[Freesurfer] Convert non-surface labels to volume masks
Dear Freesurfers, I am trying to convert a non-surface label into a binary volume mask (does that make sense?). To create the label I used tkmedit (brush tool) to select the voxels I need on the appropriate slices and saved as a label file. Then I tried to use mri_label2vol to convert this label to a binary volume mask by doing: mri_label2vol --label lh-test.label --temp 100101AA/bold/006/f.nii --reg 100101AA/bold/register.dat --proj frac 0 1 .01 --subject AA --hemi lh --o 100101AA/bold/masks/lh-volmask.nii I got an error: Loading ./lh-test.label ERROR: label ./lh-test.label is not a surface label. So looks like mri_label2vol only works on surface labels. Is there a way to convert a label defined by tkmedit on the volume into a binary volume mask? Or is there a better way to do this? Thank you. Lingqiang Kong ___ 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] How to display the dtrecon results
Dear Lilla, Sorry I am bother you one more time with a question: I was trying to display the dtrecon result smore exactly the GLM group analysis results. After I did the mri_concat */fa-tal.nii --o group-fa-tal.nii I created a mask: mri_concat */mask-tal.nii --o group-masksum-tal.nii --mean mri_binarize --i group-masksum-tal.nii --min .999 --o group-mask-tal.nii then I ran the GLM Fit: mri_glmfit --y group-fa-tal.nii --mask group-mask-tal.nii\ --fsgd your.fsgd --C contrast --glmdir group_analysis.glmdir My questions are: 1) How I can display the uncorrected significance map values for the group analysis? What files should I use? I checked the DTI basic tutorial and I was trying the following: freeview -v /media/1Tra/Antonella_2011/DTI_FS/dtrecon/group-masksum-tal.nii \ /media/1Tra/Antonella_2011/DTI_FS/dtrecon/group_analysis.glmdir/contrast/sig.mgh:colormap=heat Is this right? Or I should use the mask.mgh 2) If my contrast is C = +1.0 -1.0 (I am not accounting for age nor for gender) the what the colours represents and how I can get the p values for the forming clusters? THANK YOU VERY MUCH! 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] TAL-to-avg35
Dear experts, I would appreciate if you can provide me with the TAL-to-avg35 template. Thank you very much! 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] Students for position (fwd)
FYI -- Forwarded message -- Date: Tue, 29 Nov 2011 14:26:21 -0500 From: Thomas Talavage To: "Sutton, Brad" , Bruce Fischl , Noam Harel , dn...@umich.edu, Peter A. Bandettini , x...@emory.edu, Steve Wright Subject: Students for position Hey folks --- If you could do one last ping of folks, anyone who wishes to apply for a position in BME here at Purdue should do so in the next few days (letters not needed immediately). We anticipate doing a first review of the imaging-related apps in the next week or so. https://engineering.purdue.edu/BME/AboutUs/FacultyPositions Thanks immensely! Tom ___ 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.
