Hi Joost,

great, but make sure the recon-all processing went OK also. If you had the same directory name twice (for base and for the first time point) stuff will be messed up. Usually recon-all should complain if that happens, but who knows what exactly happened.

Best Martin

On Mon, 2012-07-02 at 12:28 +0200, j janssen wrote:

Hi Martin,

changing the dir-names and qdec table to:

fsid fsid-base ISI_years Group Gender Age ICV 11298_1 11298_template 0 patient F 16 1441 11298_2 11298_template 1.83 patient F 17.92 1396

solved my problem.

-joost

On Sun, Jul 1, 2012 at 4:33 PM, j janssen joost.janssen76@gmail.com wrote: Hi Martin,

    thanks.

    i changed 11298 to 11298_1 and got the same error. are you
    suggesting that some recon-all error may have happened because
    of the file names? no error messages were reported in any of
    the log files, all (cross-sectional and longitudinal) finished
    without error. does the error point to two intra-subject
    surfaces which should have the same # of vertices but do not
    have so? if so, which surfaces? 

    thanks,
    -joost




    On Fri, Jun 29, 2012 at 8:50 PM, Martin Reuter
    <mreuter@nmr.mgh.harvard.edu> wrote:
            Hi Joost,

            the tp id cannot be the same as the base id:

            fsid fsid-base ISI_years Group Gender Age ICV
            11298 11298 0 patient F 16 1441
            11298_2 11298 1.83 patient F 17.92 1396

            I am amazed that you were able to process it this way?

            So either call the first time point
            11298_1
            or call the base 11298_base in both cases.

            Also make sure your longitudinal processing is correct
            (I mean the
            recon-all, not the post processing that you are trying
            here).

            Best, Martin

            On Fri, 2012-06-29 at 13:35 +0200, j janssen wrote:
            > Hi (Martin),
            >
            > - version 5.1 (Ubuntu 64b)
            > - command: long_mris_slopes
            --qdec ./qdec/long.qdec.table.n114.dat
            > --meas thickness --hemi lh --do-avg --do-rate
            --do-pc1 --do-spc
            > --do-stack --do-label --time ISI_years --qcache
            fsaverage
            > - attached: first 3 lines of qdec table containing
            the info for
            > subject 11298
            > - attached: on screen error output.
            > - i have 2 timepoints/subject.
            >
            > things go awry in the "SUBJECT 11298  Running
            Within-Subject GLM" step
            > (see attachment):
            >
            > Reshaping mriglm->mask...
            > ERROR: mri_reshape: number of elements cannot change
            >
            > what am i doing wrong?
            >
            > -joost
            >

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