All right, I have found the load_mgh functionat
https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/MghFormat?action=At
tachFile&do=view&target=load_mgh.mThank you so much!!
But I cannot get a full understand on its usage. In particular, the "fname"
option is obvious, but i cannot understand the explanations for rest three
of "<slices>", "<frames>", and "<headeronly>". So could you pls just provide
an example?
--Given that I want to get all the thickness values from the file
"lh.thickness.fwhm10.fsaverage.mgh", so the command should be "[vol, M,
mr_parms, Mdc, volsz] = load_mgh('lh.thickness.fwhm10.fsaverage.mgh', ????,
????, ????)
"
Thank you so much!!!!!
kai
____________________________________________________________________________
From: li...@hotmail.com
To: freesurfer@nmr.mgh.harvard.edu
Subject: RE: Freesurfer Digest, Vol 135, Issue 23
Date: Sat, 16 May 2015 16:22:09 +0000
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_free
view)
>
>
> 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
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> ------------------------------
>
> 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
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>
> ------------------------------
>
> 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
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>
> ------------------------------
>
> 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 --------------
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>
> ------------------------------
>
> 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...
>
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>
> ------------------------------
>
> 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 --------------
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> ------------------------------
>
> 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
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> ------------------------------
>
> _______________________________________________
> 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
> *******************************************
>
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