New subject: Freesurfer Digest, Vol 79, Issue 32

2 Oct 2010


      When I ran this command, " mri_segstats --seg  
"$fsaveragesurfpath"/"$hemi".fsaverage."$hemi"_"$roi"_"$subj".mgh --in  
"$hemi".thickness.fsaverage.mgh --sum  segstats-"$hemi"_"$roi"_"$subj".txt, this 
kind of output came out
"mghRead(/usr/local/freesurfer/subjects/100905lsy/surf/lh.thickness.fsaverage.mgh,
  -1): could not open file--> which indicated that there was no  
lh.thickness.fsaverage.mgh created. Well, basically, when I ran  recon-all, 
lh.thickness.fsaverage.mgh should be created, but it wasn't.   So, again with my 
question,is this situation happened due to the new  freesurfer software that I 
installed or was it caused by other source? The skull strip result was ok
________________________________
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.edu
Message-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.edu
Subject: 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 marco@nmr.mgh.harvard.edu

Re: [Freesurfer] Freesurfer Digest, Vol 79, Issue 32