not sure what is going on. Is the script stem2fname in your path? If so,
run selxavg3-sess with -debug as the first option and send the terminal
output
On 5/16/17 3:08 AM, std...@virgilio.it wrote:
Hi list,
this error occurs during selxavg3-sess in FS-FAST fcMRI
meanval --i stem2fname stem L
Thank you, I'll try!
Best
Francesca
On Wednesday, June 15, 2016, Douglas N Greve
wrote:
> Sorry for the delay. Do you have polar angle data? Unfortunately, FSFAST
> needs both. If you don't have polar, just copy the eccen data and call
> it polar. for what you want to do it won't make much diff
Sorry for the delay. Do you have polar angle data? Unfortunately, FSFAST
needs both. If you don't have polar, just copy the eccen data and call
it polar. for what you want to do it won't make much difference.
On 06/08/2016 09:55 AM, Francesca Strappini wrote:
> I have only something similar in t
Hi Doug, it looks like my email with attached the Xtmp.mat file didn't
arrive.
How can I send it to you?
Thanks!
Francesca
2016-06-08 15:44 GMT+02:00 Douglas Greve :
> Do you have both polar and eccen data? If so, can you send the Xtmp.mat
> file?
>
>
> On 6/8/16 6:08 AM, Francesca Strappini wro
Do you have both polar and eccen data? If so, can you send the Xtmp.mat
file?
On 6/8/16 6:08 AM, Francesca Strappini wrote:
Hi Freesurfer experts,
I'm re-posting this message because I think it got lost.
I'm trying to analyze some phase-encoded data with the eccentricity
protocol for retinoto
I see, here is a copy of my paradigm
0. 2
11.100 0
21.100 3
32.200 0
42.200 2
53.300 0
63.300 2
74.400 0
84.400 1
95.500 0
105.500 1
116.600 0
126.600 3
137.700 0
147.700 3
158.800 0
168.800 1
179.900 0
I don’t see how this setup reflects one of the two potential errors you
outlined.
.par
That means that your design matrix is ill-conditioned.
This error means one of two things is wrong with your .par file (located
in each run of each subjects bold directory): 1) there are not two or
more occurrences of one of your conditions; or 2) there is a pattern to
your conditions (for exa
hi doug,
thank you so much for your quick reply.
yes - I saw this error after I sent you the error log.
I checked the paradigm file, corrected it and rerun everything.
now this error is gone but I still get the following:
Error using svd
Input to SVD must not contain NaN or Inf.
Error in cond
Did you see the error description:
ERROR:
/space/mdeh5/1/halgdev/projects/christina/FSFAST/Project/NC211_fmri_060515/Sess01/bold/004/oddeven.par
is not correctly formatted. Line 19 only has 0 items
did you check this file?
On 12/09/2015 12:38 PM, Christina Pressl wrote:
> Dear Freesurfer Ex
On 11/19/15 9:53 AM, Danielle Miller wrote:
> Hi Doug,
>
> Thanks for your response. So you are saying to rename a correctly
> identified condition as the empty condition? That is if I have a
> correct trial, rename it to an incorrect trial? Won't this pull onset
> times from the wrong cond
There is not a way to model empty conditions. The easiest thing to do is
to just change another condition to say it is the missing condition. It
should have little effect on the final results.
On 11/18/2015 02:06 PM, Danielle Miller wrote:
> Hello Freesurfer Experts,
>
> I am reposting this as t
glas Greve
[gr...@nmr.mgh.harvard.edu]
Sent: Friday, August 21, 2015 1:46 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] selxavg3-sess error
I thought this problem was fixed when you eliminated the multiple
formats (?)
On 8/20/15 12:03 PM, Rodriguez-Thompson, Anais wrote:
> Hi Dou
t; [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Rodriguez-Thompson,
> Anais [arodriguez-thomp...@mgh.harvard.edu]
> Sent: Thursday, July 30, 2015 6:34 PM
> To: Freesurfer support list
> Subject: Re: [Freesurfer] selxavg3-sess error
>
> Hi Doug,
>
> Attached is doug2.log.
:34 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] selxavg3-sess error
Hi Doug,
Attached is doug2.log.
Thanks,
Anais
From: freesurfer-boun...@nmr.mgh.harvard.edu
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve
[gr
@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] selxavg3-sess error
ok, still not sure what is happening. Can you try
preproc-sess -debug -s GDDA001 -d
/autofs/cluster/roffman/users/Stable5_PerRun -a
SIRP_LoadRegression_Stable5_072915 |& tee doug2.log
and send me doug2.log
On 07/30/2015 12:5
gt; echo anadir = $anadir | tee -a $LF
> echo anadir =
> /autofs/cluster/roffman/users/Stable5_PerRun/GDDA001/bold/SIRP_LoadRegression_Stable5_072915
> tee -a
> /autofs/cluster/roffman/users/Stable5_PerRun/log/selxavg3-sess-bold-SIRP_LoadRegression_Stable5_072915-150730125217.log
> anadir =
> /autofs/cluster
un/GDDA001/bold/016/fmcpr.sm5
ERROR: cannot find
/autofs/cluster/roffman/users/Stable5_PerRun/GDDA001/bold/016/fmcpr.sm5
exit 1 ;
exit 1
Thanks,
Anais
From: freesurfer-boun...@nmr.mgh.harvard.edu
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve
[
Greve
> [gr...@nmr.mgh.harvard.edu]
> Sent: Thursday, July 30, 2015 12:02 PM
> To: freesurfer@nmr.mgh.harvard.edu
> Subject: Re: [Freesurfer] selxavg3-sess error
>
> What is your preproc-sess command and your mkanalysis-sess command?
>
>
> On 07/30/2015 12:00 PM, Rodriguez-Tho
, July 30, 2015 12:02 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] selxavg3-sess error
What is your preproc-sess command and your mkanalysis-sess command?
On 07/30/2015 12:00 PM, Rodriguez-Thompson, Anais wrote:
> Hi Freesurfer experts,
>
> I'm having trouble ru
What is your preproc-sess command and your mkanalysis-sess command?
On 07/30/2015 12:00 PM, Rodriguez-Thompson, Anais wrote:
> Hi Freesurfer experts,
>
> I'm having trouble running selxavg3-sess in 5.3 because it is looking for a
> file that does not exist (fmcpr.sm5.nii.gz). I read in another f
>
>
>
> *From:* freesurfer-boun...@nmr.mgh.harvard.edu
> [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas Greve
> [gr...@nmr.mgh.harvard.edu]
> *Sent:* Monday, March 09, 2015 2:49 PM
> *To:* f
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas Greve
[gr...@nmr.mgh.harvard.edu]
Sent: Monday, March 09, 2015 2:49 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] selxavg3-sess error
What is your mris_preproc command? And your mkanalysis-sess command?
On 3/9/15 2:
Hamdi
*From:* freesurfer-boun...@nmr.mgh.harvard.edu
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas Greve
[gr...@nmr.mgh.harvard.edu]
*Sent:* Monday, March 09, 2015 2:38 PM
*To:* freesurfer@nmr.mgh.harvard.edu
*Subject:* Re: [Freesurfer] selxavg3-sess error
It looks like diff
onday, March 09, 2015 2:38 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] selxavg3-sess error
It looks like different runs have different number of slices. Is that right?
On 3/9/15 1:13 PM, Eryilmaz, H. Hamdi wrote:
Dear FS experts,
I got an error while running selxavg3-sess
It looks like different runs have different number of slices. Is that right?
On 3/9/15 1:13 PM, Eryilmaz, H. Hamdi wrote:
Dear FS experts,
I got an error while running selxavg3-sess for a single subject. The
log (attached) says the following:
Thank you, now it works!
Best
Francesca
2014-09-08 15:24 GMT+03:00 Douglas Greve :
> It is not looking for fmc.sm5.DM.lh.nii.gz but rather fmcsm5.nii.gz in
>
> /usr/local/freesurfer/fsfast/MeytalRetinotopy/SUBJ01/bold/001
>
> does that file exist? Have you run preproc-sess?
> doug
>
> On 8/28/14
It is not looking for fmc.sm5.DM.lh.nii.gz but rather fmcsm5.nii.gz in
/usr/local/freesurfer/fsfast/MeytalRetinotopy/SUBJ01/bold/001
does that file exist? Have you run preproc-sess?
doug
On 8/28/14 9:49 AM, Francesca Strappini wrote:
> Dear all,
>
> I've run selxavg3-sess and I got this error me
Thank you for your Help. I figured out that it was a problem with the data
which caused this error.
On Wed, 04 Jun 2014 12:00:08 -0400
Douglas N Greve wrote:
>
> This is a strange error that I cannot figure out from the terminal
> output. What version of FS are you using? Here's something
This is a strange error that I cannot figure out from the terminal
output. What version of FS are you using? Here's something you can try:
Run selxavg3-sess with --monly sxa3.m This will return right away having
created sxa3.m
Start matlab and run sxa3. It will stop at the error below. Then ty
Hopefully this is the last problem with per-run analysis (in native space)
but as far as I see, preproc-sess and selxavg3-sess do not generate
/autofs/cluster/tootell/pitcairn/1/shahin/ColorPrj/7T/Sbj/myla2/bold_Color/register.dof6.dat
Because of that, when I use tksurfer-sess it faces an error:
yes, or you can just
register-sess -per-session ...
that should create just the register.dof6.dat you need
doug
On 03/19/2014 03:10 PM, SHAHIN NASR wrote:
> Hopefully this is the last problem with per-run analysis (in native
> space) but as far as I see, preproc-sess and selxavg3-sess do not
I used "-nuisreg mcprextreg" in mkanalysis-sess. Got this error:
Error: -nuisreg requires two arguments"
> -nuisreg
>
> On 03/19/2014 11:24 AM, sha...@nmr.mgh.harvard.edu wrote:
>> Does not accept "-nuis" flag. I changed my mkanalysis-sess to this:
>>
>> mkanalysis-sess -analysis ColorPrj_TR4_1
I think it is just confused because it expects native to be per-session.
One way around this is to just specify -nuis mcprextreg instead of
-mcprextreg
doug
On 03/19/2014 11:15 AM, sha...@nmr.mgh.harvard.edu wrote:
> But this is a per-run analysis and preproc-sess is -per-run (in native
> spac
use
-nuisreg mcprextreg 3
On 03/19/2014 11:34 AM, sha...@nmr.mgh.harvard.edu wrote:
> I used "-nuisreg mcprextreg" in mkanalysis-sess. Got this error:
>
> Error: -nuisreg requires two arguments"
>
>
>
>> -nuisreg
>>
>> On 03/19/2014 11:24 AM, sha...@nmr.mgh.harvard.edu wrote:
>>> Does not accept "
Does not accept "-nuis" flag. I changed my mkanalysis-sess to this:
mkanalysis-sess -analysis ColorPrj_TR4_1p5mm_PR_ANOVA -fwhm 1.5 -paradigm
Conds.par -native -event-related -polyfit 2 -gammafit 2.25 1.25 -nuis
mcprextreg -TR 4 -nconditions 8 -refeventdur 14 -force -fsd bold_Color
-per-run
and g
YES! Started to work.
Thanks Doug!
> use
> -nuisreg mcprextreg 3
>
> On 03/19/2014 11:34 AM, sha...@nmr.mgh.harvard.edu wrote:
>> I used "-nuisreg mcprextreg" in mkanalysis-sess. Got this error:
>>
>> Error: -nuisreg requires two arguments"
>>
>>
>>
>>> -nuisreg
>>>
>>> On 03/19/2014 11:24 AM, sh
-nuisreg
On 03/19/2014 11:24 AM, sha...@nmr.mgh.harvard.edu wrote:
> Does not accept "-nuis" flag. I changed my mkanalysis-sess to this:
>
> mkanalysis-sess -analysis ColorPrj_TR4_1p5mm_PR_ANOVA -fwhm 1.5 -paradigm
> Conds.par -native -event-related -polyfit 2 -gammafit 2.25 1.25 -nuis
> mcprextre
There is not an mcextreg file there. There is mcprextreg file. I think
you need to run preproc with -per-session to get the mcextreg file
doug
On 03/18/2014 02:34 PM, SHAHIN NASR wrote:
> Hi,
>When I run selxavg3-sess, I face this error:
>
> ERROR: cannot find volume matching
> /autofs/clus
Original Message
Subject: Re: selxavg3-sess error
From:sha...@nmr.mgh.harvard.edu
Date:Wed, March 19, 2014 11:15 am
To: "Douglas N Greve"
--
But this is a
Hi Doug,
Yes, that was the problem. I think Freesurfer expects that you start Matlab by
typing "matlab" in the terminal (as opposed to "matlab2010a" which is what I
usually do). So I created a new symbolic that takes care of that.
Now I got the error message "ERROR: TR mismatch between analysis
yes, B is correct. The error says that it cannot find matlab. Is it in
your path?
doug
On 5/25/12 9:16 AM, Michael Bannert wrote:
Hi Doug,
Thanks for your help! No, the current directory is the "Project"
directory (refering to naming conventions in
http://www.freesurfer.net/fswiki/FsFastTuto
Hi Doug,
Thanks for your help! No, the current directory is the "Project" directory
(refering to naming conventions in
http://www.freesurfer.net/fswiki/FsFastTutorialV5.1/FsFastDirStruct). It is
identical to $FUNCTIONALS_DIR.
The rtopy.self.lh folder is in the "Sess0x" directory and contains o
Hi Michael, is rtopy.self.lh in the current directory (the one that you
are running selxavg from)?
doug
On 05/24/2012 07:57 AM, Michael Bannert wrote:
> Hi all,
>
> I'm trying to analyze a retinotopic mapping dataset using FsFast but
> some things don't seem to work the way they should.
>
> When
I have not set path for afni.
After setting the correct path, that runs fine.
From: freesurfer-boun...@nmr.mgh.harvard.edu
[mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Oya, Hiroyuki (UI
Health Care)
Sent: 30 March 2012 07:53
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfe
It does not look too bad to me. That is a significance map and it is
covering most of the occipital region. If you want to see the angle,
add -angle to your tksurfer-sess command.
doug
Daniel Cole wrote:
> I was mistaken, I only have *Polar* (Rotating wedge) not Eccentricity
> stimuli.
> Aft
Hi Daniel, can you send me the analysis.info and Xtmp.mat files?
doug
Daniel Cole wrote:
>
> Hello Freesurfers,
>
> I think my last email failed to send so here it is again -
>
>
> I'm running into problems using fs-fast for a polar only, retinotopic
> analysis.
>
>
> The error message I get is:
Hi Reagan, I was not able to recreate this error. Can you send me the
full terminal output?
thanks
doug
Wetherill, Reagan wrote:
> Hello FreeSurfers!
>
> I am new to FSFast and am attempting to run selxavg3-sess, but I keep
> receiving the following errors:
>
> ERROR: model ??? In an assignment
try it with a prestim of 0
Ben Letham wrote:
> Yes, the paradigm came from optseq2 with a PSD window 0 19.2 0.4.
>
> Looking more into the details, it seems that the design is pretty
> ill-conditioned, cond(Xn'*Xn) is 6.2e5, and the cut-off in
> fast_selxavg3.m is 1e4.
>
> Like I said, the design
Yes, the paradigm came from optseq2 with a PSD window 0 19.2 0.4.
Looking more into the details, it seems that the design is pretty
ill-conditioned, cond(Xn'*Xn) is 6.2e5, and the cut-off in
fast_selxavg3.m is 1e4.
Like I said, the design came from optseq2 and the cost/efficiency is
the same as o
Did you optimize the stimulus schedule with the idea that you would do
sub-TR FIR estimation? Eg, you would have had to have run optseq2 with
this in mind. If not, then you probably cannot do an FIR analysis.
Instead, assume a shape (eg, -gammafit 2.25 1.25)
doug
Ben Letham wrote:
> Hello,
>
>
Hmmm, not sure. Can you send your par file?
Jeremy Elman wrote:
Hello all,
I am trying to run a first level analysis on a subject with
selxavg3-sess but keep running into the same error. The dof file is
created, but that is it. Any ideas what might be causing this? Below
is the error given.
All,
Nevermind. It looks like the error was being caused by a space issue.
Sorry for eating up your time,
Avram
On 2/16/2009 1:34 PM, Avram Holmes wrote:
All,
I'm encountering an error when I run selxavg3-sess and I am not sure
how to get around the problem, or what it means.
I am running
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