The problem is that you have a version 4 analysis that you are trying to view with version 5 tools. To use version 5 visualization, you'll need to remake the analysis in version 5 and then reanalyze. Otherwise, you'll have to use the version 4 stream (instructions attached). It is somewhat difficult for me to support the version 4 stream because it is so old.

doug



On 12/06/2012 03:27 PM, Julia Foecker wrote:
I have the two versions 4 and 5 , but I am receiving the same error messages with 5.1
For example when I type in preproc-see there is no -surface as well.
Isn't there any other possibility to solve that issue?

It may have also sth. to do with the computer. I have a new Mac, not sure if this may be the reason. As I said, I do not think this is due to the version...I just tried that and similar requirements are missing when I am doing that with 5.1

Thanks again for further advices,
Julia



On 12/6/12 11:56 AM, Douglas N Greve wrote:
Julia, what version of FS are you using? It looks like pre-5.0. Can you upgrade to 5.1? There were a lot of changes in going from 4 to 5, and it is becoming increasingly hard to support version 4.

doug



On 12/06/2012 02:45 AM, Julia Foecker wrote:
thanks.
attached the info file.

When I run the surf-sess command after that, it shows the functional on a surface (see attached but the values at the occip regions show "inf." (see
figure 1 attached).
Moreover, when I try to load the occipital patch it shows me the attached file
(fig.3) and I cannot use the command -> configure -> overlay to change
settings.

I have used fake ecc. runs (I have recorded only polar runs).

Would you have any further suggestions?
Thanks,
Julia

On Wed, 05 Dec 2012 17:03:31 -0500 Douglas N Greve <gr...@nmr.mgh.harvard.edu>
wrote

It should automatically detect that this was a retinotopy analysis and
then load the polar and eccen. Was this configured as a retinotopy
analysis? Can you send me the

$ANALYSIS_PHASE/analysis.info file?

doug



On 12/05/2012 04:12 PM, Julia Foecker wrote:
Hi Doug,

I tried now several ways to get the maps on the surface:

1. When I am deleting -retinotopy flag and type in:


tksurfer-sess -debug -s $SESSIONNAME -hemi lh -d $SESSIONDIRECTORY
-analysis $ANALYSIS_PHASE
I got the message:no contrast has been specified

(I do not have any contrasts in the analysis, just use polar angle maps)


2. I tried to use the commands on the website you referred to, but I do not
have -surface in the preproc-sess (see attached)
The other commands depend on this preproc-sess command.


3. I tried the following command
paint-sess -s $SESSIONNAME -d $SESSIONDIRECTORY -analysis $ANALYSIS_PHASE


and I got the errors listed below...

I am not sure how to procede. Would you have any further suggestions?
Many thanks,
Julia

Thanks,
Julia



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--
Douglas N. Greve, Ph.D.
MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html
Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/

Retinotopy analysis in FS-FAST


For each session, create retinotopy paradigm files in each of the run
directories.  These paradigm files are different than an event-related
or block paradigm (which list which stimulus was presented when).  A
retinotopy paradigm file has information about whether the run was an
eccentricity or polar stimulus and in what direction the stimulus was
presented.

For polar, the direction is indicates whether the spoke was traveling
clockwise or counter-clockwise.  For eccen, the direction is indicates
whether the ring was expanding or contracting.  The definition of
what's positive and what's negative is arbitrary, though it must be
consistent.  If you don't have both directions, just use positive.

For example, if there were four runs (001, 002, 003, 004), two eccen
and two polar, both in the positive and negative directions.  Create a
file (eg, rtopy.par) in each run.  Assuming run 001 was eccen in the
negative direction, then the rtopy.par for run 001 would look like:

--------cut here --------
stimtype  eccen
direction neg
--------cut here --------

If needed, create a run-list file with the all retinotopy runs
(regardless of whether it was eccen or polar).

Create the analysis:

mkanalysis-sess \
 -a rtopy   \
 -TR 2   \
 -designtype retinotopy  \
 -paradigm rtopy.par  \
 -funcstem fmcsm5  \
 -ncycles 8


Preprocess
  preproc-sess -s avdk -fwhm 8

Run the analysis:
  sfa-sess -s avdk -a rtopy

This will create avdk/bold/rtopy in which will be:
  1. volume h-offset (the mean function intensity)
  2. eccen - eccentricity folder (with h volume)
  3. polar - polar folder (with h volume)

The task-related activation can be viewed as with any other contrast
in a non-retinotopy application.  Just use eccen or polar as the
contrast and specify h as the map.

The task-related activation for eccen can be viewed with:
  sliceview-sess -s avdk -a rtopy -c eccen -map h -slice mos
The task-related activation for polar can be viewed with:
  sliceview-sess -s avdk -a rtopy -c polar -map h -slice mos

Run paint:

  paint-sess -a rtopy -s avdk

This will create map-imag-lh.w (the imaginary or sine part multiplied
by the log10(sig)), map-real-lh.w (the real or cosine part multiplied
by the log10(sig)), and sig-0-lh.w (the task related activation) for
both the polar and eccen.  It will also create a directory called
fieldsign in bold/rtopy in which fieldsign-lh (or -rh) along with
fieldsignmask-lh will be found.

To view the field-sign on the flattened patch (occip.patch.flat):
  surf-sess -s avdk  -a rtopy -retinotopy fieldsign -flat

To view the eccen on the flattened patch (occip.patch.flat):
  surf-sess -s avdk  -a rtopy -retinotopy eccen -flat

To view the polar on the flattened patch (occip.patch.flat):
  surf-sess -s avdk  -a rtopy -retinotopy polar -flat

To view the task-related polar activation on the flattened patch
  surf-sess -s avdk  -a rtopy -c polar -flat
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