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 salso...@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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status file for recon-all
Thu May 23 01:32:10 BRT 2013
#@# MotionCor Thu May 23 01:32:10 BRT 2013
#@# Talairach Thu May 23 01:35:39 BRT 2013
#@# Talairach Failure Detection Thu May 23 01:37:16 BRT 2013
#@# Nu Intensity Correction Thu May 23 01:37:16 BRT 2013
#@# Intensity Normalization Thu May 23 01:38:35 BRT 2013
#@# Skull Stripping Thu May 23 01:41:00 BRT 2013
#@# EM Registration Thu May 23 02:16:10 BRT 2013
#@# CA Normalize Thu May 23 02:42:59 BRT 2013
#@# CA Reg Thu May 23 02:44:52 BRT 2013
#@# CA Reg Inv Thu May 23 07:28:41 BRT 2013
#@# Remove Neck Thu May 23 07:29:49 BRT 2013
#@# SkullLTA Thu May 23 07:30:59 BRT 2013
#@# SubCort Seg Thu May 23 08:02:06 BRT 2013
#@# Merge ASeg Thu May 23 08:23:51 BRT 2013
#@# Intensity Normalization2 Thu May 23 08:23:51 BRT 2013
#@# Mask BFS Thu May 23 08:28:03 BRT 2013
#@# WM Segmentation Thu May 23 08:28:06 BRT 2013
#@# Fill Thu May 23 08:31:06 BRT 2013
#@# Tessellate lh Thu May 23 08:32:01 BRT 2013
#@# Smooth1 lh Thu May 23 08:32:09 BRT 2013
#@# Inflation1 lh Thu May 23 08:32:14 BRT 2013
#@# QSphere lh Thu May 23 08:32:50 BRT 2013
#@# Fix Topology lh Thu May 23 08:37:40 BRT 2013
#@# Make White Surf lh Thu May 23 09:03:51 BRT 2013
#@# Smooth2 lh Thu May 23 09:10:51 BRT 2013
#@# Inflation2 lh Thu May 23 09:10:55 BRT 2013
#@# Curvature Stats lh Thu May 23 09:13:12 BRT 2013
#@# Sphere lh Thu May 23 09:13:16 BRT 2013
#@# Surf Reg lh Thu May 23 10:08:23 BRT 2013
#@# Jacobian white lh Thu May 23 10:45:12 BRT 2013
#@# AvgCurv lh Thu May 23 10:45:15 BRT 2013
#@# Cortical Parc lh Thu May 23 10:45:17 BRT 2013
#@# Make Pial Surf lh Thu May 23 10:46:15 BRT 2013
#@# Surf Volume lh Thu May 23 11:00:00 BRT 2013
#@# WM/GM Contrast lh Thu May 23 11:00:00 BRT 2013
#@# Parcellation Stats lh Thu May 23 11:00:11 BRT 2013
#@# Cortical Parc 2 lh Thu May 23 11:00:32 BRT 2013
#@# Parcellation Stats 2 lh Thu May 23 11:01:36 BRT 2013
#@# Cortical Parc 3 lh Thu May 23 11:01:56 BRT 2013
#@# Parcellation Stats 3 lh Thu May 23 11:02:52 BRT 2013
#@# Tessellate rh Thu May 23 11:03:09 BRT 2013
#@# Smooth1 rh Thu May 23 11:03:18 BRT 2013
#@# Inflation1 rh Thu May
