[Freesurfer] mri_cc
Dear all, mri_cc does not seem to be working properly to parcellate corpus callosum. As per one of the previous posts, there is a bug in the current release of mri_cc. However, the link provided in the same thread for an updated version of mri_cc is no longer existent. Our cluster runs on 64bit Ubuntu 14.04 systems. I'd be grateful if someone can post a new link for the corrected mri_cc. Thanks in advance. Cheers, Arash ___ 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_cc
Dear Freesurfer experts, Sorry for resending this post. mri_cc does not seem to be working properly to parcellate corpus callosum. As per one of the previous posts, there is a bug in the current release of mri_cc. However, the link provided in the same thread for an updated version of mri_cc is no longer existent. Our cluster runs on 64bit Ubuntu 14.04 systems. I'd be grateful if someone can post a new link for the corrected mri_cc. Thanks in advance. Cheers, Arash ___ 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] Projecting voxel intensities to a surface file
Dear all, I'm new to the freesurfer. I want to project surrounding cortical voxel values (intensities) from a given map (e.g. mean diffusivity map in a nifti format) to a surface file (e.g. mid-cortical surface in a gifti fromat) to generate scalar maps like ?h.thickness for group-wise statistics. Can this be carried out using freesurfer commands? Cheers, Arash ___ 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] Projecting voxel intensities to a surface file
Sorry. I meant to do that. Original Message From: Bruce Fischl To: Arash Nazeri Sent: Wed, Oct 23, 2013 8:25 am Subject: Re: [Freesurfer] Projecting voxel intensities to a surface file Hi Arash can you cc the list on this type of email so that others can answer? Particularly Matt Glasser! I suspect that they have already run bbregister, but I'm not sure. cheers Bruce On Wed, 23 Oct 2013, Arash Nazeri wrote: > Hi Bruce, > Thanks for your response. I think this will do the trick generally, is it > also possible to apply mri_vol2surf to the Human Connectome Project > preprocessed files, or should I rerun the recon-all? In the HCP dataset, the > surface files are in the gifti format and the diffusion images are already > registered to the structural volumes. Based on the documentations it seems > that mri_vol2surf is hard-wired for outputs generated from recon-all. > > Cheers, > Arash > > > > -Original Message- > From: Bruce Fischl > To: Arash Nazeri > Cc: freesurfer > Sent: Tue, Oct 22, 2013 10:17 pm > Subject: Re: [Freesurfer] Projecting voxel intensities to a surface file > > Hi Arash > Yes. Register the surface to the volume with bbregister, then use > mri_vol2surf to do the sampling > Cheers > Bruce > > > > On Oct 22, 2013, at 12:13 PM, Arash Nazeri wrote: > > Dear all, > I'm new to the freesurfer. I want to project surrounding cortical > voxel values (intensities) from a given map (e.g. mean diffusivity map > in a nifti format) to a surface file (e.g. mid-cortical surface in a > gifti fromat) to generate scalar maps like ?h.thickness for group-wise > statistics. Can this be carried out using freesurfer commands? > > Cheers, > Arash > > ___ > 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 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_vol2surf
Hi all, I wanted to make sure how one could assign intensities from the subjacent white matter voxels to the cortical surfaces using mri_vol2surf. Based on the documentation page --projfrac, if used with negative values, would assign white matter values to the surface. I was wondering if this holds true for other options such as projfrac-avg, projfrac-max, projdist-max ... . Further, I wanted to make sure if the third value, designated as del, means the minimum value that could be projected to the surface. For instance: --projdist-max 0 -4 0.1 means to assign the maximum value in the distance 0-4 mm of the gray/white matter boundary to the white matter, that is larger than 0.1 . In case of the local/global outliers, is there any good way of finding, discarding, and replacement of these values, through thresholding+resampling for instance? Finally, I was wondering how it is possible to use these resulting mgh files for group comparison in an uncached dataset, presumably using mris_preproc. Bests, Arash ___ 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] mri_vol2surf
Thank you very much for all the help. > On Dec 2, 2013, at 11:27 AM, Douglas N Greve > wrote: > > >> On 12/01/2013 11:40 PM, Arash Nazeri wrote: >> Hi all, >> >> I wanted to make sure how one could assign intensities from the >> subjacent white matter voxels to the cortical surfaces using mri_vol2surf. >> >> Based on the documentation page --projfrac, if used with negative >> values, would assign white matter values to the surface. I was >> wondering if this holds true for other options such as projfrac-avg, >> projfrac-max, projdist-max ... . Further, I wanted to make sure if the >> third value, designated as del, means the minimum value that could be >> projected to the surface. >> For instance: --projdist-max 0 -4 0.1 means to assign the maximum >> value in the distance 0-4 mm of the gray/white matter boundary to the >> white matter, that is larger than 0.1 . > You basically have the right idea (ie, negative values go into the white > matter). I'm not sure exactly what you are asking in your example. If > you want to go from the gray/white surface into the WM by 4 mm, I would > use --projdist-max -4 0 0.1 or --projdist-max 0 4 -0.1 > This will sample along the normal in 40 places spaced 0.1mm apart and > return the maximum. Note that this does not assure that all points will > be in WM because 4mm may put you into the GM on an adjacent bank (but > for a T1 this will be dark so probably does not affect the max). >> >> In case of the local/global outliers, is there any good way of >> finding, discarding, and replacement of these values, through >> thresholding+resampling for instance? > We don't have anything. >> >> Finally, I was wondering how it is possible to use these resulting mgh >> files for group comparison in an uncached dataset, presumably using >> mris_preproc. > You can save them in the surf folder and then use "--meas yourfile.mgh" > with mris_preproc. > > I'm not sure what you are aiming for, but David Salat did a similar > analysis http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2750073 > This was done using the pctsurfcon program, so you might want to take a > look at that > doug > > >> >> Bests, >> Arash >> >> >> ___ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > gr...@nmr.mgh.harvard.edu > Phone Number: 617-724-2358 > Fax: 617-726-7422 > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 > www.nmr.mgh.harvard.edu/facility/filedrop/index.html > Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ > > ___ > 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 mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
