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I tried that, but no luck. FS ran into issues with ?h.white.H and then ?h.w-g.pct.mgh (maybe more errors). Is there a way to use qcache in 4.5? Could I simply download and install v.4.5 ( https://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/4.5.0/) and go from there? I couldn't find instructions for v.4.5, but would the syntax of 'recon-all -s $sub -qcache' work?

Thanks much!

On Wed, Jun 13, 2018 at 11:20 AM Douglas N. Greve dgreve@mgh.harvard.edu wrote:

I have no idea how to make it work with data that old. You can "fool" it by copying or soft linking lh.curv to lh.white.K. You can probably get it to at least finish.

On 06/06/2018 03:41 PM, Jamie Hanson wrote:

...

    External Email - Use Caution

Hello all,

I was trying to run qcache on some previously processed Freesurfer data from a colleague, but ran into some issues with missing files and wondered how best to proceed.

Details: -The data was processed with (Freesurfer) v4.5.0 and I would ideally like to not reprocess it with a newer version (to keep in concordance with past published work, and also it's a large number of subjects, n=800+). -The qcache flag was not used with the data previously (to my knowledge), so I was attempting to run this command: recon-all -s $subj -qcache -When I try that command, I get an error regarding a missing lh.white.K file.

I've uploaded the log file here: https://www.dropbox.com/s/94mnsy7wrps5ce2/recon-all.log?dl=0

I wondered if it was possible to complete qcache with the data as is? I searched on the list previously and saw one or two other folks had run into this issues; I, however, didn't see a final solution to things. Any thoughts or suggestions are greatly appreciated! Thanks much!

Best, Jamie.

-- Jamie Hanson Assistant Professor, Psychology Research Scientist, Learning Research and Development Center University of Pittsburgh Personal website: jamiehanson.org http://jamiehanson.org

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Sorry, I don't know what the problem is and I am not highly motivated to debug a 10-year-old version of FS. Instead of using qdec, why not just use the command-line stream (ie, mris_preproc, mri_surf2surf, mri_glmfit, and mri_glmfit-sim). There are tutorials for it on the wiki. We are also getting away from supporting qdec anyway.j

On 06/18/2018 12:00 PM, Jamie Hanson wrote:

I installed Freesurfer v.4.5 and tried to qcache this old data, but ran into an error (segmentation fault). I wondered if there were some settings or files I might be missing? (Or if I had old libraries that stopped FS from completing?)

I downloaded freesurfer-Linux-centos4_x86_64-stable-pub-v4.5.0-full.tar.gz (from https://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/4.5.0/).

A log file is located here-- https://www.dropbox.com/s/9c3d0kgbafqpgx3/P0008_000_01-FS_recon-all.log?dl=0... the error output is a bit sparse).

Additional suggestions to try? Thanks much!

On Thu, Jun 14, 2018 at 12:47 PM Jamie Hanson <jamielarshanson@gmail.com mailto:jamielarshanson@gmail.com> wrote:

I tried that, but no luck. FS ran into issues with ?h.white.H and
then ?h.w-g.pct.mgh (maybe more errors). Is there a way to use
qcache in 4.5? Could I simply download and install v.4.5
(https://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/4.5.0/)
and go from there? I couldn't find instructions for v.4.5, but
would the syntax of 'recon-all -s $sub -qcache' work?

Thanks much!


On Wed, Jun 13, 2018 at 11:20 AM Douglas N. Greve
<dgreve@mgh.harvard.edu <mailto:dgreve@mgh.harvard.edu>> wrote:

    I have no idea how to make it work with data that old. You can
    "fool" it
    by copying or soft linking lh.curv to lh.white.K. You can
    probably get
    it to at least finish.


    On 06/06/2018 03:41 PM, Jamie Hanson wrote:
    >
    >         External Email - Use Caution
    >
    >
    > Hello all,
    >
    > I was trying to run qcache on some previously processed
    Freesurfer
    > data from a colleague, but ran into some issues with missing
    files and
    > wondered how best to proceed.
    >
    > Details:
    > -The data was processed with (Freesurfer) v4.5.0 and I would
    ideally
    > like to not reprocess it with a newer version (to keep in
    concordance
    > with past published work, and also it's a large number of
    subjects,
    > n=800+).
    > -The qcache flag was not used with the data previously (to my
    > knowledge), so I was attempting to run this command:
    recon-all -s
    > $subj -qcache
    > -When I try that command, I get an error regarding a
    > missing lh.white.K file.
    >
    > I've uploaded the log file here:
    > https://www.dropbox.com/s/94mnsy7wrps5ce2/recon-all.log?dl=0
    >
    > I wondered if it was possible to complete qcache with the
    data as is?
    > I searched on the list previously and saw one or two other
    folks had
    > run into this issues; I, however, didn't see a final
    solution to
    > things. Any thoughts or suggestions are greatly appreciated!
    Thanks much!
    >
    > Best,
    > Jamie.
    >
    > --
    > Jamie Hanson
    > Assistant Professor, Psychology
    > Research Scientist, Learning Research and Development Center
    > University of Pittsburgh
    > Personal website: jamiehanson.org <http://jamiehanson.org>
    <http://jamiehanson.org>
    >
    >
    >
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    Compliance HelpLine at
    http://www.partners.org/complianceline . If the e-mail was
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