[Freesurfer] beta value
Hi, During the processing of functional data, can fsfast generate outputs of the significants for each beta values modeled in the design matrix? Thanks,XIaomin___ 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] dt_recon
Thanks, Doug! Pedro Rosa On Monday, May 11, 2015 at 6:51 PM, Douglas N Greve wrote: > It sounds like you did the right thing. > > On 05/10/2015 02:41 PM, Pedro Rosa - GMail wrote: > > Dear developers, > > I am running an analysis with dt_recon, and it seems that my DWI files > > are organized into three series (one larger, and two smaller, that I > > believe are ADC and Trace). Inputing a DICOM file to dt_recon > > generates a .nii file from one of the series only (the larger one, > > once it has many more .dcm files). Thus, it ignores the smaller series. > > This is the first time I am working with DWI series, so I not quite > > sure if this way of organizing data is usual. > > I would appreciate help in regard of how to deal with this data and > > input it into dt_recon. > > Regards, > > Pedro Rosa. > > > > > > ___ > > Freesurfer mailing list > > Freesurfer@nmr.mgh.harvard.edu (mailto: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 (mailto: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 > (http://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 (mailto: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.
Re: [Freesurfer] Freesurfer Digest, Vol 135, Issue 23
f Southern California > imacp...@usc.edu > -- next part -- > An HTML attachment was scrubbed... > URL:http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20150515/f f813e5f/attachment.html > > -- > > Message: 3 > Date: Fri, 15 May 2015 12:40:46 -0600 > From: Chris Wertz > Subject: [Freesurfer] Qdec not receiving keyboard input > To: Freesurfer support list > Message-ID: > > Content-Type: text/plain; charset="utf-8" > > Hi Freesurfer Experts, > > Recently, Qdec 1.5 has not been receiving any keyboard input on the > Subjects page, yet it does receive keyboard input on the Design page, when > I change the Design name for example, and then does not accept keyboard > entries on the the Display page, like when I try to change the threshold. > Qdec was working just fine up until recently so I don't know what's > happening? I've noticed there are a couple of other people who've had > similar problems but I didn't see any possible causes or solutions > provided. > > Thanks in advance, > Chris > -- next part -- > An HTML attachment was scrubbed... > URL:http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20150515/c 59dbb76/attachment.html > > -- > > Message: 4 > Date: Fri, 15 May 2015 19:03:52 + > From: "Chiu, Bryan (PHTH)" > Subject: [Freesurfer] freeview data checking for longitudinal > To: "freesurfer@nmr.mgh.harvard.edu" > Message-ID: > <680d9b8d5feaaf40a1a5878265424ca49e30d...@s-itsv-mbx06p.ead.ubc.ca> > Content-Type: text/plain; charset="iso-8859-1" > > Hi, > > I am trying to create a command line for data checking the same participant over multiple longitudinal timepoints in freeview. However at the moment I am running into issues. > > Can someone provide me an example of a freeview command to be used if I wanted to overlay the scans? > > Any help is greatly appreciated. > ___ > Bryan Chiu > Undergraduate Research Assistant > Aging, Mobility, and Cognitive Neuroscience Lab > Djavad Mowafaghian Centre for Brain Health > Department of Physical Therapy > Faculty of Medicine > University of British Columbia > -- next part -- > An HTML attachment was scrubbed... > URL:http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20150515/0 9c91356/attachment.html > > -- > > Message: 5 > Date: Fri, 15 May 2015 16:11:44 -0400 > From: Martin Reuter > Subject: Re: [Freesurfer] freeview data checking for longitudinal > To: Freesurfer support list > Message-ID: <55565300.3060...@nmr.mgh.harvard.edu> > Content-Type: text/plain; charset="windows-1252" > > Hi Bryan, > > what issues are you running into? > > Just open the images from all time points on top of each other. Make > sure to load the ones from the .long.base dirs. The same can be done for > surfaces. > > freeview tp1.long.base/mri/norm.mgz tp2.long.base/mri/norm.mgz ... > > Martin > > On 05/15/2015 03:03 PM, Chiu, Bryan (PHTH) wrote: > > Hi, > > > > I am trying to create a command line for data checking the same > > participant over multiple longitudinal timepoints in freeview. However > > at the moment I am running into issues. > > > > Can someone provide me an example of a freeview command to be used if > > I wanted to overlay the scans? > > > > Any help is greatly appreciated. > > ___ > > Bryan Chiu > > Undergraduate Research Assistant > > Aging, Mobility, and Cognitive Neuroscience Lab > > Djavad Mowafaghian Centre for Brain Health > > Department of Physical Therapy > > Faculty of Medicine > > University of British Columbia > > > > > > ___ > > Freesurfer mailing list > > Freesurfer@nmr.mgh.harvard.edu > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > -- > Dr. Martin Reuter > > Instructor in Neurology > Harvard Medical School > Assistant in Neuroscience > Dept. of Radiology, Massachusetts General Hospital > Dept. of Neurology, Massachusetts General Hospital > Research Affiliate > Computer Science and Artificial Intelligence Lab, > Dept. of Electrical Engineering and Computer Science, > Massachusetts Institute of Technology > > A.A.Martinos Center for Biomedical Imaging > 149 Thirteenth Street, Suite 2301 > Charlestown, MA 02129 > > Phone: +1-617-724-5652 > Email: > mreu...@nmr.mgh.harvard.edu
Re: [Freesurfer] Freesurfer Digest, Vol 135, Issue 23
@usc.edu > -- next part -- > An HTML attachment was scrubbed... > URL: > http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20150515/ff813e5f/attachment.html > > > -- > > Message: 3 > Date: Fri, 15 May 2015 12:40:46 -0600 > From: Chris Wertz > Subject: [Freesurfer] Qdec not receiving keyboard input > To: Freesurfer support list > Message-ID: > > Content-Type: text/plain; charset="utf-8" > > Hi Freesurfer Experts, > > Recently, Qdec 1.5 has not been receiving any keyboard input on the > Subjects page, yet it does receive keyboard input on the Design page, when > I change the Design name for example, and then does not accept keyboard > entries on the the Display page, like when I try to change the threshold. > Qdec was working just fine up until recently so I don't know what's > happening? I've noticed there are a couple of other people who've had > similar problems but I didn't see any possible causes or solutions > provided. > > Thanks in advance, > Chris > -- next part -- > An HTML attachment was scrubbed... > URL: > http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20150515/c59dbb76/attachment.html > > > -- > > Message: 4 > Date: Fri, 15 May 2015 19:03:52 + > From: "Chiu, Bryan (PHTH)" > Subject: [Freesurfer] freeview data checking for longitudinal > To: "freesurfer@nmr.mgh.harvard.edu" > Message-ID: > <680d9b8d5feaaf40a1a5878265424ca49e30d...@s-itsv-mbx06p.ead.ubc.ca> > Content-Type: text/plain; charset="iso-8859-1" > > Hi, > > I am trying to create a command line for data checking the same participant > over multiple longitudinal timepoints in freeview. However at the moment I am > running into issues. > > Can someone provide me an example of a freeview command to be used if I > wanted to overlay the scans? > > Any help is greatly appreciated. > ___ > Bryan Chiu > Undergraduate Research Assistant > Aging, Mobility, and Cognitive Neuroscience Lab > Djavad Mowafaghian Centre for Brain Health > Department of Physical Therapy > Faculty of Medicine > University of British Columbia > -- next part -- > An HTML attachment was scrubbed... > URL: > http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20150515/09c91356/attachment.html > > > -- > > Message: 5 > Date: Fri, 15 May 2015 16:11:44 -0400 > From: Martin Reuter > Subject: Re: [Freesurfer] freeview data checking for longitudinal > To: Freesurfer support list > Message-ID: <55565300.3060...@nmr.mgh.harvard.edu> > Content-Type: text/plain; charset="windows-1252" > > Hi Bryan, > > what issues are you running into? > > Just open the images from all time points on top of each other. Make > sure to load the ones from the .long.base dirs. The same can be done for > surfaces. > > freeview tp1.long.base/mri/norm.mgz tp2.long.base/mri/norm.mgz ... > > Martin > > On 05/15/2015 03:03 PM, Chiu, Bryan (PHTH) wrote: > > Hi, > > > > I am trying to create a command line for data checking the same > > participant over multiple longitudinal timepoints in freeview. However > > at the moment I am running into issues. > > > > Can someone provide me an example of a freeview command to be used if > > I wanted to overlay the scans? > > > > Any help is greatly appreciated. > > ___ > > Bryan Chiu > > Undergraduate Research Assistant > > Aging, Mobility, and Cognitive Neuroscience Lab > > Djavad Mowafaghian Centre for Brain Health > > Department of Physical Therapy > > Faculty of Medicine > > University of British Columbia > > > > > > ___ > > Freesurfer mailing list > > Freesurfer@nmr.mgh.harvard.edu > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > -- > Dr. Martin Reuter > > Instructor in Neurology >Harvard Medical School > Assistant in Neuroscience >Dept. of Radiology, Massachusetts General Hospital >Dept. of Neurology, Massachusetts General Hospital > Research Affiliate >Computer Science and Artificial Intelligence Lab, >Dept. of Electrical Engineering and Computer Science, >Massachusetts Institute of Technology > > A.A.Martinos Center for Biomedical Imaging > 149 Thirteenth Street, Suite 2301 > Charlestown, MA 0212
[Freesurfer] Segmenting the olfactory bulb
Hello, Is there a way to segment and extract volumes of the olfactory bulb in Freesurfer based on T1-MPRAGE? Cheers. Best Wishes, Elijah -- Elijah Mak, Gates Scholar PhD Candidate *|* Psychiatry University of Cambridge Trinity College, Cambridge, CB2 1TQ ___ 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] Export value for each vertex in mgh file
Hi Kai you can load mgh files into matlab using load_mgh - is that sufficient for what you want to do? cheers Bruce On Sat, 16 May 2015, LiuKai wrote: > Hi dear freesurfer expert, > Is there any command which can be used to export the value of each vertex of > a mgh file (e.g., lh.thickness.fsaverage.mgh) and list all the values by > generating a file (may be a .txt file)? Because I want to plot the values > for further steps. > > Thank you!! > > kai > > The Chinese University of Hong 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.
