Yes, it is. I forgot that version 5.3 uses the brain mask from the first run. This is fixed in version 6.

On 03/09/2016 02:42 PM, Ji Won Bang wrote:

Dear. Freesurfer experts.

Hi.

I'm pretty sure that this error is due to the different number of slices in different runs....

I ran preproc-sess -s $SUBJECT -df sessdirfile -fsd bold_Retino -nosmmth -per-run -force Then I ran selxavg3-sess -s $SUBJECT -analysis retino -df sessdirfile

I thought preproc-sess -per-run creates mask for each run.. but probably not...

Could you please advise me how to correct this dimension mismatch between mask and 2th run?

Thank you very much!

Best, Ji Won

2016-03-09 12:08 GMT-05:00 Ji Won Bang <kirstens03@gmail.com mailto:kirstens03@gmail.com>:

Dear. Freesurfer experts.

Hi.

i appreciate your help in advance!

I'm using freesurfer version 5.3.0.

I tried selxavg3-sess and got the error dimension mismatch between
mask and 2th run.
Actually, the number of slices of the 1st run and the rest are
different. Is it the reason why I get this error message?
Please let me know what I should do to correct this error!

Below are command and error lines.

command: selxavg3-sess -s $SUBJECT -analysis retino -df sessdirfile

error:
--------------------------------------------------------------
selxavg3-sess logfile is
/home/jbang/Projects/replay/log/log/selxavg3-sess-bold_retino-retino-160309115326.log
--------------------------------------------------------------
-------------------------------------------
/home/jbang/Projects/replay/epi/replay06
Wed Mar  9 11:53:33 EST 2016
anadir = /home/jbang/Projects/replay/epi/replay06/bold_retino/retino
DoGLMFit = 1
DoContrasts = 1
UpdateNeeded = 1
------------------------------------------
------- matlab output --------------------
Warning: Unable to open display 'iconic'.  You will not be able to
display graphics on the screen.

                            < M A T L A B (R) >
                  Copyright 1984-2009 The MathWorks, Inc.
                Version 7.8.0.347 (R2009a) 64-bit (glnxa64)
                             February 12, 2009


  To get started, type one of these: helpwin, helpdesk, or demo.
  For product information, visit www.mathworks.com
<http://www.mathworks.com>.

>> >> >> >> >> >> >>
sxa3pwd =

/home/jbang/Projects/replay/log

>>
sxa3cmd =

/usr/local/freesurfer//fsfast/bin/selxavg3-sess -s replay06
-analysis retino -df sessdirfile

>> /usr/local/freesurfer/fsfast/toolbox/fast_selxavg3.m
>> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >>

#@# replay06 ###############################
/home/jbang/Projects/replay/epi/replay06
-------------------------
$Id: fast_selxavg3.m,v 1.100.2.2 2012/11/30 18:40:38 greve Exp $
/usr/local/freesurfer/fsfast/toolbox/fast_selxavg3.m
/usr/local/freesurfer/fsfast/toolbox/fast_ldanaflac.m
/usr/local/freesurfer/matlab/MRIread.m
-------------------------
outtop = /home/jbang/Projects/replay/epi
Extension format = nii.gz
 1 HorVer.mat
 2 UpperLower.mat
nruns = 4
autostimdur =


outanadir =
/home/jbang/Projects/replay/epi/replay06/bold_retino/retino
Found 62211/180708 (34.4) voxels in mask
Creating Design Matrix
 ... creation time =  0.008 sec
DoMCFit = 0
ntptot = 480, nX = 28, DOF = 452
Saving X matrix to
/home/jbang/Projects/replay/epi/replay06/bold_retino/retino/Xtmp.mat
XCond = 199.451 (normalized)
Computing compensation for resdual AR1 bias
 1  -0.5  -0.499283    (t=0.024843)
 2  -0.25  -0.268756    (t=0.047925)
 3  0  -0.0441607    (t=0.069497)
 4  0.25  0.16942    (t=0.093633)
 5  0.5  0.359032    (t=0.117433)
AR1 Correction M: 0.0657489 1.15858
Computing contrast matrices
OLS Beta Pass
  run 1    t= 0.0
    Global Mean   855.07
  run 2    t= 3.1
ERROR: dimension mismatch between mask and 2th run
>> ------------------------------------------
ERROR: fast_selxavg3() failed\n

Thank you very much!

Best,
Ji Won

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