grep -H -R "/usr/pubsw/bin/perl -w" $FREESURFER_HOME/*
Produced the results below, which appear to be the only files with hard
links to the "/usr/pubsw/bin/perl."
grep -H -R "/usr/pubsw/bin/perl -w" $FREESURFER_HOME/*
$FREESURFER_HOME/lib/mni/bin/make_template:#!/usr/pubsw/bin/perl -w
$FREESURFER_HOME/lib/mni/bin/nu_estimate_np_and_em:#!/usr/pubsw/bin/perl -w
$FREESURFER_HOME/lib/mni/bin/sharpen_volume:#!/usr/pubsw/bin/perl -w
$FREESURFER_HOME/lib/mni/bin/imp2field:#!/usr/pubsw/bin/perl -w
$FREESURFER_HOME/lib/mni/bin/nu_estimate:#!/usr/pubsw/bin/perl -w
$FREESURFER_HOME/lib/mni/bin/mritotal:#! /usr/pubsw/bin/perl -w
$FREESURFER_HOME/lib/mni/bin/autocrop:#! /usr/pubsw/bin/perl -w
$FREESURFER_HOME/lib/mni/bin/nu_correct:#!/usr/pubsw/bin/perl -w
$FREESURFER_HOME/lib/mni/bin/xfmtool:#! /usr/pubsw/bin/perl -w
$FREESURFER_HOME/lib/mni/bin/mritoself:#! /usr/pubsw/bin/perl -w
$FREESURFER_HOME/lib/mni/bin/nu_evaluate:#!/usr/pubsw/bin/perl -w
$FREESURFER_HOME/lib/mni/bin/field2imp:#!/usr/pubsw/bin/perl -w
The recon-all -subjid XXX -autorecon-all completed successfully in 27 hours
on my Fedora Core 4 (AMD sempron 2600+) with surfaces having 0 holes. No
manual edits were done.
The aseg.stats file is wonderful. Is there a way to overlay an individual's
subcortical/cortical segmentation results on their t1.mgz volume (i.e,
colorize voxels belonging to a specific structures)?
--
Brian C. Schweinsburg, Ph.D.
Assistant Adjunct Professor of Psychiatry
University of California, San Diego
Office: 858-552-8585 x6109
Cell: 858-354-3756
> From: Nick Schmansky
nicks@nmr.mgh.harvard.edu
> Date: Tue, 06 Sep 2005 11:16:22 -0400
> To: "Brian Schweinsburg, Ph.D."
bschweinsburg@ucsd.edu
> Cc: Freesurfer Mailing List
freesurfer@nmr.mgh.harvard.edu
> Subject: Re: [Freesurfer] new 'dev' release for Linux rh9, centos4 and
> centos4_x86_64
>
> Brian,
>
> I'm glad to hear that the installation is now working for you.
>
> The recon-all -autorecon-all command can take 24 or more hours to
> complete, depending on the quality of the scan, and the difficulty of
> auto-fixing any defects, and of course the machine upon which it is
> running. Your machine appears to be more than adequate.
>
> Concerning the perl scripts which needed editing, which files (with
> paths) required editing? I'd like to remove any hard-coded paths in our
> installation.
>
> Concerning the mgz files, recon-all does expect to find each structural
> scan in the mri/orig directory, with filenames 001.mgz, 002.mgz, etc..
> Given a subject having three sets of DICOMS (three runs of structural
> scans), I do the following to setup a subject:
>
> cd $SUBJECTS_DIR
> mksubjdirs <subjid>
> cd <subjid>
> cd mri/orig
> mkdir 001
> mkdir 002
> mkdir 003
> cp -r <path_to_dicoms>/95555-2-*.dcm 001/
> cp -r <path_to_dicoms>/95555-3-*.dcm 002/
> cp -r <path_to_dicoms>/95555-7-*.dcm 003/
> mri_convert -it dicom -ot mgz 001/ 001.mgz
> mri_convert -it dicom -ot mgz 002/ 002.mgz
> mri_convert -it dicom -ot mgz 003/ 003.mgz
>
> Now you will have three .mgz files in mri/orig, and recon-all will
> automatically take these three structural scans and average/motion-
> correct them.
>
> The reason that we now encourage .mgz files over the COR format is
> because the COR format is limited to storage of volume data in unsigned
> char format only, and does not allow int, float, double or long formats.
> Also, the COR format historically assumes a slice size of 256 by 256
> voxels. For these reasons, the COR format is deprecated in favor of the
> newer mgh (and mgz) format.
>
> Concerning csurf, we no longer actively maintain csurf, in favor of
> recon-all. csurf is essentially an older copy of the recon-all script,
> and is not kept in-line with recon-all. We encourage using the recon-
> all script because it is easier to see what is going on, and to
> maintain. But we'll look into the possibility of at least csurf
> supporting the opening of .mgz files.
>
> Nick
>
>
> On Mon, 2005-09-05 at 21:58 -0700, Brian Schweinsburg, Ph.D. wrote:
>> Hi Nick,
>>
>> I downloaded freesurfer-Linux-rh9-dev20050905-full.tar.gz and installed it
>> on the following system:
>> Fedora Core 4; AMD Sempron 2600+ on an ECS KT600-A board; Nvidia GeForce 2;
>> 1 GB DDR 400 RAM.
>>
>> 'recon-all -subjid XXX -autorecon-all' would not run at first because it
>> could not find some of the mni tools. The ones that it was having difficulty
>> with were the perl scripts (not the binary MNI files). I noticed the first
>> line in each of the scripts points to what looks like the MGH specific perl
>> installation (i.e., /usr/pubsw/bin/perl), which does not exist on my system.
>> I tested two different solutions 1) change the first line of each file and
>> 2) mkdir -p /usr/pubsw/bin and then add a symbolic link to my perl binary.
>> Both methods appear to work, and 'recon-all -subjid XXX -autorecon-all' has
>> been running successfully for about 12 hours. I assume it is working!
>>
>> I also noticed that recon-all expected the mgz files for each separate
>> anatomical to both be located in $FREESURFER_HOME/subjects/XXX/mri/orig.
>> This is opposed to what I recall for the old COR method of placing separate
>> anats in 001 002 etc (for obvious overwriting reasons). I believe this is
>> documented in the recon-all help file, but could be confusing for some users
>> at first.
>>
>> Csurf, tkmedit, and tksurfer gui's loaded without a problem on my FC4
>> machine. Csurf loads surfaces fine, but I cannot get it to load mgz files.
>> It seems to expect COR files. Out of habit, I did all of my volume edits
>> using 'Edit Segmentation' in csurf, but may have to switch tkmedit/tksurfer.
>> No problem there.
>>
>> In sum, the current dev version for Redhat 9 appears to be running fine on a
>> basic Fedora Core 4 machine.
>>
>> Thanks,
>> Brian
>>
>
