Hi Carolina,
probably you are not interested in the average thickness, so you can
drop --do-avg . Also usually people decide between pc1 and spc. The
stack is also not really necessary unless you want to look at it.
Try to remove the trailing / at fsaverage and --sd $SUBJECTS_DIR
that should fix your error.
Best, Martin
On 02/24/2015 01:54 PM, carolina.mr wrote:
Hi FreeSurfer experts,
I am trying to run Longitudinal Two Steps analysis.
In the long_mris_slopes I run the following command:
long_mris_slopes --qdec $SUBJECTS_DIR/qdec/longRRMSP01.qdec.table.dat
--meas thickness --hemi lh --do-avg --do-rate --do-pc1 --do-spc
--do-stack --do-label --time years --qcache fsaverage/ --sd $SUBJECTS_DIR/
And, after some processing, it appears the error message:
mv ./tmp-P01_TP_lh_thickness_C8c_pE/lh.tmp0000.mgh
/analise//P01_TP/surf/lh.long.thickness-spc.fwhm0.fsaverage/.mgh
mv: rename ./tmp-P01_TP_lh_thickness_C8c_pE/lh.tmp0000.mgh to
/analise//P01_TP/surf/lh.long.thickness-spc.fwhm0.fsaverage/.mgh: No
such file or directory
ERROR 1 : mv ./tmp-P01_TP_lh_thickness_C8c_pE/lh.tmp0000.mgh
/analise//P01_TP/surf/lh.long.thickness-spc.fwhm0.fsaverage/.mgh did
not work?
In the base folder, /surf, I can find many .mgh archives, for example:
lh.long.thickness-spc.fwhm0.mgh (and others with other fwhm smoothing
factors). But I can't find any lh.long.thickness....fsaverage files.
I did all the previous processing as it appears in the Longitudinal FS
Tutorials. I also tried to run qcache with the base file, but it says
it is not necessary, since it is a base file.
Should I run qcache first with each subject / time point before?
Thank you,
Carolina
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--
Dr. Martin Reuter
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
Phone: +1-617-724-5652
Email:
mreu...@nmr.mgh.harvard.edu
reu...@mit.edu
Web : http://reuter.mit.edu
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