Re: [Freesurfer] Visualizing individual ROI labels
Hi Elissa, you can load the labels into tksurfer or freeview and give them whatever color you like. Is that what you are trying to do? I think that's how Rahul created the figures in that paper. cheers Bruce On Sat, 4 Oct 2014, Elissa McIntosh wrote: Hello freesurfer experts, I am hoping that someone can tell me how I can create 3D representations of individual cortical ROIs (labels based on the Desikan/Killiany Atlas) to be used in figures. I'm trying to make figures that show the ROIs that I investigated (like this figure in Desikan et al. paper http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0012853) . I know that I can manually make a label in qdec, but I was hoping that there was an automated method to highlighting individual labels/ROIs. Thank you, Elissa ___ 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] Gyrification index vs cortical surface area
Dear FreeSurfer experts I have run analyses on gyrification index. I was wondering if anybody could tell me what exactly is the relationship between gyrification index and cortical area. My gyrification results and area results are to a large extent similar. Am I measuring approximately the same thing? Thank you Knut Jørgen Bjuland PhD candidate The Norwegian University of Science and Technology (NTNU) Trondheim, Norway ___ 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] rawfunc2surf-sess with a limited set of surface files
Hi, I want to use rawfunc2surf-sess to project the functional data onto the surface in the source subject and then in the target subject. My source subject has been processed in Freesurfer. However, my target subject has been processed in Caret, so I do not have all the surface files for the target subject. To get rawfunc2surf-sess to work for my situation, I have to make some minor changes in its code. By looking at the code, I realized that rawfunc2surf-sess calls mri_vol2surf for mask and raw data, then it calls mris_fwhm to smooth raw data within mask. I am describing the changes that I have to make in these two commands, plus a specific question for each change: 1) mri_vol2surf includes the --cortex flag. Since I do not have cortex.label in the target subject, I am removing this flag. Would this be problematic later on? I will eventually do specific analyses on the occipito-temporal vertices in Matlab. Since I have lobar labels in the target subject, I can select/mask those vertices later on. 2) For the source subject, I have the white and pial surfaces. For the target subject, I have the midthickness surface which is somewhere between white and pial. I am adding --surf midthickness in mri_vol2surf to specify the target surface to be midthickness (instead of white). Will this be a problem when the source subject does not have such surface? 3) There is --projfrac 0.5 in mri_vol2surf. The help says "When [the projfrac is] set at 0.5 with the white surface, this should sample in the middle of the cortical surface. This requires that a ?h.thickness file exist for the source subject". I have the thickness file in the source subject - though I don't have it in the target subject. Does 'projfracing' happen only for the source subject? 4) I assume that mris_fwhm will work fine for my situation, unless it requires the white surface in the target subject. Which file is used in mris_fwhm for extracting the vertices coordinates? Thanks in advance for your advice, Reza ___ 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] White matter and white matter lesions
Hi Douglas Thanks for your answers. I have two more questions: 1) In which file(s) do I find the labels 151-255? 2) What do the columns of zeros and the numbers 64, 112, 160, 208 and 255 in your answer mean? Leise -Original Message- From: Douglas Greve [mailto:gr...@nmr.mgh.harvard.edu] Sent: 4. oktober 2014 18:22 To: Leise Borg; freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] White matter and white matter lesions On 10/4/14 12:35 AM, Leise Borg wrote: > So - just to be sure - if I take labels 2, 7, 41, and 46 from aseg.mgz, then > I have ALL white matter in the entire brain? You should also add 251-255 251 CC_Posterior0 0 64 0 252 CC_Mid_Posterior0 0 112 0 253 CC_Central 0 0 160 0 254 CC_Mid_Anterior 0 0 208 0 255 CC_Anterior 0 0 255 0 > > And another question: I also need the white matter hypointensities. Until > now, I used label 77 of aparc.a2009s+aseg.mgz. Is that sufficient? Or should > I use the aseg.mgz file for this too? That is sufficient > > -Leise > > -Original Message- > From: Douglas N Greve [mailto:gr...@nmr.mgh.harvard.edu] > Sent: 3. oktober 2014 18:55 > To: Leise Borg; Freesurfer@nmr.mgh.harvard.edu > Subject: Re: [Freesurfer] White matter and white matter lesions > > > Those are the only WM labels present in the aseg. You may or may not want to > include brain stem as WM. > > > On 10/03/2014 04:03 AM, Leise Borg wrote: >> Hi again >> >> Labels 7 and 46 in the aseg-file gives me the cerebellum white matter >> - which I can see from the aseg.stat-file. From the list at >> http://www.slicer.org/slicerWiki/index.php/Slicer3:Freesurfer_labels >> I can see that I also need the labels 2 and 41. It looks ok to me >> when I plot it, but can I be sure that it gives me all white matter >> (NOT white matter hypointensities)? I can see that there are several >> other labels referring to white matter, such as label 219, 223, 3000 >> etc. Do those labels point at subsets of the labels 2 and 41 (and 7 and 46)? >> >> -Leise >> >> *From:*Leise Borg >> *Sent:* 3. oktober 2014 08:48 >> *To:* 'gr...@nmr.mgh.harvard.edu' >> *Subject:* Re: [Freesurfer] White matter and white matter lesions >> >> Hi Douglas >> >> Thanks a lot for your answer. I will definitely do that. Can you tell >> me how I load this aseg.stats file into Matlab? I do not have >> FreeSurfer downloaded on my own computer. Do I need that to load this >> file? >> >> -Leise. >> >> Why not just use the values in aseg.stats? >> >> On 10/01/2014 07:44 AM, Leise Borg wrote: >> >>> Hi FreeSurfer >>> I am working on a project concerning Alzheimer's patients and I need >>> to know the positions of white matter (WM) and white matter lesions >>> (WML) from your segmentations. >>> To find the WML, I use label 77 in the aparc.a2009s+aseg.mgz-files. >>> To find the WM, I use labels 2 and 41 in the ribbon.mgz-files and >>> subtract the ventricles by subtracting labels: 4, 5 14, 15, 43 44 >>> found in the aseg.mgz-files. >>> However, in the two sets of positions - one for WML and one for WM >>> -there is an overlap. It is not big, but it is there. >>> Can you help me finding the true WML- and WM-segmentations? >>> With kind regards, Leise. 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
