Heidi,
first: you probably need to keep the .nii in the table for now
(depending on how your cross sectional directories are really named?).
If they have the .nii extension, you need to do the same in the qdec table.
If down the road the extension creates problems, it will be very
complicated to solve this as the naming is propagated to many places (in
the cross runs, base and long). Cleaning that up retrospectively is
possible but lot's of work and if you miss a place things will fail. So
it might be easier to re-run from scratch (depending on the size of the
data and the edits)? Let's first wait and see what happens.
Best, Martin
On 11/04/2015 09:34 AM, Heidi Foo wrote:
Hi Martin,
Thanks so much for your reply, I really appreciate it.
I will change my qdec file for fsid accordingly from
FS_PD002_1.nii.long.FSBASE_002 to FS_PD002_1. If the file name and
file extension are causing the problem, do you have any suggestions
for me overcome this? Would changing the file name help?
Thanks again.
Regards,
Heidi
On Wed, Nov 4, 2015 at 9:51 PM, Martin Reuter
<mreu...@nmr.mgh.harvard.edu <mailto:mreu...@nmr.mgh.harvard.edu>> wrote:
Dear Heidi,
maybe there is a problem with your long.qdec.table.dat file? It is
used to create the <fsid>.long.<fs_baseid> file names and
obviously that filename is wrong (containing two .long. in it).
Make sure that the first column is only the cross sectional id and
the second one is the base id, so in your case:
fsid fsid-base
FS_PD002_1.nii FSBASE_002
Also it is not a good idea to have the ".nii" as part of the
subject id, as that is a file extension. Next time, when running
the cross sectionals, make sure you call the subject "FS_PD002_1"
without extension. Could be that this leads to other problems (or
it could just work, we'll see).
Best, Martin
On 11/04/2015 08:38 AM, Heidi Foo wrote:
Dear FreeSurfer experts,
I was running the first stage of analysis of preparing of data -
qcache - and I encountered some problems.
When using this command, /long_mris_slopes --qdec
./qdec/long.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/, an error message saying:"
FS_PD002_1.nii.long.FSBASE_002.long.FSBASE_002/label/lh.cortex.label
does not exist!" appears.
I tried several other ways such as using long_stats_slopes, but I
keep receiving error messages similar to the one above.
Please advice?
Thank you so much for your kind help!
Regards,
Heidi Foo
--
Martin Reuter, PhD
Assistant Professor of Radiology, Harvard Medical School
Assistant Professor of Neurology, Harvard Medical School
A.A.Martinos Center for Biomedical Imaging
Massachusetts General Hospital
Research Affiliate, CSAIL, MIT
Phone:+1-617-724-5652 <tel:%2B1-617-724-5652>
Web :http://reuter.mit.edu
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--
Martin Reuter, PhD
Assistant Professor of Radiology, Harvard Medical School
Assistant Professor of Neurology, Harvard Medical School
A.A.Martinos Center for Biomedical Imaging
Massachusetts General Hospital
Research Affiliate, CSAIL, MIT
Phone: +1-617-724-5652
Web : http://reuter.mit.edu
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