[Freesurfer] issues about pial and wm edit
Dear all, I will really appreciate if you can help me with some issues about editing the pial surface. I have carefully followed the information on the web and looked up the mailing list but I still have the same doubts: 1) I have noticed that pial surface usually includes more than GM (dura, vessels...). My first question is if should we edit this kind of error. Sometimes I am completely sure what I need to correct, but I don't want to put human error in it. Moreover, we will spend to much time with big samples. 2) I have tried to edit the pial surface following the tutorial. After re-running -autorecon2-pial nothing seems to change. The voxels I deleted before are still there and the pial surface looks the same. What could be happening? 3) I have had the same problem with WM edit. After -autorecon2-wm everything remain as before edit. 4) I have read about regenerate the new pial surface with make_final_surfaces or from inside recon-all with -finalsurfs. The command could be something like this? recon-all -s mysubjectname -finalsurfs 5) If I need to fix pial and wm lesions in the same subject, do I need to run autorecon2-pial and -autorecon2-wm separately? Can I do it at the same time? And if I could, what command do I have to use? I hope these are not too much questions. Thank you very much in advance. Daniel Ferreira ___ 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] adding control points
Dear FS experts, we have run autorecon2 on a set of subjects and now we are in the process of manual editing adding control points. We read the tutorial about the manual editing; however, sometimes we have some doubts about adding or not adding control points in some regions. We had a look at the subject bert (included in FS distribution) to have a reference on what can be considered a good output and what is necessary to be edited. Can this subject be considered as a good one and used as reference, or do you have any additional reference subjects to look at? Thank you in advance Kind regards, Paola - DAI IL TUO 5 X MILLE AL SAN RAFFAELE. BASTA UNA FIRMA. SE FIRMI PER LA RICERCA SANITARIA DEL SAN RAFFAELE DI MILANO, FIRMI PER TUTTI. C.F. 03 06 42 80 153 INFO: 5permi...@hsr.it - www.5xmille.org ___ 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] tksurfer problems
Dear all: I installed Freesurfer, tested it with the recommended commands listed in http://surfer.nmr.mgh.harvard.edu/fswiki/TestingFreeSurfer and encountered a problem only in tksurfer. When I hit tksurfer yc (or bert) lh pial I get two kinds of error messages: can't find talairach file '/Volumes/Sophomore/ncku_KMU_fMRI/surfaces/yc/surf/../mri/orig/COR-.info/../transforms/talairach.xfm' surfer: single buffered window surfer: tkoInitWindow(yc) surfer: using interface /Applications/freesurfer/lib/tcl/tksurfer.new.tcl Error sourcing /Applications/freesurfer/lib/tcl/tksurfer.new.tcl: can't read env(MRI_DIR): no such variable I found both problems have been asked before (one at http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg02372.html another http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg00029.html and I tried to mimic the solution provided, but no luck so far. The problem persists. So I wonder if gurus in this forum might be kind enough to suggest some directions? I was baffled by this small problems for almost 1 week, so many thanks, chun-chia p.s., I checked the .xdebug_tksurfer returned empty files, and I am not sure where is the log file located... ___ 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] setting segmentation brush information from command line in tkmedit
Hi Folks, Currently I set the segmentation brush information from tkmedit buttons. (For example: Set Segmentation as Use as source and also set the color) I need to do this for a large number of subjects and I was wondering if it was possible to do this from command line ? thanks Mehul ___ 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.
