Dear Bruce, Thank you so much, i guess this would be exactly what i expected. But could you pls help provide some more information about the "load_mgh" function (either some links or descriptions are good to me)? Because it's not a default function in matlab and I failed to find a detailed description on google about how to install this function into matlab and its specific usages. Thank you so much!!! kai
> From: freesurfer-requ...@nmr.mgh.harvard.edu > Subject: Freesurfer Digest, Vol 135, Issue 23 > To: freesurfer@nmr.mgh.harvard.edu > Date: Sat, 16 May 2015 12:00:02 -0400 > > Send Freesurfer mailing list submissions to > freesurfer@nmr.mgh.harvard.edu > > To subscribe or unsubscribe via the World Wide Web, visit > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > or, via email, send a message with subject or body 'help' to > freesurfer-requ...@nmr.mgh.harvard.edu > > You can reach the person managing the list at > freesurfer-ow...@nmr.mgh.harvard.edu > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of Freesurfer digest..." > > > Today's Topics: > > 1. Re: xhemi final iteration (Douglas N Greve) > 2. White Matter Corrections (Imola MacPhee) > 3. Qdec not receiving keyboard input (Chris Wertz) > 4. freeview data checking for longitudinal (Chiu, Bryan (PHTH)) > 5. Re: freeview data checking for longitudinal (Martin Reuter) > 6. Manual labels in terms of anatomical regions (Andreas Werner) > 7. Export value for each vertex in mgh file (LiuKai) > 8. Re: Export value for each vertex in mgh file (Bruce Fischl) > 9. Segmenting the olfactory bulb (Elijah Mak) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Fri, 15 May 2015 14:32:03 -0400 > From: Douglas N Greve <gr...@nmr.mgh.harvard.edu> > Subject: Re: [Freesurfer] xhemi final iteration > To: freesurfer@nmr.mgh.harvard.edu > Message-ID: <55563ba3.8080...@nmr.mgh.harvard.edu> > Content-Type: text/plain; charset=windows-1252; format=flowed > > > You will need a new version of make_average_surface, which you can get > from here: > ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/make_average_surface > > make a back up of your current version, ie, > cp $FREESURFER_HOME/bin/make_average_surface > $FREESURFER_HOME/bin/make_average_surface.backup > The copy the above into $FREESURFER_HOME/bin/make_average_surface > > I have not tried this with 5.3, so i'm not sure it will work > > doug > > > On 05/14/2015 06:51 PM, Derek James Dean wrote: > > Sorry about that, Outlook seems to be preventing me from sending the > > code in email. I have attached a text document of the output. > > > > > > _______________________________________________ > > 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/ > > > > ------------------------------ > > Message: 2 > Date: Fri, 15 May 2015 11:34:09 -0700 > From: Imola MacPhee <imacp...@usc.edu> > Subject: [Freesurfer] White Matter Corrections > To: freesurfer@nmr.mgh.harvard.edu > Message-ID: > <CALmBsk=w9d2bbkqanafs40uqmhhiwevrbeqoqqnu8slbnbg...@mail.gmail.com> > Content-Type: text/plain; charset="utf-8" > > Dear FreeSurfer Team, > > I am quite new to FreeSurfer/Freeview (and neuroimaging in general) and was > wondering about "fixing" white matter holes that are identified using the > ?h.smoothwm.nofix surface. This is based on the error spotting techniques > suggested in the online troubleshooting tutorial, topological defects > example ( > https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/TopologicalDefect_freeview) > > > Specifically, should all of the holes be filled using wm.mgz recon edits? > My experience thus far is that each image has at least 4-5 holes and some > have many more. > > If the answer is no, is there a logical way to decide which should and > should not be filled? > > I have included an image here as an example. > > ? > > Any guidance that you can provide will be greatly appreciated. > > Best Regards, > > -- > Imola X. MacPhee, Au.D. > > Neuroscience Graduate Program > University of Southern California > imacp...@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 <cwert...@gmail.com> > Subject: [Freesurfer] Qdec not receiving keyboard input > To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu> > Message-ID: > <ca++f89wfff5vvbdzt88o30wfghe9wy+2_+hmy0gupv6hjl_...@mail.gmail.com> > 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 +0000 > From: "Chiu, Bryan (PHTH)" <bryan.c...@ubc.ca> > Subject: [Freesurfer] freeview data checking for longitudinal > To: "freesurfer@nmr.mgh.harvard.edu" <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 <mreu...@nmr.mgh.harvard.edu> > Subject: Re: [Freesurfer] freeview data checking for longitudinal > To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu> > 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 > reu...@mit.edu > Web : http://reuter.mit.edu > > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: > http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20150515/3743e218/attachment.html > > > ------------------------------ > > Message: 6 > Date: Sat, 16 May 2015 00:44:55 +0200 > From: "Andreas Werner" <derandreaswer...@gmx.de> > Subject: [Freesurfer] Manual labels in terms of anatomical regions > To: freesurfer <freesurfer@nmr.mgh.harvard.edu> > Message-ID: > > <trinity-19bd9e04-b118-4b0d-80c5-e2634e513a5d-1431729895073@3capp-gmx-bs06> > > Content-Type: text/plain; charset="us-ascii" > > An HTML attachment was scrubbed... > URL: > http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20150516/055b043d/attachment.html > > > ------------------------------ > > Message: 7 > Date: Sat, 16 May 2015 05:39:10 +0000 > From: LiuKai <li...@hotmail.com> > Subject: [Freesurfer] Export value for each vertex in mgh file > To: "freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu> > Message-ID: <bay178-w38637d55f5ff44a9228b34f9...@phx.gbl> > Content-Type: text/plain; charset="gb2312" > > > > > 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!!kaiThe Chinese University of > Hong Kong > > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: > http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20150516/bb64a16a/attachment.html > > > ------------------------------ > > Message: 8 > Date: Sat, 16 May 2015 09:27:14 -0400 (EDT) > From: Bruce Fischl <fis...@nmr.mgh.harvard.edu> > Subject: Re: [Freesurfer] Export value for each vertex in mgh file > To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu> > Message-ID: > <alpine.lrh.2.11.1505160926560.14...@gate.nmr.mgh.harvard.edu> > Content-Type: TEXT/PLAIN; charset=US-ASCII; format=flowed > > 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 > > > > > > > ------------------------------ > > Message: 9 > Date: Sat, 16 May 2015 15:01:45 +0100 > From: Elijah Mak <fk...@medschl.cam.ac.uk> > Subject: [Freesurfer] Segmenting the olfactory bulb > To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu> > Message-ID: > <CAAuUvMzey-Y8ez63xbkjbzCMJX=YWLvD=AS05cHTC=Ua8Y=8...@mail.gmail.com> > Content-Type: text/plain; charset="utf-8" > > 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 > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: > http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20150516/9515038e/attachment.html > > > ------------------------------ > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > End of Freesurfer Digest, Vol 135, Issue 23 > ******************************************* > > > 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. >
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