[Freesurfer] question about preprocessing and analysis in FS 4.5 vs FS5
I had a question about using different components of Freesurfer 4.5 and Freesurfer 5 in an analysis. We were wondering whether it is possible to do preprocessing in Freesufer 5, but run the analysis on Freesufer 4.5 or whether the output from preprocessing in Freesurfer 5 is not compatible with the analysis methods in 4.5. For reasons I don't want to go into, it is not possible to switch to doing the analysis in Freesurfer 5, but we would like to incorporate some of the improvements in the preprocessing stream in Freesufer 5 if possible. Any guidance would be appreciated. Katie Bettencourt ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] Average for each voxel across all conditions
Yes, in each analysis directory there is a meanfunc.nii. Maybe this summer I will switch to FS5, but I have a bunch of experiments in 4.5 and am not 100% comfortable with the way the retinotopy analysis needs to be done in FS5, which is a vital component of my work. Katie On Thu, May 30, 2013 at 4:50 PM, Douglas N Greve gr...@nmr.mgh.harvard.eduwrote: Hi Katie, I don't remember what 4.5 outputs. Is there a meanfunc volume there? Itwould be much easier to support you if you were using version 5.x:) doug On 05/30/2013 04:36 PM, Katie Bettencourt wrote: Hi, I have an experiment where I have 3 conditions in a FIR event related analysis (running FS 4.5). I need to get the mean activity level for each voxel across all conditions across the run, so that I can calculate percent signal change for each individual voxel. Is this available (I have analyzed each run separately) somewhere? Katie ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- 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: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] Average for each voxel across all conditions
Hi, I have an experiment where I have 3 conditions in a FIR event related analysis (running FS 4.5). I need to get the mean activity level for each voxel across all conditions across the run, so that I can calculate percent signal change for each individual voxel. Is this available (I have analyzed each run separately) somewhere? Katie ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] selxavg3-sess illconditioned error
Ok, I understand that, except that all of my runs are like that, but only a
few of them errored out. Why is that?
Katie
On Fri, Mar 1, 2013 at 3:38 PM, Douglas N Greve
gr...@nmr.mgh.harvard.eduwrote:
Hi Katie, the problem is that eventtypes 1 and 2 are synchronized 32 sec
apart. What this means is that they are effectively one event if you set
the time window longer than 32 sec (you have it set to 34). There is no way
around this. If you want a longer window, use 30 sec (32 might work).
doug
On 02/28/2013 04:46 PM, Katie Bettencourt wrote:
Here it is for one of the failed runs. Let me know if you need anything
else.
Katie
On Thu, Feb 28, 2013 at 3:27 PM, Douglas N Greve
gr...@nmr.mgh.harvard.edu
mailto:gr...@nmr.mgh.harvard.**edugr...@nmr.mgh.harvard.edu
wrote:
Can you send me the Xtmp.mat file from the outputdirectory?
doug
On 02/28/2013 07:34 AM, Katie Bettencourt wrote:
Still looking for an answer why my analysis gives me an ill
conditioned error. I have run this analysis fine before, with
a timewindow of 22, but when I tried to change the time
window to 34, selxavg3-sess gives me an ill conditioned error
on some of the runs (each run is being analyzed separately),
but not all of them. All the runs are identical except for
the order the conditions appear in, but each condition appears
an equal number of times and for an equal duration in each
run. There is nothing specific about the runs that fail or
the subjects that they fail in (for some subjects all 8 runs
work fine, others lost between 1-3 runs to this error). I'm
doing svm with this data so I need all conditions to be
analyzed correctly.
Any help?
Katie
On Mon, Feb 25, 2013 at 10:23 AM, Katie Bettencourt
k...@wjh.harvard.edu mailto:k...@wjh.harvard.edu
mailto:k...@wjh.harvard.edu mailto:k...@wjh.harvard.edu wrote:
No, each condition has at least 3 instances of it in each run.
The runs are all set up exactly the same, just the order
changes,
so there is nothing different about the runs that work
than the
runs that fail, and again, all of these runs worked fine
with the
exact same paradigm files and set up, but only the
timewindow at
22 instead of 34.
Katie
On Mon, Feb 25, 2013 at 10:21 AM, Douglas N Greve
gr...@nmr.mgh.harvard.edu
mailto:gr...@nmr.mgh.harvard.**edu gr...@nmr.mgh.harvard.edu
mailto:gr...@nmr.mgh.harvard.**edu gr...@nmr.mgh.harvard.edu
mailto:gr...@nmr.mgh.harvard.**edu gr...@nmr.mgh.harvard.edu
wrote:
Hi katie, I'm guessing that you have one event type
that only
has one event? If so, you can do what Sebastian
suggests, but
you won't be able to look at contrasts related to that
condition.
doug
On 02/19/2013 03:24 PM, Katie Bettencourt wrote:
I am having a problem with selxavg3-sess (for FS 4.5)
where it is giving me an Ill-conditioned error that I
can't trace out.
I have 8 runs that I am running separately (same basic
analysis for each run, but each run gets it's own
analysis
for svm purposes). Originally for this subject, I
created
an analysis and it ran fine for all 8 runs. I
went back
and changed the timewindow on the analysis (and
only the
timewindow) and now, while it runs fine for 7 or the 8
runs, one of them gives me an ill conditioned
error during
selxavg3-sess. I double checked the paradigm file
and all
conditions are listed, and the only change between
when
the analysis ran fine and when it gave me this
error was
changing the timewindow. The mkanalysis commands
I used
both times are listed below.
Original analysis (worked fine):
foreach r (1 2 3 4 5 6 7 8)
mkanalysis-sess -analysis
grating_nodist_ld_run${r} -TR 2
-paradigm grating.dat -designtype event-related
-funcstem
fmc -motioncor -runlistfile nodist_run${r}.txt -inorm
-tpexclude tpexclude.dat -nconditions 3 -timewindow 22
-TER 2 -noautostimdur -polyfit 2
end
new analysis (illconditioned on one run only):
foreach r (1 2 3 4 5 6 7 8
Re: [Freesurfer] selxavg3-sess illconditioned error
Still looking for an answer why my analysis gives me an ill conditioned
error. I have run this analysis fine before, with a timewindow of 22, but
when I tried to change the time window to 34, selxavg3-sess gives me an ill
conditioned error on some of the runs (each run is being analyzed
separately), but not all of them. All the runs are identical except for
the order the conditions appear in, but each condition appears an equal
number of times and for an equal duration in each run. There is nothing
specific about the runs that fail or the subjects that they fail in (for
some subjects all 8 runs work fine, others lost between 1-3 runs to this
error). I'm doing svm with this data so I need all conditions to be
analyzed correctly.
Any help?
Katie
On Mon, Feb 25, 2013 at 10:23 AM, Katie Bettencourt k...@wjh.harvard.eduwrote:
No, each condition has at least 3 instances of it in each run. The runs
are all set up exactly the same, just the order changes, so there is
nothing different about the runs that work than the runs that fail, and
again, all of these runs worked fine with the exact same paradigm files and
set up, but only the timewindow at 22 instead of 34.
Katie
On Mon, Feb 25, 2013 at 10:21 AM, Douglas N Greve
gr...@nmr.mgh.harvard.edu wrote:
Hi katie, I'm guessing that you have one event type that only has one
event? If so, you can do what Sebastian suggests, but you won't be able to
look at contrasts related to that condition.
doug
On 02/19/2013 03:24 PM, Katie Bettencourt wrote:
I am having a problem with selxavg3-sess (for FS 4.5) where it is giving
me an Ill-conditioned error that I can't trace out.
I have 8 runs that I am running separately (same basic analysis for each
run, but each run gets it's own analysis for svm purposes). Originally for
this subject, I created an analysis and it ran fine for all 8 runs. I went
back and changed the timewindow on the analysis (and only the timewindow)
and now, while it runs fine for 7 or the 8 runs, one of them gives me an
ill conditioned error during selxavg3-sess. I double checked the paradigm
file and all conditions are listed, and the only change between when the
analysis ran fine and when it gave me this error was changing the
timewindow. The mkanalysis commands I used both times are listed below.
Original analysis (worked fine):
foreach r (1 2 3 4 5 6 7 8)
mkanalysis-sess -analysis grating_nodist_ld_run${r} -TR 2 -paradigm
grating.dat -designtype event-related -funcstem fmc -motioncor -runlistfile
nodist_run${r}.txt -inorm -tpexclude tpexclude.dat -nconditions 3
-timewindow 22 -TER 2 -noautostimdur -polyfit 2
end
new analysis (illconditioned on one run only):
foreach r (1 2 3 4 5 6 7 8)
mkanalysis-sess -analysis grating_nodist_ld_34_run${r} -TR 2 -paradigm
grating.dat -designtype event-related -funcstem fmc -motioncor -runlistfile
nodist_run${r}.txt -inorm -tpexclude tpexclude.dat -nconditions 3
-timewindow 34 -TER 2 -noautostimdur -polyfit 2
end
Katie
--
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/BugReportinghttp://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop:
www.nmr.mgh.harvard.edu/**facility/filedrop/index.htmlhttp://www.nmr.mgh.harvard.edu/facility/filedrop/index.html
Outgoing: ftp://surfer.nmr.mgh.harvard.**edu/transfer/outgoing/flat/**
greve/ ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
The information in this e-mail is intended only for the person to whom it
is
addressed. If you believe this e-mail was sent to you in error and the
e-mail
contains patient information, please contact the Partners Compliance
HelpLine at
http://www.partners.org/**compliancelinehttp://www.partners.org/complianceline.
If the e-mail was sent to you in error
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The information in this e-mail is intended only for the person to whom it is
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contains patient information, please contact the Partners Compliance HelpLine at
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but does not contain patient information, please contact the sender and properly
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Re: [Freesurfer] selxavg3-sess illconditioned error
Here it is for one of the failed runs. Let me know if you need anything
else.
Katie
On Thu, Feb 28, 2013 at 3:27 PM, Douglas N Greve
gr...@nmr.mgh.harvard.eduwrote:
Can you send me the Xtmp.mat file from the outputdirectory?
doug
On 02/28/2013 07:34 AM, Katie Bettencourt wrote:
Still looking for an answer why my analysis gives me an ill conditioned
error. I have run this analysis fine before, with a timewindow of 22, but
when I tried to change the time window to 34, selxavg3-sess gives me an ill
conditioned error on some of the runs (each run is being analyzed
separately), but not all of them. All the runs are identical except for
the order the conditions appear in, but each condition appears an equal
number of times and for an equal duration in each run. There is nothing
specific about the runs that fail or the subjects that they fail in (for
some subjects all 8 runs work fine, others lost between 1-3 runs to this
error). I'm doing svm with this data so I need all conditions to be
analyzed correctly.
Any help?
Katie
On Mon, Feb 25, 2013 at 10:23 AM, Katie Bettencourt
k...@wjh.harvard.edumailto:
k...@wjh.harvard.edu wrote:
No, each condition has at least 3 instances of it in each run.
The runs are all set up exactly the same, just the order changes,
so there is nothing different about the runs that work than the
runs that fail, and again, all of these runs worked fine with the
exact same paradigm files and set up, but only the timewindow at
22 instead of 34.
Katie
On Mon, Feb 25, 2013 at 10:21 AM, Douglas N Greve
gr...@nmr.mgh.harvard.edu
mailto:gr...@nmr.mgh.harvard.**edugr...@nmr.mgh.harvard.edu
wrote:
Hi katie, I'm guessing that you have one event type that only
has one event? If so, you can do what Sebastian suggests, but
you won't be able to look at contrasts related to that condition.
doug
On 02/19/2013 03:24 PM, Katie Bettencourt wrote:
I am having a problem with selxavg3-sess (for FS 4.5)
where it is giving me an Ill-conditioned error that I
can't trace out.
I have 8 runs that I am running separately (same basic
analysis for each run, but each run gets it's own analysis
for svm purposes). Originally for this subject, I created
an analysis and it ran fine for all 8 runs. I went back
and changed the timewindow on the analysis (and only the
timewindow) and now, while it runs fine for 7 or the 8
runs, one of them gives me an ill conditioned error during
selxavg3-sess. I double checked the paradigm file and all
conditions are listed, and the only change between when
the analysis ran fine and when it gave me this error was
changing the timewindow. The mkanalysis commands I used
both times are listed below.
Original analysis (worked fine):
foreach r (1 2 3 4 5 6 7 8)
mkanalysis-sess -analysis grating_nodist_ld_run${r} -TR 2
-paradigm grating.dat -designtype event-related -funcstem
fmc -motioncor -runlistfile nodist_run${r}.txt -inorm
-tpexclude tpexclude.dat -nconditions 3 -timewindow 22
-TER 2 -noautostimdur -polyfit 2
end
new analysis (illconditioned on one run only):
foreach r (1 2 3 4 5 6 7 8)
mkanalysis-sess -analysis grating_nodist_ld_34_run${r} -TR
2 -paradigm grating.dat -designtype event-related
-funcstem fmc -motioncor -runlistfile nodist_run${r}.txt
-inorm -tpexclude tpexclude.dat -nconditions 3 -timewindow
34 -TER 2 -noautostimdur -polyfit 2
end
Katie
-- Douglas N. Greve, Ph.D.
MGH-NMR Center
gr...@nmr.mgh.harvard.edu
mailto:gr...@nmr.mgh.harvard.**edugr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422
Bugs:
surfer.nmr.mgh.harvard.edu/**fswiki/BugReportinghttp://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
http://surfer.nmr.mgh.**harvard.edu/fswiki/**BugReportinghttp://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop:
www.nmr.mgh.harvard.edu/**facility/filedrop/index.htmlhttp://www.nmr.mgh.harvard.edu/facility/filedrop/index.html
http://www.nmr.mgh.harvard.**edu/facility/filedrop/index.**htmlhttp://www.nmr.mgh.harvard.edu/facility/filedrop/index.html
Outgoing:
ftp://surfer.nmr.mgh.harvard.**edu/transfer/outgoing/flat/**
greve/ ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
The information in this e-mail is intended only for the person
to whom it is
addressed. If you believe this e-mail was sent to you in error
and the e-mail
Re: [Freesurfer] selxavg3-sess illconditioned error
Hmm, I think that might not help given that I get an XCond = 2.75109e+17
right before that error, so bumping to 6 probably isn't going to help.
I can't figure out why it is doing this now with just the change in
timewindow, but I'm obviously missing something. I actually only have 3
conditions in this experiment and 4 repetitions of each across the run
(which is the same as all the other runs that are working fine).
Katie
On Tue, Feb 19, 2013 at 4:46 PM, Sebastian Moeller
sebastian.moell...@rwth-aachen.de wrote:
Hi Katie,
what about just modifying the matlab code that gives the ill-conditioned
error? So for free surfer 4.5 you will find in
$FREESURFER_HOME/fsfast/toolbox/fast_selxavg3.m:
XCond = cond(XtX);
fprintf('XCond = %g (normalized)\n',XCond);
if(XCond 1e4)
fprintf('ERROR: design is ill-conditioned\n');
return;
end
While in freesurfer 5.1 it reads:
XCond = cond(XtX);
fprintf('XCond = %g (normalized)\n',XCond);
if(XCond 1e6)
fprintf('ERROR: design is ill-conditioned\n');
return;
end
So just try to change the threshold in fast_selxavg3.m to 1e6 and be done
with (because if this works you are not doing any worse than you would do
using free surfer 5.1). @Doug: Is that justifiable, or is 1e4 really the
better threshold? (We have run into this issue in the past when we used
very many conditions per run, and few repetitions of each condition per
run).
best regards
sebastian
On Feb 19, 2013, at 12:24 , Katie Bettencourt wrote:
I am having a problem with selxavg3-sess (for FS 4.5) where it is giving
me an Ill-conditioned error that I can't trace out.
I have 8 runs that I am running separately (same basic analysis for each
run, but each run gets it's own analysis for svm purposes). Originally for
this subject, I created an analysis and it ran fine for all 8 runs. I went
back and changed the timewindow on the analysis (and only the timewindow)
and now, while it runs fine for 7 or the 8 runs, one of them gives me an
ill conditioned error during selxavg3-sess. I double checked the paradigm
file and all conditions are listed, and the only change between when the
analysis ran fine and when it gave me this error was changing the
timewindow. The mkanalysis commands I used both times are listed below.
Original analysis (worked fine):
foreach r (1 2 3 4 5 6 7 8)
mkanalysis-sess -analysis grating_nodist_ld_run${r} -TR 2 -paradigm
grating.dat -designtype event-related -funcstem fmc -motioncor -runlistfile
nodist_run${r}.txt -inorm -tpexclude tpexclude.dat -nconditions 3
-timewindow 22 -TER 2 -noautostimdur -polyfit 2
end
new analysis (illconditioned on one run only):
foreach r (1 2 3 4 5 6 7 8)
mkanalysis-sess -analysis grating_nodist_ld_34_run${r} -TR 2 -paradigm
grating.dat -designtype event-related -funcstem fmc -motioncor -runlistfile
nodist_run${r}.txt -inorm -tpexclude tpexclude.dat -nconditions 3
-timewindow 34 -TER 2 -noautostimdur -polyfit 2
end
Katie
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--
Sebastian Moeller
telephone: +1-626-325-8598 /+1-626-395-6523 / +1-626-395-6616
fax: 626-395-8826
German GSM: +49 - 15 77 - 1 90 31 41
mobile: +1-626-325-8598
+1-626-807-5242
US CDMA: +1-626-807-5242
moel...@caltech.edu
Division of Biology
MC 114-96
California Institute of Technology
1200 East California Boulevard
CA 91125, Pasadena
USA
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[Freesurfer] slice timing correction and motion correction order
Can you tell me the order of the slice timing and motion correction steps in preproc-sess (freesurfer v 4.5)? From the wiki it looks like motion correction is done first (For MC the input will be f and the output will be fmc For STC the input will be fmc and the output will be fmcstc. However, wouldn't doing the motion correction first cause an issue? Because, otherwise, after motion correction, the slices are realigned and the timing of a slice at a particular location is no longer what it is before, correct? Can you clarify this for me? ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] mapping an set of talairach points
I am still having some trouble with this. As a test, used mri_label2label to convert a label I had in freesurfer to the fsaverage brain, as I couldn't get it to covert just to talairach (see my last email, included below as well). Then I removed all the vertex numbers and replaced them with -1. I could not then use mri_label2label to convert using --regmethod surface (gave me a error: there is a vertex in the label that cannot be match to the surface...) and when I tried the volume method it ran, but then loading the label into tksurfer showed that it was really incorrect (several disjointed blobs across the brain instead of one focus label). However, if I first loaded the label file with the -1 for the vertices into the fsaverage brain, it came up correctly, if I then saved it again, and used mri_label2label and --regmethod surface to convert it back to my original subject brain, it ended up being very close to the original label it was made from. So, my questions are: 1). Should I be using the fsaverage brain for the talairach coordinates I get from Brain Voyager, even though my understanding was that the fsaverage brain was MNI not talairach? 2). Do I need to bring the label up on the fsaverage brain and save it before converting it to the appropriate subject? Or should it work without this intermediate step? 3). What is the difference between regmethod volume and regmethod surface and why does this cause me to get very different results? Is there something I need to do to the volume method ones to display them on the surface? Thanks, Katie On Tue, Sep 18, 2012 at 12:48 PM, Katie Bettencourt k...@wjh.harvard.eduwrote: So I was looking into mri_label2label and it suggests you can map a label to talairach by using --trgsubject talairach, which I thought may be good to do as a test, creating a label I already have in talairach space, then doing the back transformation you suggested. However, when I tried to do this, I ran across 2 problems. 1) it appears you can't register a subject label to talairach in surface space (ie. --regmethod surface), is this correct? and 2) when I tried to do it in volume, it gave me the error: Cannot find subject talairach in my subject directory. I have the fsaverage brain in there, but is there a talairach brain I need to download as well? Katie On Mon, Sep 17, 2012 at 1:25 PM, Bruce Fischl fis...@nmr.mgh.harvard.eduwrote: Hi Katie if you set the vertex numbers to -1 then tksurfer will search for the closest vertex to each point and fill them in. So start with a list of tal points (and -1 for the vertex), then use mri_label2label to map them to the individual subject space and visualize it in tkmedit or freeview to make sure it is right. Then load it into tksurfer, which will assign vertex #s to each point, after which you can save the label again to make them permanent. cheers Bruce On Mon, 17 Sep 2012, Katie Bettencourt wrote: Hi Bruce, So my understanding of the label file is that it has a list of the # of vertices in the label, then each line is the vertex number followed by the RAS coordinates and then some 5th column. I think you are saying that I could use my text file of talairach coordinates (with each line as a new coordinate) like a label file for the talairach brain (is this different from the fsaverage brain?). However, I'm not exactly how to create that sort of file from a list of talairach points since I don't have the vertex number for each coordinate. Am I misunderstanding something? Is there someway to do some sort of scripting where I create a label from the vertex selected by select_talairach_point using the first talairach point I have and then repeatedly use select_talairach point to load each talairach point onto a subject, then add that point to the label file? I don't quite understand all the tcl commands to understand if this is possible. In then end, our issue is that we seem to be getting different results between freesurfer and brain voyager from identical data analyzed in a ROI defined off of identical data in identical subjects (ie. we take data set 1, define a ROI in FS and BV, then take data set 2, analyzed the response in the ROI, and get different results). We aren't sure why we are getting different results and so wanted to check on where the ROIs were located in relation to each other. Since there doesn't seem to be a way to load BV ROIs into FS, we were trying to work around it by using what we can get out of BV that should be transferrable, the talairach coordinates). Unfortunately, we have to cross platforms like this because historically the data has been done in BV and has produced consistent, published results, but we need to use FS's retinotopic analysis capabilities for future work, but aren't getting the same results on these ROIs and can't figure out why, or even begin to understand it until we can examine whether we
Re: [Freesurfer] mapping an set of talairach points
So I was looking into mri_label2label and it suggests you can map a label to talairach by using --trgsubject talairach, which I thought may be good to do as a test, creating a label I already have in talairach space, then doing the back transformation you suggested. However, when I tried to do this, I ran across 2 problems. 1) it appears you can't register a subject label to talairach in surface space (ie. --regmethod surface), is this correct? and 2) when I tried to do it in volume, it gave me the error: Cannot find subject talairach in my subject directory. I have the fsaverage brain in there, but is there a talairach brain I need to download as well? Katie On Mon, Sep 17, 2012 at 1:25 PM, Bruce Fischl fis...@nmr.mgh.harvard.eduwrote: Hi Katie if you set the vertex numbers to -1 then tksurfer will search for the closest vertex to each point and fill them in. So start with a list of tal points (and -1 for the vertex), then use mri_label2label to map them to the individual subject space and visualize it in tkmedit or freeview to make sure it is right. Then load it into tksurfer, which will assign vertex #s to each point, after which you can save the label again to make them permanent. cheers Bruce On Mon, 17 Sep 2012, Katie Bettencourt wrote: Hi Bruce, So my understanding of the label file is that it has a list of the # of vertices in the label, then each line is the vertex number followed by the RAS coordinates and then some 5th column. I think you are saying that I could use my text file of talairach coordinates (with each line as a new coordinate) like a label file for the talairach brain (is this different from the fsaverage brain?). However, I'm not exactly how to create that sort of file from a list of talairach points since I don't have the vertex number for each coordinate. Am I misunderstanding something? Is there someway to do some sort of scripting where I create a label from the vertex selected by select_talairach_point using the first talairach point I have and then repeatedly use select_talairach point to load each talairach point onto a subject, then add that point to the label file? I don't quite understand all the tcl commands to understand if this is possible. In then end, our issue is that we seem to be getting different results between freesurfer and brain voyager from identical data analyzed in a ROI defined off of identical data in identical subjects (ie. we take data set 1, define a ROI in FS and BV, then take data set 2, analyzed the response in the ROI, and get different results). We aren't sure why we are getting different results and so wanted to check on where the ROIs were located in relation to each other. Since there doesn't seem to be a way to load BV ROIs into FS, we were trying to work around it by using what we can get out of BV that should be transferrable, the talairach coordinates). Unfortunately, we have to cross platforms like this because historically the data has been done in BV and has produced consistent, published results, but we need to use FS's retinotopic analysis capabilities for future work, but aren't getting the same results on these ROIs and can't figure out why, or even begin to understand it until we can examine whether we are in the same brain space for our ROIs. Thanks, Katie On Mon, Sep 17, 2012 at 12:14 PM, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote: Hi Katie you might be able to create a label file with the tal coords, then use mri_label2label to map it from tal to the individual subject, then load it in tksurfer which will map it to the surface. It will probably look spotty though. cheers Bruce On Mon, 17 Sep 2012, Katie Bettencourt wrote: I'm still trying to figure out a way to display an ROI made elsewhere on my freesurfer data. I can get all ROI I need in freesurfer in talairach points (ie. a list of talairach points that cover the entirety of the ROI space), but as far as I can see, I can only load one talairach point at a time (using select_talairach_point), and then the last point is lost with each subsequent call. What I really want to do is select a region on the surface that covers a set of talairach coordinates (instead of say, dilating from 1 talairach point). Is there any way to do this? Should I use something like the talairach transform file to change it into surface coordinates and load those like a label somehow, or is there some other way? Katie The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains
[Freesurfer] mapping an set of talairach points
I'm still trying to figure out a way to display an ROI made elsewhere on my freesurfer data. I can get all ROI I need in freesurfer in talairach points (ie. a list of talairach points that cover the entirety of the ROI space), but as far as I can see, I can only load one talairach point at a time (using select_talairach_point), and then the last point is lost with each subsequent call. What I really want to do is select a region on the surface that covers a set of talairach coordinates (instead of say, dilating from 1 talairach point). Is there any way to do this? Should I use something like the talairach transform file to change it into surface coordinates and load those like a label somehow, or is there some other way? Katie ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] mapping an set of talairach points
Hi Bruce, So my understanding of the label file is that it has a list of the # of vertices in the label, then each line is the vertex number followed by the RAS coordinates and then some 5th column. I think you are saying that I could use my text file of talairach coordinates (with each line as a new coordinate) like a label file for the talairach brain (is this different from the fsaverage brain?). However, I'm not exactly how to create that sort of file from a list of talairach points since I don't have the vertex number for each coordinate. Am I misunderstanding something? Is there someway to do some sort of scripting where I create a label from the vertex selected by select_talairach_point using the first talairach point I have and then repeatedly use select_talairach point to load each talairach point onto a subject, then add that point to the label file? I don't quite understand all the tcl commands to understand if this is possible. In then end, our issue is that we seem to be getting different results between freesurfer and brain voyager from identical data analyzed in a ROI defined off of identical data in identical subjects (ie. we take data set 1, define a ROI in FS and BV, then take data set 2, analyzed the response in the ROI, and get different results). We aren't sure why we are getting different results and so wanted to check on where the ROIs were located in relation to each other. Since there doesn't seem to be a way to load BV ROIs into FS, we were trying to work around it by using what we can get out of BV that should be transferrable, the talairach coordinates). Unfortunately, we have to cross platforms like this because historically the data has been done in BV and has produced consistent, published results, but we need to use FS's retinotopic analysis capabilities for future work, but aren't getting the same results on these ROIs and can't figure out why, or even begin to understand it until we can examine whether we are in the same brain space for our ROIs. Thanks, Katie On Mon, Sep 17, 2012 at 12:14 PM, Bruce Fischl fis...@nmr.mgh.harvard.eduwrote: Hi Katie you might be able to create a label file with the tal coords, then use mri_label2label to map it from tal to the individual subject, then load it in tksurfer which will map it to the surface. It will probably look spotty though. cheers Bruce On Mon, 17 Sep 2012, Katie Bettencourt wrote: I'm still trying to figure out a way to display an ROI made elsewhere on my freesurfer data. I can get all ROI I need in freesurfer in talairach points (ie. a list of talairach points that cover the entirety of the ROI space), but as far as I can see, I can only load one talairach point at a time (using select_talairach_point), and then the last point is lost with each subsequent call. What I really want to do is select a region on the surface that covers a set of talairach coordinates (instead of say, dilating from 1 talairach point). Is there any way to do this? Should I use something like the talairach transform file to change it into surface coordinates and load those like a label somehow, or is there some other way? Katie The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/**compliancelinehttp://www.partners.org/complianceline. If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] Repost: Converting BV ROIs to FS
Another question. If I have a list of talairach coordinates, is there someway to load those without having to do it individually? Or someway to save the points after scripting to run through select_talairach_point individually (as just redoing the command will lose the previous point each time)? Katie On Wed, Sep 5, 2012 at 2:02 PM, Katie Bettencourt k...@wjh.harvard.eduwrote: Nevermind, it turns out it was due to an permissions error. Thanks again. Katie On Wed, Sep 5, 2012 at 12:53 PM, Katie Bettencourt k...@wjh.harvard.eduwrote: Ok, I am trying to use the select_talairach_point command, and I have it in part of a script that uses tksurfer to load up a subject's inflated surface, load the curvature, and load an overlay, but it doesn't seem to be doing anything. Is there a step I am missing? What should I see if it works correctly? Thanks for all your help! Katie On Wed, Sep 5, 2012 at 9:19 AM, Bruce Fischl fis...@nmr.mgh.harvard.eduwrote: Hi Katie you can view data on a tal brain by mapping the data using the talairach.xfm transform. Since you can also use the inverse of the transform you can map both ways. I think there is a tcl command in tksurfer for finding the vertex that is closest to a given tal coord. Try: select_talairach_point xtal ytal ztal cheers Bruce On Tue, 4 Sep 2012, Katie Bettencourt wrote: Hrm. Ok, is there any way to view data for a subject in Freesurfer on a talairach transformed brain? What I would be hoping to do is bring up the data in native subject space, make any ROI label, then also bring the data up on a talairach transformed brain, make a ROI label, then put both labels on the same brain (either native or talairach transformed) and see if they are any different. Also, is there a way to input a particular talairach vertex and jump to that in freesurfer, instead of just moving the mouse around and hoping to find the right spot? Katie On Tue, Sep 4, 2012 at 12:24 PM, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote: Hi Katie I don't think anyone here knows how to do this as we don't use it. Perhaps the Brain Voyager people do? sorry, Bruce On Tue, 4 Sep 2012, Katie Bettencourt wrote: So our lab is running a couple analyses and we are getting different results based on whether we use Brain Voyager or Freesurfer that we think is due to different ROI selection across the two platforms. Is there anyway to load a BrainVoyager ROI into freesurfer? The BV data has been talairach transformed, does that matter? Less optimal would be loading a freesurfer ROI into BV, but if that's easier, we could try that way too. Any help would be appreciated. Katie The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/**compliancelinehttp://www.partners.org/complianceline. If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] Repost: Converting BV ROIs to FS
Ok, I am trying to use the select_talairach_point command, and I have it in part of a script that uses tksurfer to load up a subject's inflated surface, load the curvature, and load an overlay, but it doesn't seem to be doing anything. Is there a step I am missing? What should I see if it works correctly? Thanks for all your help! Katie On Wed, Sep 5, 2012 at 9:19 AM, Bruce Fischl fis...@nmr.mgh.harvard.eduwrote: Hi Katie you can view data on a tal brain by mapping the data using the talairach.xfm transform. Since you can also use the inverse of the transform you can map both ways. I think there is a tcl command in tksurfer for finding the vertex that is closest to a given tal coord. Try: select_talairach_point xtal ytal ztal cheers Bruce On Tue, 4 Sep 2012, Katie Bettencourt wrote: Hrm. Ok, is there any way to view data for a subject in Freesurfer on a talairach transformed brain? What I would be hoping to do is bring up the data in native subject space, make any ROI label, then also bring the data up on a talairach transformed brain, make a ROI label, then put both labels on the same brain (either native or talairach transformed) and see if they are any different. Also, is there a way to input a particular talairach vertex and jump to that in freesurfer, instead of just moving the mouse around and hoping to find the right spot? Katie On Tue, Sep 4, 2012 at 12:24 PM, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote: Hi Katie I don't think anyone here knows how to do this as we don't use it. Perhaps the Brain Voyager people do? sorry, Bruce On Tue, 4 Sep 2012, Katie Bettencourt wrote: So our lab is running a couple analyses and we are getting different results based on whether we use Brain Voyager or Freesurfer that we think is due to different ROI selection across the two platforms. Is there anyway to load a BrainVoyager ROI into freesurfer? The BV data has been talairach transformed, does that matter? Less optimal would be loading a freesurfer ROI into BV, but if that's easier, we could try that way too. Any help would be appreciated. Katie The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/**compliancelinehttp://www.partners.org/complianceline. If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] Repost: Converting BV ROIs to FS
Nevermind, it turns out it was due to an permissions error. Thanks again. Katie On Wed, Sep 5, 2012 at 12:53 PM, Katie Bettencourt k...@wjh.harvard.eduwrote: Ok, I am trying to use the select_talairach_point command, and I have it in part of a script that uses tksurfer to load up a subject's inflated surface, load the curvature, and load an overlay, but it doesn't seem to be doing anything. Is there a step I am missing? What should I see if it works correctly? Thanks for all your help! Katie On Wed, Sep 5, 2012 at 9:19 AM, Bruce Fischl fis...@nmr.mgh.harvard.eduwrote: Hi Katie you can view data on a tal brain by mapping the data using the talairach.xfm transform. Since you can also use the inverse of the transform you can map both ways. I think there is a tcl command in tksurfer for finding the vertex that is closest to a given tal coord. Try: select_talairach_point xtal ytal ztal cheers Bruce On Tue, 4 Sep 2012, Katie Bettencourt wrote: Hrm. Ok, is there any way to view data for a subject in Freesurfer on a talairach transformed brain? What I would be hoping to do is bring up the data in native subject space, make any ROI label, then also bring the data up on a talairach transformed brain, make a ROI label, then put both labels on the same brain (either native or talairach transformed) and see if they are any different. Also, is there a way to input a particular talairach vertex and jump to that in freesurfer, instead of just moving the mouse around and hoping to find the right spot? Katie On Tue, Sep 4, 2012 at 12:24 PM, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote: Hi Katie I don't think anyone here knows how to do this as we don't use it. Perhaps the Brain Voyager people do? sorry, Bruce On Tue, 4 Sep 2012, Katie Bettencourt wrote: So our lab is running a couple analyses and we are getting different results based on whether we use Brain Voyager or Freesurfer that we think is due to different ROI selection across the two platforms. Is there anyway to load a BrainVoyager ROI into freesurfer? The BV data has been talairach transformed, does that matter? Less optimal would be loading a freesurfer ROI into BV, but if that's easier, we could try that way too. Any help would be appreciated. Katie The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/**compliancelinehttp://www.partners.org/complianceline. If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] Converting BV ROIs to FS
So our lab is running a couple analyses and we are getting different results based on whether we use Brain Voyager or Freesurfer that we think is due to different ROI selection across the two platforms. Is there anyway to load a BrainVoyager ROI into freesurfer? The BV data has been talairach transformed, does that matter? Less optimal would be loading a freesurfer ROI into BV, but if that's easier, we could try that way too. Any help would be appreciated. Katie ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] retinotopy analysis viewing in Freesurfer 5
Without the color wheel, how are you supposed to see the different meridians so that you can draw the boundaries for visual areas? I know that field sign can do that in occipital if you have polar and eccen, but it doesn't work well with parietal retinotopy or if you don't have eccen data (which so far is not worthwhile to collect for parietal retinotopy). What do you recommend using? We looked at the sig maps and the angle maps per the instructions on the wiki page, but neither of them gave us the boundaries, even within occipital, and we've done this data with 4.5 and know that it comes out correctly there, so it's not an error in our data. Katie On Thu, Feb 16, 2012 at 3:26 PM, Douglas N Greve gr...@nmr.mgh.harvard.eduwrote: Hi Katie, the color wheel became difficult to support (and I think it is inferior for viewing for various reasons). There is an alternative called rtview. It is not in the distribution, but you can get it from ftp://surfer.nmr.mgh.harvard.**edu/transfer/outgoing/flat/**greve/rtviewftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/rtview Look at the --help to see how to run it. doug Katie Bettencourt wrote: I have a question about the retinotopy analysis in freesurfer 5. I was following these instructions : http://surfer.nmr.mgh.harvard.** edu/fswiki/**FsFastIndividualRetinotopyAnal**ysishttp://surfer.nmr.mgh.harvard.edu/fswiki/FsFastIndividualRetinotopyAnalysis with some minor edits because we don't have eccen data. And now I'm ready to view the data, but I'm confused by what I am seeing. I have a lot of previous retinotopy experience with older versions of freesurfer, and have this data all analyzed using Freesurfer4.5 and it works fine. However, with Freesurfer 5 when I use this command (with the correct sessid and hemisphere added in): tksurfer-sess -a rtopy.self.?h -s sessid it gives me a heat map, instead of the standard colors that match to the upper, lower, and horizontal meridians (i.e. red, green, and blue). I also tried using the raw angle code: tksurfer-sess -a rtopy.self.?h -s sessid -map angle but it doesn't give me the three colors either, but a sort of heat like map with 2 colors, but the colors don't map to the different visual areas, even in occipital cortex. Field sign doesn't work because I don't have the eccen data (and because I'm care about parietal retinotopy, not occipital). Is there a way to get the standard view of retinotopy out of freesurfer 5? For reference in freesurfer4.5, I would load retinotopy data by using this command: tksurfer subjname ?h inflated and then load the map-imag-lh.w in one overlay layer, and map-real-lh.w in the second overlay layer, then configuring the overlay to display the color wheel color scale and complex display options, and then configuring the phase encoding display to 2 angle cycles and an appropriate angle offset. Can you help me figure out how to get my data to display correctly? Thanks, Katie -- 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/BugReportinghttp://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/**facility/filedrop/index.htmlhttp://www.nmr.mgh.harvard.edu/facility/filedrop/index.html The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/**compliancelinehttp://www.partners.org/complianceline. If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] retinotopy analysis viewing in Freesurfer 5
I have a question about the retinotopy analysis in freesurfer 5. I was following these instructions : http://surfer.nmr.mgh.harvard.edu/fswiki/FsFastIndividualRetinotopyAnalysis with some minor edits because we don't have eccen data. And now I'm ready to view the data, but I'm confused by what I am seeing. I have a lot of previous retinotopy experience with older versions of freesurfer, and have this data all analyzed using Freesurfer4.5 and it works fine. However, with Freesurfer 5 when I use this command (with the correct sessid and hemisphere added in): tksurfer-sess -a rtopy.self.?h -s sessid it gives me a heat map, instead of the standard colors that match to the upper, lower, and horizontal meridians (i.e. red, green, and blue). I also tried using the raw angle code: tksurfer-sess -a rtopy.self.?h -s sessid -map angle but it doesn't give me the three colors either, but a sort of heat like map with 2 colors, but the colors don't map to the different visual areas, even in occipital cortex. Field sign doesn't work because I don't have the eccen data (and because I'm care about parietal retinotopy, not occipital). Is there a way to get the standard view of retinotopy out of freesurfer 5? For reference in freesurfer4.5, I would load retinotopy data by using this command: tksurfer subjname ?h inflated and then load the map-imag-lh.w in one overlay layer, and map-real-lh.w in the second overlay layer, then configuring the overlay to display the color wheel color scale and complex display options, and then configuring the phase encoding display to 2 angle cycles and an appropriate angle offset. Can you help me figure out how to get my data to display correctly? Thanks, Katie ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] ROI analysis with label in both hemispheres -still looking for an answer
No errors, I hadn't actually tried it because everything else was so hemispheric based, and I didn't want to just blindly try it and be unsure of the data I got out. So I should be able to (in surface space) draw a LH and RH ROI, combine them using labels_union and do an standard ROI analysis on that? Katie On Tue, Jul 26, 2011 at 11:31 AM, Douglas N Greve gr...@nmr.mgh.harvard.edu wrote: Hi Katie, it should not matter that they are across hemispheres. Are you getting an error? doug Katie Bettencourt wrote: I'm still looking for an answer on this. If the answer is you can't do it, I'm ok with that, I just would like to know! Thanks! Hi all, I was wondering if anyone had any idea if it was possible to combine together ROIs from the separate hemispheres into one ROI (for example LH V1 and RH V1) and then perform a functional ROI analysis on it. I know how to combine ROIs (through labels_union) and how to do a functional ROI analysis (using func2roi-sess and roisummary-sess), but I don't know if it is possible to do it with a label that runs across both hemispheres. Thoughts? Thanks, Katie -- 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/BugReportinghttp://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/**facility/filedrop/index.htmlhttp://www.nmr.mgh.harvard.edu/facility/filedrop/index.html The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/**compliancelinehttp://www.partners.org/complianceline. If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] ROI analysis with label in both hemispheres -still looking for an answer
I'm still looking for an answer on this. If the answer is you can't do it, I'm ok with that, I just would like to know! Thanks! Hi all, I was wondering if anyone had any idea if it was possible to combine together ROIs from the separate hemispheres into one ROI (for example LH V1 and RH V1) and then perform a functional ROI analysis on it. I know how to combine ROIs (through labels_union) and how to do a functional ROI analysis (using func2roi-sess and roisummary-sess), but I don't know if it is possible to do it with a label that runs across both hemispheres. Thoughts? Thanks, Katie ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] ROI analysis with label in both hemispheres -still looking for an answer
Are there instructions for how to do volume functional analysis and how to do it that way? I've only ever done surface based analysis. Katie On Mon, Jul 25, 2011 at 3:58 PM, Bruce Fischl fis...@nmr.mgh.harvard.eduwrote: Hi Katie, you could do it in the volume, but I doubt there's any way to do it on the surface. cheers Bruce On Mon, 25 Jul 2011, Katie Bettencourt wrote: I'm still looking for an answer on this. If the answer is you can't do it, I'm ok with that, I just would like to know! Thanks! Hi all, I was wondering if anyone had any idea if it was possible to combine together ROIs from the separate hemispheres into one ROI (for example LH V1 and RH V1) and then perform a functional ROI analysis on it. I know how to combine ROIs (through labels_union) and how to do a functional ROI analysis (using func2roi-sess and roisummary-sess), but I don't know if it is possible to do it with a label that runs across both hemispheres. Thoughts? Thanks, Katie The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/**compliancelinehttp://www.partners.org/complianceline. If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] ROI analysis with label in both hemispheres
Hi all, I was wondering if anyone had any idea if it was possible to combine together ROIs from the separate hemispheres into one ROI (for example LH V1 and RH V1) and then perform a functional ROI analysis on it. I know how to combine ROIs (through labels_union) and how to do a functional ROI analysis (using func2roi-sess and roisummary-sess), but I don't know if it is possible to do it with a label that runs across both hemispheres. Thoughts? Thanks, Katie ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] questions about drawing functional rois
I'm trying to draw an ROI by selecting the center of activation for a particular contrast and then selecting nearby voxels within a certain range (for example. say 20 voxels). Ideally I'd like to select only the voxels within this range that are activated by my contrast. However, I can't see how to do this, any help would be appreciated. Thanks, Katie ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] questions about drawing functional rois
Hi Bruce, That's how I normally make my ROIs, but my boss is concerned that we are going from one area to a nearby area that is also activated by this contrast, so she wants to restrict it by a certain number of voxels from the center of activation. Katie On Fri, Jul 1, 2011 at 1:55 PM, Bruce Fischl fis...@nmr.mgh.harvard.eduwrote: Hi Katie, you can use the custom fill tool in tksurfer for this. Display your activation map at whatever threshold you want, then click in the middle of the blob you want to create an ROI for and do custom fill with up to functional threshold. This will floodfill from that point outwards stopping when it reaches vertices that are below threshold cheers Bruce On Fri, 1 Jul 2011, Katie Bettencourt wrote: I'm trying to draw an ROI by selecting the center of activation for a particular contrast and then selecting nearby voxels within a certain range (for example. say 20 voxels). Ideally I'd like to select only the voxels within this range that are activated by my contrast. However, I can't see how to do this, any help would be appreciated. Thanks, Katie The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/**compliancelinehttp://www.partners.org/complianceline. If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] questions about drawing functional rois
What do you mean by dilate it? Katie On Fri, Jul 1, 2011 at 2:28 PM, Bruce Fischl fis...@nmr.mgh.harvard.eduwrote: you can draw a boundary between them and also click up to boundaries or something like that. Or just click the center and dilate it a few times or some combination of thresholding and dilation. It's quite flexible cheers Bruce On Fri, 1 Jul 2011, Katie Bettencourt wrote: Hi Bruce, That's how I normally make my ROIs, but my boss is concerned that we are going from one area to a nearby area that is also activated by this contrast, so she wants to restrict it by a certain number of voxels from the center of activation. Katie On Fri, Jul 1, 2011 at 1:55 PM, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote: Hi Katie, you can use the custom fill tool in tksurfer for this. Display your activation map at whatever threshold you want, then click in the middle of the blob you want to create an ROI for and do custom fill with up to functional threshold. This will floodfill from that point outwards stopping when it reaches vertices that are below threshold cheers Bruce On Fri, 1 Jul 2011, Katie Bettencourt wrote: I'm trying to draw an ROI by selecting the center of activation for a particular contrast and then selecting nearby voxels within a certain range (for example. say 20 voxels). Ideally I'd like to select only the voxels within this range that are activated by my contrast. However, I can't see how to do this, any help would be appreciated. Thanks, Katie The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/**compliancelinehttp://www.partners.org/complianceline. If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] questions about drawing functional rois
Ok, I see it. I'll see what I can do with this, but I guess that means there's no way to do it and enter an explicit number of voxels to select from that central point? Katie On Fri, Jul 1, 2011 at 2:39 PM, Bruce Fischl fis...@nmr.mgh.harvard.eduwrote: under tools-label in tksurfer (I think) there's an option to dilate or erode the boundary (expand or contract) cheers Bruce On Fri, 1 Jul 2011, Katie Bettencourt wrote: What do you mean by dilate it? Katie On Fri, Jul 1, 2011 at 2:28 PM, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote: you can draw a boundary between them and also click up to boundaries or something like that. Or just click the center and dilate it a few times or some combination of thresholding and dilation. It's quite flexible cheers Bruce On Fri, 1 Jul 2011, Katie Bettencourt wrote: Hi Bruce, That's how I normally make my ROIs, but my boss is concerned that we are going from one area to a nearby area that is also activated by this contrast, so she wants to restrict it by a certain number of voxels from the center of activation. Katie On Fri, Jul 1, 2011 at 1:55 PM, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote: Hi Katie, you can use the custom fill tool in tksurfer for this. Display your activation map at whatever threshold you want, then click in the middle of the blob you want to create an ROI for and do custom fill with up to functional threshold. This will floodfill from that point outwards stopping when it reaches vertices that are below threshold cheers Bruce On Fri, 1 Jul 2011, Katie Bettencourt wrote: I'm trying to draw an ROI by selecting the center of activation for a particular contrast and then selecting nearby voxels within a certain range (for example. say 20 voxels). Ideally I'd like to select only the voxels within this range that are activated by my contrast. However, I can't see how to do this, any help would be appreciated. Thanks, Katie The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/**compliancelinehttp://www.partners.org/complianceline. If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. __**_ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.**edu/mailman/listinfo/**freesurferhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/**compliancelinehttp://www.partners.org/complianceline. If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] autostimdur vs noautostimdur
I'm a bit confused about what the -autostimdur and -noautostimdur flags in mkanalysis-sess do. I've checked the help files, but the wording is a bit confusing, and when I run them on my event related design, I get different results depending on which flag I use, with the -noautostimdur being more of what I expect as far as results go. Also, they are only used in event related and AB designs, not blocked, correct? Katie ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] autostimdur vs noautostimdur
Wait, I'm confused, in v 4.5 (which I'm using) the paradigm files have 4 values per line (starting time, condition, length, and weight), so don't they have the lengths in there? I know you could use an older paradigm file with only 2 columns (starting time, condition), and in this case I would list each TR and the condition there, but the wiki says that v. 4.5 can use the 4 column paradigm files. Is that not true? I mean it obviously uses the weights I ran an event related analysis with -noautostimdur in the analysis, with a 4 column paradigm file. I did not list every TR, but used the 3rd column to list the length of time. I got what appears to be valid data out. When I redid it with -autostimdur, I got very little activation. But if the -noautostimdur assumes that each event is equal to the TR (which is shorter than the actual durations I have), then wouldn't the analysis have had problems because I didn't cover all the TRs in the paradigm file? But it worked fine. I'm very confused here. Also, is there a difference between the way this is used in FIR and Gamma analyses? Katie On Fri, Apr 15, 2011 at 2:33 PM, Douglas N Greve gr...@nmr.mgh.harvard.eduwrote: FYI: autostimdur is not valid in version 5.X because the stimulus duration is supplied in the paradigm file. For earlier versions, there was no info in the par file about the duration. The -autostimdur will compute the duration of the stimulus from the paradigm file based upon the time to the next stimulus entry this works as long as all time is accounted for in the parfile and no stimuli overlap. If you use -no-autostimdur, then it will assume that the duration of the event is equal to the TR. doug Katie Bettencourt wrote: I'm a bit confused about what the -autostimdur and -noautostimdur flags in mkanalysis-sess do. I've checked the help files, but the wording is a bit confusing, and when I run them on my event related design, I get different results depending on which flag I use, with the -noautostimdur being more of what I expect as far as results go. Also, they are only used in event related and AB designs, not blocked, correct? Katie -- 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 The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] autostimdur vs noautostimdur
Ok, so if I use the 4 col I don't need to use -autostimdur, I can use -noautostimdur or can I leave it out all together? I noticed that FIR ignored the stimulus duration entirely, so I only need the -autostimdur/noautostimdur for gamma event related or AB designs? However, I did get a difference (and a fairly large one) for a FIR event related analysis with 4 col paradigm files when I did mkanalysis-sess -noautostimdur and mkanalysis-sess -autostimdur. Should i just ignore the -autostimdur one? Katie On Fri, Apr 15, 2011 at 2:51 PM, Douglas N Greve gr...@nmr.mgh.harvard.eduwrote: Oh, sorry, I had forgotten when I introduced the 4col format. Yes, 4.5 does take the 4 col. I actually dont remember exactly what 4.5 does when you give it autostimdur with a 4col. It might ignore the duration in the parfile and compute it from the stimulus timing. If you represent all time in your paradigm file, this should do the same thing. For the FIR, the stimulus duration is ignored entirely. doug Katie Bettencourt wrote: Wait, I'm confused, in v 4.5 (which I'm using) the paradigm files have 4 values per line (starting time, condition, length, and weight), so don't they have the lengths in there? I know you could use an older paradigm file with only 2 columns (starting time, condition), and in this case I would list each TR and the condition there, but the wiki says that v. 4.5 can use the 4 column paradigm files. Is that not true? I mean it obviously uses the weights I ran an event related analysis with -noautostimdur in the analysis, with a 4 column paradigm file. I did not list every TR, but used the 3rd column to list the length of time. I got what appears to be valid data out. When I redid it with -autostimdur, I got very little activation. But if the -noautostimdur assumes that each event is equal to the TR (which is shorter than the actual durations I have), then wouldn't the analysis have had problems because I didn't cover all the TRs in the paradigm file? But it worked fine. I'm very confused here. Also, is there a difference between the way this is used in FIR and Gamma analyses? Katie On Fri, Apr 15, 2011 at 2:33 PM, Douglas N Greve gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu wrote: FYI: autostimdur is not valid in version 5.X because the stimulus duration is supplied in the paradigm file. For earlier versions, there was no info in the par file about the duration. The -autostimdur will compute the duration of the stimulus from the paradigm file based upon the time to the next stimulus entry this works as long as all time is accounted for in the parfile and no stimuli overlap. If you use -no-autostimdur, then it will assume that the duration of the event is equal to the TR. doug Katie Bettencourt wrote: I'm a bit confused about what the -autostimdur and -noautostimdur flags in mkanalysis-sess do. I've checked the help files, but the wording is a bit confusing, and when I run them on my event related design, I get different results depending on which flag I use, with the -noautostimdur being more of what I expect as far as results go. Also, they are only used in event related and AB designs, not blocked, correct? Katie -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. -- 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 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient
Re: [Freesurfer] functional ROI analysis problem
Ok, I ran that and a couple questions. I ran it on 2 different subjects and
got the exact same value, is that expected? Do I need to run it for each
subject?
Also, do I need to do this for event-related designs as well, or just block
designs? I tried to run it on another analysis I did, an event-related one,
but got this error:
??? Error using == times
Matrix dimensions must agree.
Katie
On Mon, Apr 11, 2011 at 12:22 PM, Douglas N Greve
gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu wrote:
You can run it anytime after the analysis. The 'X' file below is
an actual file that is there (X.mat). The value that you get out
of this procedure should be used to multiply the values you get
out of roisummary-sess.
doug
Katie Bettencourt wrote:
I'm working with Yaoda Xu. Thanks for the percent signal
change fix, but Im a little
confused by what you wrote. When do I run that? after running
roisummary-sess? Or after the analysis is run?
Also, is the load('X' a placeholder where I need to put
load('filename')? or will it just work as is? Obviously I
change the session and analysis in the cd line. And is
that a flat scale factor for all conditions for that
subject?
Katie
On Fri, Apr 8, 2011 at 10:59 AM, Douglas N Greve
gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu
mailto:gr...@nmr.mgh.harvard.edu
mailto:gr...@nmr.mgh.harvard.edu wrote:
btw, I notice that you have a harvard email now (was BU).
who are
you working with there?
doug
Katie Bettencourt wrote:
Hi all,
I'm doing ROI analysis on functional data with an
anatomical
label, and while the activity looks strong and robust in
tksurfer, the % signal changes I am getting are very
low (and
much lower than we've previously found), and I'm not sure
what's going on.
I'm running Freesurfer 4.5 on red hat linux.
The design is a blocked design with 4 non-null conditions,
baseline is fixation. Attached is a picture of the
activity I
get for 2 subjects for on of the conditions vs fixation
(baseline) at a p0.05 threshold with the ROI outlined in
black as well as the output from roisummary-sess for
these two
subjects in that roi. I calculate % signal change based of
the output from roisummary-sess, dividing each condition by
the baseline in that file and then multiplying by 100. %
signal changes are listed below, along with all
commands run.
% signal change:
110222SKJ_connected 110222SP_connected
0.000988998467052 0.000533852720367
0.001053498367080.000556814127695
0.000408499366826 0.000327200054419
0.000440749316839 0.000436266739225
commands:
mkanalysis-sess -analysis connect -TR 2 -paradigm
connect.dat
-designtype blocked -funcstem fmc -motioncor -runlistfile
connect_runs.txt -inorm -tpexclude tpexclude.dat
-nconditions
4 -timewindow 20 -gammafit 2.25 1.25 -noautostimdur
mkcontrast-sess -analysis connect -contrast
connected_vs_unconnected -a 1 -c 2
mkcontrast-sess -analysis connect -contrast
connected_vs_noise
-a 1 -c 3
mkcontrast-sess -analysis connect -contrast
connected_vs_phase
-a 1 -c 4
mkcontrast-sess -analysis connect -contrast
connected_vs_fix
-a 1 -c 0
mkcontrast-sess -analysis connect -contrast
unconnected_vs_noise -a 2 -c 3
mkcontrast-sess -analysis connect -contrast
unconnected_vs_phase -a 2 -c 4
mkcontrast-sess -analysis connect -contrast
unconnected_vs_fix
-a 2 -c 0
mkcontrast-sess -analysis connect -contrast
noise_vs_phase -a
3 -c 4
mkcontrast-sess -analysis connect -contrast
noise_vs_fix -a 3 -c 0
mkcontrast-sess -analysis connect -contrast
shape_vs_noise -a
1 -a 2 -c 3
mkcontrast-sess -analysis connect -contrast
shape_vs_phase -a
2 -a 1 -c 4
mkcontrast-sess -analysis connect -contrast
shape_vs_noisephase -a 2 -a 1 -c 3 -c 4
mkcontrast-sess -analysis connect -contrast act_vs_fix
-a 2 -a
1 -a 3 -a 4 -c 0
selxavg3-sess -sf connect-sess -df connect.dir
-analysis connect
[Freesurfer] question about weighted regression analysis
So I created a weighted regression analysis to look at the effect of memory load in a particular brain region. Basically, I weighted the paradigms by a behavioral measure that reflected the number of items actually remembered (as set size was increased). As far as Doug told me there are basically 2 ways to weight your paradigm files. Version 1: Have 2 conditions, baseline (condition 0) and all the set sizes (condition 1). Condition 1 would then be weighted by the behavioral measure. Version 2: Have 3 conditions, baseline (condition 0), and then I represented each presentation as two different conditions, one with a weight that is always 1 (condition 1), the other weighted according to the behavioral measure (condition 2). The difference, as far as I understand it, in version 1, it is assumed that the response amplitude is ) when the weight is 0 (ie. that when you are attending to 0 items, brain activity = 0). Whereas, version 2, tests the slope of the HRF amplitude vs weight without the assumption above. However, I'm a bit confused as to the results I got. When I looked at the data from both versions, version 1 provided a much higher amount of activation and more areas activated than version 2. However, I believe version 2 better fits with the multiple regression analysis that is done in Brain Voyager. Can anyone give me a better explanation of what the difference between these analysis models is? Katie ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] problem with spmregister on mac
Can you tell me how to check that because Im having the same problem with spmregister-sess with my linux as well and I've never used SPM at all, and honestly can't even figure out how to open it. Katie On Thu, Feb 3, 2011 at 11:21 PM, Y.V. Jiang yuhong.ji...@gmail.com wrote: Hi Maryam, You should check your spm defaults to see whether it uses radiology or neurology convention. Most likely your spm has flipped your image, and the spmregister-sess is trying to match the left hemisphere of your functionals to the right hemisphere of your anatomical. -Yuhong On Thu, Feb 3, 2011 at 9:59 PM, Maryam Vaziri Pashkam mvazir...@gmail.com wrote: Hi, I am new to freesurfer and I am analyzing fmri data on a Mac OSX 10.5.8 computer using freesurfer 4.5. I have SPM 8 and FSL also installed. I have two versions of matlab (matlab R2009b R2008a) on my computer. I think spm runs through the R2009b on my computer. I have added the SPM path to the startup.m of both matlabs by adding the following line (they both point to the same startup.m ): path(path,'/Applications/spm8'); I run preprocessing on the data using the following command: preproc-sess -nosmooth -sf retino-sess -df retino.dir then I run automatic registration with the following command: spmregister-sess -sf retino-sess -df retino.dir It runs smoothly and there seems to be no errors. But when I try to check the registration with this command: tkregister-sess -sf retino-sess -df retino.dir -inorm what I see is not a good registration. Isn't spm register supposed to do a good job in automatic registration? The one that I get still needs a lot of manual adjustment. Am I doing something wrong? I have attached the log files for spmregister and tkregister and a screen shot of the image that I get after running tkregister. I would appreciate any help in this matter. Thanks, Maryam ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. -- -- Yuhong Vanessa Jiang, PhD, Associate Professor McKnight Presidential Fellow Department of Psychology, Univ of Minnesota jiang...@umn.edu, 612-625-7003 https://sites.google.com/site/jiang166/ -- ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] problem with spmregister on mac
The spm_flip_analyse_images.m was what I needed! Thanks so much! Katie On Fri, Feb 4, 2011 at 11:53 AM, Y.V. Jiang yuhong.ji...@gmail.com wrote: It depends on which version of SPM you're running. It's either the file called spm_defaults.m, or on my system it's file called spm_flip_analyze_images.m. There is a line that says: flip = 1; (or flip = 0). For my kind of scans I need to set flip = 0, whereas the spm defaults tend to come with flip = 1 (which turns your radiology images into neurology images). -Yuhong On Fri, Feb 4, 2011 at 10:30 AM, Katie Bettencourt k...@wjh.harvard.eduwrote: Can you tell me how to check that because Im having the same problem with spmregister-sess with my linux as well and I've never used SPM at all, and honestly can't even figure out how to open it. Katie On Thu, Feb 3, 2011 at 11:21 PM, Y.V. Jiang yuhong.ji...@gmail.comwrote: Hi Maryam, You should check your spm defaults to see whether it uses radiology or neurology convention. Most likely your spm has flipped your image, and the spmregister-sess is trying to match the left hemisphere of your functionals to the right hemisphere of your anatomical. -Yuhong On Thu, Feb 3, 2011 at 9:59 PM, Maryam Vaziri Pashkam mvazir...@gmail.com wrote: Hi, I am new to freesurfer and I am analyzing fmri data on a Mac OSX 10.5.8 computer using freesurfer 4.5. I have SPM 8 and FSL also installed. I have two versions of matlab (matlab R2009b R2008a) on my computer. I think spm runs through the R2009b on my computer. I have added the SPM path to the startup.m of both matlabs by adding the following line (they both point to the same startup.m ): path(path,'/Applications/spm8'); I run preprocessing on the data using the following command: preproc-sess -nosmooth -sf retino-sess -df retino.dir then I run automatic registration with the following command: spmregister-sess -sf retino-sess -df retino.dir It runs smoothly and there seems to be no errors. But when I try to check the registration with this command: tkregister-sess -sf retino-sess -df retino.dir -inorm what I see is not a good registration. Isn't spm register supposed to do a good job in automatic registration? The one that I get still needs a lot of manual adjustment. Am I doing something wrong? I have attached the log files for spmregister and tkregister and a screen shot of the image that I get after running tkregister. I would appreciate any help in this matter. Thanks, Maryam ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. -- -- Yuhong Vanessa Jiang, PhD, Associate Professor McKnight Presidential Fellow Department of Psychology, Univ of Minnesota jiang...@umn.edu, 612-625-7003 https://sites.google.com/site/jiang166/ -- ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. -- -- Yuhong Vanessa Jiang, PhD, Associate Professor McKnight Presidential Fellow Department of Psychology, Univ of Minnesota jiang...@umn.edu, 612-625-7003 https://sites.google.com/site/jiang166/ -- ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] taskreg in version 5
I'm not sure if that's exactly what I am saying. Basically, there is an area in the brain (which I am trying to localize) that tracks the number of items you are holding in memory so that the more items you hold in memory, the higher the bold activation. We have behavioral results saying how many items people are holding in each of the conditions, and we want to use this to get out an area in which the BOLD activation mirrors this. In Brain Voyager, this is done by weighting the conditions by the behavior, which is what I am trying to do here. I'm not sure that that translates exactly into what you are saying. Katie On Wed, Dec 8, 2010 at 11:47 AM, Douglas N Greve gr...@nmr.mgh.harvard.eduwrote: It depends on what you want to test exactly. You can just weight each presentation and test against fixation as you suggest. This implies that the response amp is 0 when your weight is 0. If that's not the case, then you need to make a modification. Let me know if you need that. doug Katie Bettencourt wrote: Ah, there was one condition (the throw away one) that was all weighted 0, I will just change the weight on that one back to 1. For looking at what shows up in the weighted analysis, if I want to see areas that increase along my weights, would I just make a contrast of all of them vs fixation, and then any area that shows up in that comparison would be an area that followed my weighting (if that makes sense)? Katie On Tue, Dec 7, 2010 at 4:16 PM, Douglas N Greve gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu wrote: They do not need to be whole numbers. 0s should be ok, unless there are some conditions that only have 0 weighting. For throw aways conditions, you usually just create a separate condition and leave the weight at 1. Katie Bettencourt wrote: It does run ok when the FIR is all weighted to 1. There are weights of 0 for the couple conditions that were essentially throwaway trials for counterbalancing reasons. Is that what is causing the trouble? Do the numbers need to be whole numbers? katie On Tue, Dec 7, 2010 at 3:23 PM, Douglas N Greve gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu wrote: It should work in 4.5 too. The numbers are weights. So if you think that the response to presentation A of condition 1 will be twice that of presentation B of condition 1, then you would have a weight of 2 for pres A and 1 for pres B. The weight of fixation (condition 0) is unimportant. I can't tell from the error msg below whether the error is caused by the weighting or by the FIR. Does the FIR run ok when it is not weighted? Are there any task weights that are 0? doug Katie Bettencourt wrote: Ah, what I want is the 2nd one then. I was trying to do this in freesurfer v 4.5 but I can't figure out how to use the 4th column in a way that doesn't crash during selxavg3-sess and there isn't much on the wiki about how to use it, what sorts of numbers are acceptable in the 4th column? I have 6 conditions plus fixation. one condition I want to be ignored (so I set the weight to 0), and then I want an increase as set size increases but with a plateau at large set sizes. I tried weighting them as whole numbers above 1 (which was what fixation was set to), weighing them as all less than 1 (but with fixation still as 1), weighing them less than 1 and so that combined they add up to 1 (fixation still as 1), but all errored our in selxavg3-sess. the same data analyzes fine unweighted (all 1s in the 4th column of the paradigm file). This is the output I get when I try to change the 4th column of the paradigm file: selxavg3-sess -s 101103TM_supIPS -df supIPS.dir -analysis supIPS-fir-weighted -overwrite -- selxavg3-sess logfile is /home/kcb/mri-space/supIPS_loc/log/selxavg3-sess-bold-supIPS-fir-weighted-101207145505.log -- --- /home/kcb/mri-space/101103TM_supIPS Tue Dec 7 14:55:05 EST 2010 anadir = /home/kcb/mri-space/101103TM_supIPS/bold/supIPS-fir-weighted analysis supIPS-fir-weighted alread exists for 101103TM_supIPS ... reanalyzing (deleting old analysis
[Freesurfer] taskreg in version 5
I'm trying to set up an analysis using an external regressor (as part of the mkanalysis-sess stream, -taskreg flag) in version 5, but I'm not sure what the taskreg.dat file should look like. The only thing I can find is that it should have a line for each time point. Does anyone have any more guidance than this? Katie ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] taskreg in version 5
So I just need 1 column with a line for each time point that has the weight I want to give the condition that is occuring at that time point? And what do you mean a contrast will automatically be created for it? I was trying to use this to find an area that increases with load but then plateaus at a point where subject's behavioral performance plateaus (so essentially looking for a mirroring of the behavioral data in the neural data), will there just be a contrast created after I run selxavg3-sess that I can bring up with tksurfer-sess afterwards? katie On Tue, Dec 7, 2010 at 11:40 AM, Douglas N Greve gr...@nmr.mgh.harvard.eduwrote: It is just a text file with a value for each time point. You can have multiple columns, but if it is a task, then you probably want to keep one to make the interpretation easier. A contrast will automatically be created for it. You can look at the mcprextreg file created by the motion correction to get an idea. doug Katie Bettencourt wrote: I'm trying to set up an analysis using an external regressor (as part of the mkanalysis-sess stream, -taskreg flag) in version 5, but I'm not sure what the taskreg.dat file should look like. The only thing I can find is that it should have a line for each time point. Does anyone have any more guidance than this? Katie ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- 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 The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] analysis in v5 vs v4.5
So we won't actually be doing group analysis on this except ROI analysis. We are using this data to look at overlap in activations on individual subject levels. Since the v5 whiten seems much more extreme than v4.5, I'm not really sure how to interprete this in terms of what I need to do for accurate represenations of the data for my experiments, if that makes sense. Katie On Tue, Dec 7, 2010 at 2:46 PM, Douglas N Greve gr...@nmr.mgh.harvard.eduwrote: selxavg3-sess checks to see whether preproc has been run and runs it if it is needed, so all that stuff can go on in the background. It does look like the differences you are seeing come from the whitening. This attempts to account for temporal correlation in the noise. Whether you need it or not depends on what you actually report. If you report the volume of activation for each subject, then you'll probably want some sort of whitening. In general, people don't report this. If you are going to just hand the 1st level results up to the next higher level (eg, group analysis), then I don't think it makes a difference. A reviewer may balk if there has not been whitening performed at the first level, but this is usually just a misunderstanding on their part. doug Katie Bettencourt wrote: When I registered the 4.5 version, I did it fully manually, using tkregister2, but with the version5 one I initially didn't do anything outside of the commands I listed below (though the register.dat was present from the 4.5 version), but then to check that I went through and ran register-sess on the version 5, and then double checked it in tkregister2 (as the output to register-sess suggested I do) and at least at a coarse look it looked fairly well aligned, and rerunning selxavg3-sess after running register-sess didn't change the output (in fact, the picture I attached before was from the register-sess version). Does selxavg3-sess automatically run this registration in version 5 or do you need to do the registration separately everytime? Similarly, I didn't run preproc-sess separately for version5, did I need to? rerunning it with the -no-whiten flag seems to have pushed it in the other direction. I now get more activation in v5 than v4.5 (see attached pictures) which honestly I guess I like better... Do I need to run it with the -no-whiten flag each time? Exactly what is this flag doing? Katie On Tue, Dec 7, 2010 at 2:20 PM, Douglas N Greve gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu wrote: Hmmm, not sure what's going on with that. Can you verify that the registration is correct in the v5 results? The only other thing that I can think of is that the whitening may be a bit different between 4.5 and 5.0. Try turning off the whitening in v5 (-no-whiten when running mkanalysis-sess). doug Katie Bettencourt wrote: I was attempting to run an analysis that was previously done in freesurfer 4.5 in version 5 to see if I cuold switch over to the new version. However, I am getting very different results for the two versions. Below are the commands I ran in both and attached are pictures of the differences. I get much much less activation (and much less than expected) when using version 5. I assume this is because I've done something wrong with the way I set up my version 5 analysis, but I don't knwo what it is. Any help would be appreciated. version 5: mkanalysis-sess -analysis supIPS-gamma-5rh -TR 1.5 -paradigm supIPS.dat -event-related -runlistfile supIPSruns.txt -nskip 2 -nconditions 6 -gammafit 2.25 1.25 -surface self rh -fwhm 0 -refeventdur 6 mkcontrast-sess -analysis supIPS-gamma-5rh -contrast act_vs_fix -a 1 -a 2 -a 3 -a 4 -a 5 -c 0 selxavg3-sess -s 101103TM_supIPS -df supIPS.dir -analysis supIPS-gamma-5rh tksurfer-sess -s 101103TM_supIPS -a supIPS-gamma-5rh-c act_vs_fix -df supIPS.dir version 4.5 mkanalysis-sess -analysis supIPS-gamma -TR 1.5 -paradigm supIPS.dat -designtype event-related -funcstem fmc -motioncor -runlistfile supIPSruns.txt -inorm -tpexclude tpexclude.dat -nconditions 6 -gammafit 2.25 1.25 -noautostimdur mkcontrast-sess -analysis supIPS-gamma -contrast act_vs_fix -a 1 -a 2 -a 3 -a 4 -a 5 -c 0 tksurfer-sess -s 101103TM_supIPS -df supIPS.dir -a supIPS-gamma -c act_vs_fix -hemi rh Katie ___ Freesurfer mailing list
Re: [Freesurfer] taskreg in version 5
Ah, what I want is the 2nd one then. I was trying to do this in freesurfer v 4.5 but I can't figure out how to use the 4th column in a way that doesn't crash during selxavg3-sess and there isn't much on the wiki about how to use it, what sorts of numbers are acceptable in the 4th column? I have 6 conditions plus fixation. one condition I want to be ignored (so I set the weight to 0), and then I want an increase as set size increases but with a plateau at large set sizes. I tried weighting them as whole numbers above 1 (which was what fixation was set to), weighing them as all less than 1 (but with fixation still as 1), weighing them less than 1 and so that combined they add up to 1 (fixation still as 1), but all errored our in selxavg3-sess. the same data analyzes fine unweighted (all 1s in the 4th column of the paradigm file). This is the output I get when I try to change the 4th column of the paradigm file: selxavg3-sess -s 101103TM_supIPS -df supIPS.dir -analysis supIPS-fir-weighted -overwrite -- selxavg3-sess logfile is /home/kcb/mri-space/supIPS_loc/log/selxavg3-sess-bold-supIPS-fir-weighted-101207145505.log -- --- /home/kcb/mri-space/101103TM_supIPS Tue Dec 7 14:55:05 EST 2010 anadir = /home/kcb/mri-space/101103TM_supIPS/bold/supIPS-fir-weighted analysis supIPS-fir-weighted alread exists for 101103TM_supIPS ... reanalyzing (deleting old analysis) -- --- 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 1984-2010 The MathWorks, Inc. Version 7.10.0.499 (R2010a) 64-bit (glnxa64) February 5, 2010 To get started, type one of these: helpwin, helpdesk, or demo. For product information, visit www.mathworks.com. /usr/local/freesurfer4.5/fsfast/toolbox/fast_selxavg3.m $Id: fast_selxavg3.m,v 1.55.2.8 2009/04/17 20:09:46 greve Exp $ outtop = /home/kcb/mri-space Extension format = nii UseFloat = 0 INFO: mask is not set, setting to brain 1 act_vs_fix-delay.mat Ignoring stimulus duration for FIR model Ignoring stimulus duration for FIR model Ignoring stimulus duration for FIR model Ignoring stimulus duration for FIR model Ignoring stimulus duration for FIR model Ignoring stimulus duration for FIR model Excluding 2 points nruns = 2 autostimdur = 0 outanadir = /home/kcb/mri-space/101103TM_supIPS/bold/supIPS-fir-weighted Found 48212/124416 (38.8) voxels in mask Creating Design Matrix Ignoring stimulus duration for FIR model Ignoring stimulus duration for FIR model Ignoring stimulus duration for FIR model Ignoring stimulus duration for FIR model Ignoring stimulus duration for FIR model Ignoring stimulus duration for FIR model Excluding 2 points Warning: Matrix is singular to working precision. In fast_selxavg3 at 212 Ignoring stimulus duration for FIR model Ignoring stimulus duration for FIR model Ignoring stimulus duration for FIR model Ignoring stimulus duration for FIR model Ignoring stimulus duration for FIR model Ignoring stimulus duration for FIR model Excluding 2 points Warning: Matrix is singular to working precision. In fast_selxavg3 at 212 ntptot = 616, nX = 80, DOF = 536 Saving X matrix to /home/kcb/mri-space/101103TM_supIPS/bold/supIPS-fir-weighted/Xtmp.mat ??? Error using == svd Input to SVD must not contain NaN or Inf. Error in == cond at 40 s = svd(A); Error in == fast_selxavg3 at 248 XCond = cond(XtX); -- ERROR: fast_selxavg3() failed\n katie On Tue, Dec 7, 2010 at 2:50 PM, Douglas N Greve gr...@nmr.mgh.harvard.eduwrote: what are you trying to do exactly? The external regressor is usually used with a continuous measure (eg, skin conductance, it can also be used to seed-based functional connectivity). If you expect the hemodynamic response to be scaled by something (eg, reaction time), then that should be incorporated into the paradigm file in the 4th column. doug Katie Bettencourt wrote: So I just need 1 column with a line for each time point that has the weight I want to give the condition that is occuring at that time point? And what do you mean a contrast will automatically be created for it? I was trying to use this to find an area that increases with load but then plateaus at a point where subject's behavioral performance plateaus (so essentially looking for a mirroring of the behavioral data in the neural data), will there just be a contrast created after I run selxavg3-sess that I can bring up with tksurfer-sess afterwards? katie On Tue, Dec 7, 2010 at 11:40 AM, Douglas N Greve gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu wrote: It is just a text
Re: [Freesurfer] taskreg in version 5
It does run ok when the FIR is all weighted to 1. There are weights of 0 for the couple conditions that were essentially throwaway trials for counterbalancing reasons. Is that what is causing the trouble? Do the numbers need to be whole numbers? katie On Tue, Dec 7, 2010 at 3:23 PM, Douglas N Greve gr...@nmr.mgh.harvard.eduwrote: It should work in 4.5 too. The numbers are weights. So if you think that the response to presentation A of condition 1 will be twice that of presentation B of condition 1, then you would have a weight of 2 for pres A and 1 for pres B. The weight of fixation (condition 0) is unimportant. I can't tell from the error msg below whether the error is caused by the weighting or by the FIR. Does the FIR run ok when it is not weighted? Are there any task weights that are 0? doug Katie Bettencourt wrote: Ah, what I want is the 2nd one then. I was trying to do this in freesurfer v 4.5 but I can't figure out how to use the 4th column in a way that doesn't crash during selxavg3-sess and there isn't much on the wiki about how to use it, what sorts of numbers are acceptable in the 4th column? I have 6 conditions plus fixation. one condition I want to be ignored (so I set the weight to 0), and then I want an increase as set size increases but with a plateau at large set sizes. I tried weighting them as whole numbers above 1 (which was what fixation was set to), weighing them as all less than 1 (but with fixation still as 1), weighing them less than 1 and so that combined they add up to 1 (fixation still as 1), but all errored our in selxavg3-sess. the same data analyzes fine unweighted (all 1s in the 4th column of the paradigm file). This is the output I get when I try to change the 4th column of the paradigm file: selxavg3-sess -s 101103TM_supIPS -df supIPS.dir -analysis supIPS-fir-weighted -overwrite -- selxavg3-sess logfile is /home/kcb/mri-space/supIPS_loc/log/selxavg3-sess-bold-supIPS-fir-weighted-101207145505.log -- --- /home/kcb/mri-space/101103TM_supIPS Tue Dec 7 14:55:05 EST 2010 anadir = /home/kcb/mri-space/101103TM_supIPS/bold/supIPS-fir-weighted analysis supIPS-fir-weighted alread exists for 101103TM_supIPS ... reanalyzing (deleting old analysis) -- --- 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 1984-2010 The MathWorks, Inc. Version 7.10.0.499 (R2010a) 64-bit (glnxa64) February 5, 2010 To get started, type one of these: helpwin, helpdesk, or demo. For product information, visit www.mathworks.com http://www.mathworks.com. /usr/local/freesurfer4.5/fsfast/toolbox/fast_selxavg3.m $Id: fast_selxavg3.m,v 1.55.2.8 2009/04/17 20:09:46 greve Exp $ outtop = /home/kcb/mri-space Extension format = nii UseFloat = 0 INFO: mask is not set, setting to brain 1 act_vs_fix-delay.mat Ignoring stimulus duration for FIR model Ignoring stimulus duration for FIR model Ignoring stimulus duration for FIR model Ignoring stimulus duration for FIR model Ignoring stimulus duration for FIR model Ignoring stimulus duration for FIR model Excluding 2 points nruns = 2 autostimdur = 0 outanadir = /home/kcb/mri-space/101103TM_supIPS/bold/supIPS-fir-weighted Found 48212/124416 (38.8) voxels in mask Creating Design Matrix Ignoring stimulus duration for FIR model Ignoring stimulus duration for FIR model Ignoring stimulus duration for FIR model Ignoring stimulus duration for FIR model Ignoring stimulus duration for FIR model Ignoring stimulus duration for FIR model Excluding 2 points Warning: Matrix is singular to working precision. In fast_selxavg3 at 212 Ignoring stimulus duration for FIR model Ignoring stimulus duration for FIR model Ignoring stimulus duration for FIR model Ignoring stimulus duration for FIR model Ignoring stimulus duration for FIR model Ignoring stimulus duration for FIR model Excluding 2 points Warning: Matrix is singular to working precision. In fast_selxavg3 at 212 ntptot = 616, nX = 80, DOF = 536 Saving X matrix to /home/kcb/mri-space/101103TM_supIPS/bold/supIPS-fir-weighted/Xtmp.mat ??? Error using == svd Input to SVD must not contain NaN or Inf. Error in == cond at 40 s = svd(A); Error in == fast_selxavg3 at 248 XCond = cond(XtX); -- ERROR: fast_selxavg3() failed\n katie On Tue, Dec 7, 2010 at 2:50 PM, Douglas N Greve gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu wrote: what are you trying to do exactly? The external regressor is usually used with a continuous
Re: [Freesurfer] taskreg in version 5
Ah, there was one condition (the throw away one) that was all weighted 0, I will just change the weight on that one back to 1. For looking at what shows up in the weighted analysis, if I want to see areas that increase along my weights, would I just make a contrast of all of them vs fixation, and then any area that shows up in that comparison would be an area that followed my weighting (if that makes sense)? Katie On Tue, Dec 7, 2010 at 4:16 PM, Douglas N Greve gr...@nmr.mgh.harvard.eduwrote: They do not need to be whole numbers. 0s should be ok, unless there are some conditions that only have 0 weighting. For throw aways conditions, you usually just create a separate condition and leave the weight at 1. Katie Bettencourt wrote: It does run ok when the FIR is all weighted to 1. There are weights of 0 for the couple conditions that were essentially throwaway trials for counterbalancing reasons. Is that what is causing the trouble? Do the numbers need to be whole numbers? katie On Tue, Dec 7, 2010 at 3:23 PM, Douglas N Greve gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu wrote: It should work in 4.5 too. The numbers are weights. So if you think that the response to presentation A of condition 1 will be twice that of presentation B of condition 1, then you would have a weight of 2 for pres A and 1 for pres B. The weight of fixation (condition 0) is unimportant. I can't tell from the error msg below whether the error is caused by the weighting or by the FIR. Does the FIR run ok when it is not weighted? Are there any task weights that are 0? doug Katie Bettencourt wrote: Ah, what I want is the 2nd one then. I was trying to do this in freesurfer v 4.5 but I can't figure out how to use the 4th column in a way that doesn't crash during selxavg3-sess and there isn't much on the wiki about how to use it, what sorts of numbers are acceptable in the 4th column? I have 6 conditions plus fixation. one condition I want to be ignored (so I set the weight to 0), and then I want an increase as set size increases but with a plateau at large set sizes. I tried weighting them as whole numbers above 1 (which was what fixation was set to), weighing them as all less than 1 (but with fixation still as 1), weighing them less than 1 and so that combined they add up to 1 (fixation still as 1), but all errored our in selxavg3-sess. the same data analyzes fine unweighted (all 1s in the 4th column of the paradigm file). This is the output I get when I try to change the 4th column of the paradigm file: selxavg3-sess -s 101103TM_supIPS -df supIPS.dir -analysis supIPS-fir-weighted -overwrite -- selxavg3-sess logfile is /home/kcb/mri-space/supIPS_loc/log/selxavg3-sess-bold-supIPS-fir-weighted-101207145505.log -- --- /home/kcb/mri-space/101103TM_supIPS Tue Dec 7 14:55:05 EST 2010 anadir = /home/kcb/mri-space/101103TM_supIPS/bold/supIPS-fir-weighted analysis supIPS-fir-weighted alread exists for 101103TM_supIPS ... reanalyzing (deleting old analysis) -- --- 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 1984-2010 The MathWorks, Inc. Version 7.10.0.499 (R2010a) 64-bit (glnxa64) February 5, 2010 To get started, type one of these: helpwin, helpdesk, or demo. For product information, visit www.mathworks.com http://www.mathworks.com http://www.mathworks.com. /usr/local/freesurfer4.5/fsfast/toolbox/fast_selxavg3.m $Id: fast_selxavg3.m,v 1.55.2.8 2009/04/17 20:09:46 greve Exp $ outtop = /home/kcb/mri-space Extension format = nii UseFloat = 0 INFO: mask is not set, setting to brain 1 act_vs_fix-delay.mat Ignoring stimulus duration for FIR model Ignoring stimulus duration for FIR model Ignoring stimulus duration for FIR model Ignoring stimulus duration for FIR model Ignoring stimulus duration for FIR model Ignoring stimulus duration for FIR model Excluding 2 points nruns = 2 autostimdur = 0 outanadir = /home/kcb/mri-space/101103TM_supIPS/bold/supIPS-fir-weighted Found 48212/124416 (38.8) voxels in mask Creating Design Matrix Ignoring
[Freesurfer] looking for load dependent effects - task regressors?
Hi all, I was running an event-related analysis where the number of targets change, and I would really like to find an area that tracks their behavioral performance so that it would increase as set size increases, but then level off when performance does. Basically I have 5 set sizes, 1,2,3,4,6 items. performance increases to set size 4 then plateaus. And I want to find an area of the brain that reflects this same pattern. For now, I've been looking at areas that are more active for the higher set sizes than lower ones, but I'd really like to weight the set sizes by their performance so that where performance is flat, we'd see flat activity too. Does that make sense? I see that in Freesurfer version 5 you can use external task regressors, is that what I want to use? And if so, how do I do that? Is there any way to do this in version 4.5? Katie ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] Questions about event related processing and selxavg-sess and selxavg3-sess
Ok, so looking at the FIR analysis, when I advance it to time point 5, I see my activation (yay!) but does this mean my timewindow, etc is set up wrong, or is this just something you have to do when you do a FIR analysis? Katie On Wed, Nov 3, 2010 at 7:05 PM, Douglas N Greve gr...@nmr.mgh.harvard.eduwrote: The FIR does not assume a shape to the HRF but fits each point within the given time window. You might not be seeing activation for several reasons. FIRs are much less efficient than gamma functions. Also, by default, the FIR analysis gives you a sig map at each time point in the FIR, so you might be looking at the activation 1.5 sec *before* stimulus onset (so it would be a good thing not to see any activation!). Try advancing the time point from the overlay config window. You can see the map from the gamma and the timecourse from the FIR with something like tksurfer-sess -analysis fir-analysis -map-analysis gamma-analysis ... I'm not sure about the diffs with version 3. Why are you using such an old version? doug Katie Bettencourt wrote: Hi all, I've been trying to analyses both an event related and block design experiments and have noticed a couple things that are confusing me and I would appreciate any help anyone could give me. 1. In trying do the event-related analysis, I'm am a bit confused by the FIR vs Gamma analysis and the use of the time window and tprestim in the FIR analysis. I have an experiment with 6 set size conditions and 1 fixation condition. each trial is 6s long with a TR of 1.5 I have run both of these commands: mkanalysis-sess.new -analysis supIPS_loc -TR 1.5 -paradigm supIPS.dat -designtype event-related -funcstem fmc -motioncor -runlistfile supIPSruns.txt -inorm -nskip 2 -nconditions 6 -gammafit 2.25 1.25 mkanalysis-sess.new -analysis supIPS_loc -TR 1.5 -paradigm supIPS.dat -designtype event-related -funcstem fmc -motioncor -runlistfile supIPSruns.txt -inorm -nskip 2 -nconditions 6 -tprestim 2 -timewindow 20 The FIR gives me a time course window, which makes me think that perhaps that is the one I want to use, but it shows very little activation. This data has been previously analyzed in Brain Voyager, so I know it's not a case of the conditions not actually causing activation, but for some reason, the FIR analysis doesn't show any. I'm not sure if this is due to a bad time window/tprestim settings, or something else. However the gamma fit analysis shows a bunch of activity where I expect to see it, but no time course window. (attached are pngs of the differences for the act_vs_fixation comparison). 2. In addition, in both the event related (gamma) and a normal block design (different experiment) I get very different results (at least for certain comparisons) depending on whether I use selxavg-sess (with stxgrinder-sess for each contrast) or selxavg3-sess. The differences are shown in the attached pngs (act_vs_fix-gamma.png (which is the selxavg-sess and stxgrinder-sess analysis and act_vs_fix-gamma-selxavg3). In the block design, both selxavg3 and selxavg (+stxgrinder) give me very similar activation when comparing two non-null conditions (ie. shape_vs_noise) but very different (and similar to the differences in the attached pictures) activations when comparing against the null (ie shape_vs_fix or noise_vs_fix). What am I doing wrong here? Thanks for your help! Katie ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- 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 The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http
Re: [Freesurfer] Questions about event related processing and selxavg-sess and selxavg3-sess
I'm not sure about the diffs with version 3. Why are you using such an old version? I'm not sure I understand your question, why am I using the old version selxavg-sess or selxavg3-sess? I'm using Freesurfer 4.5, but I tried using selxavg-sess because I was confused by the results I was getting from selxavg3-sess (which is what the wiki says to use), and I was used to using selxavg-sess in my old lab, which was probably because we were using a much older version of Freesurfer. I assumed that selxavg3-sess was the newer version as it didnt' seem to need to have stxgrinder done on it to get maps out. am I wrong? It really is only when you compare against the baseline condition that you see differences in the two, but the selxavg3-sess is what is giving me the really weird whole brain more active for baseline maps. Katie doug Katie Bettencourt wrote: Hi all, I've been trying to analyses both an event related and block design experiments and have noticed a couple things that are confusing me and I would appreciate any help anyone could give me. 1. In trying do the event-related analysis, I'm am a bit confused by the FIR vs Gamma analysis and the use of the time window and tprestim in the FIR analysis. I have an experiment with 6 set size conditions and 1 fixation condition. each trial is 6s long with a TR of 1.5 I have run both of these commands: mkanalysis-sess.new -analysis supIPS_loc -TR 1.5 -paradigm supIPS.dat -designtype event-related -funcstem fmc -motioncor -runlistfile supIPSruns.txt -inorm -nskip 2 -nconditions 6 -gammafit 2.25 1.25 mkanalysis-sess.new -analysis supIPS_loc -TR 1.5 -paradigm supIPS.dat -designtype event-related -funcstem fmc -motioncor -runlistfile supIPSruns.txt -inorm -nskip 2 -nconditions 6 -tprestim 2 -timewindow 20 The FIR gives me a time course window, which makes me think that perhaps that is the one I want to use, but it shows very little activation. This data has been previously analyzed in Brain Voyager, so I know it's not a case of the conditions not actually causing activation, but for some reason, the FIR analysis doesn't show any. I'm not sure if this is due to a bad time window/tprestim settings, or something else. However the gamma fit analysis shows a bunch of activity where I expect to see it, but no time course window. (attached are pngs of the differences for the act_vs_fixation comparison). 2. In addition, in both the event related (gamma) and a normal block design (different experiment) I get very different results (at least for certain comparisons) depending on whether I use selxavg-sess (with stxgrinder-sess for each contrast) or selxavg3-sess. The differences are shown in the attached pngs (act_vs_fix-gamma.png (which is the selxavg-sess and stxgrinder-sess analysis and act_vs_fix-gamma-selxavg3). In the block design, both selxavg3 and selxavg (+stxgrinder) give me very similar activation when comparing two non-null conditions (ie. shape_vs_noise) but very different (and similar to the differences in the attached pictures) activations when comparing against the null (ie shape_vs_fix or noise_vs_fix). What am I doing wrong here? Thanks for your help! Katie ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- 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 The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] Questions about event related processing and selxavg-sess and selxavg3-sess
In fact, I had to use selxavg-sess and not selxavg3-sess to do the FIR analysis because fast-selxavg3-sess failed during the FIR analysis (I dont' have the error on me right now, but I can send it in tomorrow if it's important). Katie On Thu, Nov 4, 2010 at 12:29 PM, Katie Bettencourt kc...@bu.edu wrote: I'm not sure about the diffs with version 3. Why are you using such an old version? I'm not sure I understand your question, why am I using the old version selxavg-sess or selxavg3-sess? I'm using Freesurfer 4.5, but I tried using selxavg-sess because I was confused by the results I was getting from selxavg3-sess (which is what the wiki says to use), and I was used to using selxavg-sess in my old lab, which was probably because we were using a much older version of Freesurfer. I assumed that selxavg3-sess was the newer version as it didnt' seem to need to have stxgrinder done on it to get maps out. am I wrong? It really is only when you compare against the baseline condition that you see differences in the two, but the selxavg3-sess is what is giving me the really weird whole brain more active for baseline maps. Katie doug Katie Bettencourt wrote: Hi all, I've been trying to analyses both an event related and block design experiments and have noticed a couple things that are confusing me and I would appreciate any help anyone could give me. 1. In trying do the event-related analysis, I'm am a bit confused by the FIR vs Gamma analysis and the use of the time window and tprestim in the FIR analysis. I have an experiment with 6 set size conditions and 1 fixation condition. each trial is 6s long with a TR of 1.5 I have run both of these commands: mkanalysis-sess.new -analysis supIPS_loc -TR 1.5 -paradigm supIPS.dat -designtype event-related -funcstem fmc -motioncor -runlistfile supIPSruns.txt -inorm -nskip 2 -nconditions 6 -gammafit 2.25 1.25 mkanalysis-sess.new -analysis supIPS_loc -TR 1.5 -paradigm supIPS.dat -designtype event-related -funcstem fmc -motioncor -runlistfile supIPSruns.txt -inorm -nskip 2 -nconditions 6 -tprestim 2 -timewindow 20 The FIR gives me a time course window, which makes me think that perhaps that is the one I want to use, but it shows very little activation. This data has been previously analyzed in Brain Voyager, so I know it's not a case of the conditions not actually causing activation, but for some reason, the FIR analysis doesn't show any. I'm not sure if this is due to a bad time window/tprestim settings, or something else. However the gamma fit analysis shows a bunch of activity where I expect to see it, but no time course window. (attached are pngs of the differences for the act_vs_fixation comparison). 2. In addition, in both the event related (gamma) and a normal block design (different experiment) I get very different results (at least for certain comparisons) depending on whether I use selxavg-sess (with stxgrinder-sess for each contrast) or selxavg3-sess. The differences are shown in the attached pngs (act_vs_fix-gamma.png (which is the selxavg-sess and stxgrinder-sess analysis and act_vs_fix-gamma-selxavg3). In the block design, both selxavg3 and selxavg (+stxgrinder) give me very similar activation when comparing two non-null conditions (ie. shape_vs_noise) but very different (and similar to the differences in the attached pictures) activations when comparing against the null (ie shape_vs_fix or noise_vs_fix). What am I doing wrong here? Thanks for your help! Katie ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- 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 The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent
[Freesurfer] retinotopy in Freesurfer 5.0
I had a couple questions relating to how to perform retinotopic analysis and view the results in the new Freesurfer 5.0 distribution (bear with me, previous I was using Freesurfer 4.0.2, so there's probably a bunch of changes that are confusing me). 1. I was able to create a new analysis with mkanalysis-sess, and compute the stats with selxavg3-sess. But I'm a bit confused on displaying the data. When I use tksurfer-sess I can see the sig map (which isn't really helpful for determining regions) or use the -map angle command and see something that looks a bit like retintopy but in the heat overlay display type (sorry, not sure the correct terminology here) instead of the standard color wheel. When I try to change the overlay display settings to color wheel and complex it becomes all a single color (green). Perviously I also had to change the phase encoding display settings to 2.0 plus some offset (which I can't actually do right now do to a bug I'm having), but you would at least still see some color differences with the 1.0 phase setting, and I'm not getting any of that. What am I doing wrong? 2. Previously, you could load the brain with tksurfer (not tksurfer-sess) and load data through overlays and loading the real and imag .w files created with paint-sess. I know that now paint-sess isn't needed, but when I try to load the real.nii and imag.nii or even angle.nii this doesn't work. Can you only load retinotopic data through tksurfer-sess command line now? 3. When I try to change the fthresh in the command line, it seems to read it, but then overwrite it with retinotopic data. Is there no way in the command line to change the fthresh value? 4. In the analysis example I was following you had to create a separate analysis for lh and rh, why is this? thanks! Katie ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] retinotopy - Freesurfer 5.0 problem
I was trying to do retinotopic analysis on a dataset using the new Freesurfer v5.0.0 on a 64bit Linux (Red Hat 4.1.2-48 CentOS 5.5) computer and have run across a problem. I set up the analysis using mkanalysis-sess as suggested in an earlier email to the list, but when I try to run selxavg3-sess it errors out. The commands I ran were: mkanalysis-sess -analysis retino26-lh -surface self lh -fwhm 0 -retinotopy 55.467 -paradigm retino.par -TR 2.6 -runlistfile polar_runs.txt selxavg3-sess -a retino26-lh -s spicyrobin -df retino-dirfile It gets through all the preprocessing and then this is the output (the matlab error is one I know about, if that is causing the problem I can talk to our IT here about getting it fixed): preproc-sess done --- /home/kcb/mri-space/spicyrobin Tue Aug 31 15:29:38 EDT 2010 anadir = /home/kcb/mri-space/spicyrobin/bold/retino26-lh 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 1984-2010 The MathWorks, Inc. Version 7.10.0.499 (R2010a) 64-bit (glnxa64) February 5, 2010 To get started, type one of these: helpwin, helpdesk, or demo. For product information, visit www.mathworks.com. Warning: Executing startup failed in matlabrc. This indicates a potentially serious problem in your MATLAB setup, which should be resolved as soon as possible. Error detected was: MATLAB:TooManyInputs Too many input arguments. In matlabrc at 227 /usr/local/freesurfer/fsfast/toolbox/fast_selxavg3.m $Id: fast_selxavg3.m,v 1.88.2.2 2010/07/16 15:31:24 greve Exp $ outtop = /home/kcb/mri-space Extension format = nii nruns = 4 autostimdur = outanadir = /home/kcb/mri-space/spicyrobin/bold/retino26-lh Found 117359/125110 (93.8) voxels in mask Creating Design Matrix ... creation time = 0.008 sec DoMCFit = 1 ntptot = 1024, nX = 36, DOF = 988 Saving X matrix to /home/kcb/mri-space/spicyrobin/bold/retino26-lh/Xtmp.mat ??? Error using == svd Input to SVD must not contain NaN or Inf. Error in == cond at 40 s = svd(A); Error in == fast_selxavg3 at 247 XCond = cond(XtX); -- ERROR: fast_selxavg3() failed\n thanks, Katie ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] keyboard problem in freesurfer
Centos 5.5, which seems to be the newest one. I guess I could try reinstalling it. Katie On Thu, Aug 5, 2010 at 9:40 AM, Bruce Fischl fis...@nmr.mgh.harvard.eduwrote: thanks Don, Katie: what OS are you running? Bruce On Wed, 4 Aug 2010, Don Hagler wrote: We had exactly that problem on machines running RedHat 5, but it was solved by reinstalling with the latest CentOS. From: kc...@bu.edu Date: Wed, 4 Aug 2010 15:44:52 -0400 To: fis...@nmr.mgh.harvard.edu CC: freesurfer@nmr.mgh.harvard.edu; ni...@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] keyboard problem in freesurfer Nope, no errors when tksurfer starts, and I've tried running it with both my own data/folder and with the tutorial data/folders, and have the same problem. I don't currently have freesurfer installed on a laptop, and the only laptop I have access to is a mac (whereas I am using linux for most of my analysis). I can see what happens if I try installing it on the mac and see if it has the same problem, but I assume it's somehow specific to my linux machine if others aren't having the same problem. Katie On Wed, Aug 4, 2010 at 3:19 PM, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote: Hi Katie, can you replicate this problem on a laptop? If so, maybe you want to swing by MGH with it and we can take a look? There are no errors when tksurfer starts? Bruce On Wed, 4 Aug 2010, Katie Bettencourt wrote: Ok, I tried to unset the FSLTCLSH variable (which is the only one that came up when I grep TCL) to see if that allowed me to use keyboard input with tksurfer, but it didn't work. I really need to be able to use the keyboard with tksurfer so that I can save label files and rgbs, etc. Is there any way I can get this fixed? Please? Katie The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] keyboard problem in freesurfer
Ok, I tried to unset the FSLTCLSH variable (which is the only one that came up when I grep TCL) to see if that allowed me to use keyboard input with tksurfer, but it didn't work. I really need to be able to use the keyboard with tksurfer so that I can save label files and rgbs, etc. Is there any way I can get this fixed? Please? Katie ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] keyboard problem in freesurfer
Nope, no errors when tksurfer starts, and I've tried running it with both my own data/folder and with the tutorial data/folders, and have the same problem. I don't currently have freesurfer installed on a laptop, and the only laptop I have access to is a mac (whereas I am using linux for most of my analysis). I can see what happens if I try installing it on the mac and see if it has the same problem, but I assume it's somehow specific to my linux machine if others aren't having the same problem. Katie On Wed, Aug 4, 2010 at 3:19 PM, Bruce Fischl fis...@nmr.mgh.harvard.eduwrote: Hi Katie, can you replicate this problem on a laptop? If so, maybe you want to swing by MGH with it and we can take a look? There are no errors when tksurfer starts? Bruce On Wed, 4 Aug 2010, Katie Bettencourt wrote: Ok, I tried to unset the FSLTCLSH variable (which is the only one that came up when I grep TCL) to see if that allowed me to use keyboard input with tksurfer, but it didn't work. I really need to be able to use the keyboard with tksurfer so that I can save label files and rgbs, etc. Is there any way I can get this fixed? Please? Katie The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] keyboard problem in freesurfer
Nope, all I get is a Warning: No colortable found! Katie On Mon, Jul 26, 2010 at 3:34 PM, Bruce Fischl fis...@nmr.mgh.harvard.eduwrote: Hi Katie, do you see any errors in the window that you typed the tksurfer command? Bruce On Mon, 26 Jul 2010, Katie Bettencourt wrote: I am having a problem others have had before, but that I can't seem to see any resolution to in the archives. When I open tksurfer I can't use my keyboard to input anything. I don't get any errors, it just doesn't let me type or delete anything, making it next to impossible to use. I'm running Freesurfer4.5.0 on linux - Red Hat 4.1.2-48 (Centos 5.5) I checked my .cshrc file and couldn't find any issues there. Any other help please? Katie The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] keyboard problem in freesurfer
I am having a problem others have had before, but that I can't seem to see any resolution to in the archives. When I open tksurfer I can't use my keyboard to input anything. I don't get any errors, it just doesn't let me type or delete anything, making it next to impossible to use. I'm running Freesurfer4.5.0 on linux - Red Hat 4.1.2-48 (Centos 5.5) I checked my .cshrc file and couldn't find any issues there. Any other help please? Katie ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] within subject regression analysis and qdec
Hi, I'm still trying to figure out how to run a regression analysis using functional data. I found the information in using qdec, however, the example uses a between subject design (with age/gender) and looks at thickness measures. I tried creating a qdec.table.dat, but I am unsure how to do it with a within subject design, as when I ended up with it reading the file as me having 16 subjects instead of 8. What I have is a discrete variable of load (high and low) and a continuous variable of set size (1,3,6), but I want to correlate the data with the performance at each set size for each load as well as load. This is what my qdec table looked like: fsid dist k1k3 k6 subj1 low 1 2.94.0 subj1 high 0.81.32.0 subj2 low 0.9 2.9 5.7 subj2 high 0.9 1.91.4 ... subj8 low 0.8 2.42.5 subj8 high0.8 1.4 2.7 Can anyone tell me how to appropriately structure this to do what I want? Thank you! Katie ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
