Dear Experts, With your help, I recalculated the surface area, now using the pial surface instead of the wm/gm boundary. I am, however, somewhat surprised by the discrepancy between my previous and current results, because the cortical surface area that is calculated using the pial is surface is consistently (a lot) larger than the SA that was calculated using the WM/GM boundary (please see below for an example). While computing the new SA measure, FS also automatically calculated both volume and thickness. Since these two measures are exactly the same as previously when SA was calculated using the wm/gm boundary (as was to be expected), I assume that the calculation of SA using the pial surface was correctly executed.
Nonetheless, I am wondering: 1) is such a large difference to be expected, and 2) what could be a physiological explanation for this discrepancy? All suggestions are much appreciated! Best wishes, Niels Gerrits LH_cuneus_area LH_entorhinal_area LH_fusiform_area LH_inferiorparietal_area PP_01 1305 349 2563 3699 PP_02 1351 368 2989 4803 PP_03 1324 490 3489 3963 PP_04 1714 518 4107 4473 PP_05 1573 566 3750 5697 PP_06 1419 387 3206 4543 PP_07 1249 364 2636 4518 PP_08 1386 362 3174 5105 PP_09 1322 562 3239 6264 PP_10 1696 517 3926 5989 LH_cuneus_area LH_entorhinal_area LH_fusiform_area LH_inferiorparietal_area PP_01 1617 575 3231 4446 PP_02 1555 661 3970 5983 PP_03 1769 886 5059 5143 PP_04 1964 809 5402 5662 PP_05 1788 946 4832 6907 PP_06 1752 667 3944 5449 PP_07 1595 674 3631 5783 PP_08 1779 634 4074 6364 PP_09 1648 912 4353 7395 PP_10 1915 816 4758 7358 -----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/mri/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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