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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