[Freesurfer] Problem about vol2surf
Dear FS experts,I got into a trouble when used the command of mri_vol2surf.I planned to project a volume file (left hemisphere) onto the surface (lh) of the same subject. While i got nothing (value=0 for nearly all the vertexes except for a few valued vertexes on the medial surface). However, i tried to project this volume (lh) file onto the surface of rh, some vertexes were valued, but the dimension seems abnormal. I guess there may be something wrong with the coordinate system of this volume file. This volume file was initially generated from the command of mri_surf2vol as a mask (which can be projected to the surface correctly), and i assigned some values to this mask volume then generated this problematic volume file (as attached). So where is the problem?Thank you so much for any help!!!Best Regards,kaiThe 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.
[Freesurfer] Export value for each vertex in mgh file
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 ___ 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
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 > 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 > Subject: [Freesurfer] White Matter Corrections > To: freesurfer@nmr.mgh.harvard.edu > Message-ID: > > 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...
Re: [Freesurfer] Freesurfer Digest, Vol 135, Issue 23
All right, I have found the load_mgh function at
https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/MghFormat?action=AttachFile&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
"", "", and "". 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 +
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
> 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
> Subject: [Freesurfer] White Matter Corrections
> To: freesurfer@nmr.mgh.harvard.edu
> Message-ID:
>
> 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 i
Re: [Freesurfer] Freesurfer Digest, Vol 135, Issue 23
Ok, I ve figured it out: the "strlen" in the code is not a matlab function.
Thus I deleted the lines 38-46, then it works well by just define the fname.
Thank you very much!!
kai
From: li...@hotmail.com
To: freesurfer@nmr.mgh.harvard.edu
Subject: RE: Freesurfer Digest, Vol 135, Issue 23
Date: Sun, 17 May 2015 08:57:58 +
All right, I have found the load_mgh function at
https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/MghFormat?action=AttachFile&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
"", "", and "". 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 +
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
> 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
> Subject: [
[Freesurfer] Load a .label as a mask in tksurfer
Dear experts,Is there a way in tksurfer which could enable us to load a surface mask (e.g., lh.cortex.label) to confine the visualization of annotation files within certain cortical region? For example, now I want to confine the visualization of brain surface values within cortex (with corpus callosum etc. exluded), and I have tried to load the lh.cortex.label as a filed mask, while it seemed not work. Besides, I also tried the -mask option in command line, it seemed that this option didn't accept a .label file.So, how should a add a certain .label file as a mask in tksurfer?Thank you!!kaiThe 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.
