Dear All,
I have run into problems with a longitudinal analysis using v5.0.0 (freesurfer-Linux-centos4_x86_64-stable-pub-v5.0.0) that seemed to work fine under v4.5.0. For both analyses I processed the raw data from scratch since they were run on different clusters.
Following the instructions at http://surfer.nmr.mgh.harvard.edu/fswiki/LongitudinalProcessing I initially processed all images using the cross sectional stream, eg
recon-all -s PATIENT016_TIMEPOINT1 -i PATIENT016_TIMEPOINT1 then created a template from all time points for each subject, eg recon-all -base PATIENT016 -tp PATIENT016_TIMEPOINT1 -tp PATIENT016_TIMEPOINT2 -tp PATIENT016_TIMEPOINT3 -all Finally I tried to run the longitudinal processing stream, eg recon-all -long PATIENT016_TIMEPOINT1 PATIENT016 -all
where I ran into the following error message
"ERROR: longitudinal base ID cannot be the same as a timepoint subject ID (in /home/asimmons/images/FREESURFER/PATIENT016/base-tps) Find more info at: http://surfer.nmr.mgh.harvard.edu/fswiki/LongitudinalProcessing"
The longitudinal base ID is however not the same as any of the timepoints in /home/asimmons/images/FREESURFER/LNDMCI016/base-tps which just contains a list of the time points as expected -
PATIENT016_TIMEPOINT1 PATIENT016_TIMEPOINT2 PATIENT016_TIMEPOINT3
Best wishes,
Andy Simmons
----
Dr Andy Simmons Reader in Neuroimaging & Consultant Clinical Scientist Centre for Neuroimaging Sciences and NIHR Biomedical Research Centre Institute of Psychiatry, Box P089 Kings College London De Crespigny Park London, SE5 8AF, UK
Email - andy.simmons@kcl.ac.uk Webpage - http://www.iop.kcl.ac.uk/staff/profile/default.aspx?go=10338 Directions - http://www.iop.kcl.ac.uk/virtual/?path=/about/how-to-find-the-institute-of-p... ResearcherID - http://www.researcherid.com/rid/B-8848-2008 Fax +44 (0)203 228 2116
you will need to make the following edit to recon-all:
find and change:
grep $tpNid
to:
grep -w $tpNid
and find and change:
grep $longbaseid
to:
grep -w $longbaseid
Nick
On Tue, 2010-08-31 at 13:14 +0100, Simmons, Andy wrote:
Dear All,
I have run into problems with a longitudinal analysis using v5.0.0 (freesurfer-Linux-centos4_x86_64-stable-pub-v5.0.0) that seemed to work fine under v4.5.0. For both analyses I processed the raw data from scratch since they were run on different clusters.
Following the instructions at http://surfer.nmr.mgh.harvard.edu/fswiki/LongitudinalProcessing I initially processed all images using the cross sectional stream, eg
recon-all -s PATIENT016_TIMEPOINT1 -i PATIENT016_TIMEPOINT1
then created a template from all time points for each subject, eg
recon-all -base PATIENT016 -tp PATIENT016_TIMEPOINT1 -tp PATIENT016_TIMEPOINT2 -tp PATIENT016_TIMEPOINT3 -all
Finally I tried to run the longitudinal processing stream, eg
recon-all -long PATIENT016_TIMEPOINT1 PATIENT016 -all
where I ran into the following error message
“ERROR: longitudinal base ID cannot be the same as a timepoint subject ID (in /home/asimmons/images/FREESURFER/PATIENT016/base-tps)
Find more info at: http://surfer.nmr.mgh.harvard.edu/fswiki/LongitudinalProcessing%E2%80%9D
The longitudinal base ID is however not the same as any of the timepoints in /home/asimmons/images/FREESURFER/LNDMCI016/base-tps which just contains a list of the time points as expected -
PATIENT016_TIMEPOINT1
PATIENT016_TIMEPOINT2
PATIENT016_TIMEPOINT3
Best wishes,
Andy Simmons
Dr Andy Simmons
Reader in Neuroimaging & Consultant Clinical Scientist
Centre for Neuroimaging Sciences and NIHR Biomedical Research Centre
Institute of Psychiatry, Box P089
Kings College London
De Crespigny Park
London, SE5 8AF, UK
Email - andy.simmons@kcl.ac.uk
Webpage - http://www.iop.kcl.ac.uk/staff/profile/default.aspx?go=10338
Directions - http://www.iop.kcl.ac.uk/virtual/?path=/about/how-to-find-the-institute-of-p...
ResearcherID - http://www.researcherid.com/rid/B-8848-2008
Fax +44 (0)203 228 2116
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
See this as a feature to prevent at least some people from accidentally running 5.0 longitudinally :-)
Martin
On Aug 31, 2010, at 8:55, Nick Schmansky nicks@nmr.mgh.harvard.edu wrote:
you will need to make the following edit to recon-all:
find and change:
grep $tpNid
to:
grep -w $tpNid
and find and change:
grep $longbaseid
to:
grep -w $longbaseid
Nick
On Tue, 2010-08-31 at 13:14 +0100, Simmons, Andy wrote:
Dear All,
I have run into problems with a longitudinal analysis using v5.0.0 (freesurfer-Linux-centos4_x86_64-stable-pub-v5.0.0) that seemed to work fine under v4.5.0. For both analyses I processed the raw data from scratch since they were run on different clusters.
Following the instructions at http://surfer.nmr.mgh.harvard.edu/fswiki/LongitudinalProcessing I initially processed all images using the cross sectional stream, eg
recon-all -s PATIENT016_TIMEPOINT1 -i PATIENT016_TIMEPOINT1
then created a template from all time points for each subject, eg
recon-all -base PATIENT016 -tp PATIENT016_TIMEPOINT1 -tp PATIENT016_TIMEPOINT2 -tp PATIENT016_TIMEPOINT3 -all
Finally I tried to run the longitudinal processing stream, eg
recon-all -long PATIENT016_TIMEPOINT1 PATIENT016 -all
where I ran into the following error message
“ERROR: longitudinal base ID cannot be the same as a timepoint subject ID (in /home/asimmons/images/FREESURFER/PATIENT016/base-tps)
Find more info at: http://surfer.nmr.mgh.harvard.edu/fswiki/LongitudinalProcessing%E2%80%9D
The longitudinal base ID is however not the same as any of the timepoints in /home/asimmons/images/FREESURFER/LNDMCI016/base-tps which just contains a list of the time points as expected -
PATIENT016_TIMEPOINT1
PATIENT016_TIMEPOINT2
PATIENT016_TIMEPOINT3
Best wishes,
Andy Simmons
Dr Andy Simmons
Reader in Neuroimaging & Consultant Clinical Scientist
Centre for Neuroimaging Sciences and NIHR Biomedical Research Centre
Institute of Psychiatry, Box P089
Kings College London
De Crespigny Park
London, SE5 8AF, UK
Email - andy.simmons@kcl.ac.uk
Webpage - http://www.iop.kcl.ac.uk/staff/profile/default.aspx?go=10338
Directions - http://www.iop.kcl.ac.uk/virtual/?path=/about/how-to-find-the-institute-of-p...
ResearcherID - http://www.researcherid.com/rid/B-8848-2008
Fax +44 (0)203 228 2116
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
freesurfer@nmr.mgh.harvard.edu
-
Martin Reuter -
Nick Schmansky -
Simmons, Andy