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.
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
analy
at 4:50 PM, Douglas N Greve
wrote:
>
> 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:
> >
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 tra
> 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
> tal
PM, Bruce Fischl 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
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
>
> cheers
>
> Bruce
>
>
> On Tue, 4 Sep 2012, Katie Bettencourt wrote:
>
> Hrm. Ok, is there any way to view d
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 wrote:
> 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'
)?
Katie
On Wed, Sep 5, 2012 at 2:02 PM, Katie Bettencourt wrote:
> 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
> wrote:
>
>> Ok, I am trying to use the select
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
gt; 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
>
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 fol
ing 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 wrote:
> So I was looking into mri_label2label and it suggests you can map a label
> to talairach by using --trgsubject talairach, which I thought
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,
w
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
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-s
sts 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
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 wrote:
> No, each condition has at least 3 instances of it in each run.
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
wrote:
> Can you send me the Xtmp.mat file from the outputdirectory?
> doug
>
> On 02/28/2013 07:34 AM, Katie Bettencourt wrote:
>
>> Still
ey 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 th
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
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
nalysis on
that?
Katie
On Tue, Jul 26, 2011 at 11:31 AM, Douglas N Greve 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. I
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
> rtview. It is not in the distribution, but you can get it from
>
> ftp://surfer.nmr.mgh.harvard.**edu/transfer/outgoing/flat/**greve/rtview<ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/rtview>
>
> Look at the --help to see how to run it.
>
> doug
>
>
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
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 F
Nope, all I get is a "Warning: No colortable found!"
Katie
On Mon, Jul 26, 2010 at 3:34 PM, Bruce Fischl wrote:
> 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:
>
l or tcl or something. Nick: any ideas?
> > On Tue, 27 Jul
> > 2010, Katie Bettencourt wrote:
> >
> > > Nope, all I get is a "Warning: No colortable found!"
> > >
> > > Katie
> > >
> > > On Mon, Jul 26, 2010 at 3:34 PM, Bruce Fisch
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
ie,
> 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
pecific to my
>> linux machine if others aren't having the same problem.
>>
>>
>> Katie
>>
>> On Wed, Aug 4, 2010 at 3:19 PM, Bruce Fischl
>> wrote:
>>
>>
>> Hi Katie,
>>
>> can you replicate this problem on a laptop? If so
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
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 mka
s 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.
Ka
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 Bettenco
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
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 i
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 gu
e 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
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
&g
xternal 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 fi
dition 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
ghting. 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
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
Can you tell me how to check that because I"m 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 wrote:
> Hi Maryam,
>
> You should check your sp
yze_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
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
ime 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
>>
>>
>
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
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:
>
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 tim
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
d". 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
&
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 acti
e'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
>> wrot
Ok, thanks!
Katie
On Fri, Jul 1, 2011 at 2:54 PM, Bruce Fischl wrote:
> not really
>
> On Fri, 1 Jul 2011, Katie Bettencourt wrote:
>
> 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 num
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 an
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