Not sure what is going on. can you find (from the log) the command it runs just before that (something with mris_label_calc) and run it in a terminal (with the SUBJECT_DIR set etc). It could be that it get's confused by the .nii extension, but could also be something else.

Martin

On 11/04/2015 10:09 AM, Heidi Foo wrote:

Hi Martin,

I understand what you mean now. Thanks for your advice!

But I have another error message now: /ERROR 64 : mris_label_calc intersect did not work? /Is there something I am doing wrong?

Regards, Heidi

On Wed, Nov 4, 2015 at 10:39 PM, Martin Reuter <mreuter@nmr.mgh.harvard.edu mailto:mreuter@nmr.mgh.harvard.edu> wrote:

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
<mreuter@nmr.mgh.harvard.edu
<mailto:mreuter@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 <tel:%2B1-617-724-5652>
Web  :http://reuter.mit.edu