lists values between 0 and 255.
The MNC is unsigned byte.
Caspar
2014/1/22 Bruce Fischl
> how do you know that the values were there before? Try running mri_diff on
> the .nii and the .mnc and see if it finds any differences
>
> Bruce
>
>
> On Wed, 22 Jan 2014, Caspar
Bruce Fischl
> Hi Caspar
>
> hmm, I don't know why that would be the case. Can you send the full
> command line and screen output?
> cheers
> Bruce
>
> On Wed, 22 Jan 2014, Caspar M. Schwiedrzik wrote:
>
> Hi!
>> I am having some troubles converting MNC f
Hi!
I am having some troubles converting MNC files to NII while preserving the
exact values in the MNC file. I have tried to use mri_convert and mnc2nii,
but in both cases, the values in the file output get changed. The help of
mri_convert mentions that the output for MNC files may not work.
Is the
Hi Freesurfer Experts,
I was wondering what the best way to apply two registration matrices to the
same data set would be, ideally without re-slicing after the first
registration?
Thanks, Caspar
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h
> one and I'll verify it is the right thing.
> doug
>
>
>
> On 01/09/2014 10:21 PM, Caspar M. Schwiedrzik wrote:
>
>> Hi Doug, I found a way to build it in myself. I am using
>> spatialsmooth-sess from v5.1. I need to smooth some functional data that I
>>
Thursday, January 9, 2014, Douglas Greve wrote:
>
> No, sorry. Why are you using such an old version?
> doug
>
>
>
>
>
> On 1/9/14 5:26 PM, Caspar M. Schwiedrzik wrote:
>
> Hi Doug,
> do you have a version of spatialsmooth-sess with the option to set
Hi Doug,
do you have a version of spatialsmooth-sess with the option to set mask
file name?
Thanks, Caspar
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The information in this e-
Hi Freesurfer Experts,
I would like to do a whole brain group analysis of functional data with
mri_glmfit using a custom volume space instead of the MNI space Freesurfer
provides. This is for primate data.
I was wondering what the best way to do this would be.
I have a T1 template in volume space
e with
>> the --replace option in your volumes.
>>
>> --replace V1 V2 : replace voxels=V1 with V2
>>
>> For label descriptions you can loook up
>> $FREESURFER_HOME/FreeSurferColorLUT.txt.
>>
>> --Lilla
>>
>>
olorLUT.txt.
>
> --Lilla
>
>
> On Mon, 6 Jan 2014, Caspar M. Schwiedrzik wrote:
>
> Hi!
>> I have a volume in MNC format that contains labels, and I was wondering
>> whether there is a way to quickly convert them into Freesurfer labels?
>> Within the MNC file, v
Hi!
I have a volume in MNC format that contains labels, and I was wondering
whether there is a way to quickly convert them into Freesurfer labels?
Within the MNC file, voxels belonging to one label all have the same
intensity value, which is, however, not in RGB space but just a single
number, rang
and see if you get 1s and 0s. If not, then try
> that file as input. You can also try fscalc, something like
>
> fscalc input.nii mul mask.nii -o output.nii
>
> should accomplish the same thing
>
> doug
>
>
>
>
>
> On 12/30/13 1:12 PM, Caspar M. Schwiedrzik
os in the image.
Is there a way to rescale the file?
Thanks, Caspar
2013/12/30 Douglas Greve
> And macaque_25_model-MNI.nii is the non-binary image? And
> macaque_stripped_mask.nii.gz is the binary mask? If so, the command looks
> right to me.
> doug
>
>
> On 12/30/13 12:08
nii.gz or mgz files.
Caspar
2013/12/30 Douglas Greve
>
> what is your command line and terminal output?
>
>
>
> On 12/30/13 10:22 AM, Caspar M. Schwiedrzik wrote:
>
> Hi Freesurfer Experts,
> I am trying to apply a mask that I made with FSL's bet to a NIFTI fil
Hi Freesurfer Experts,
I am trying to apply a mask that I made with FSL's bet to a NIFTI file that
I got from someone else.
The mask looks fine, the NIFTI file is in float format, does not contain
NaNs or negative values, but the overall values are all pretty low (in the
40ies). When I try to apply
when I ran it with --checkopts.
Caspar
2013/10/30 Douglas N Greve
> OK, I put a centos4 build there, that should work
>
>
> On 10/30/2013 11:05 AM, Caspar M. Schwiedrzik wrote:
>
>> Hi Doug,
>>
>> that would be Red Hat Enterprise Linux Server release 5.9 (Tikan
Hi Doug,
that would be Red Hat Enterprise Linux Server release 5.9 (Tikanga)
Caspar
2013/10/30 Douglas N Greve
> what OS platform are you using?
>
> On 10/30/2013 11:00 AM, Caspar M. Schwiedrzik wrote:
>
>> Hi Doug,
>>
>> thanks for the advice.
>> When I
aspar
2013/10/30 Douglas N Greve
>
>
>
>
>
> On 10/30/2013 08:51 AM, Caspar M. Schwiedrzik wrote:
>
>> Hi Doug,
>> thank you very much!
>> I have two follow-up questions for your two suggestions:
>> 1) If I want to use mri_glmfit-sim but my conjunctions
than using cached
> data.
>
> 2. Create cached data by running mri_mcsim. This may take longer than
> #1, but once you have the cached data you do not need to run it again,
> which could be useful if you are going to do more analyses with this
> template
>
> doug
>
>
Hi,
I have a question regarding cluster size thresholding using mri_glmfit-sim.
Namely, I have a sig.nii conjunction map that I made with mri_concat.
The analyses that serve as input to the conjunction map are done on a
custom surface template.
If I want to run mri_glmfit-sim, how would that work?
Hi Freesurfer Experts,
is it possible to run a 2x2 repeated measures ANOVA for functional data on
the surface in Freesurfer (both factors have two levels and are fully
within subjects)?
If not, is there a way to use mri_glmfit-sim on results calculated in
Matlab to correct for multiple comparisons?
Hi Freesurfer experts,
I am running a group analysis of functional data on a custom
template/average subject for which I do not have a talairach.xfm file, an
orig.mgz nor aparc data (it is a primate dataset). I ran into some error
messages when trying to use mri_glmfit-sim.
1) I get an error messa
mgh/rstd.mgh
> doug
>
> On 10/09/2013 01:39 PM, Caspar M. Schwiedrzik wrote:
>
>> Hi Doug,
>> this is coming from a seed-based resting state analysis. I would like to
>> show effect size instead of p-values.
>> I thought you calculate them from the slopes or the t-
e this
> is a one-sample group mean (design matrix a column of all 1s). What are you
> trying to compute the correlation between? Or do you just want to convert
> the p-values to a correlation coefficient?
>
>
>
> On 10/09/2013 01:26 PM, Caspar M. Schwiedrzik wrote:
>
>
Hi Doug, did you already have a chance to look into this? Thanks, Caspar
2013/10/4 Caspar M. Schwiedrzik
> Done. Thank you very much for looking into this.
> Caspar
>
>
> 2013/10/4 Douglas N Greve
>
>> Can you tar up you glmfit dir and drop it to me on our file drop?
&
> cheers
> Bruce
>
>
>
> On Fri, 4 Oct 2013, Caspar M. Schwiedrzik wrote:
>
> Hi Bruce,
>> another update: I now set more than 2000 control points which
>> significantly
>> improved the pial surface. I am still fighting with a few places though,
>>
Done. Thank you very much for looking into this.
Caspar
2013/10/4 Douglas N Greve
> Can you tar up you glmfit dir and drop it to me on our file drop?
>
>
> On 10/04/2013 05:29 PM, Caspar M. Schwiedrzik wrote:
>
>> Hi Doug,
>>
>> thank you very much for sendin
> On 10/04/2013 03:33 PM, Caspar M. Schwiedrzik wrote:
>
>> Hi Doug,
>> I guess it boils down to the question how to get a group PCC map after a
>> RFX GLM?
>> Using -m PCC seems to only give me a map per subject. Are you calculating
>> PCC from the t- value
Hi Doug,
I guess it boils down to the question how to get a group PCC map after a
RFX GLM?
Using -m PCC seems to only give me a map per subject. Are you calculating
PCC from the t- values? Thanks,
Caspar
On Thursday, October 3, 2013, Caspar M. Schwiedrzik wrote:
> Hi Doug,
>
> On
. See occipital lobe.
Caspar
2013/10/3 Bruce Fischl
> Hi Caspar,
>
> that's probably part of the problem. Is this human data? If you actually
> run it at 1mm (conforming it) does it work better?
>
> Bruce
>
>
> On Thu, 3 Oct 2013, Caspar M. Schwiedrzik wrote:
>
y not use -m pcc?
Isn't that giving me a map per subject? How do I get the group map that is
consistent with the results of mri_glmfit run on ces.nii?
Thanks, Caspar
>
> doug
>
>
> On 10/03/2013 01:10 PM, Caspar M. Schwiedrzik wrote:
>
>> Hi Doug,
>> I loaded
It is originally 0.5x0.5x0.5 mm but we are pretending it's 1x1x1 mm.
Caspar
2013/10/3 Bruce Fischl
> what resolution?
>
> On Thu, 3 Oct 2013, Caspar M. Schwiedrzik wrote:
>
> This was a fairly regular MPRAGE, unfortunately not very well optimized
>> for
>> c
drop from above 90 to below 90.
Caspar
2013/10/3 Bruce Fischl
> h. Can you tell us more about the acquisition?
>
> On Thu, 3 Oct 2013, Caspar M. Schwiedrzik wrote:
>
> the white matter is mostly between 100 and 110 in these regions. at least
>> in
>> the cente
. However, I'd still like to get pcc maps from them, if there is a
way to do so in FSFAST.
Thanks, Caspar
2013/10/3 Douglas N Greve
>
> On 10/03/2013 10:39 AM, Caspar M. Schwiedrzik wrote:
>
>> Hi Doug,
>>
>> when I run a two-tailed t-test against 0 in Matlab on the
ogical variability over the
> brain)
>
>
> On Thu, 3 Oct 2013, Caspar M. Schwiedrzik wrote:
>
> Thanks, Bruce. The problem is fairly extensive. There is no way to do
>> normalize grey matter intensity (the white surface looks pretty
>> good)?Caspar
>>
>>
> doesn't get out far enough.
>
> cheers
> Bruce
> On Thu, 3 Oct 2013, Caspar M. Schwiedrzik wrote:
>
> Hi Freesurfer Experts,
>> I am working on a fairly noisy and inhomogeneous MPRAGE T1 and I am having
>> trouble getting the pial surface to go all the way throu
Hi Freesurfer Experts,
I am working on a fairly noisy and inhomogeneous MPRAGE T1 and I am having
trouble getting the pial surface to go all the way through the grey matter.
Please see screenshot attached. These data were acquired with a surface
coil and the grey matter varies a lot in intensity. I
ry to selxavg3-sess on the single subject
level). How would I get those?
Thanks, Caspar
2013/10/1 Douglas N Greve
>
> On 10/01/2013 01:13 PM, Caspar M. Schwiedrzik wrote:
> > Hi Doug,
> > it would be great if you could give me some further advise on the
> > group analysis of
Hi Doug,
it would be great if you could give me some further advise on the group
analysis of functional connectivity maps.
Specifically, I am trying to get PCC maps for certain seeds, and am not
planning any comparison between groups.
Following your previous advise, I am running isxconcat-sess with
this up but I'd need to know where I can find
this information.
Thanks, Caspar
2013/9/24 Caspar M. Schwiedrzik
> Hi Doug,
> thanks for the clarification.
> If I understand your instructions and the walktrough correctly, I would be
> running something like this after isxconca
.,
2007. Intrinsic functional architecture in the anaesthetized monkey brain.
Nature. 447:83-86)?
Thanks, Caspar
2013/9/23 Douglas N Greve
>
> Use ppc.nii as input to mri_glmfit and proceed as usual with the group
> analysis.
> doug
>
>
>
> On 09/23/2013 12:31 PM, Cas
ess and continue as normal with
> the group analysis
> doug
>
> On 09/23/2013 09:50 AM, Caspar M. Schwiedrzik wrote:
> > Hi Freesurfer Experts,
> > I am trying to calculate group pcc maps for resting state functional
> > connectivity analyses. Unfortunately, the wa
Hi Freesurfer Experts,
I am trying to calculate group pcc maps for resting state functional
connectivity analyses. Unfortunately, the walkthrough does not cover this.
I found several posts regarding this on the mailing list, but I am not sure
which one is the right way to go:
There is -m pcc in i
t (at least at the group level), that I cannot imagine that
> it will make much difference.
> doug
>
> On 09/19/2013 09:36 AM, Caspar M. Schwiedrzik wrote:
> > Hi Freesurfer Experts,
> > mkanalysis-sess seems to default to a FWHM of 20 for the smooting of
> > the ACF
Hi FreeSurfer Experts,
I am trying to run a group analysis with a custom fsaverage for which I do
not have a cortex.label file. It seems that in version 5.1, --cortex is
called by default. I did not find a flag to turn this off in the
documentation or the help.
Is there a way to run mri_glmfit with
Hi Freesurfer Experts,
mkanalysis-sess seems to default to a FWHM of 20 for the smooting of the
ACF (in version 5.1). I was wondering whether it makes sense to use the
same FWHM for volume and surface based analyses of functional data in
FSFAST? I seem to remember that the autocorrelations differ b
volume.
> Not sure that will work, but make sure to use --no-aseg
>
> doug
>
>
>
> On 8/19/13 8:43 PM, Caspar M. Schwiedrzik wrote:
>
> Hi Doug,
> I ran make_average_surface.no-aparc and identity matrices on my data, and
> I seems to have completed the averaging
if you display your results on those instead of on the
> inflated). If you are not going to display on the white or the pial, then
> you can just leave it as the identity
>
> doug
>
>
>
>
> On 08/19/2013 03:57 PM, Caspar M. Schwiedrzik wrote:
>
>> Hi Doug,
>>
//surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/make_average_surface.no-aparc
>
>
> On 08/19/2013 02:53 PM, Caspar M. Schwiedrzik wrote:
> > Hi Freesurfer experts,
> > I am trying to make an average surface from several monkey surfaces,
> > and I ran into a proble
Hi Freesurfer experts,
I am trying to make an average surface from several monkey surfaces, and I
ran into a problem with make_average_subject. Specifically, I do not have
an aparc file nor a talairach.xfm. It seems that these problems have come
up on the list before (
http://www.mail-archive.com/f
not sure whether others are experiencing this as well, but the
freesurfer wiki seems to be down.
caspar
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The information in this e-mai
I guess the solution is -nofill...
2013/7/20 Caspar M. Schwiedrzik :
> Hi Freesurfer Experts,
> I am working on a primate anatomy and I am having problems with the
> white matter filling in the temporal lobe in version 4.5.
> I manually edited wm.mgz and recreated filled.mgz using
Hi Freesurfer Experts,
I am working on a primate anatomy and I am having problems with the
white matter filling in the temporal lobe in version 4.5.
I manually edited wm.mgz and recreated filled.mgz using mri_fill. I
then manually edited filled.mgz.
However, when I then run autorecon-all -autorecon
Hi!
I am doing motion correction outside Freesurfer and would like to use
motion nuisance regressors in my GLM, which I run in FSFAST.
I am externally creating mcextreg.bhdr, mcextreg_000.blfoat and
mcextreg_000.hdr for analyses in Freesurfer v4.5, but I was wondering
whether I can use the same fil
Thanks, Doug!
Caspar
On Wednesday, June 26, 2013, Douglas N Greve wrote:
>
> They are accounted for as nuisance predictors in the GLM. They are not
> removed from the time series.
> doug
>
>
> On 06/26/2013 06:59 PM, Caspar M. Schwiedrzik wrote:
> > Hi Freesurfer exper
Hi Freesurfer experts,
I was wondering how exactly time point exclude files are used by FSFAST.
Are the time points removed from the time series before the GLM, or is
the time point exclude file used to build a nuisance predictor (as in
FSL's motion outliers routine,
http://fsl.fmrib.ox.ac.uk/fsl/f
Hi Freesurfers,
I am getting a segmentation fault with the 4.5 version of mri_convert
when trying to convert an AFNI BRIK file into nii.
This is my command line:
mri_convert -i input+orig.BRIK -o fde.nii --in_like f.nii
Strangely, I only get the segmentation fault when I run mri_convert in
a bash s
Hi Maria,
if the warp around is such that the wrapped part of the brain ends up
outside the brain but on the other side of the FOV, you can maybe fix it
partially (e.g., if the frontal cortex is wrapped to the back but not into
the occipital cortex). You would just need to copy the respective rows
same as -b 15)
>
> cheers
> Bruce
>
>
>
> On Fri, 31 May 2013, Caspar M. Schwiedrzik wrote:
>
>> yes, but recon-all just calls mri_segment with -mprage and mri_normalize
>> with -mprage.
>> I would like to know what -mprage does in these two function
gt;
> cheers,
> -MH
>
> --
> Michael Harms, Ph.D.
> ---
> Conte Center for the Neuroscience of Mental Disorders
> Washington University School of Medicine
> Department of Psychiatry, Box 8134
> 660 South Euclid Ave. Tel: 314-747-6173
ount for the lower SNR and increased CNR in the mprage. You'll need
> to look in the recon-all script for the details
>
> cheers
> Bruce
>
>
>
> On Thu, 30 May 2013, Caspar M. Schwiedrzik wrote:
>
> Hi!
>> Is there more documentation on what settings the mprage f
Hi!
Is there more documentation on what settings the mprage flag enables in
recon-all?
Specifically, I would be interested which individual steps it affects and
what the parameters are for each of the steps.
Thanks!
Caspar
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Fre
es the smallest p-value (and so implements
> Nichols). I think I'd to the multiple comparisons correction after
> conjunction (but I'd like to hear opinions). Not sure about the FWHM,
> probably take the max of the contrasts that go into it.
>
> doug
>
>
>
> On 05/24
lue at each voxel (this is what
> mri_concat does).
> doug
>
>
>
> On 05/24/2013 02:10 PM, Caspar M. Schwiedrzik wrote:
>>
>> Hi Doug,
>> I am trying to implement something like the MS/CN conjunction
>> suggested by Nichols.
>> For that, I am finding t
not sure about
> your fsfast question. There is nothing to automatically do it (ie,
> you'll need to run mri_concat)
> doug
> On 05/23/2013 03:06 PM, Caspar M. Schwiedrzik wrote:
>> Hi!
>> I am trying to do a conjunction analysis using mri_concat --conjunct
>> with
Hi!
I am trying to do a conjunction analysis using mri_concat --conjunct
with 2 to three sig.nii as input.
It seems to me that the resulting map is what Nichols et al. refer to
as MS/GN, i.e., a test against the global null (at least one effect).
Is that correct, and does that depends on v4.5 / 5.x
gt;
> 2013/5/17 Bruce Fischl :
>> Try leaving out the -i and -seg
>> Those are mandatory parameters and don't need hyphens
>>
>> On May 17, 2013, at 3:11 PM, "Caspar M. Schwiedrzik"
>> wrote:
>>
>>> Hi Matt and Bruce,
>>> sti
out the -i and -seg
> Those are mandatory parameters and don't need hyphens
>
> On May 17, 2013, at 3:11 PM, "Caspar M. Schwiedrzik"
> wrote:
>
>> Hi Matt and Bruce,
>> still the same problem. What about the fix that was mentioned in the
>> earlier
t fixes the problem.
>
> Matt.
>
> On 5/17/13 1:37 PM, "Caspar M. Schwiedrzik"
> wrote:
>
>>set threshold = `echo "7/10" | bc -l`
>>set segment_options = "-v -fillv -fillbg -wlo 104 -ghi 118 -whi 140
>>-n 4 -p $threshold -keep"
chl :
> Hi Caspar
>
> can you include the command line and all the output?
>
>
> Bruce
> On Fri, 17 May 2013, Caspar M. Schwiedrzik wrote:
>
>> filling ventricles
>> filling basal ganglia
>> using white lolim = 104.0
>> using gray hilim = 11
scussion on the mailing list, there
should be a fix available somewhere:
http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg18824.html
Thanks, Caspar
2013/5/17 Bruce Fischl :
> and what happens? Can you send the full screen output?
>
> On Fri, 17 May 2013, Caspar M. Schwiedrzik
our command line? You are probably better off setting gray_hi,
> gray_low, wm_hi, wm_low, etc...
>
> Bruce
> On Fri, 17 May 2013, Caspar M. Schwiedrzik wrote:
>
>> When I try to specify a different threshold using -p, mri_segment
>> reads in the threshold as the input vol
gt;sure what to advise you. Perhaps one of the other people on list who have
>>done a bunch can comment?
>>Bruce
>>On Fri, 17 May 2013, Caspar M. Schwiedrzik wrote:
>>
>>> Hi Bruce,
>>> I tried adding control points in the white matter in that region,
&g
ite matter).
>
>
> Bruce
>
> On Thu, 16 May 2013, Caspar M. Schwiedrzik wrote:
>
>> Hi Bruce,
>> ok.
>> But in theory, what would you recommend to get around the darkening
>> issue? Unfortunately, I do not have a field map available for this
>> data
white matter (original voxel size
0.5x0.5x0.5 mm).
Thanks, Caspar
2013/5/16 Bruce Fischl :
> Hi Caspar
>
> if it's primate I don't think I'm going to be able to help - you'll need
> someone more familiar with primate anatomy
>
> sorry
> Bruce
> On Thu
ce,
>
> Matt.
>
> On 5/16/13 11:43 AM, "Caspar M. Schwiedrzik"
> wrote:
>
>>Hi!
>>I am failing to get a proper pial surface in orbitofrontal cortex.
>>See attached screenshot.
>>This is NHP data, processed with version 4.5.
>>I am not sure how to
Dear Freesurfer Team,
when I am trying to set control points in tkmedit (FS 5.1 or 4.5) or to see
control points in Freeview (FS 5.1), I run into a strange problem when I
connect to our server through X11.
Namely, I cannot see the control points, although they are being set when I
place them (they
*[posting for colleagues, please write to them, not to me]
*
*
*
Research Assistant Position in Cognitive Neuroscience
Department of Neurology, School of Medicine, New York University
We are seeking a full-time Research Assistant to assist with cognitive
neuroscience experiments involving human
hm, I just realized that I should probably run selxavg3-sess with
-svres and then take the residuals from the res folder, right?
caspar
2013/2/22 Caspar M. Schwiedrzik :
> Dear Freesurfer experts,
> I am running some functional connectivity analyses using FSFAST in
> Freesurfer 5.1.
Dear Freesurfer experts,
I am running some functional connectivity analyses using FSFAST in
Freesurfer 5.1.
I would like to compare seed time courses (which I later use as
predictors) obtained after regular pre-processing with seed time
courses obtained after regressing out several nuisance paramet
trictly
> prohibited and may be unlawful. If you have received this e-mail
> unintentionally, please immediately notify the sender via telephone at
> (773)
> 406-2464 or email.
>
>
> On Tue, Feb 12, 2013 at 4:16 PM, Caspar M. Schwiedrzik
> wrote:
> > Hi Doug,
> > the
as to create ?h.sphere.reg
> doug
>
>
>
> On 02/12/2013 03:57 PM, Caspar M. Schwiedrzik wrote:
>
>> Hi Doug,
>> thank you very much.
>> One more question: From the documentation, I wasn't really sure whether
>> it would also be possible to do the analysis
t; directory structure.
>
> doug
>
>
> On 02/12/2013 07:55 AM, Caspar M. Schwiedrzik wrote:
> > Dear Freesurfer experts,
> > I am trying to prepare some NHP functional data for a whole brain
> > group analysis, and I was wondering which sequence of steps you would
&
Dear Freesurfer experts,
I am trying to prepare some NHP functional data for a whole brain group
analysis, and I was wondering which sequence of steps you would recommend,
given that the data cannot be processed with recon-all.
I have surfaces from 4 subjects, but one subject for which I do not hav
sorry, -log10(1) gives 0 of course.
caspar
2012/11/30 Caspar M. Schwiedrzik :
> Hi Doug and Sebastian,
> thanks for your input. I think I can confirm that it is the problem
> that Sebastian described. FS 5.1 uses betainc, which returns 0, even
> in Matlab R2011b.
> The workaround
uns do you
>> have? Is is a contrast that has a huge amount of power(eg, something vs
>> fixation)? Does it happen in other subjects? One path to debugging is to
>> run selxavg3-sess with -run-wise. This will create an analysis for each
>> run separately. You can then see whe
following:
mkanalysis-sess v1.64.2.1
mkcontrast-sess v1.17
selxavg3-sess v1.57
fast_selxavg3.m v1.100
Thank you very much!
Caspar
2012/11/27 Caspar M. Schwiedrzik :
> Hi Doug,
> I am afraid the p values are still too small in Free Surfer
> Linux-centos4_x86_64-stable-pub-v5.1.0-full.
,
Caspar
2012/11/26 Douglas Greve :
>
> No, it does not. With version 5 I went to a simple AR1 model instead.
> doug
>
>
>
> On 11/26/12 10:34 PM, Caspar M. Schwiedrzik wrote:
>>
>> Hi Doug,
>> thanks for the input. What I meant is that in version 5.1,
>> m
Hi Doug,
thanks for the input. What I meant is that in version 5.1,
mkanalysis-sess does not seem to recognize the -taumax flag to set the
maximum delay for the autocorrelation function.
Caspar
2012/11/26 Douglas N Greve :
>
>
> On 11/26/2012 02:12 PM, Caspar M. Schwiedrzik wrote:
>
Hi!
I ran into a funny problem when calculating contrasts in Freesurfer 4.5.0.
Namely, the center of my cluster of significant voxels has a p-value
of -0.0, resulting in a funny whole where you would otherwise expect
to find the most significant voxel(s).
It seems that the p-value is too small. Is
Hi all,
when specifying -hpf and -polyfit in mkanalysis-sess, I understand
that fourier pairs and polynomials are implemented in the design
matrix.
I was wondering whether the filtering is also applied to the predictors?
I am doing a seed-based resting state analysis and applying the
filters to the
Hi!
Is it possible to have slice-by-slice predictors in Freesurfer, and if so,
how?
Thanks,
Caspar
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Hi Doug,
I think M is automatically computed, but t needs to be given (in addition
to indpeak).
What is t?
Thanks, Caspar
2012/7/18 Douglas N Greve
> M is the number of regressor pairs. Leave out the others and it will
> figure them out.
>
> On 07/18/2012 01:43 PM, Caspar M. Schwi
and some more questions: in fast_retroicor(t,indpeak,M,peakamp,troughamp)
what is t / M?
how do I get peakamp and throughamp?
thanks again, caspar
2012/7/18 Caspar M. Schwiedrzik
> great!
> one more question: how do I choose fmin and fmax?
> thanks, caspar
>
> 2012/7/18
>
>
> On 07/18/2012 01:25 PM, Caspar M. Schwiedrzik wrote:
>
>> Hi Doug,
>> thanks for your advice. I am using
>> freesurfer-Linux-centos4_x86_**64-stable-pub-v5.1.0-full,
>> while I have a copy of peakfinder.m, fast_retroicor.m does not seem to be
>> part o
on) to peakfinder.m, then call fast_retroicor.m passing it the
> peaks and returning the regressors. Then save the regressors you want in
> a text file and specify them using -nuisreg option to mkanalysis-sess.
> doug
>
> On 07/18/2012 11:28 AM, Caspar M. Schwiedrzik wrote:
>
Hi!
Has someone used retroicor (retroactive correction of physiological noise;
Glover at al. 2000) with Freesurfer?
I would like to create nuisance regressors for EPI data based on cardiac
and respiratory signals.
The AFNI version of retroicor produces slice-based regressors, and I am not
sure how
if i come up with the code for the newey white standard error, where in
selxavg3-sess would i need to plug that in?
caspar
2012/6/15 Douglas N Greve
> I don't know anything about it. Looks interesting.
> doug
>
>
> On 06/15/2012 02:14 PM, Caspar M. Schwiedrzik wrote:
&
implemented in FSFAST.
> doug
>
> On 06/15/2012 01:36 PM, Caspar M. Schwiedrzik wrote:
> > Hi!
> > I am processing a resting state data set, which I would like to low
> > pass filter to get rid of some artifacts. The sample will be very
> > small, so I won't ru
Hi!
I am processing a resting state data set, which I would like to low pass
filter to get rid of some artifacts. The sample will be very small, so I
won't run a RFX GLM, but an FFX GLM and/or single subject analyses.
Since the low pass filter introduces high autocorrelations, it does not
make sens
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