Hey Krish,

Thanks for your input.  Good idea too, never thought about doing that.  Tried this in command line and worked without a hitch.  Then i realized if you just use command line what I did before works as well.  The error must somehow be resulting from issues with tcsh or something.  But I found a way to get it to work in tcsh shell script, going off of what you suggested.  Here is what works for me in tcsh script:

cd $FSsubjDir
mkdir $subjID
cd $subjID
mkdir mri
cd mri
mkdir orig
cd orig
mv ../../Volume_ns+orig* ./

mri_convert --in_type brik Volume_ns+orig.BRIK 001.mgz

etc etc

That's probably a primitive way to write the script, but hey, it works.  Thanks for the help!

John

On Wed, Oct 22, 2008 at 10:34 PM, Krish Subramaniam <krish@nmr.mgh.harvard.edu> wrote:
John

Is orig/ already there ? Otherwise try

mkdir orig
mri_convert --in_type brik Volume_ns+orig.BRIK 001.mgz
mv 001.mgz orig/

Thanks
Krish



On Oct 22, 2008, at 10:01 PM, John Sheppard wrote:

Hey everyone,

I'm having some issues trying to run the volume pipeline using .BRIK input from afni (hence running mri_convert command directly).  The problem occurs at the end of mri_convert at the very beginning when Freesurfer fails to write orig/001.mgz, and I'm not sure if I'm making a mistake without realizing it or if something weirder is going on.  I've tried this on both a Mac and a linux station running RHEL, with the same results.  I ran the script using sudo in RHEL so I do not think this is a permissions issue.

The error occurs right when it tries to write orig/001.mgz: writing to orig/001.mgz...
sh: orig/001.mgz: No such file or directory
Broken pipe

I'm not really familiar with working with pipes but I'm guessing I shouldn't have to deal with that.

Just curious if anyone has encoutered this before and knows what's going on.  Didn't find this issue in prior mailing list emails, so I hope this isn't a repeat question.

Thanks!

John Sheppard

Recon output below:

mri_convert --in_type brik Volume_ns+orig.BRIK orig/001.mgz
$Id: mri_convert.c,v 1.146.2.3 2008/08/11 22:18:58 nicks Exp $
reading from Volume_ns+orig.BRIK...
AFNI Header Information ============================================
DATASET_RANK      : spatial dims 3, sub-bricks 1
DATASET_DIMENSIONS: (256, 256, 160)
TYPESTRING        : 3DIM_HEAD_ANAT
SCENE_DATA        : view type 0, func type 0, verify 0
ORIGIN            : (-172.926697, 84.177513, -82.874474)
DELTA             : (1.000000, -1.000000, 1.000000)
IDCODE_STRING     : XYZ_FSWwmSca-raNtz0oRbtKow
BYTEORDER_STRING  : LSB_FIRST
BRICK_STATS       : min 0.000000         max 950.000000
BRICK_TYPES       : short
BRICK_FLOAT_FACS  : 0.000000
====================================================================
BRICK_STATS min = 0.000000 <--> actual min = 0.000000
BRICK_STATS max = 950.000000 <--> actual max = 950.000000
TR=0.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (0, -1, 0)
j_ras = (0, 0, -1)
k_ras = (-1, 0, 0)
writing to orig/001.mgz...
sh: orig/001.mgz: No such file or directory
Broken pipe
Subject Stamp: freesurfer-Linux-centos4-stable-pub-v4.1.0
Current Stamp: freesurfer-Linux-centos4-stable-pub-v4.1.0
INFO: SUBJECTS_DIR is /mnt/win/MTLD1/autorecon
Actual FREESURFER_HOME /usr/local/freesurfer
Linux SLR10.soc.northwestern.edu 2.6.18-92.1.13.el5 #1 SMP Thu Sep 4 03:51:01 EDT 2008 i686 i686 i386 GNU/Linux
#--------------------------------------------
#@# MotionCor Wed Oct 22 20:45:32 CDT 2008
ERROR: no run data found in /mnt/win/MTLD1/autorecon/E-05-010-2-afni-test/mri. Make sure to
have a volume called 001.mgz in  /mnt/win/MTLD1/autorecon/E-05-010-2-afni-test/mri/orig.


--
John Sheppard
Undergraduate Student (Class of 2010)
Department of Biomedical Engineering
Northwestern University

Phone: (630) 957-8321
E-mail: john-sheppard@northwestern.edu
Address: 1927 Orrington Ave. Rm 8203
             Evanston, IL 60201

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--
John Sheppard
Undergraduate Student (Class of 2010)
Department of Biomedical Engineering
Northwestern University

Phone: (630) 957-8321
E-mail: john-sheppard@northwestern.edu
Address: 1927 Orrington Ave. Rm 8203
              Evanston, IL 60201