I usually use this little bash script (named myrecon) to process my images.

#!/bin/bash mkdir ~/freesurfer/subjects/$1/mri/orig -p cp ~/freesurfer/ImgOrig/$1/* ~/freesurfer/subjects/$1/mri/orig/ recon-all -all -s $1 -cw256 -hippo-subfields -qcache

With this script I get the entire -all pipeline, plus hippocampal segmentation and the cache for posterior analysis with qdec. All in a once and just typing myrecon subject. You can check if the hippo-subfields were correctly processed reading the recon-all-status.log and with more detail reading hippo-subfields.log. Both files are in freesurfer/subjects/yoursubject/scripts. I attached one of my recon-all-status.log so you can compare. The last line is related to hippo-subfields processing. After recon-all you will see several posterior*.mgz files inside freesurfer/subjects/yoursubject/mri/.

BTW, ImgOrig is a custom folder where I have one folder for each subject with the original 00X.mgz file(s).

Marcos

Em Seg, 2013-05-27 às 09:45 -0700, Salil Soman escreveu:

I can add that running the -hippo-subfields flag separately did work:

recon-all -s SUBJECTIDENTIFIER -hippo-subfields

Is there a reason the order of processing should matter? Is there a way I can change my recon-all call (below) so that hippo-subfields will get processed (so I do not have to make a separate call)?

recon-all -i SPGR/*.gz -s SUBJECTIDENTIFIER -nuintensitycor-3T -nocanorm -openmp 50 -hippo-subfields -all

Thank you,

Sal

On Sun, May 26, 2013 at 2:33 PM, Salil Soman salsoman@stanford.edu wrote:

    Dear Freesurfer Experts,


    I have been running freesurfer 5.3 without any reported errors
    using the following command:

    recon-all -i SPGR/*.gz -s SUBJECTIDENTIFIER -nuintensitycor-3T
    -nocanorm -openmp 50 -hippo-subfields -all


    However, when I look for any of the hippocampal subfield stats
    (as described on
    http://ftp.nmr.mgh.harvard.edu/fswiki/HippocampalSubfieldSegmentation), I do not find any of them.


    Any suggestions on what I am doing incorrectly?

    Best wishes,

    Salil Soman, MD, MS 

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