Hi,
Thank you very much for this prompt response.
I don't think that it is a disk space problem. I have ~40GB of disk
space available (out of 60GB) and I haven't set any quotas.
I still cannot figure out why it analyzes example data but not my
data. One difference is the data size. My data is bigger, 256x256x15,
90 volumes (~177MB). Example data is 64x64x21, 180 volumes (~31MB). I
don't know if this is making a difference.
Here's the directory listing:
Contents of feat directory:
[tugan@amd2 GG++++.feat]$ ls -l
total 172500
-rw-rw-r-- 1 tugan tugan 86 Apr 24 16:19 design.con
-rw-rw-r-- 1 tugan tugan 13910 Apr 24 16:19 design_cov.gif
-rw-rw-r-- 1 tugan tugan 70965 Apr 24 16:19 design_cov.ppm
-rw-rw-r-- 1 tugan tugan 6313 Apr 24 16:19 design.fsf
-rw-rw-r-- 1 tugan tugan 62 Apr 24 16:19 design.fts
-rw-rw-r-- 1 tugan tugan 81843 Apr 24 16:19 design.gif
-rw-rw-r-- 1 tugan tugan 2565 Apr 24 16:19 design.mat
-rw-rw-r-- 1 tugan tugan 241410 Apr 24 16:19 design.ppm
-rw-rw-r-- 1 tugan tugan 124 Apr 24 16:19 design.trg
-rw-rw-r-- 1 tugan tugan 348 Apr 24 16:19 example_func.hdr
-rw-rw-r-- 1 tugan tugan 1966080 Apr 24 16:19 example_func.img
-rw-rw-r-- 1 tugan tugan 348 Apr 24 17:29 filtered_func_data.hdr
-rw-rw-r-- 1 tugan tugan 173015040 Apr 24 17:29
filtered_func_data.img
-rw-rw-r-- 1 tugan tugan 348 Apr 24 17:27 mask.hdr
-rw-rw-r-- 1 tugan tugan 983040 Apr 24 17:27 mask.img
drwxrwxr-x 2 tugan tugan 4096 Apr 24 17:25 mc
drwxrwxr-x 2 tugan tugan 4096 Apr 24 17:31 reg
-rw-rw-r-- 1 tugan tugan 3285 Apr 24 17:31 report.com
-rw-rw-r-- 1 tugan tugan 2573 Apr 24 17:31 report.html
-rw-rw-r-- 1 tugan tugan 3828 Apr 24 17:31 report.log
drwxrwxr-x 2 tugan tugan 4096 Apr 24 17:29 stats
drwxrwxr-x 2 tugan tugan 4096 Apr 24 17:31 tsplot
Contents of stats:
[tugan@amd2 GG++++.feat]$ ls -l stats
total 8
-rw-rw-r-- 1 tugan tugan 112 Apr 24 17:29 cmlogfile
-rw-rw-r-- 1 tugan tugan 176 Apr 24 17:29 logfile
[tugan@amd2 GG++++.feat]$
>Hi - it looks like the output from ip was not successful so film_gls
>wasn't happy - this is most likely that you ran out of disk space or
>quota?
>
>Can you send us the result of running in the FEAT directory:
>
>ls -l
>ls -l stats
>
>thanks :)
>
>
>On Thu, 24 Apr 2003, Tugan Muftuler wrote:
>
>> Hi,
>>
>> I sent an inquiry yesterday but for some reason it did not go through.
>> Anyway, I am trying it again:
>>
>> I recently donwloaded FSL both to my Mac with OSX and RedHat 7.3 machines. I
>> ran the example data set on both computers and they run without any
>> problems. However, when I run an old data of mine on both machines, the one
>> on Mac runs smoothly but the same data fails during FEAT analysis on the
>> RedHat 7.3 machine. The 3D images are converted from a set of images ran
>> under SPM. They are converted to 4D using avwmerge and merging was checked
>> with slicer/display. I also checked the headers with avwhd.
>>
>> I checked all the header infromation, they seem fine on both machines. I
>> used slicer/display to make sure that they display correctly on both
>> machines. It actually does motion correction on both machines, so there
>> should not be a problem with reading the images. I cannot figure out why it
>> fails during the stats.
>>
>> It should not be an installation/configuration problem either, since it runs
>> example fmri data in feeds.
>>
>> My redhat machine is much faster, has bigger memory and a huge hard drive.
>> It takes 25-30 minutes on the Mac, so I am certainly inclined to use it on
>> the linux box.
>>
>> So, any inputs to this matter will be greatly appreciated.
>>
>> Thanks,
>>
>> Tugan Muftuler
>>
>>
>> Below, I have included the report.log for any clues you might catch.
> > Actually, every time I run it, I get the following, which seems unusual:
>>
>> /home/tugan/fsl/bin/contrast_mgr stats design.con
>> AvwOpen: Error while opening header!: No such file or directory
>>
>> *********************************
>> The whole report.log:
>>
>> Started FEAT at Wed Apr 23 18:39:36 PDT 2003
>>
>> /bin/mkdir /ric_data1/users/tugan/motor/GG+++.feat
>>
>> /bin/cp /tmp/feat_TEeG4S.fsf design.fsf
>>
>> /home/tugan/fsl/bin/feat_model design
>>
>> Started FEAT at Wed Apr 23 18:39:36 PDT 2003 on amd2.ric.uci.edu
>> Total original volumes = 88
>> /home/tugan/fsl/bin/avwroi /ric_data1/users/tugan/motor/GG example_func 44 1
>>
>> /home/tugan/fsl/bin/betfunc /ric_data1/users/tugan/motor/GG
>> prefiltered_func_data_bet
>>
>> /home/tugan/fsl/bin/ip prefiltered_func_data_bet filtered_func_data 10 -s
>> 2.12314225053 -m mask -I 10000 -t 16.6666666667 -1 | grep THRESHOLD | awk '{
> > print $2 }' -
> > 1000.000000
> > rm -rf prefiltered_func_data*
> >
> > /home/tugan/fsl/bin/film_gls -rn stats -sa -ms 5 -sp
> > /home/tugan/fsl/bin/susan_smooth filtered_func_data design.mat 1000.000000
>> Log directory is: stats
>> Loading image...
>> /home/tugan/fsl/bin/contrast_mgr stats design.con
>> AvwOpen: Error while opening header!: No such file or directory
>> Rendering using zmin=2.3 zmax=8
>> /home/tugan/fsl/bin/tsplot . -f filtered_func_data
>> Cannot open volume ./stats/pe1.hdr for reading!
>> mkdir grot; mv *tsplot* grot; mv grot tsplot
>> mv: cannot stat `*tsplot*': No such file or directory
>> /bin/mkdir reg
>>
>> /bin/rm -f example_func.hdr example_func.img
>>
>> ln -s ../example_func.hdr example_func.hdr
>>
>> ln -s ../example_func.img example_func.img
>>
>> /bin/rm -f standard.hdr standard.img
>>
>> ln -s /home/tugan/fsl/etc/standard/avg152T1_brain.hdr standard.hdr
>>
>> ln -s /home/tugan/fsl/etc/standard/avg152T1_brain.img standard.img
>>
>> /home/tugan/fsl/bin/flirt -ref standard -in example_func -out
>> example_func2standard -omedx example_func2standard.xfm -omat
>> example_func2standard.mat -cost corratio -dof 6 -schedule
>> /home/tugan/fsl/etc/flirtsch/xyztrans.sch -searchrx -90 90 -searchry -90 90
>> -searchrz -90 90 -interp trilinear
>>
>> /home/tugan/fsl/bin/convert_xfm -matonly -inverse -omat
>> standard2example_func.mat example_func2standard.mat
>>
>> /home/tugan/fsl/bin/slicer example_func2standard standard -s 1 -x 0.35 sla
>> -x 0.45 slb -x 0.55 slc -x 0.65 sld -y 0.35 sle -y 0.45 slf -y 0.55 slg -y
>> 0.65 slh -z 0.35 sli -z 0.45 slj -z 0.55 slk -z 0.65 sll ;
>> /home/tugan/fsl/bin/convert -colors 100 +append sla slb slc sld sle slf slg
>> slh sli slj slk sll example_func2standard.gif ; /bin/rm -f sla slb slc sld
>> sle slf slg slh sli slj slk sll
>>
>> /bin/rm -f example_func2standard.hdr example_func2standard.img
>>
>> Finished registration at Wed Apr 23 18:46:07 PDT 2003
>> Finished FEAT at Wed Apr 23 18:46:07 PDT 2003
>> To view the FEAT report point your web browser at
>> /ric_data1/users/tugan/motor/GG+++.feat/report.html
>>
>
> Stephen M. Smith MA DPhil CEng MIEE
> Associate Director, FMRIB and Analysis Research Coordinator
>
> Oxford University Centre for Functional MRI of the Brain
> John Radcliffe Hospital, Headington, Oxford OX3 9DU, UK
> +44 (0) 1865 222726 (fax 222717)
>
> [log in to unmask] http://www.fmrib.ox.ac.uk/~steve
--
****************************************
L. Tugan Muftuler, Ph.D.
Center for Functional Onco-Imaging
Irvine Hall 164
University of California
Irvine, CA, 92697-5020
Tel: (949) 824-6290
fax: (949) 824-3481
E-mail: [log in to unmask]
****************************************
