Hello,

I forgot to mention another query regarding recon-all –make all:

If I do end up running this command on the subjects that fail the qcache processing (so effectively rerunning the whole recon-all stream), will any edits I have made to fix errors (such as control points, wm.mgz edits and pial edits) be erased, or will they be incorporated into the new reconstruction?

Many thanks (again),

Rysia

From: Burmicz, Ryzarda
Sent: 11 December 2008 15:19
To: 'freesurfer@nmr.mgh.harvard.edu'
Cc: Santo, Susan
Subject: qcache error and recon-all -make all

Hello,

When running recon-all –qcache –s <subject> with a view to running qdec analyses I get the following error message, which I think I understand, however I am having trouble with the –make all option of recon-all that is recommended in a previous thread:

“Reading curvature file /PICKACARDB01/surf/lh.jacobian_white

ERROR: number of vertices in /PICKACARDB01/surf/lh.jacobian_white does not match surface (150934, 150818)

ERROR: reading curvature file

recon-all exited with ERRORS at Tue Dec 9 ...”

This subject was originally run on 4.0.1 (Linux-centos4_x86_64 version)

And then corrected and rerun on 4.0.3 (Linux-centos4_x86_64 version)

(I understand that this is not always a good thing to do rerunning on a different version so don’t know if this has anything to do with it..). I think I am correct in saying that they problem might be due to rerunning portions of recon-all (in this case we reran from –autorecon2-wm to correct a wm error) such that the new surface vertices do not match such that the lh.jacobian_white file in this case is now invalid.

My query is as follows:

I have experimented with running “recon-all –s <subject> -make all” to fix the above problem but it seems to be going through the entirety of the recon-all processing stream... I thought it only ran the parts that were missing, or in the case that dependency files are older than a particular file.  Have I misunderstood this flag, or is it running through the whole of recon-all simply because we are running it on 4.0.3, so it is updating all of the recon-all files up to autorecon2-wm that were created from version 4.0.1?

It is interesting that the error happens in this case only on the jacobian_white surface, in other subjects it has occurred for all smoothing surface files on a single hemisphere (.e.g. volume, sulc, curv, thickness, jacobian_white ..) and in many just the .volume files are missing... it is confusing.

Naturally I would love to avoid reprocessing these subjects from scratch! But I can see how this might not be possible.

Thanks very much for your time,

Rysia