Re: [Freesurfer] 2D sphere co-ordinates
That worked perfectly! Thanks ___ 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] mni152reg
Hello Doug, Thank you for your reply.I'm using version 1.9 of mni152reg, which is located at http://ftp.nmr.mgh.harvard.edu/pub/dist/freesurfer/5.3.0-patch/mni152reg. Best, Nao > Date: Mon, 29 Jun 2015 18:58:28 -0400 > From: gr...@nmr.mgh.harvard.edu > To: freesurfer@nmr.mgh.harvard.edu > Subject: Re: [Freesurfer] mni152reg > > What version of mni152reg are you using? > > On 06/22/2015 05:17 AM, OKADA NAOHIRO wrote: > > Hello Freesurfer Experts, > > > > I am trying to create a registration matrix from subject space to MNI152: > > > > mni152reg --s bert > > > > However, this error appeared: > > > > fslregister --mov > > /usr/local/fsl/data/standard/MNI152_T1_2mm_brain.nii.gz --s bert --reg > > /usr/local/freesurfer/subjects/bert/mri/transforms/reg.mni152.2mm.dat > > --dof 12 --tmp /usr/local/freesurfer/subjects/bert/tmp/mni152reg.4901 > > --cleanup --lta > > /usr/local/freesurfer/subjects/bert/mri/transforms/reg.mni152.2mm.lta > > ERROR: Flag --lta unrecognized. > > --mov /usr/local/fsl/data/standard/MNI152_T1_2mm_brain.nii.gz --s bert > > --reg > > /usr/local/freesurfer/subjects/bert/mri/transforms/reg.mni152.2mm.dat > > --dof 12 --tmp /usr/local/freesurfer/subjects/bert/tmp/mni152reg.4901 > > --cleanup --lta > > /usr/local/freesurfer/subjects/bert/mri/transforms/reg.mni152.2mm.lta > > > > How can I make the mni152reg command work? > > > > Thanks in advance. > > > > Best, > > Nao > > > > > > > > ___ > > 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 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_label2vol in matlab
Hi Freesurfer experts, I have a label with 1500+ vertices I'd like to convert to a nifti file. Right now I use mri_label2vol and output a file I'd like to do this in matlab, is there any way? More specifically, I'd like to get the native co-ordinate for each vertex in the nifti file. The vox2ras co-ordinates in the label file aren't suited for me, I need a co-ordinate in the same size as the template nifti file (in my case a 96*96*31 matrix). Thanks! Jonathan ___ 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] TRACULA analyses in glmfit
Dear Developers, Tracula’s Statistics wiki suggests one to use the statistical software of choice. Could it be glmfit? For that, I think I would need to concatenate each tract-by-voxel diffusion data from each subject (e.g., each diffusion data of course separately) in common space (e.g., MNI) and then input it to mri_glmfit / mri_glmfit-sim, whose output sig.mgh would be loaded in Freeview as a heatmap. I understood that diffusion data in Tracula is saved in .txt files, which cannot be inputed into mri_preproc or mri_label2vol. Is it possible to use glmfit with Tracula outputs? Thanks in advance, Pedro Rosa. ___ 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] basic request on cortical thickness analysis
Hi Alessandro you can do it either way. qdec gives you a GUI interface to guide you through the process, but is limited in terms of the hypotheses you can test with it. You can choose to smooth or not either way cheers Bruce On Sat, 4 Jul 2015, Alessandro Calamuneri wrote: > Hi freesurfer users, > > I am new to freesurer and have a basic question about how to perform > statistics on cortical thickness. > > I basically have two groups and a structure of interest. Would it be > sufficient to perform analysis (like 2-samples t test) on manually extracted > thickness from stats obtained after recon-all finished up or should I use > qdec as explained in tutorial? I know one of the differences could be that i > did not use -qcache flag as it is pointed out in qdec tutorial for smoothing > my data. > Thanks in advance. > > Best Regards, > > Alessandro > > ___ 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.
