[Freesurfer] longitudinal stream: adding a time point
Dear all, We have run recon-all longitudinal stream on two time points and now have an additional time point we would like to integrate. Since edits and analysis were already done using the 2 time points template, we would like to avoid creation of a new template (by combining all time points) and instead register the third time point to the pre-existing template. What is the best way to do so? Is there a way to force recon-all to use a specific template? Many thanks! Best, ruthi ___ 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] WM segmentation error longitudinal stream
Hi all, We have run longitudinal analysis on two time points. The resulting longitudinal WM surface for both time points excludes large parts of the cortex. The cross sectional surfaces and the wm.mgz are correct. The base wm.mgz also seems to be fine, however, the base white and pial surfaces do not follow the wm volume properly. We have rerun the longitudinal anlaysis (recon-all -long) according to the cheat sheet: 1. marking the base wm.mgz border with 255 voxel value (instead of 110) 2. adding control points to the base wm.mgz but it did not change the original result. Any idea how this can be fixed? Thank you very much in advance! Best, ruthi ___ 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] excluding labels
Hi,Would that make a difference?I would like to use the stats file, unless you recommend otherwise. Thanks!Best,ruthiOn 14 Oct 2014, at 17:43, Douglas N Greve <gr...@nmr.mgh.harvard.edu> wrote:Which cortical thickness measure? The value in the stats file or the values in the map prior to voxel-wise analysis?On 10/10/2014 03:57 AM, Adam, Ruth wrote:Hi,I would like to exclude areas which were incorrectly segmented and could not be corrected after editing and re-running recon-all from the cortical thickness measure.Thank you again.Best,ruthiOn 09 Oct 2014, at 19:57, Douglas Greve <gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu>> wrote:What analysis?On 10/9/14 11:35 AM, Adam, Ruth wrote:Hi all,Would be great is someone can tell me how to exclude user-defined labels from the analysis.As far as I understand after creating all labels, mris_label2annot with a custom colortable should be used.-Is this correct or is there a more efficient way to exclude labels form analysis?-How can the new annotation file be incorporated with old annotation files to mark what should be excluded/included in the analysis?-Can a similar operation be done directly for labels created in Tkmedit and volumes?Thank you very much in advance!Best,ruthi___Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer___Freesurfer mailing listFreesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurferThe information in this e-mail is intended only for the person to whom it isaddressed. If you believe this e-mail was sent to you in error and the e-mailcontains patient information, please contact the Partners Compliance HelpLine athttp://www.partners.org/complianceline . If the e-mail was sent to you in errorbut does not contain patient information, please contact the sender and properlydispose of the e-mail.___Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer-- Douglas N. Greve, Ph.D.MGH-NMR Centergr...@nmr.mgh.harvard.eduPhone Number: 617-724-2358Fax: 617-726-7422Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReportingFileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2www.nmr.mgh.harvard.edu/facility/filedrop/index.htmlOutgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/___Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://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] excluding labels
Hi,I would like to exclude areas which were incorrectly segmented and could not be corrected after editing and re-running recon-all from the cortical thickness measure. Thank you again.Best,ruthiOn 09 Oct 2014, at 19:57, Douglas Greve <gr...@nmr.mgh.harvard.edu> wrote: What analysis? On 10/9/14 11:35 AM, Adam, Ruth wrote: Hi all, Would be great is someone can tell me how to exclude user-defined labels from the analysis. As far as I understand after creating all labels, mris_label2annot with a custom colortable should be used. -Is this correct or is there a more efficient way to exclude labels form analysis? -How can the new annotation file be incorporated with old annotation files to mark what should be excluded/included in the analysis? -Can a similar operation be done directly for labels created in Tkmedit and volumes? Thank you very much in advance! Best, ruthi ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurferThe information in this e-mail is intended only for the person to whom it isaddressed. If you believe this e-mail was sent to you in error and the e-mailcontains patient information, please contact the Partners Compliance HelpLine athttp://www.partners.org/complianceline . If the e-mail was sent to you in errorbut does not contain patient information, please contact the sender and properlydispose 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] excluding labels
Hi all,Would be great is someone can tell me how to exclude user-defined labels from the analysis.As far as I understand after creating all labels, mris_label2annot with a custom colortable should be used.-Is this correct or is there a more efficient way to exclude labels form analysis?-How can the new annotation file be incorporated with old annotation files to mark what should be excluded/included in the analysis? -Can a similar operation be done directly for labels created in Tkmedit and volumes?Thank you very much in advance!Best,ruthi___ 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] excluding labels from analysis
Hi all,I would like to exclude user-defined labels from the analysis. As far as I understand after creating all labels, mris_label2annot with a custom colortable should be used.-Is this correct or is there a more efficient way to exclude labels form analysis?-How can the new annotation file be incorporated with old annotation files to mark what should be excluded/included in the analysis? -Can a similar operation be done directly for labels created in Tkmedit and volumes?Hope this is not too much for the beginning of the week.Thank you very much & Have a lovely week!Best,ruthi___ 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] create a label file in tkmedit
Hi all, I am creating a label file using the select voxels tool in TkMedit. However this doesn't work properly with e.g. all saved vertex IDs are set to -1. Example file: #!ascii label ….. , from subject ….. vox2ras=TkReg 19 -1 -40.000 52.000 21.000 110.00 -1 -39.000 52.000 21.000 110.00 -1 -38.000 52.000 21.000 110.00 -1 -37.000 52.000 21.000 110.00 -1 -37.000 52.000 19.000 110.00 -1 -37.000 52.000 17.000 102.00 -1 -38.000 52.000 17.000 108.00 -1 -39.000 52.000 18.000 110.00 -1 -39.000 52.000 19.000 110.00 -1 -39.000 52.000 20.000 110.00 -1 -38.000 52.000 20.000 110.00 -1 -38.000 52.000 19.000 110.00 -1 -38.000 52.000 23.000 110.00 -1 -38.000 52.000 22.000 110.00 -1 -37.000 52.000 22.000 109.00 -1 -37.000 52.000 20.000 110.00 -1 -39.000 52.000 22.000 110.00 -1 -39.000 52.000 24.000 108.00 -1 -39.000 52.000 23.000 110.00 Any ideas how this can be solved? Many thanks in advance! Best, ruthi ___ 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.
