Hi Martin,
Thanks for your reply! Yes, that definitely makes sense. I had an additional probably elementary question: I tried to reconstruct the base after I added some control points to it, using the command recon-all -autorecon2-cp -autorecon3 -subjid <base_subject_name>
but the following error pops up:
ERROR: It appears that this subject ID is an existing base/template from longitudinal processing (-base). Please make sure you pass all necessary flags. For example, if you are trying to re-run a -base:
' -base <templateid> -tp <tpNid> ... '
Exit 1
In order to reconstruct the base do I need to run again the command that created the base in the first place and then add the flag -autorecon2-cp -autorecon3 that is:
recon-all -autorecon2-cp -autorecon3 -base <base_subject_name> -tp <tmp1> -tp <tmp2> ... -tp <tmpN> -all ?
Thanks in advance, Panos
Hi Panos,
- you need to edit the base. That is actually more important than
editing the individual (cross) time points from the first stage, especially when the edits are supposed to improve the surface. The reason is that the surface is taken from the base to initialize all time points in the -long step. So accurate surfaces, brainmasks and talairach transforms are very important in the base.
- Yes, that is generally OK. It would be bad if one group has only 3
time points the other 5 though, but if that is relatively balanced across your groups, you'll be fine.
Best, Martin
On 03/28/2014 03:43 PM, pfotiad@nmr.mgh.harvard.edu wrote:
Hi FS community,
I am using FS 5.3 to do a longitudinal analysis on some data of mine. I have manually edited some of the reconstructed scans (i.e. addition of control points and white voxels) where the reconstruction was not as precise:
- Is the base template created from the recon-all -base command in the
wiki preserving those edits or do I need to reapply them in the base template? I know that this has been answered for previous versions of FS but I was wondering whether anything has changed in more recent versions.
- Is it ok to run the longitudinal analysis described in the wiki when
my subjects have an unequal number of timepoints (i.e. one person has 3 different timepoints, whereas another one has five) or should they all have the same number of timepoints? Thanks in advance!
Best, Panos _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-- Martin Reuter, Ph.D.
Instructor in Neurology Harvard Medical School Assistant in Neuroscience Dept. of Radiology, Massachusetts General Hospital Dept. of Neurology, Massachusetts General Hospital Research Affiliate Computer Science and Artificial Intelligence Lab, Dept. of Electrical Engineering and Computer Science, Massachusetts Institute of Technology
A.A.Martinos Center for Biomedical Imaging 149 Thirteenth Street, Suite 2301 Charlestown, MA 02129
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