[Freesurfer] tkmedit
Hi freesurfer experts, I am trying to correct the pial surfaces for my cortical thickness analysis. I assume that I have to load my pial surface into tkmedit and that I have to specify the subject image_type and the absolute path. However, every time I specify the image_type of the subject, the terminal says that it cannot find the subject in the file I indicate, although I am of the opinion that it is the right file. Do I have to add something to the file where all the subject data is stored so that tkmedit can find the right data? Thanks for your help, Julia ___ 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] Structural images quality
Hi everyone, I am going to use FreeSurfer to analyze cortical thickness in some structural images. In order to generate the individual output, Freesurfer asks for 2 different input images. If I have two acquisitions from the same subject, but they present different degrees of quality (such as movement index), would it be better to use just one of them? Is there any problem in doing that? Also, is there a reliable index to assess the images level of movement before I use them on FreeSurfer? Thanks for that! ___ 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] Structural images quality
Hi Cícero there's no easy answer for this question. If one of them is seriously motion corrected you are probably better off only using the other, but it depends on what coil you used, what field strength, voxel res, etc Basically if one has sufficient CNR than it can be better than two, particularly if the 2nd is corrupted. In general we don't require 2 images cheers Bruce On Wed, 21 Mar 2012, Cícero Nardini Querido wrote: Hi everyone, I am going to use FreeSurfer to analyze cortical thickness in some structural images. In order to generate the individual output, Freesurfer asks for 2 different input images. If I have two acquisitions from the same subject, but they present different degrees of quality (such as movement index), would it be better to use just one of them? Is there any problem in doing that? Also, is there a reliable index to assess the images level of movement before I use them on FreeSurfer? Thanks for that! ___ 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] tkmedit
what is your command line? On Wed, 21 Mar 2012, Richter, Julia wrote: Hi freesurfer experts, I am trying to correct the pial surfaces for my cortical thickness analysis. I assume that I have to load my pial surface into tkmedit and that I have to specify the subject image_type and the absolute path. However, every time I specify the image_type of the subject, the terminal says that it cannot find the subject in the file I indicate, although I am of the opinion that it is the right file. Do I have to add something to the file where all the subject data is stored so that tkmedit can find the right data? Thanks for your help, Julia ___ 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] Structural images quality
Thanks for the answer, Bruce. Best, Cícero. 2012/3/21 Bruce Fischl fis...@nmr.mgh.harvard.edu Hi Cícero there's no easy answer for this question. If one of them is seriously motion corrected you are probably better off only using the other, but it depends on what coil you used, what field strength, voxel res, etc Basically if one has sufficient CNR than it can be better than two, particularly if the 2nd is corrupted. In general we don't require 2 images cheers Bruce On Wed, 21 Mar 2012, Cícero Nardini Querido wrote: Hi everyone, I am going to use FreeSurfer to analyze cortical thickness in some structural images. In order to generate the individual output, Freesurfer asks for 2 different input images. If I have two acquisitions from the same subject, but they present different degrees of quality (such as movement index), would it be better to use just one of them? Is there any problem in doing that? Also, is there a reliable index to assess the images level of movement before I use them on FreeSurfer? Thanks for that! 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. ___ 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] [BUG] epidewarp.fsl
epidewarp.fsl does not take non-integer smoothing kernel sizes. cheers, satra ___ 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] Tkmedit question
Dear All, I am trying to understand what should be my -fthresh and -fmax or -fmin and -fmax values while visualizing in tkmedit the significant map of uncorrected results so I can see all the clusters in this map. Further,I want to see what clusters from this map did not survived after corrections by multiple comparison for cluster voxel-wise equal 3. Thank you. Antonella ___ 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] Tkmedit question
Hi Antonella it's hard for us to know without seeing your data, but certainly setting them both to 0 will show you everything Bruce On Wed, 21 Mar 2012, Antonella Kis wrote: Dear All, I am trying to understand what should be my -fthresh and -fmax or -fmin and -fmax values while visualizing in tkmedit the significant map of uncorrected results so I can see all the clusters in this map. Further,I want to see what clusters from this map did not survived after corrections by multiple comparison for cluster voxel-wise equal 3. Thank you. Antonella ___ 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] interpreting cluster results
Dear FS group, This may be a trivial question. Could not find answer in the archives. When Freesurfer outputs cluster summary files, it displays number of vertices (NVtxs). What is the size of each of these vertices. In other words, is there a standard correspondence between number of vertices and area of the cluster. Thanks Koushik ___ 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] interpreting cluster results
Hi Koushik the vertices start out evenly spaced at 1mm, but various processing steps along the way change that. You can get a rough idea of how much area is devoted to each vertex by dividing the total surface area by the number of vertices, but of course there is a fair amount of variability, particularly in the vicinity of topological defects. cheers Bruce On Wed, 21 Mar 2012, Govindarajan, Koushik Athreya wrote: Dear FS group, This may be a trivial question. Could not find answer in the archives. When Freesurfer outputs cluster summary files, it displays number of vertices (NVtxs). What is the size of each of these vertices. In other words, is there a standard correspondence between number of vertices and area of the cluster. Thanks Koushik ___ 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] Skull strip and white matter
Hi, I am having an issue where some dura remains behind after the skull strip and is being mistakenly classified as white matter. Since it is just dura, and not skull, would it be better to edit the white matter volume or should I start by adjusting the skull strip since occurs earlier in the recon-all processing stream? --Vincent ___ 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] Skull strip and white matter
Hi Vincent is it affecting the surfaces? If not you can ignore it. Otherwise you might try the graph cuts skull stripping and/or changing the preflooding heights cheers Bruce On Wed, 21 Mar 2012, Vincent wrote: Hi, I am having an issue where some dura remains behind after the skull strip and is being mistakenly classified as white matter. Since it is just dura, and not skull, would it be better to edit the white matter volume or should I start by adjusting the skull strip since occurs earlier in the recon-all processing stream? --Vincent ___ 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] fsaverage documentation
Hi All, I was looking for documentation on the fsaverage brain but I do not have permission to access the *Buckner40http://surfer.nmr.mgh.harvard.edu/fswiki/Buckner40page for notes on building fsaverage*. http://surfer.nmr.mgh.harvard.edu/fswiki/Buckner40 Has the information on this page been relocated? If so, can you point me to the new location? Thanks Emily -- Emily J Rogalski, PhD Assistant Research Professor Northwestern University Cognitive Neurology and Alzheimer's Disease Center (CNADC) 320 E Superior Street Searle Building 11th Floor Chicago, IL 60611 312-503-1155 phone 312-908-8789 fax erogal...@gmail.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.
[Freesurfer] custom making an overlay
Hi freesurfers, Is it possible to make an overlay to load into tksurfer containing any type of data (for instance, centrality measures computed with graph theory) for a particular annotation? In the mailing archive, I've found tips about creating a custom LUT table and making it a segmentation, but you need the coordinates of the labels for that. In my case, I've made my own parcellation by using mris_divide_parcellation, so then I would have to know where to find the coordinates (I don't). And do you think this is the most efficient method? Thanks! -- Linda Douw, Ph.D. ___ 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] custom making an overlay
Hi Linda it should be easy enough to make a scalar map and save it from matlab using save_mgh or MRIwrite.m. If it's first dimension has nvertices then tksurfer will know it's a surface overlay and not a volume. cheers, Bruce On Wed, 21 Mar 2012, Linda Douw wrote: Hi freesurfers, Is it possible to make an overlay to load into tksurfer containing any type of data (for instance, centrality measures computed with graph theory) for a particular annotation? In the mailing archive, I've found tips about creating a custom LUT table and making it a segmentation, but you need the coordinates of the labels for that. In my case, I've made my own parcellation by using mris_divide_parcellation, so then I would have to know where to find the coordinates (I don't). And do you think this is the most efficient method? Thanks! ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] Skull strip failure
Hi, I have an image that is completing the skull strip with a lot of skull remaining and it is have a large effect on the surfaces. I've tried lowering the watershed threshold as low as 5 and I've tried adding the -gcut option, but the low threshold by itself does not eliminate the skull and gcut not only fails to remove the skull but it removes cerebellum as well. There is so much skull left that I am hesitant to try manual edits, but I don't know any other options. Are there any? By the way, this brain is from an older individual with pretty substantial atrophy. --Vincent ___ 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] Skull strip failure
Why don't you upload the subject and we'll take a look On Mar 21, 2012, at 8:24 PM, Vincent cloud@gmail.com wrote: Hi, I have an image that is completing the skull strip with a lot of skull remaining and it is have a large effect on the surfaces. I've tried lowering the watershed threshold as low as 5 and I've tried adding the -gcut option, but the low threshold by itself does not eliminate the skull and gcut not only fails to remove the skull but it removes cerebellum as well. There is so much skull left that I am hesitant to try manual edits, but I don't know any other options. Are there any? By the way, this brain is from an older individual with pretty substantial atrophy. --Vincent ___ 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] mkheadsurf and smseghead
Hi, In my previous lab, which I no longer have access to, we ran mkheadsurf as part of postprocessing, and it generated smseghead files. The latest version of Freesurfer which I recently downloaded (with mkheadsurf version v 1.8 2011/03/02 20:16:39 nicks Exp) does not generate these files - and moreover the smheadsurf environment variable (which defaults to 'smseghead') in the mkheadsurf script does not appear to be used for anything in that script. Have I forgotten to do something in the earlier processing stages, or have things changed? Will ___ 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.
