[Freesurfer] From flat map to mesh representation
Dear list, I have created flat maps of Freesurfer ROIs and manipulated them in Matlab to extract only the area of the ROI that I am interested in. Now, I would like to project the selected region onto the cortical mesh representation. Is there a way to know the correspondence between points on a flat map and vertices of the corresponding cortical mesh representation? Thanks a lot for your help! Best, Roberta ___ 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] Group analysis
Dear all, I created an average subject from my dataset and I would like to use it to run a group analysis of thickness. I am using the command: recon-all -s subjid -qcache -target MyAverage When looking at the terminal, I noticed that the srcsurfreg and the trgsurfreg are both sphere.reg: shouldn’t one of the two be sphere.reg.MyAverage? Otherwise, how is the alignment achieved? Thanks for your help. Best, Roberta ___ 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] mri_label2label
Dear all, I would like to draw a ROI on a group average surface (template) and map it back to the surface of individual subjects. For this, I would like to create the template based on my subjects, rather than using fsaverage. As far as I understood, I should first create the template by using: make_average_subject –out myAvg –subjects s1 s2 … Then, I should register each subject to the template with: mris_register --curv s1/surf/lh.sphere SUBJECTS_DIR/myAvg/lh.reg.template.tif s1/surf/lh.sphere.reg.myAvg. At this point, I can map the ROI to a given subject by using the command mri_label2label: mri_label2label --srclabel labelName --srcsubject myAvg --trgsubject s1 trglabel OutputLabelName --hemi lh --regmethod surface. There is one thing I don’t understand: how can I tell the command mri_label2label that it should use the registration file that I have created in the previous step (namely lh.sphere.reg.myAvg)? If I don't specify anything, is the function going to use the sphere.reg file that refers to the registration between subject s1 and fsaverage? In general, is the pipeline I described correct? Thanks a lot for your help. Best Roberta ___ 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] Overlay transparency
Dear all, I have selected some vertices that I would like to overlay on an inflated surface and I would like the overlay to have opacity1 such that I can see the curvature underneath. I am using a script for doing this and everything works, but the opacity doesn’t change when I use the command sclv_set_overlay_alpha 0.5. Does anyone know how to fix this problem? Thanks a lot Roberta ___ 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] Overlay transparency
Thanks a lot for your input, I’ll give it a try. Roberta On 27 Oct 2014, at 17:58, Ruopeng Wang rpw...@nmr.mgh.harvard.edumailto:rpw...@nmr.mgh.harvard.edu wrote: Hi Roberta, not sure how well you know freeview. You can set the opacity of overlay either from 'Configure Overlay' button on the GUI or from the command-line by ':opacity=0.5'. Ruopeng On 10/27/2014 12:53 PM, Bruce Fischl wrote: Hi Roberta you are probably better off doing this in freeview - Ruopeng can help you there. cheers Bruce On Mon, 27 Oct 2014, Roberta Santoro wrote: Dear all, I have selected some vertices that I would like to overlay on an inflated surface and I would like the overlay to have opacity1 such that I can see the curvature underneath. I am using a script for doing this and everything works, but the opacity doesn’t change when I use the command sclv_set_overlay_alpha 0.5. Does anyone know how to fix this problem? Thanks a lot Roberta ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto: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] Convert curv into volume
Dear all, I am trying to convert the curv surface into a volume by using the following command: mri_surf2vol –surf curv –hemi lh –template $subj/mri/T1.mgz –surfval $subj/surf/lh.curv –projfrac 0 –volregidentity $subj –o CurvatureVolume.nii I get the following error: the lh.curv has many more faces than vertices! If the curv file is not a surface, is it possible at all to convert it into a volume? Thanks a lot for your help. Best, Roberta ___ 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] Talairach transformation
Dear list, I am new to Freesurfer and I have a doubt about the Talairach transformation. As far I understand, the Talairach transformation is applied to compute the surface representations. However, this seems to be a “hidden“ step, i.e. no volume is saved as Talairach transformed. Is this correct? Do the final surfaces (and parcellations) show the brain before or after Talairach transformation? I am asking this because I need to extract ROIs in the original space, i.e. before Talairach transform. Thanks a lot for your help Roberta ___ 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.
