Also, in case anyone is interested -- if you have a brik volume in the subject folder, specifying mri/orig/001.mgz gives the same error as specifying orig/001.mgz, at least for me. So that wasn't the cause of the problem.
John On Thu, Oct 23, 2008 at 7:44 AM, John Sheppard < [EMAIL PROTECTED]> wrote: > 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 < > [EMAIL PROTECTED]> 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 >>> #-------------------------------------------- >>> [EMAIL PROTECTED] 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: [EMAIL PROTECTED] >>> Address: 1927 Orrington Ave. Rm 8203 >>> Evanston, IL 60201 >>> >>> _______________________________________________ >>> Freesurfer mailing list >>> Freesurfer@nmr.mgh.harvard.edu >>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>> >> >> > > > -- > John Sheppard > Undergraduate Student (Class of 2010) > Department of Biomedical Engineering > Northwestern University > > Phone: (630) 957-8321 > E-mail: [EMAIL PROTECTED] > Address: 1927 Orrington Ave. Rm 8203 > Evanston, IL 60201 > > -- John Sheppard Undergraduate Student (Class of 2010) Department of Biomedical Engineering Northwestern University Phone: (630) 957-8321 E-mail: [EMAIL PROTECTED] Address: 1927 Orrington Ave. Rm 8203 Evanston, IL 60201
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