From: "freesurfer-request@nmr.mgh.harvard.edu" <freesurfer-request@nmr.mgh.harvard.edu>
To: freesurfer@nmr.mgh.harvard.edu
Sent: Mon, September 20, 2010 9:49:16 PM
Subject: Freesurfer Digest, Vol 79, Issue 32
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Today's Topics:
1. Re: mri_label2volume issues (Michael Waskom)
2. Generating a 'non-zero' group mask (Marco Loggia, PhD)
3. Re: recon-all quality control checks on large numbers of
subjects (Nick Schmansky)
4. lh.thickness.fsaverage (Siti Hajar)
5. Re: lh.thickness.fsaverage (Douglas Greve)
----------------------------------------------------------------------
Message: 1
Date: Fri, 17 Sep 2010 11:04:00 -0400
From: Michael Waskom <
mwaskom@mit.edu>
Subject: Re: [Freesurfer] mri_label2volume issues
To:
Freesurfer@nmr.mgh.harvard.eduMessage-ID:
<AANLkTi=
5ZnihXybQu0Wwf-ysJN6oPoQk2bFuf2_iirzb@mail.gmail.com>
Content-Type: text/plain; charset=ISO-8859-1
Hi Prapti,
Basically, you just need to have a label file that you can turn into a
lh.your_annot_name.annot (assuming your actual ROI is in the right
hemisphere), so that mri_label2annot runs properly.
The easiest thing to do would be to rename any old label you have in
your subject's label directory to lh.dummy.label, and then create an
annotation from that label with mri_label2annot. Then run
mris_aparc2aseg as you tried to do before, which will create a volume
that has 0's everywhere except in the area where your actual and dummy
labels were projected. Figure out the voxel values for the ROI you
want (using Freeview or tkmedit), and then
run:
mri_binarize --i your_annot_name+aseg.mgz --match <that voxel value>
--o you_roi_name.mgz
Which will have 1s where your ROI is and 0s everywhere else.
Best,
Mike
-------Original Message-------
Hi Doug,
Thanks for the reply. I am sorry, I am a bit confused about what you
mean by creating a dummy label. I am also not sure at which step I need
to do this.
As I understand it, I use mri_label2annot to transform my label into a
annotation file and this will be separate for the two hemispheres. Do I
then edit these files ? where exactly do I use mri_binarize?
Thanks,
Prapti
-----Original Message-----
From: Douglas N Greve [mailto:
gr...@nmr.mgh.harvard.edu]
Sent: Friday, 17 September 2010 12:44 AM
To: Prapti Gautam
Cc:
freesurfer@nmr.mgh.harvard.eduSubject: Re: [Freesurfer] mri_label2volume issues
Right, I see, mri_aparc2aseg is hard-coded to expect both lh and rh. The
easiest thing is to make a dummy label for the other hemisphere. In the
final segmentation, left hemisphere will have an index of
1000+something, the right will have 2000+something. You can then use
mri_binarize with --match create a new binary volume with just your
hemisphere.
doug
Prapti Gautam wrote:
> Hi Doug,
>
> Thanks for the reply. I have tried using the method you've suggested,
> however, I'm stuck because mri_label2annot which I use to turn my
label
> into a annot file only works in one hemisphere while mri_aparc2aseg
> works for the whole brain. Do you know a work around for this?
>
> Can I merge the
annot files created from each hemisphere so that I can
> pass it to mri_aparc2aseg?
>
>
> Thanks,
>
> Prapti
>
>
>
------------------------------
Message: 2
Date: Fri, 17 Sep 2010 11:38:22 -0400
From: "Marco Loggia, PhD" <
marco@nmr.mgh.harvard.edu>
Subject: [Freesurfer] Generating a 'non-zero' group mask
To: <
freesurfer@nmr.mgh.harvard.edu>
Message-ID: <5EA6CF4FA3914BC49D4CC51BD03A8618@MARCOWORK>
Content-Type: text/plain; charset="us-ascii"
Dear all,
I am performing surface analyses on ASL CBF maps. As these maps do not cover
the whole brain, and some masks have larger brain coverage than others, I
would need to create a binary
surface mask (in the fsaverage space) which
would zero out the vertices where at least one of my subjects have a zero
value. This map would then be used to spatially limit my statistical
analyses in mri_glmfit.
Any suggestions?
Thanks a lot,
Marco
_____________________
Marco L. Loggia, PhD
Postdoctoral Fellow, Mass General Hospital & Brigham and Women's Hospital
Harvard Medical School
CNY Building 120, suite 101E
Charlestown, Massachusetts 02129
Phone: (617) 643-7267
Fax: (617) 643-7340
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Message: 3
Date: Fri, 17 Sep 2010 18:41:09 -0400
From: Nick Schmansky <
nicks@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] recon-all quality control checks on large
numbers of subjects
To: Pradeep <
tpradeep@gmail.com>, Freesurfer Mailing List
<
freesurfer@nmr.mgh.harvard.edu>
Cc: kewei chen <
keweichen7921@gmail.com>
Message-ID: <
1284763269.543.5.camel@terrier.nmr.mgh.harvard.edu>
Content-Type: text/plain
consult this page:
http://surfer.nmr.mgh.harvard.edu/fswiki/TksurferDisplayProblemstypically the problem is resolved by upgrading the nvidia driver
(assuming you have such a graphics card).
n.
On Fri, 2010-09-17 at 15:17 -0700, Pradeep wrote:
> Hello Nick,
>
> The data_check program works after some minor fixes.
>
> I now a have problem with tksurfer on our server
>
> The recon-all step ran with out any
errors
>
> But
> tksurfer AD_C165 lh smoothwm
> displays only a part of the image and dose not give any error
> messages.
>
> Machine Details: x86_64 GNU/Linux
> FreeSurefer Version: freesurfer-Linux-centos4_x86_64-stable-pub-v5.0.0
>
> So i downloaded the images to another computer and the display is good
> here.
>
> Machine Details: i686 GNU/Linux
> FreeSurfer Version: freesurfer-Linux-centos4-stable-pub-v5.0.0
>
>
> Any suggestions on this would be greately appreciated.
>
> Thanks,
> Pradeep
>
>
>
>
> On Thu, Sep 16, 2010 at 5:32 PM, Pradeep <
tpradeep@gmail.com> wrote:
> Thanks for letting us know.
>
> Is
there any other way to do the QA in batch ?
>
> Thanks,
> Pradeep
>
> On Thu, Sep 16, 2010 at 3:52 PM, Nick Schmansky
>
> <
nicks@nmr.mgh.harvard.edu> wrote:
> > sorry, this is no longer supported. it was created by an ra
> who left
> > the center a few years ago. i suppose i should have
> mentioned that in
> > my original email.
> >
> > n.
>
>
> > On Thu, 2010-09-16 at 15:51 -0700, Pradeep wrote:
> >> Hell Nick,
> >>
> >> Looks like the recon_checker has some problems to fix
> >>
> >> Below is my log file.
> >>
> >> ############
> >> surf/rh.sphere surf/rh.sphere.reg surf/rh.lh.sphere.reg
> >> surf/rh.avg_curv label/rh.aparc.annot stats/rh.aparc.stats
> >> label/rh.aparc.a2005s.annot mri/aparc+aseg
> >> .mgz
> >> check to see if all files exist...
>
>> AD_C165 missing output files
> >> AD_C165 has no surf/lh.rh.sphere.reg
> >>
> >> In recon_all_status_log_checker
> >>
> >>
> WARNING: /working/pthiyyagura/freesurfer/data_checker/data_checker/sample-recon-all-status.log
> >> does not exist. Skipping this
> >> complete status log file...
> >>
> >> #############
> >>
> >>
> >> Its looking for lh.rh.sphere.reg. which would not exist.
>
>> Could you please look into this.
> >>
> >> Thanks,
> >> Pradeep
> >>
> >> P.S also please chage
> >> set scriptsDir =
> >>
> >>
> >>
> >>
> >>
> >>
> >>
> >> On Thu, Sep 16, 2010 at 11:41 AM, Nick Schmansky
> >> <
nicks@nmr.mgh.harvard.edu> wrote:
>
>> > see also this page:
> >> >
> >> > http://surfer.nmr.mgh.harvard.edu/fswiki/QATools> >> >
> >> > On Thu, 2010-09-16 at 14:13 -0400, Bruce Fischl wrote:
> >> >> Hi Avram,
> >> >>
> >> >> that all souds reasonable to me.
> >> >>
> >> >> cheers
> >> >> Bruce
> >> >> On Thu, 16 Sep 2010, Avram Holmes wrote:
>
>> >>
> >> >> > All,
> >> >> >
> >> >> > I'm setting up a processing stream for a sizable
> dataset and I'd like
> >> >> > to use .tcl scripts to save out images for some
> preliminary quality
> >> >> > control checks. It was my intention to output images
> of the the
> >> >> > curvature and structural parcelation overlaid on the
> inflated surface
> >> >> > (6 views for each hemi) and the lh/rh.white and
> aseg.mgz
segmentation
> >> >> > overlaid on the volume (a midline coronal, sagital,
> and axial slice).
> >> >> > The idea would be that then we could go through and
> quickly check
> >> >> > which subjects may need manual intervention.
> >> >> >
> >> >> > I wanted to double check that the images I am saving
> out are
> >> >> > consistent with the checks that other folks are doing
> and I'd love to
> >> >> > get some feedback on what else I should look save.
>
>> >> >
> >> >> > Thanks,
> >> >> > Avram
> >> >> >
> >> >> >
> >> >> _______________________________________________
> >> >> Freesurfer mailing list
> >> >>
Freesurfer@nmr.mgh.harvard.edu> >> >>
>
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> >> >>
>
>> >>
> >> >
> >> > _______________________________________________
> >> > 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.
> >> >
> >> >
> >>
>
>>
> >>
> >
> >
>
>
>
>
>
> --
> Pradeep Thiyyagura
> Research Assistant
> School of Mathematical and Statistical Sciences
> Graduate Student
> Computational Biosciences
> Arizona State University
> Tempe, AZ 85287-1804
>
Pradeep.Thiyyagura@asu.edu>
>
>
>
> --
> Pradeep Thiyyagura
> Research Assistant
> School of Mathematical and Statistical Sciences
> Graduate Student
> Computational Biosciences
> Arizona State University
> Tempe, AZ 85287-1804
>
Pradeep.Thiyyagura@asu.edu------------------------------
Message: 4
Date: Sun, 19 Sep 2010 22:45:30 -0700 (PDT)
From: Siti Hajar <
s.hajar432@yahoo.com>
Subject: [Freesurfer] lh.thickness.fsaverage
To:
freesurfer@nmr.mgh.harvard.eduMessage-ID: <
510347.11762.qm@web111606.mail.gq1.yahoo.com>
Content-Type: text/plain; charset="us-ascii"
When I run recon all for my subject, I couldn't open lh.thickness.fsaverage.mgh
(/usr/local/freesurfer/subjects/.../surf/lh.thickness.fsaverage.mgh.) I need to
use that information to obtain the cortical thickness.Is it because the new
updated freesurfer or it might come from other source of problem?
Thank you...
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Message: 5
Date: Mon, 20 Sep 2010
08:49:12 -0400
From: Douglas Greve <
greve@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] lh.thickness.fsaverage
To:
freesurfer@nmr.mgh.harvard.eduMessage-ID: <
4C975848.3050300@nmr.mgh.harvard.edu>
Content-Type: text/plain; charset="iso-8859-1"
Hi Siti, you'll need to give us more information about what you did.
What was your command line? Did the command finish without error? Have
you gone through the checks to make sure that the other results (eg,
skull strip) are ok? See
surfer.nmr.mgh.harvard.edu/fswiki/BugReporting for what else might be useful to send to us so that we can more
efficiently help you.
doug
On 9/20/10 1:45 AM, Siti Hajar wrote:
> When I run recon all for my subject, I couldn't open
> lh.thickness.fsaverage.mgh
> (/usr/local/freesurfer/subjects/.../surf/lh.thickness.fsaverage.mgh.)
> I need to use that information to obtain the cortical thickness.Is it
> because the new updated freesurfer or it might come from other source
> of problem?
>
> Thank you...
>
>
> _______________________________________________
> Freesurfer mailing list
>
Freesurfer@nmr.mgh.harvard.edu>
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