Hey Bruce,

Here's the command line I'm using - sorry realized I should've included it after sending the email: It just goes to the subject folder ($subject-$scan) and then does it's thing - already in tcsh shell with all the environment variables set and the .csh file sourced. Volume_ns+orig.BRIK is located right in the subject folder.

cd $subject-$scan

mri_convert --in_type brik Volume_ns+orig.BRIK orig/001.mgz recon-all -motioncor -s $subjID recon-all -nuintensitycor -s $subjID recon-all -talairach -s $subjID recon-all -normalization -s $subjID recon-all -skullstrip -s $subjID

recon-all -autorecon2 -s $subjID

By the way, thanks so much for working more with the data I sent you. I really appreciate it. Wonder whether you found ways to improve the intensity normalization automatically? (Right now I am trying giving AFNI pre-processing a shot using their 3dUniformize which is what I'm doing now, but obviously you will know what the best way to go is. We've gotten acceptable results using extensive control points, but just want to optimize the inhomogeneity correction/ intensity normalization and get the best possible automatic segs as we can to start with.)

Cheers,

John

On Wed, Oct 22, 2008 at 9:41 PM, Bruce Fischl fischl@nmr.mgh.harvard.eduwrote:

Hi John,

can you send us the command line you are running?

cheers, Bruce

On Wed, 22 Oct 2008, 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.