no worries, glad to hear we sorted it out
Bruce
On Mon, 13 Jul 2015, Gerrits,
Niels wrote:
Hi Bruce,
Thank you so much and I’m sorry for the newbie question(s). It’s working
now!
Cheers,
Niels
-----Original Message-----
From: freesurfer-boun...@nmr.mgh.harvard.edu
[mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Bruce Fischl
Sent: maandag 13 juli 2015 14:46
To: Freesurfer support list
Subject: Re: [Freesurfer] Computing SA from an older FS version
Hi Niels
the matlab commands should be:
>> [v, M,mr] = load_mgh('wm.mgz') ;
>> save_mgh(v, 'wm.mgz', M,mr);
cheers
Bruce
On Mon, 13 Jul 2015, Gerrits, Niels
wrote:
>
> Dear Bruce,
>
>
>
> Thanks for the quick reply! I think it might be possible that we used an
> unrelased or developmental version of FreeSurfer, because the
building-stamp
> said: freesurfer-Linux-centos5_86_64_dev-20110315. I’m not sure how this
> version ended up onto the server I was working on. Do you think this is a
> problem?
>
>
>
> With respect to the error: you were right, it was longer. I copied the
> command line below:
>
>
>
> $ mris_anatomical_stats -mgz -cortex label/lh.cortex.label -f
> stats/lh.aparc.pial.stats -b -a label/lh.aparc.annot -c
> label/aparc.annot.ctab 0007 lh pial
> INFO: assuming MGZ format for volumes.
> INFO: using label/lh.cortex.label as mask to calc cortex NumVert, SurfArea
> and MeanThickness. computing statistics for each annotation in
> label/lh.aparc.annot. reading
>volume/data2/projects/ysbrand-vumc/pddatabase-freesurfer/niels_test//0007/m
ri/wm.
> mgz... znzTAGskip: tag=825050957, failed to calloc 1969843200 bytes!
>
>
>
> I then loaded wm.mgh into matlab and then saved it as you suggested and
ran
> the command again to calculate SA of the pial surface, but it produces the
> exact same error…
>
>
>
> >> load.mgh wm.mgz;
>
> >> save.mgh wm.mgz;
>
>
>
> Am I doing anything wrong?
>
>
>
> Thanks again!
>
>
>
> Cheers,
>
> Niels
>
>
>
> -----Original Message-----
> From: freesurfer-boun...@nmr.mgh.harvard.edu
> [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Bruce Fischl
> Sent: zondag 12 juli 2015 16:44
> To: Freesurfer support list
> Subject: Re: [Freesurfer] Computing SA from an older FS version
>
>
>
> Hi Niels
>
>
>
> is that the entire error? Does it not say what volume produces the error?
>
> That was a bug we had briefly some time ago, but I didn't think it made it
>
> into anything we released. If you can track down which volume is causing
>
> this problem you can just load it into matlab with load_mgh.m then save it
>
> with save_mgh.m and the error will go away (since the matlab code doesn't
>
> try to read or write the tagged information). Make sure to save all the
>
> volumes that you do this to somewhere before overwriting them.
>
>
>
> cheers
>
> Bruce
>
>
>
> On
>
> Sun, 12 Jul 2015, Gerrits, Niels wrote:
>
>
>
> > Dear FreeSurfer-experts,
>
> >
>
> > Unfortunately, nobody replied to my question so this is a repost (see
the
>
> > original question below). Could anybody please give some advise on how
to
>
> > proceed? The deadline for the revisions is drawing near, so any help is
>
> > greatly appreciated!
>
> >
>
> > Best wishes,
>
> > Niels
>
> >
>
>>--------------------------------------------------------------------------
-
>
> > ---------------------------------------------
>
> >
>
> > Dear FreeSurfer-experts,
>
> >
>
> > In 2012 I used a (currently outdated) version of FreeSurfer to analyze
my
>
> > data on an external server and wrote an article about our findings. Now
> the
>
> > reviewers asked us to recalculate surface area using the pial surface,
>
> > instead of the WM/GM boundary. I found the command on the mailing list
to
> do
>
> > so, but I got an error, which is probably related to the fact that there
> is
>
> > a new version of FreeSurfer installed on the server and that the old
> version
>
> > has been deleted.
>
> >
>
> > Command to obtain SA from the pial surface:
>
> >
>
> > mris_anatomical_stats -mgz -cortex label/lh.cortex.label -f
>
> > stats/lh.aparc.pial.stats -b –a label/lh.aparc.annot -c
>
> > label/aparc.annot.ctab subject lh pial
>
> >
>
> > Error:
>
> >
>
> > znzTAGskip: tag=825050957, failed to alloc 1969843200 bytes!
>
> >
>
> > Cannot allocate memory!
>
> >
>
> > Now I have two questions:
>
> >
>
> > 1) When trying to find in which version of FreeSurfer the existing files
>
> > were created, I checked both the build-stamp.txt file and the
> recon-all.log
>
> > file, and both say that the version of Freesurfer that was used was
>
> > freesurfer-Linux-centos5_86_64_dev-20110315. Is this an actual version?
I
>
> > cannot find anything on the Internet about it. If not, what version
could
>
> > this have been?
>
> >
>
> > 2) I understood that running two different versions of FreeSurfer on the
>
> > same data is not favourable. However, the numbers we are looking for are
>
> > already computed and now we only need to get them out of the existing
> files.
>
> > Do you have any advice on how to do that?
>
> >
>
> > Running recon-all again using the new version (5.3) does not seem to be
an
>
> > option, since manual edits were made during the preprocessing. It is
>
> > therefore likely that we will obtain different results when compared
with
>
> > our current findings when running recon-all again using the new version,
> and
>
> > we would have to rewrite our entire article.
>
> >
>
> > Any help is greatly appreciated!
>
> >
>
> > Best wishes,
>
> > Niels Gerrits
>
> >
>
> >
>
> >
>
> >
>
> >
>
> >
>
> >
>
>
>
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