu/mailman/listinfo/** freesurfer 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.**edugr...@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/BugReportinghttp://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting http://surfer.nmr.mgh.**harvard.edu/fswiki/**BugReportinghttp://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.**edu/filedrop2https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/**facility/filedrop/index.htmlhttp://www.nmr.mgh.harvard.edu/facility/filedrop/index.html http://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/ ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ __**_ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu mailto:freesur...@nmr.mgh.**harvard.eduFreesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.**edu/mailman/listinfo/** freesurfer https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this
Re: [Freesurfer] large SD of aparc in one group
Laura, what is the coefficient of variation? Ie, the stddev/mean doug On 07/11/2013 08:54 AM, L. Koenders wrote: Dear FreeSurfer experts, We have a question regarding the aparc output from the stats files, and hopefulle you can help us. We have 4 independent groups, of about 30 subjects per group, all scanned using the same protocal on the same MRI scanner. We ran the cross sectional FreeSurfer (5.2.0, Linux centos4_x86_64) pipeline, and extracted the volume information per person from the .stat files using Matlab. We transfered the volume information into SPSS, to calculate the Means and Standard Deviations per group. We are interested in a couple of regions of interest (anterior + posterior cingulate, OFC, parahippocamus and insula). What strange is though, it that the means and standard deviations of 3 groups are comparable across all regions, but the SDs of 1 group are very (very!) large. This is not a group in which we expect brain atrophy or anything like that. Below you see the SD values of all groups, with SD values up to four times bigger in group 1! 1 2 3 4 caudal ACC 618 516 643 589 rostral ACC 1583578 692 623 PCC 1942721 616 749 OFC 2632134518441652 parahip 1198346 271 394 insula 1410103310961017 The outliers are different subject in every region, and I checked the parcellation output of them, that looks fine. We are wondering what could be the cause of this, do you have any ideas? Thank you in advance, Kind regards, Laura AMC Disclaimer : http://www.amc.nl/disclaimer ___ 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] Inflated surface smooth but white matter surface has holes
Dear Freesurfers, My inflated surface looks smooth in tksurfer, but white matter surface has holes in it. Is this an indication of topological defects? Thank you very much! Sincerely, Ye ___ 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] Inflated surface smooth but white matter surface has holes
Hi Ye almost certainly not. Try running mris_euler_number - it will tell you the topology of the surface (which is the same for inflated/white/pial/...) cheers Bruce On Fri, 12 Jul 2013, ye tian wrote: Dear Freesurfers, My inflated surface looks smooth in tksurfer, but white matter surface has holes in it. Is this an indication of topological defects? Thank you very much! Sincerely, Ye ___ 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] Xhemi results
Thanks a lot! On Fri, Jul 12, 2013 at 6:58 PM, Douglas N Greve gr...@nmr.mgh.harvard.eduwrote: It is the difference but it is on the tesselation of the left hemisphere. If you want it on the right hemisphere, then you need to perform the analysis on the right hemisphere. doug On 07/12/2013 02:37 AM, amirhossein manzouri wrote: Is lh.lh-rh.thickness.sm00.mgh the left hemisphere overlay or the stack of voxel-wise cortical thickness difference between left and right hemisphere of each subject? I need to see the difference map of left and right (lh-rh) overlaid on both hemispheres! On Thu, Jul 11, 2013 at 6:01 PM, Douglas N Greve gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.**edugr...@nmr.mgh.harvard.edu wrote: The first command loads the left hemisphere overlay onto the right hemisphere. Why do you want to do this? doug On 07/11/2013 11:13 AM, amirhossein manzouri wrote: As I mentioned before in my second question : tksurfer fsaverage_sym rh inflated -aparc -overlay lh.lh-rh.thickness.sm00.mgh tksurfer fsaverage_sym lh inflated -aparc -overlay lh.lh-rh.thickness.sm00.mgh For Right and Left side! BR On Thu, Jul 11, 2013 at 4:38 PM, Douglas Greve gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.**edugr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.**edu gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.**edu gr...@nmr.mgh.harvard.edu wrote: I don't know what you mean by overlaying the results on L R. What is your command line? On 7/11/13 3:34 AM, amirhossein manzouri wrote: Thanks Doug, When I overlay the results on L R , I see different patterns on each hemisphere. Is it something that I don't understand correctly? BR On Wed, Jul 10, 2013 at 5:45 PM, Douglas N Greve gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.**edugr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.**edugr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.**edugr...@nmr.mgh.harvard.edu wrote: On 07/10/2013 01:26 AM, amirhossein manzouri wrote: Dear Doug and FS experts, I am trying to use Xhemi tool to study asymmetry in the brain. I have done the exact procedure you mentioned in WiKi for a group of 40 controls. 1) Is lh.lh-rh.thickness.sm00.mgh the stack of voxel-wise cortical thickness difference between left and right hemisphere of each subject? Yes. 2) If yes, shouldn't I see the similar mapping by overlaying this to lh and rh? (tksurfer fsaverage_sym rh inflated -aparc -overlay lh.lh-rh.thickness.sm00.mgh) I don't know what you mean. Can you elaborate/ 3) How do you interpret the result after analyzing within one group? ( tksurfer fsaverage_sym lh inflated -aparc -overlay glm.lh.lh-rh.thickness.sm05/**osgm/sig.mgh) It is the difference between left and right hemisphere at each vertex. 4) Is there any way to look at the results through the brain per slice and also the whole brain? Do you mean mapping the difference into the volume and then viewing it as a volume? If so, You can try mri_surf2vol doug -- Best regards, Amirhossein Manzouri __**_ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu mailto:freesur...@nmr.mgh.**harvard.eduFreesurfer@nmr.mgh.harvard.edu mailto:freesur...@nmr.mgh.**harvard.eduFreesurfer@nmr.mgh.harvard.edu mailto:freesur...@nmr.mgh.**harvard.eduFreesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.**edu/mailman/listinfo/** freesurfer https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D.
[Freesurfer] integrating another atlas into Freesurfer
I have the Yeo resting-state fMRI atlases which I downloaded from http://www.freesurfer.net/fswiki/CorticalParcellation_Yeo2011 They consist of 3 versions, fsaverage being of interest here. The fsaverage folder provided includes the typical FS folders corresponding a recon-all for the average brain for this atlas. I wish to use this high resolution atlas to parcellate my individual subjects. I am unclear how to go about this. I have perused wiki pages on Annotation files FS labels Automatic surface labeling process Surface registration process but still do not find a clear path to my goal. Specifically I would like to end up with a matching set of surface and annot files, as high of resolution as possible, for each of my subjects. Using some specific numbers, the Yeo atlas has around 300,000 vertices when combining the lh.pial and rh.pial surfaces. The matching annot files I believe are lrh.Yeo2011_17Networks_N1000.annot, which together should also have 300,000 vertices. I suppose what I need to do is align each of my subjects to this atlas and project the atlas onto each subject to get a new surface and annot file for that subject, which will have some unique number of vertices for each subject. Please point me to the right set of documentation that will tell me how to do this. Thanks, -Jeff ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] FSFAST funcroi-sess problem
I'm using Freesurfer 5.3.0
(well, actually I ran the original analyses with 5.2.0 and then am running this
ROI follow-up with 5.2.0, could that be a problem? From the release notes, it
didn't look like it would be an issue)
Anyway, I've run the following set of commands:
funcroi-config -roi
/Volumes/Data/CP1/fsfast/secondLevel/CPA.sm05.lh/AR-v-CS/AR-v-CS_HC.wls/HC/roi.AR-v-CS_HC.HC.th2.neg.cluster1.roicfg
-annot
/Volumes/Data/CP1/fsfast/secondLevel/CPA.sm05.lh/AR-v-CS/AR-v-CS_HC.wls/HC/cache.th20.neg.sig.ocn.annot
cluster-001 -analysis CPA.sm05.lh
funcroi-sess -roi
/Volumes/Data/CP1/fsfast/secondLevel/CPA.sm05.lh/AR-v-CS/AR-v-CS_HC.wls/HC/roi.AR-v-CS_HC.HC.th2.neg.cluster1.roicfg
-s CPA003 -d .
I get the following output.
When I checked the results with:
tksurfer fsaverage lh inflated -overlay
roi.AR-v-CS_HC.HC.th2.neg.cluster1.nii.gz -fthresh .5
sure enough, it didn't look right. Instead of the cluster, I got speckles all
over the surface.
I used the Matlab command:
[vertex_coords, faces] = read_surf('lh.white');
and found sure enough that the size of the vertex array was only 143827 whereas
mri_info indicates that the ocn file has 163842
Any suggestions what I might be doing wrong?
Thanks!
Joe
---
/Volumes/Data/CP1/fsfast/CPA003
Fri Jul 12 18:23:28 EDT 2013
mri_annotation2label --subject CPA003 --hemi lh --annotation
/Volumes/Data/CP1/fsfast/secondLevel/CPA.sm05.lh/AR-v-CS/AR-v-CS_HC.wls/HC/cache.th20.neg.sig.ocn.annot
--outdir
/Volumes/Data/CP1/fsfast/CPA003/bold/CPA.sm05.lh/tmp.funcroi-sess.roi.AR-v-CS_HC.HC.th2.neg.cluster1/label
subject = CPA003
annotation =
/Volumes/Data/CP1/fsfast/secondLevel/CPA.sm05.lh/AR-v-CS/AR-v-CS_HC.wls/HC/cache.th20.neg.sig.ocn.annot
hemi = lh
outdir =
/Volumes/Data/CP1/fsfast/CPA003/bold/CPA.sm05.lh/tmp.funcroi-sess.roi.AR-v-CS_HC.HC.th2.neg.cluster1/label
surface = white
Reading surface
/Volumes/Data/CP1/freesurfer/CPA003/surf/lh.white
Loading annotations from
/Volumes/Data/CP1/fsfast/secondLevel/CPA.sm05.lh/AR-v-CS/AR-v-CS_HC.wls/HC/cache.th20.neg.sig.ocn.annot
MRISreadAnnotationIntoArray: vertex index out of range: 143827 i=,
in_array_size=143827
annot file:
/Volumes/Data/CP1/fsfast/secondLevel/CPA.sm05.lh/AR-v-CS/AR-v-CS_HC.wls/HC/cache.th20.neg.sig.ocn.annot
MRISreadAnnotationIntoArray: vertex index out of range: 143828 i=,
in_array_size=143827
annot file:
/Volumes/Data/CP1/fsfast/secondLevel/CPA.sm05.lh/AR-v-CS/AR-v-CS_HC.wls/HC/cache.th20.neg.sig.ocn.annot
MRISreadAnnotationIntoArray: vertex index out of range: 143829 i=,
in_array_size=143827
annot file:
/Volumes/Data/CP1/fsfast/secondLevel/CPA.sm05.lh/AR-v-CS/AR-v-CS_HC.wls/HC/cache.th20.neg.sig.ocn.annot
MRISreadAnnotationIntoArray: vertex index out of range: 143830 i=,
in_array_size=143827
annot file:
/Volumes/Data/CP1/fsfast/secondLevel/CPA.sm05.lh/AR-v-CS/AR-v-CS_HC.wls/HC/cache.th20.neg.sig.ocn.annot
MRISreadAnnotationIntoArray: vertex index out of range: 143831 i=,
in_array_size=143827
annot file:
/Volumes/Data/CP1/fsfast/secondLevel/CPA.sm05.lh/AR-v-CS/AR-v-CS_HC.wls/HC/cache.th20.neg.sig.ocn.annot
MRISreadAnnotationIntoArray: vertex index out of range: 143832 i=,
in_array_size=143827
annot file:
/Volumes/Data/CP1/fsfast/secondLevel/CPA.sm05.lh/AR-v-CS/AR-v-CS_HC.wls/HC/cache.th20.neg.sig.ocn.annot
MRISreadAnnotationIntoArray: vertex index out of range: 143833 i=,
in_array_size=143827
…
MRISreadAnnotationIntoArray: vertex index out of range: 163838 i=,
in_array_size=143827
annot file:
/Volumes/Data/CP1/fsfast/secondLevel/CPA.sm05.lh/AR-v-CS/AR-v-CS_HC.wls/HC/cache.th20.neg.sig.ocn.annot
MRISreadAnnotationIntoArray: vertex index out of range: 163839 i=,
in_array_size=143827
annot file:
/Volumes/Data/CP1/fsfast/secondLevel/CPA.sm05.lh/AR-v-CS/AR-v-CS_HC.wls/HC/cache.th20.neg.sig.ocn.annot
MRISreadAnnotationIntoArray: vertex index out of range: 163840 i=,
in_array_size=143827
annot file:
/Volumes/Data/CP1/fsfast/secondLevel/CPA.sm05.lh/AR-v-CS/AR-v-CS_HC.wls/HC/cache.th20.neg.sig.ocn.annot
MRISreadAnnotationIntoArray: vertex index out of range: 163841 i=,
in_array_size=143827
annot file:
/Volumes/Data/CP1/fsfast/secondLevel/CPA.sm05.lh/AR-v-CS/AR-v-CS_HC.wls/HC/cache.th20.neg.sig.ocn.annot
reading colortable from annotation file...
colortable with 3 entries read (originally none)
Seg base 0
max index = 2
1952
/Volumes/Data/CP1/fsfast/CPA003/bold/CPA.sm05.lh/tmp.funcroi-sess.roi.AR-v-CS_HC.HC.th2.neg.cluster1/label/lh.cluster-001.label
2532
/Volumes/Data/CP1/fsfast/CPA003/bold/CPA.sm05.lh/tmp.funcroi-sess.roi.AR-v-CS_HC.HC.th2.neg.cluster1/label/lh.cluster2.label
mri_label2label --hemi lh --srclabel
/Volumes/Data/CP1/fsfast/CPA003/bold/CPA.sm05.lh/tmp.funcroi-sess.roi.AR-v-CS_HC.HC.th2.neg.cluster1/label/lh.cluster-001.label
--srcsubject CPA003 --trglabel
[Freesurfer] AC/PC positions and other questions
Dear freesurfers, I'm working on a function to import automatically the segmentation folder into a Brainstorm database. I have a few questions: - Is there a way to read/get the position of the anterior and posterior commissures (AC/PC)? - What file should I read to get the labels corresponding to the aseg.mgz file? - Is there an easy way to generate surfaces for all the regions defined in aseg.mgz? - How do you create a mesh from a volume mask? Thanks, Francois ___ 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] FSFAST funcroi-sess problem
Hi Joe,
On 07/12/2013 06:51 PM, Joseph Dien wrote:
I'm using Freesurfer 5.3.0
(well, actually I ran the original analyses with 5.2.0 and then am
running this ROI follow-up with 5.2.0, could that be a problem? From
the release notes, it didn't look like it would be an issue)
No, that is fine.
Anyway, I've run the following set of commands:
funcroi-config -roi
/Volumes/Data/CP1/fsfast/secondLevel/CPA.sm05.lh/AR-v-CS/AR-v-CS_HC.wls/HC/roi.AR-v-CS_HC.HC.th2.neg.cluster1.roicfg
-annot
/Volumes/Data/CP1/fsfast/secondLevel/CPA.sm05.lh/AR-v-CS/AR-v-CS_HC.wls/HC/cache.th20.neg.sig.ocn.annot
cluster-001 -analysis CPA.sm05.lh
funcroi-sess -roi
/Volumes/Data/CP1/fsfast/secondLevel/CPA.sm05.lh/AR-v-CS/AR-v-CS_HC.wls/HC/roi.AR-v-CS_HC.HC.th2.neg.cluster1.roicfg
-s CPA003 -d .
I get the following output.
When I checked the results with:
tksurfer fsaverage lh inflated -overlay
roi.AR-v-CS_HC.HC.th2.neg.cluster1.nii.gz -fthresh .5
sure enough, it didn't look right. Instead of the cluster, I got
speckles all over the surface.
I used the Matlab command:
[vertex_coords, faces] = read_surf('lh.white');
and found sure enough that the size of the vertex array was only
143827 whereas mri_info indicates that the ocn file has 163842
When you made the analysis (mkanalysis-sess), do you specify the subject
as self or fsaverage?
doug
Any suggestions what I might be doing wrong?
Thanks!
Joe
---
/Volumes/Data/CP1/fsfast/CPA003
Fri Jul 12 18:23:28 EDT 2013
mri_annotation2label --subject CPA003 --hemi lh --annotation
/Volumes/Data/CP1/fsfast/secondLevel/CPA.sm05.lh/AR-v-CS/AR-v-CS_HC.wls/HC/cache.th20.neg.sig.ocn.annot
--outdir
/Volumes/Data/CP1/fsfast/CPA003/bold/CPA.sm05.lh/tmp.funcroi-sess.roi.AR-v-CS_HC.HC.th2.neg.cluster1/label
subject = CPA003
annotation =
/Volumes/Data/CP1/fsfast/secondLevel/CPA.sm05.lh/AR-v-CS/AR-v-CS_HC.wls/HC/cache.th20.neg.sig.ocn.annot
hemi = lh
outdir =
/Volumes/Data/CP1/fsfast/CPA003/bold/CPA.sm05.lh/tmp.funcroi-sess.roi.AR-v-CS_HC.HC.th2.neg.cluster1/label
surface = white
Reading surface
/Volumes/Data/CP1/freesurfer/CPA003/surf/lh.white
Loading annotations from
/Volumes/Data/CP1/fsfast/secondLevel/CPA.sm05.lh/AR-v-CS/AR-v-CS_HC.wls/HC/cache.th20.neg.sig.ocn.annot
MRISreadAnnotationIntoArray: vertex index out of range: 143827
i=, in_array_size=143827
annot file:
/Volumes/Data/CP1/fsfast/secondLevel/CPA.sm05.lh/AR-v-CS/AR-v-CS_HC.wls/HC/cache.th20.neg.sig.ocn.annot
MRISreadAnnotationIntoArray: vertex index out of range: 143828
i=, in_array_size=143827
annot file:
/Volumes/Data/CP1/fsfast/secondLevel/CPA.sm05.lh/AR-v-CS/AR-v-CS_HC.wls/HC/cache.th20.neg.sig.ocn.annot
MRISreadAnnotationIntoArray: vertex index out of range: 143829
i=, in_array_size=143827
annot file:
/Volumes/Data/CP1/fsfast/secondLevel/CPA.sm05.lh/AR-v-CS/AR-v-CS_HC.wls/HC/cache.th20.neg.sig.ocn.annot
MRISreadAnnotationIntoArray: vertex index out of range: 143830
i=, in_array_size=143827
annot file:
/Volumes/Data/CP1/fsfast/secondLevel/CPA.sm05.lh/AR-v-CS/AR-v-CS_HC.wls/HC/cache.th20.neg.sig.ocn.annot
MRISreadAnnotationIntoArray: vertex index out of range: 143831
i=, in_array_size=143827
annot file:
/Volumes/Data/CP1/fsfast/secondLevel/CPA.sm05.lh/AR-v-CS/AR-v-CS_HC.wls/HC/cache.th20.neg.sig.ocn.annot
MRISreadAnnotationIntoArray: vertex index out of range: 143832
i=, in_array_size=143827
annot file:
/Volumes/Data/CP1/fsfast/secondLevel/CPA.sm05.lh/AR-v-CS/AR-v-CS_HC.wls/HC/cache.th20.neg.sig.ocn.annot
MRISreadAnnotationIntoArray: vertex index out of range: 143833
i=, in_array_size=143827
…
MRISreadAnnotationIntoArray: vertex index out of range: 163838
i=, in_array_size=143827
annot file:
/Volumes/Data/CP1/fsfast/secondLevel/CPA.sm05.lh/AR-v-CS/AR-v-CS_HC.wls/HC/cache.th20.neg.sig.ocn.annot
MRISreadAnnotationIntoArray: vertex index out of range: 163839
i=, in_array_size=143827
annot file:
/Volumes/Data/CP1/fsfast/secondLevel/CPA.sm05.lh/AR-v-CS/AR-v-CS_HC.wls/HC/cache.th20.neg.sig.ocn.annot
MRISreadAnnotationIntoArray: vertex index out of range: 163840
i=, in_array_size=143827
annot file:
/Volumes/Data/CP1/fsfast/secondLevel/CPA.sm05.lh/AR-v-CS/AR-v-CS_HC.wls/HC/cache.th20.neg.sig.ocn.annot
MRISreadAnnotationIntoArray: vertex index out of range: 163841
i=, in_array_size=143827
annot file:
/Volumes/Data/CP1/fsfast/secondLevel/CPA.sm05.lh/AR-v-CS/AR-v-CS_HC.wls/HC/cache.th20.neg.sig.ocn.annot
reading colortable from annotation file...
colortable with 3 entries read (originally none)
Seg base 0
max index = 2
1 952
/Volumes/Data/CP1/fsfast/CPA003/bold/CPA.sm05.lh/tmp.funcroi-sess.roi.AR-v-CS_HC.HC.th2.neg.cluster1/label/lh.cluster-001.label
2 532
Re: [Freesurfer] AC/PC positions and other questions
On 07/12/2013 07:18 PM, François Tadel wrote: Dear freesurfers, I'm working on a function to import automatically the segmentation folder into a Brainstorm database. I have a few questions: - Is there a way to read/get the position of the anterior and posterior commissures (AC/PC)? What do you mean by position? Do you mean the col, row, slice? For the AC, it should be possible since it is at TalXYZ=(0,0,0). Is there such a coordinate for the PC? We don't find the actual AC or PC. - What file should I read to get the labels corresponding to the aseg.mgz file? $FREESURFER_HOME/ASegStatsLUT.txt - Is there an easy way to generate surfaces for all the regions defined in aseg.mgz? Do you mean a surface for, say, hippocampus? In principle, it is possible, but the question is whether it is accurate. - How do you create a mesh from a volume mask? You can run mri_tesselate on it. Again, it might not be very accurate. It will look better if you run mris_smooth on it. doug Thanks, Francois ___ 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] combining lh.annot and rh.annot files
Is it possible to combine the lh and rh annotation files into a single annotation file? How? -Jeff ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] integrating another atlas into Freesurfer
Hi Jeff, do you just want to map the annotations from fsaverage to your individual subject? If so, you can use mri_surf2surf, something like mri_surf2surf --srcsubject fsaverage --trgsubject yoursubject --hemi lh \ --sval-annot $SUBJECTS_DIR/fsaverage/label/lh.aparc.annot \ --tval $SUBJECTS_DIR/yoursubject/label/lh.subj1.aparc.annot doug On 07/12/2013 06:45 PM, Jeff Eriksen wrote: I have the Yeo resting-state fMRI atlases which I downloaded from http://www.freesurfer.net/fswiki/CorticalParcellation_Yeo2011 They consist of 3 versions, fsaverage being of interest here. The fsaverage folder provided includes the typical FS folders corresponding a recon-all for the average brain for this atlas. I wish to use this high resolution atlas to parcellate my individual subjects. I am unclear how to go about this. I have perused wiki pages on Annotation files FS labels Automatic surface labeling process Surface registration process but still do not find a clear path to my goal. Specifically I would like to end up with a matching set of surface and annot files, as high of resolution as possible, for each of my subjects. Using some specific numbers, the Yeo atlas has around 300,000 vertices when combining the lh.pial and rh.pial surfaces. The matching annot files I believe are lrh.Yeo2011_17Networks_N1000.annot, which together should also have 300,000 vertices. I suppose what I need to do is align each of my subjects to this atlas and project the atlas onto each subject to get a new surface and annot file for that subject, which will have some unique number of vertices for each subject. Please point me to the right set of documentation that will tell me how to do this. Thanks, -Jeff ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- 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] Freesurfer surface circle of pre-defined size
Hi Sarah, I can image several ways to do this. If you can go onto the surface and find an index that you want to be the center, then you can create a label file with a single point. It would look something like this (see fsaverage/label/lh.cortex.label for example): --cut-- #!ascii label , from subject vox2ras=TkReg 1 1 -27.106 -80.730 11.969 0.00 --cut-- In this case, the only thing that matters is the vertex number (1). Replace 1 with your vertex number. Assuming this file is called lh.point.label, run mri_label2label --srclabel lh.point.label --dilate 20 --s yoursubject --hemi lh --trglabel ./lh.point20.label --regmethod surface This will create a new label that has been dilated 20 times. You can load it in tksurfer. Is this what you want to do? doug On 07/11/2013 02:55 PM, sar...@nmr.mgh.harvard.edu wrote: I'd like to make a circle of a pre-defined size on the freesurfer surface, with RAS coordinates as the center of the circle. What would be the best way to do this? ___ 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] FSFAST funcroi-sess problem
I followed the tutorial:
mkanalysis-sess -fsd bold -analysis CPA.sm05.lh -surface fsaverage lh
-fwhm 5 -event-related -paradigm CPA1.par -nconditions 20 -spmhrf 0 -TR 2
-refeventdur 20.265 -polyfit 2 -per-run -force -nuisreg nuisreg2.dat 7
-tpexclude tpexclude.dat
On Jul 12, 2013, at 7:34 PM, Douglas N Greve gr...@nmr.mgh.harvard.edu wrote:
Hi Joe,
On 07/12/2013 06:51 PM, Joseph Dien wrote:
I'm using Freesurfer 5.3.0
(well, actually I ran the original analyses with 5.2.0 and then am
running this ROI follow-up with 5.2.0, could that be a problem? From
the release notes, it didn't look like it would be an issue)
No, that is fine.
Anyway, I've run the following set of commands:
funcroi-config -roi
/Volumes/Data/CP1/fsfast/secondLevel/CPA.sm05.lh/AR-v-CS/AR-v-CS_HC.wls/HC/roi.AR-v-CS_HC.HC.th2.neg.cluster1.roicfg
-annot
/Volumes/Data/CP1/fsfast/secondLevel/CPA.sm05.lh/AR-v-CS/AR-v-CS_HC.wls/HC/cache.th20.neg.sig.ocn.annot
cluster-001 -analysis CPA.sm05.lh
funcroi-sess -roi
/Volumes/Data/CP1/fsfast/secondLevel/CPA.sm05.lh/AR-v-CS/AR-v-CS_HC.wls/HC/roi.AR-v-CS_HC.HC.th2.neg.cluster1.roicfg
-s CPA003 -d .
I get the following output.
When I checked the results with:
tksurfer fsaverage lh inflated -overlay
roi.AR-v-CS_HC.HC.th2.neg.cluster1.nii.gz -fthresh .5
sure enough, it didn't look right. Instead of the cluster, I got
speckles all over the surface.
I used the Matlab command:
[vertex_coords, faces] = read_surf('lh.white');
and found sure enough that the size of the vertex array was only
143827 whereas mri_info indicates that the ocn file has 163842
When you made the analysis (mkanalysis-sess), do you specify the subject
as self or fsaverage?
doug
Any suggestions what I might be doing wrong?
Thanks!
Joe
---
/Volumes/Data/CP1/fsfast/CPA003
Fri Jul 12 18:23:28 EDT 2013
mri_annotation2label --subject CPA003 --hemi lh --annotation
/Volumes/Data/CP1/fsfast/secondLevel/CPA.sm05.lh/AR-v-CS/AR-v-CS_HC.wls/HC/cache.th20.neg.sig.ocn.annot
--outdir
/Volumes/Data/CP1/fsfast/CPA003/bold/CPA.sm05.lh/tmp.funcroi-sess.roi.AR-v-CS_HC.HC.th2.neg.cluster1/label
subject = CPA003
annotation =
/Volumes/Data/CP1/fsfast/secondLevel/CPA.sm05.lh/AR-v-CS/AR-v-CS_HC.wls/HC/cache.th20.neg.sig.ocn.annot
hemi = lh
outdir =
/Volumes/Data/CP1/fsfast/CPA003/bold/CPA.sm05.lh/tmp.funcroi-sess.roi.AR-v-CS_HC.HC.th2.neg.cluster1/label
surface = white
Reading surface
/Volumes/Data/CP1/freesurfer/CPA003/surf/lh.white
Loading annotations from
/Volumes/Data/CP1/fsfast/secondLevel/CPA.sm05.lh/AR-v-CS/AR-v-CS_HC.wls/HC/cache.th20.neg.sig.ocn.annot
MRISreadAnnotationIntoArray: vertex index out of range: 143827
i=, in_array_size=143827
annot file:
/Volumes/Data/CP1/fsfast/secondLevel/CPA.sm05.lh/AR-v-CS/AR-v-CS_HC.wls/HC/cache.th20.neg.sig.ocn.annot
MRISreadAnnotationIntoArray: vertex index out of range: 143828
i=, in_array_size=143827
annot file:
/Volumes/Data/CP1/fsfast/secondLevel/CPA.sm05.lh/AR-v-CS/AR-v-CS_HC.wls/HC/cache.th20.neg.sig.ocn.annot
MRISreadAnnotationIntoArray: vertex index out of range: 143829
i=, in_array_size=143827
annot file:
/Volumes/Data/CP1/fsfast/secondLevel/CPA.sm05.lh/AR-v-CS/AR-v-CS_HC.wls/HC/cache.th20.neg.sig.ocn.annot
MRISreadAnnotationIntoArray: vertex index out of range: 143830
i=, in_array_size=143827
annot file:
/Volumes/Data/CP1/fsfast/secondLevel/CPA.sm05.lh/AR-v-CS/AR-v-CS_HC.wls/HC/cache.th20.neg.sig.ocn.annot
MRISreadAnnotationIntoArray: vertex index out of range: 143831
i=, in_array_size=143827
annot file:
/Volumes/Data/CP1/fsfast/secondLevel/CPA.sm05.lh/AR-v-CS/AR-v-CS_HC.wls/HC/cache.th20.neg.sig.ocn.annot
MRISreadAnnotationIntoArray: vertex index out of range: 143832
i=, in_array_size=143827
annot file:
/Volumes/Data/CP1/fsfast/secondLevel/CPA.sm05.lh/AR-v-CS/AR-v-CS_HC.wls/HC/cache.th20.neg.sig.ocn.annot
MRISreadAnnotationIntoArray: vertex index out of range: 143833
i=, in_array_size=143827
…
MRISreadAnnotationIntoArray: vertex index out of range: 163838
i=, in_array_size=143827
annot file:
/Volumes/Data/CP1/fsfast/secondLevel/CPA.sm05.lh/AR-v-CS/AR-v-CS_HC.wls/HC/cache.th20.neg.sig.ocn.annot
MRISreadAnnotationIntoArray: vertex index out of range: 163839
i=, in_array_size=143827
annot file:
/Volumes/Data/CP1/fsfast/secondLevel/CPA.sm05.lh/AR-v-CS/AR-v-CS_HC.wls/HC/cache.th20.neg.sig.ocn.annot
MRISreadAnnotationIntoArray: vertex index out of range: 163840
i=, in_array_size=143827
annot file:
/Volumes/Data/CP1/fsfast/secondLevel/CPA.sm05.lh/AR-v-CS/AR-v-CS_HC.wls/HC/cache.th20.neg.sig.ocn.annot
MRISreadAnnotationIntoArray: vertex index out of range: 163841
i=, in_array_size=143827
annot file:
[Freesurfer] minor fsfast bug report
In the annot files generated by mri_glmfit-sim in 5.2.0 (e.g., cache.th20.pos.sig.ocn.annot), the names of the clusters take the form: cluster0 cluster-001 cluster-002 … but the last one is of the form cluster6 which is to say, no dash and no zero-padding. I assume they are meant to have a consistent format. Not a big deal, but consistency would be helpful for scripts. Cheers! Joe Joseph Dien, Senior Research Scientist University of Maryland E-mail: jdie...@mac.com Phone: 202-297-8117 http://joedien.com// ___ 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.
