mgh.harvard.edu
on behalf of Mesquita, Tiago
Sent: 20 April 2024 14:29:19
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] Retinotopy error computing contrast matrices
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Hello FreeSurfer Developers,
I am trying to do a retinotopy analysis. My retinotopy h
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Hello FreeSurfer Developers,
I am trying to do a retinotopy analysis. My retinotopy has 8 bars, this bars
swipe the visual field from the 8 possible directions (all multiple of 45
degrees angle). One complete swipe takes 24 sec. I have 16 different p
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Dear experts,
While visualizing my polar angle results using angle file, I almost don't get
any interpretable results. However, if I show results with real+imag file,
taken from the following link
(http://secure-web.cisco.com/1JbJRUtZSYA97HQvtYOuYE
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Dear Experts,
I am running my polar angle and eccentricity following the freesurfer
retinotopy analysis.
Saddly, i figured out that my eccentricity script has a shorter cycle compared
to the polar angle (38sec vs 40sec pro cycle).
To bypass
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Dear Experts,
I am running my polar angle and eccentricity following the freesurfer
retinotopy analysis.
Saddly, i figured out that my eccentricity script has a shorter cycle compared
to the polar angle (38sec vs 40sec pro cycle).
I was
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Sorry, this is the actual link to the images:
https://drive.google.com/open?id=1SLPgXmPiqHCyKLHcxKYonyHBl_3pdFzS
Marco
On Thu, 6 Feb 2020 at 14:44, Marco Ninghetto
wrote:
> Dear FREESURFERs,
> I'm performing retinotopy analysis. I preprocessed data
External Email - Use Caution
Dear FREESURFERs,
I'm performing retinotopy analysis. I preprocessed data and made 1st level
analysis.
Stimuli definition is: 6 cycles of rotating wedge (counter-clockwise
rotation) and 6 cycles of expanding ring. One cycle lasts ~41 seconds. Scan
TR =
External Email - Use Caution
Thank you for your reply. I think I've better explained the situation in a
further email, which I paste in here.
I used expanding ring and rotating wedge. For my pilot, unfortunately, we
used only 2 cycles for each stimulus and 1 cycle lasted 200 secon
sorry, for the delay. The par files are both empty and that link cannot be
found (maybe expired)
On 1/15/2020 11:24 AM, Marco Ninghetto wrote:
External Email - Use Caution
Sorry for the late reply, the message was non stop bounced.
So, here You will find:
- terminal output for `selxavg
Actually, I was able to get those files from your previous emails
On 1/15/2020 11:24 AM, Marco Ninghetto wrote:
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Sorry for the late reply, the message was non stop bounced.
So, here You will find:
- terminal output for `selxavg3-sess` (filename: terminal_outp
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Sorry for the late reply, the message was non stop bounced.
So, here You will find:
- terminal output for `selxavg3-sess` (filename: terminal_output.txt). I
copied only the last part when freesurfer accesses to MATLAB and where the
error occurs;
- the
Can you send your paradigm files? Can you also send the terminal output? One
more thing, can you send the X.mat file from the output folder?
On 1/2/2020 3:19 AM, Marco Ninghetto wrote:
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Hello experts,
I'm performing retinotopy analysis but when running the co
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Hello experts,
I'm performing retinotopy analysis but when running the command
selxavg3-sess
It starts, but after some lines, I get the following error:
ERROR: design is ill-conditioned
I don't know how to proceed from here to solve the erro
Neither of these are easily fixable in FSFAST. You can remove the extra
time points for the first problem. For the 2nd one, I guess you can do
two analyses, one at each frequency, then ignore the one with the wrong
frequency
On 08/02/2016 05:55 PM, Xiaomin Yue wrote:
> Hi,
>
> I am running a re
Hi,
I am running a retinotopy analysis using fsfast 5.3. The design has 15 TR
blank before and after wedge presented for 30 TR with 7 repeats, and ring
presented for 24 TR with 7 repeats. Here is my analysis: mkanalysis -s vz -a
rtoy.self.rh -fsd bold -fwhm 2 -nskip 15 -TR 1.5 -retinotopy 48
Hello Freesurfers,
I'm re-posting this question. Where can I find any documentation about how
is the retinotopic analysis performed in Freesurfer? Thanks.
Best
--
Francesca Strappini, Ph.D.
Neurobiology Department
Weizmann Institute of Science
234 Herzl Street, Rehovot 7610001 Israel
Tel.: +972
Hello Freesurfers,
Where can I find the documentation about how is the retinotopic analysis
performed in Freesurfer? Thanks.
Best
Francesca
--
Francesca Strappini, Ph.D.
Neurobiology Department
Weizmann Institute of Science
234 Herzl Street, Rehovot 7610001 Israel
Tel.: +972 58 444 2584
E-mail:
It expects both polar and eccen. You can "fake" an eccentricity run by
just copying one of the polar runs and calling it eccen
On 05/31/2016 07:35 AM, Steinmann, Iris wrote:
>
> Dear freesurfers,
>
> I try to run a retinotopy analysis following the instruction on
>
> https://surfer.nmr.mgh.harvar
Hello everyone,
I've analyzed my polar retinotopy data (2 runs with clockwise and
counterclockwise wedge rotations) using FsFast. To better understand the
analysis, I'd be very grateful if you could help me with the following
questions:
1. I understand that freesurfer assumes that the rotating w
no, I don't think so, sorry.
On 7/31/15 4:03 PM, dgw wrote:
> Hi,
>
> I am setting up a polar angle stimulus program, and I am wondering if
> there is an option in FS-FAST to analyze data with two opposing wedges
> for the polar mapping. Participants can keep fixation better with this
> setup, whi
Hi,
I am setting up a polar angle stimulus program, and I am wondering if
there is an option in FS-FAST to analyze data with two opposing wedges
for the polar mapping. Participants can keep fixation better with this
setup, which is why we are aiming to use it.
Thanks,
Dan
This is a bug in 5.3. I've put a new version for you here. Let me know
if that works
ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mri_surf2vol
On 01/27/2015 01:26 PM, Benjamin Zimmerman wrote:
> Hello,
>
> When I try your recommended code, I am able to get the data back into
>
Ugh, that's weird, I don't know what's going on with that. I'll have to
dig into it more.
On 1/27/15 1:26 PM, Benjamin Zimmerman wrote:
Hello,
When I try your recommended code, I am able to get the data back into
volumetric space, but one hemisphere's cortex is significantly thinner
than t
Hello,
When I try your recommended code, I am able to get the data back into
volumetric space, but one hemisphere's cortex is significantly thinner than
the other. If I do mri_surf2vol separately on each hemisphere, I don't have
this problem. It seems to occur only if I try merging the two files.
I don't think we have a tool to display the color wheel in a volume.
FreeView might be able to do it. For the color wheel in tksurfer, you
are looking at the angle file (one for eccen and one for polar), so you
would map them. You can run mri_surf2vol something like
mri_surf2vol --surfval lh
I mean the individual's anatomical volumetric space.
On Thu, Dec 18, 2014 at 11:53 AM, Douglas N Greve wrote:
>
>
> What do you mean by the individual's volumetric space? The anatomical
> space or the functional space?
>
>
> On 12/16/2014 05:18 PM, Benjamin Zimmerman wrote:
> > Thanks for the adv
What do you mean by the individual's volumetric space? The anatomical
space or the functional space?
On 12/16/2014 05:18 PM, Benjamin Zimmerman wrote:
> Thanks for the advice. I thought I would like to use mri_surf2vol, but
> I am a little confused about the parameters and how they relate to
Thanks for the advice. I thought I would like to use mri_surf2vol, but I am
a little confused about the parameters and how they relate to what the
retinotopy analysis outputs.
To be explicit, I want to view the real.nii.gz and imag.nii.gz files in an
individual's volumetric space. I can load these
Hi Ben,
You should be able to map it back with mri_surf2vol. I haven't done
this, but the wiki page looks fairly detailed:
http://surfer.nmr.mgh.harvard.edu/fswiki/mri_surf2vol
HTH
D
On Mon, Dec 15, 2014 at 3:43 PM, Benjamin Zimmerman
wrote:
> Hi all,
>
> FsFast has an excellent individual reti
Hi all,
FsFast has an excellent individual retinotopy analysis that allows me to
see phase data on the inflated surface of the brain. Is there a way to view
the results of the retinotopy analysis in the subject's original volumetric
space rather than on the subject's surface space?
Thank you for
Thanks for your always support!
Mingxia
On Fri, Dec 12, 2014 at 1:52 AM, Douglas N Greve
wrote:
>
>
> imag is the imaginary (sine) part of the signal
> real is the real part (cosine)
> fsig is the significance (-log10(p)) where p is computed from an F test
> of the real and imag components
>
>
>
imag is the imaginary (sine) part of the signal
real is the real part (cosine)
fsig is the significance (-log10(p)) where p is computed from an F test
of the real and imag components
On 12/11/2014 05:09 AM, zhang mingxia wrote:
> Thank you very much!
>
> The map opened by rtview seems correct.
Thank you very much!
The map opened by rtview seems correct. As a new learner of retinotopic
analysis, I have one more basic quesion: What do the three files
(imag.nii.gz, real.nii.gz and fsig.nii.gz) represent? Hope some experienced
one can reply me!
Mingxia
On Thu, Dec 11, 2014 at 12:14 AM, Do
On 12/08/2014 09:19 PM, zhang mingxia wrote:
> Hi Doug,
>
> I followed this guide:
> https://surfer.nmr.mgh.harvard.edu/fswiki/FsFastIndividualRetinotopyAnalysis.
> I used "tksurfer-sess" to view. Does "significant activation in the
> visual cortex" mean the map from"tksurfer-sess -a rtopy.self
Hi Doug,
I followed this guide:
https://surfer.nmr.mgh.harvard.edu/fswiki/FsFastIndividualRetinotopyAnalysis.
I used "tksurfer-sess" to view. Does "significant activation in the visual
cortex" mean the map from"tksurfer-sess -a rtopy.self.?h -s sessid"? If so,
yes.
My question is (1) What do the
I'm not sure what you are asking for. Do you see significant activation
in the visual cortex? What command are you running to view?
On 12/08/2014 09:48 AM, zhang mingxia wrote:
> Dear freesurfer experts,
>
> I used Freesurfer 5 to do the retinotopic analysis followed by
> https://surfer.nmr.mg
try now
On 12/08/2014 09:59 AM, zhang mingxia wrote:
> I saw Doug recommended rtview, But I can't access this
> website:ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/rtview.
>
> On Mon, Dec 8, 2014 at 6:48 AM, zhang mingxia
> mailto:zhangmingxia1...@gmail.com>> wrote:
>
> Dea
I saw Doug recommended rtview, But I can't access this website:
ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/rtview.
On Mon, Dec 8, 2014 at 6:48 AM, zhang mingxia
wrote:
> Dear freesurfer experts,
>
> I used Freesurfer 5 to do the retinotopic analysis followed by
> https://surfe
Dear freesurfer experts,
I used Freesurfer 5 to do the retinotopic analysis followed by
https://surfer.nmr.mgh.harvard.edu/fswiki/FsFastIndividualRetinotopyAnalysis.
However, finally I didn't get a red, green and blue map as I expected.
This is the first time for me to analyze retinotopic data. I
Hi Cesar, you can use a time point exclude file. Run mkanalysis-sess
with -help to get more info. Make sure to put the time in seconds in the
file where t=0 is the first time point.
doug
On 11/27/2013 03:29 PM, Cesar Echavarria wrote:
> Hi all,
>
> I'm running a retinotopy analysis and I was wo
Hi all,
I'm running a retinotopy analysis and I was wondering if there was a way
for me to ignore the last x seconds/TRs of a given run. I want to ignore
this bit of time because each run started and ended with a 'blank screen'
period.
I appreciate any tips you guys might give me.
Cesar
_
The first 12 regressors are
1 and 2: fundamental real (cosine), fundamental imaginary (sine)
3 and 4: 1st harmonic real and imag
5 and 6: real and imag at a freq just below the fundamental
7 and 8: real and imag at a freq just above the fundamental
9 and 10: real and imag at a freq just below the
Hi,
I am examining the affect a metal artifact has on fMRI data, and I am
using Eccentricity mapping with the retinotopy analysis in FSFast. I
was recently asked to switch from examining the difference in the fsig
to examining the difference in the betas. I opened up beta.nii.gz and
I can see that
Hi,
I am examining the affect a metal artifact has on fMRI data, and I am
using Eccentricity mapping with the retinotopy analysis in FSFast. I
was recently asked to switch from examining the difference in the fsig
to examining the difference in the betas. I opened up beta.nii.gz and
I can see that
I see. Yes. Thanks a lot.
Best
Wei
Those values are radians. Does that help?
doug
On 11/29/2012 06:09 PM, Zhou, Wei wrote:
> Hi Doug,
>
> Thank you for your patient. I wanted to see how the polar angle
> correlates with the map and I expect a wheel bar which distinguish
> different polar angle
Those values are radians. Does that help?
doug
On 11/29/2012 06:09 PM, Zhou, Wei wrote:
> Hi Doug,
>
> Thank you for your patient. I wanted to see how the polar angle
> correlates with the map and I expect a wheel bar which distinguish
> different polar angles.
> I typed:
>
> rtview --s SUBJ1 -
Hi Doug,
Thank you for your patient. I wanted to see how the polar angle correlates with
the map and I expect a wheel bar which distinguish different polar angles.
I typed:
rtview --s SUBJ1 --lh --polar --real
SUBJ01/bold/rtopy.self.lh/polar/real.nii.gz --imag
SUBJ01/bold/rtopy.self.lh/polar
Hi Wei, I don't think I understand your question. Can you elaborate?
doug
On 11/29/2012 04:06 PM, Zhou, Wei wrote:
> Hi Doug,
>
> Thank you very much. I have thrown all the fixation sessions and run
> the analysis again. So in rtview how can i get the color scale bar
> which indicates the corre
Hi Doug,
Thank you very much. I have thrown all the fixation sessions and run the
analysis again. So in rtview how can i get the color scale bar which indicates
the corresponding time points of polar or eccen? Is it still supported in free
surfer 5?
Best
Wei
---
Hi Wei
Hi Wei, the argument to -retinotopy should be the period of stimuluation
(ie, how long it takes the wedge to go around 360 degrees), not the
duration of your run. Also, it is not set up to handle fixation at the
beginning or the end, so you might want to cut those frames out.
doug
On 11/29/201
Dear freesurfers,
I am doing retinotopy analysis using freesurfer 5 with
http://surfer.nmr.mgh.harvard.edu/fswiki/FsFastIndividualRetinotopyAnalysis .
I have four runs, two eccen and two polar. For each run I have 15 seconds
fixation, 300 seconds stimuli and 15s fixation at the end (total 330s
On 10/26/2012 05:10 AM, Andreas Schindler wrote:
> Dear freesurfers
>
> Have you ever tried to get an average retinotopic map across all subjects on
> freesurfer's standard surface (fsaverage)?
>
> I obtained an individual map for each subject using the fsfast stream
> (mkanalysis-sess, selxavg
Dear freesurfers
Have you ever tried to get an average retinotopic map across all subjects on
freesurfer's standard surface (fsaverage)?
I obtained an individual map for each subject using the fsfast stream
(mkanalysis-sess, selxavg3-sess) and plotted the results using
rtview: e.g.
rtview.sh
freesurfer/fstast/bin is fine
Maryam Vaziri Pashkam wrote:
> Sorry Doug this is a very basic question,
> Should I put the rtview file in the freesurfer/fstast/bin directory or
> somewhere else?
>
> Thanks,
> Maryam
>
> On Thu, Feb 16, 2012 at 3:57 PM, Douglas N Greve
> mailto:gr...@nmr.mgh.harv
Sorry Doug this is a very basic question,
Should I put the rtview file in the freesurfer/fstast/bin directory or
somewhere else?
Thanks,
Maryam
On Thu, Feb 16, 2012 at 3:57 PM, Douglas N Greve
wrote:
> rtview will give you the colorwheel, see if that works for you
> doug
>
> Katie Bettencourt wr
rtview will give you the colorwheel, see if that works for you
doug
Katie Bettencourt wrote:
> 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
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 s
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/rtview
Look at the --he
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
There are lots of changes to the actual work-flow. The docs are here:
http://surfer.nmr.mgh.harvard.edu/fswiki/FsFastIndividualRetinotopyAnalysis
doug
_andre...@sapo.pt wrote:
> Hello!
>
> I'm moving to FS 5.1 and I will be analysing retinotipic data (and the
> anatomical data bas well). I would
Hello!
I'm moving to FS 5.1 and I will be analysing retinotipic data (and the
anatomical data bas well). I would like to know if there are any
changes or issues while running this analysis in this new version
before I move.
Thanks,
Andreia
___
Fre
hi michelle,
the Sereno et al. 1995 Science paper has details about the phase encoded
retinotopic data analysis, especially in the endnotes of the article. also
for more details you can look at the MATLAB code embedded in the command
'selfreqavg', which is used for the basic retinotopy analysis a
Dear Freesurfers,
I am trying to describe how freesurfer conducts it's retinotopy analysis to
make the polar, eccen and fieldsign maps.
Is there a detailed description of this somewhere? I can't seem to find an
indepth description on the wiki.
Thanks.
Michelle
Hi Doug and Freesurfers
I didn't change any of the structural After the retinotopy analysis.
First, I ran recon-all -all.
Second, I made edits to to brainmask.mgz and wm.mgz and then ran
autorecon2-wm and autorecon3.
Third, I cut the occipital patches in tksurfer and then flattened them.
Finally,
Hi Doug,
I didn't change the structural after the analysis.
Before the retinotopy analysis, I ran recon-all -all, made some brainmask
and white matter edits, them ran autorecon2-wm and autorecon3. Finally, I
made occipital patches, then flattened them with mris_flatten.
When I ran this all before
Hi Michelle, did you change the structural after you ran the retinotopy
analysis? It looks like the number of vertices changed. If so, then
you'll need to re-run the fMRI analysis.
doug
Michelle Umali wrote:
> Dear Freesurfers,
> I am working on a retinotopy analysis and I got this error:
> ERRO
Dear Freesurfers,
I am working on a retinotopy analysis and I got this error:
ERROR: dimension mismatch between mask and surf when trying to look at
map angle in tksurfer-sess
Do I need to add --reshape flag? If so, where?
Any help would be most appreciated.
Thanks.
Michelle
Here are the analysi
Hi Freesurfers.
Is there text describing the retinotopy analysis in Freesurfer
mathematically?
Thanks.
Michelle
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in t
So when viewing with tksurfer I am assuming that -map angle shows the
polar data. It looks ok. There's a lot of yellow and red, which I am
assuming is the overall significance and not significance by position
yes?
tksurfer-sess -a rtopy.self.lh -s sj09 -map angle
To view eccen data, is it
Hi Bruce,
So for the following command:
bbregister --s bert --mov func.nii --init-fsl --reg register.dat
tkregister2 --mov func.nii --reg register.dat --surf
In the case of a retinotopy analysis, which files are register.dat and
func.nii?
Quoting Bruce Fischl :
> Hi Michelle
> Try
Hi Michelle
Try using bbregister.
Cheers
Bruce
On Jul 31, 2011, at 6:54 PM, Michelle Umali wrote:
> Dear Freesurfers,
> During my retinotopy analysis, I was getting very strange fieldsign
> data (blue and red speckles) and my polar and eccentricity data was
> limited to the occipital pol
Dear Freesurfers,
During my retinotopy analysis, I was getting very strange fieldsign
data (blue and red speckles) and my polar and eccentricity data was
limited to the occipital pole. It was suggested that I check
registration between the functional and anatomical.
I was looking up tkregi
y surfaces and volumes. I'm not sure however if I can
>> use freeview for retinotopic mapping. Could you kindly give me some insight
>> on that?
>>
>> Thanks Again,
>> Babak
>>
>> -Original Message-
>> From: Douglas N Greve [mailto:gr...
gt; Babak
>
> -Original Message-
> From: Douglas N Greve [mailto:gr...@nmr.mgh.harvard.edu]
> Sent: Friday, July 08, 2011 3:57 PM
> To: Babak
> Subject: Re: [Freesurfer] retinotopy manual?
>
> does
> /data/fMRIdata/1/users/babak/data-parent/haluk/bold/003/fmcpr.sm5.halu
Hi all,
Thank you very much!
I did 2 runs of each of the stimuli I described in one session (I previously
got some pretty decent maps from these data using the mrVista package from
Stanford).
I followed the retinotopy instructions from the FS wiki (
http://surfer.nmr.mgh.harvard.edu/fswiki/FsFas
w for 6 cycles/scan,
which would improve SNR (and increase total scan duration).
Don
> Date: Thu, 7 Jul 2011 11:30:13 -0400
> From: j...@nmr.mgh.harvard.edu
> To: ahouga...@dadlnet.dk
> CC: freesurfer@nmr.mgh.harvard.edu
> Subject: Re: [Freesurfer] Retinotopy stimuli
>
&
hi anders,
the optimal set of stimulus parameters will depend somewhat on what
cortical area(s) you are trying to map and on the details of your
acquisition. in general, stimulating with both clockwise- and
counterclockwise-rotating wedges for polar angle mapping and with both
expanding and contr
I'd also be very interested to hear about good reinotopic stimuli; we've
used 6Hz and 14 ring sizes for eccentricity mapping in the past.
Thomas Ballinger
On Thu, Jul 7, 2011 at 3:56 AM, Anders Hougaard wrote:
> Dear freesurfers,
>
>
> Which stimuli do you think provide the best retinotopic maps
Dear freesurfers,
Which stimuli do you think provide the best retinotopic maps?
I have done a retinotopy analysis using the following stimuli:
Polar angle:
- 45 deg counter-clockwise rotating wedge
- 8 unique positions
- flickering at 2 Hz
- stimulation period: 36 sec
- no. of cycles: 6
- TR =
The analysis is done by creating two regressors: a sine and cosine, both
at the stimulation frequency. Each has a regression coefficient computed
(ie, a 'beta'). The p-value is computed from an F-test on these two betas.
doug
Thomas Janssens wrote:
> Hi,
>
> I performed a retinotopy analyses wi
Hi,
I performed a retinotopy analyses with freesurfer using selxavg3-sess.
One of the nii-files that is created with this command is sig.nii.
How is the significance map in sig.nii calculated for retinotopy? which
p-values are used in this calculation?
Thanks!
Thomas
Hi Doug,
I'm trying to analyze my retinotopy data and visualizing in tksurfer.
I've been able to view the significance maps through:
tksurfer-sess -a rtopy.self.lh -s sessid
But I've had issues displaying the polar angle data using the
Configure Overlay tool. Specifically, I want to use
Michelle,
Can you give more details of what you are doing? How did you generate
the files you are trying to load?
doug
Michelle Umali wrote:
> Dear Freesurfers,
> I'm having issues trying to display the polar angle data using the
> color wheel. Unfortunately, I can't resizing the Configure Over
Dear Freesurfers,
I'm having issues trying to display the polar angle data using the
color wheel. Unfortunately, I can't resizing the Configure Overlay
Display window. No matter what I try, I can't actually see the Apply
button.
Any suggestions?
Also, is there a quickie guide on defining th
For a cycle. So for the time it take the wedge to go all the way around
or for the ring to start from center and return to center.
doug
Michelle Umali wrote:
> Hi Doug,
> When you say retinotopy 30, where 30 is the 30 second period.
>
> mkanalysis-sess -a rtopy.self.lh -surface self lh -TR 2
Hi Doug,
When you say retinotopy 30, where 30 is the 30 second period.
mkanalysis-sess -a rtopy.self.lh -surface self lh -TR 2 \
-retinotopy 30 -paradigm rtopy.par
Does period mean duration for a cycle or for the whole run?
Thanks.
Michelle
ing Douglas N Greve :
> I don't have a form
Yes, you need to run recon-all in order to run the FSFAST analysis.
doug
Michelle Umali wrote:
> Hi Doug,
> Sorry for the dumb beginner question, but to view the results
> projected onto their own anatomy, do I have to do anything special to
> their high res structural scan(like do a recon-all)
Hi Doug,
Sorry for the dumb beginner question, but to view the results
projected onto their own anatomy, do I have to do anything special to
their high res structural scan(like do a recon-all) ?
Thanks.
Michelle
Quoting Douglas N Greve :
> I don't have a formal manual yet (working on it). B
I don't have a formal manual yet (working on it). Below are a list of
steps that you need to run. The version 5 retinotopy stream is now
integrated with the rest of FSFAST, which is documented here:
http://nmr.mgh.harvard.edu/~greve/fsfast.intro.ppt
doug
1. Create retinotopy paradigm file in e
Dear All,
I was wondering if anyone knows of a step-by-step guide on how to do
retinotopic analysis with freesurfer.
Thanks.
Michelle
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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
Hi Katie, do you have eccentricity runs as well or just polar?
doug
Katie Bettencourt wrote:
> 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 analysi
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
ut an advantage of the MGH freesurfer retinotopy analysis
stream is that it is documented, supported, and consistent with the latest
cortical reconstruction stream distributed with MGH freesurfer.
> Date: Thu, 10 Jun 2010 05:59:58 -0400
> From: gr...@nmr.mgh.harvard.edu
> To: francescastrap
Hi Francesca,
There's a packet that, i think, combines Freesurfer and VistaView. I think
it is called VistaTools.
You should check it out on David Heeger's website.
ilana
On 9 June 2010 16:44, francesca strappini wrote:
> Hi all,
> I would ask you about freesurfer and retinotopy. I'm going to be
What do you mean by the UCSD freesurfer? A long time ago I re-wrote
a stream that Anders was using, and it gave similar results. I've just
re-written it again and it will be released with version 5.
doug
On Wed, 9 Jun 2010, francesca strappini wrote:
> Hi all,
> I would ask you about freesurfe
old freesurfer, or csurf, is this:
http://kamares.ucsd.edu/~sereno/csurf/tarballs/
made by Marty Sereno
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The information in this e-mai
what do you mean by "Old FreeSurfer"?
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On Wed, Jun 9, 2010 at 17:44, francesca strappini <
francescas
Hi all,
I would ask you about freesurfer and retinotopy. I'm going to begin the
analysis of some retinotopic data. I would ask if you know if the
retinotopic analysis made by MGH freesurfer is qualitatively comparable to,
or it's good as, that made by USCD freesurfer (old freesurfer).
Thank you kin
Hello Everyone,
I am a new FreeSurfer user, trying to do retinotopy. My stimulus has the
following configurations:
- 96 TRs in total per run, including 8 blanks in the beginning and 8 in
the end
- Polar angle:
- bowtie checkerboard wedges
- 16 unique positions
- 5 repetitions per run
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