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what version are you using? This is not a problem in the last two
versions ...
On 5/10/2023 3:43 AM, 朱筱 wrote:
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Hi Freesurfer Develpers,
I am attempting to preprocess fMRI by running preproc-sess based on
FS-F
External Email - Use Caution
Hi Freesurfer Develpers,
I am attempting to preprocess fMRI by running preproc-sess based on FS-Fast as
command lines:
preproc-sess -s sess01 -fsd rest -stc up -surface fsaverage lhrh -mni305 -fwmh
5 -per-run
However, it stopped at the motion
list
Subject: Re: [Freesurfer] FS FAST
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Hi Avnish,
I added those two lines to my bash profile but i still get the same error
message. is there anything else i could try?
Best,
justin oh
On Fri, Feb 10, 2023 at 11:03 AM Kumar, Avnish
mailto:avnish.ku
il.com>
> *Sent:* Thursday, February 9, 2023 12:16 PM
> *To:* Freesurfer support list
> *Subject:* Re: [Freesurfer] FS FAST
>
>
> External Email - Use Caution
>
> Hi Avnish,
>
> Justins-MacBook-Air:~ justinoh$ whereis python3
>
> python3: /usr/b
is pointing to your python3 installation.
source ~/.bash_profile
python --version
Best,
Avnish
From: freesurfer-boun...@nmr.mgh.harvard.edu
on behalf of Justin Oh
Sent: Thursday, February 9, 2023 12:16 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] FS FAST
*To:* Freesurfer support list
> *Subject:* Re: [Freesurfer] FS FAST
>
>
> External Email - Use Caution
>
> Hi all,
>
>
> I'm trying to run preproc-sess on a resting state MRI and I've tried to
> define python to python3 path. I assume it's tr
: [Freesurfer] FS FAST
External Email - Use Caution
Hi all,
I'm trying to run preproc-sess on a resting state MRI and I've tried to define
python to python3 path. I assume it's trying to call python into the
environment but I'm not sure how to do this. I'm runn
External Email - Use Caution
Hi all,
I'm trying to run preproc-sess on a resting state MRI and I've tried to
define python to python3 path. I assume it's trying to call python into the
environment but I'm not sure how to do this. I'm running a macOS m1 apple
chip.
I've tried in
External Email - Use Caution
Hello Justin,
Depending upon the OS of the machine, there may not be a “python” installed by
default on the system, i.e., you need to choose either python2 or python3.
Given some scripts may still look for “python”, then you can add an alias
in your
External Email - Use Caution
Hi all,
I am trying to run preproc-sess on a resting state MRI. I believe my
directory is set the way it should be. There was an error that stopped the
pipeline: env: python: No such file or directory
Could anybody help me out?
All the best,
Justin O
Something like
set MATLAB=/usr/pubsw/common/matlab/8.4
Now that I think about it, you may be able to use the compiled version
of fsfast. There are only two programs that use matlab, mkcontrast-sess
and selxavg3-sess. You can try adding -bin on to both of those to use
the compiled version (which
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My bash profile currently sets up my freesurfer environment with each
terminal. Should I also be exporting matlab into my environment and define
a path to the application? If so what should i include in my bash profile.
On Wed, Jan 25, 2023 at 11:00 AM
I have not idea, try it and see.
On 1/25/2023 9:25 AM, Justin Oh wrote:
External Email - Use Caution
Is the student version of MATLAB enough to run in the background? Our
institution does not provide a license unfortunately. I tried using
octave but i can't seem to get octave to work
External Email - Use Caution
Is the student version of MATLAB enough to run in the background? Our
institution does not provide a license unfortunately. I tried using octave
but i can't seem to get octave to work.
Best,
Justin Oh
On Thu, Jan 12, 2023 at 9:38 AM Douglas N. Greve
Just the basic is ok. Although I have not done it in a while, you should
also be able to use octave (which is free). Once you get octave install
and in your path, set the env variable FS_USE_OCTAVE to 1. Like I said,
I have not used it in a while, but it I think it should still work.
On 1/11/2
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Dear Freesurfer team,
I am new to freesurfer and I'm working on learning how to pre process and
analyze resting state fMRI. It's my understanding that MATLAB and FSL have
to run in the background from what I took away from online tutorials. Is
there a
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I aim at FS-FAST preprocessing of rs-fMRI data and extracting timeseries from
Yeo's Networks.
1 - I won’t perform a seed based analysis.
2 - I want to exclude the five sets of nuisance variables in mkanalysis-sess.
Please could you check whet
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Thanks.
On Tue, Oct 15, 2019 at 5:00 PM Greve, Douglas N.,Ph.D. <
dgr...@mgh.harvard.edu> wrote:
> Correct
>
> On 10/15/2019 9:38 AM, Keri Woods wrote:
>
> External Email - Use Caution
> Hi Doug
>
> Thank you very much for the very helpful rep
Correct
On 10/15/2019 9:38 AM, Keri Woods wrote:
External Email - Use Caution
Hi Doug
Thank you very much for the very helpful reply! It worked perfectly and was
exactly what I needed. I assume that these are the clusters after cluster-level
correction for multiple comparison since --
External Email - Use Caution
Hi Doug
Thank you very much for the very helpful reply! It worked perfectly and was
exactly what I needed. I assume that these are the clusters after
cluster-level correction for multiple comparison since --csd is used?
Thanks,
Keri
On Tue, Oct 15, 2
Sorry for the delay ...
First, run selxavg3-sess with -fwhm ( you might need to delete the
bold/analysis folder to get it to re-run).
cd session/bold/analyis
There will be a filed called fwhm.dat. Look in that. Depending upon how much
you smoothed it might be something like 10.395. This is the
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Hi
From the 1st level analysis of an fMRI study I'm trying to extract the size
of the clusters of activation from each subject, but don't know how to go
about this. I know that for the group analysis you can get the cluster
sizes from the output from m
External Email - Use Caution
Hi list,
I would like to use as seed the output of segmentation of the thalamic nuclei
in FS-FAST. Probably some nuclei may be too small to be used as seed. Are you
agree? I wonder if to merge the outputs in 5-10 subregions (e.g. AV, MD, MC
etc...)
You called the analysis "my-language..." not "language" . Try using
my-language... when running selxavg3-sess
On 5/29/18 8:24 AM, 高 寒 wrote:
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FS-FAST error:analysis language.sm05.lh does not exist, see mkanalysis-sess
Hello FreeSurfer Developers,
I'm att
External Email - Use Caution
FS-FAST error: analysis language.sm05.lh does not exist, see mkanalysis-sess
Hello FreeSurfer Developers,
I'm attempting to run FS-FAST on my own data, as described on the FS-FAST
tutorial
(http://www.freesurfer.net/fswiki/FsFastTutorialV5.1/FsFastF
That looks correct. You can also checkout the instructions here:
https://surfer.nmr.mgh.harvard.edu/fswiki/PairedAnalysis
On 9/17/17 6:07 PM, std...@virgilio.it wrote:
Hi list,
I'm not sure that the files reported below are correct to assess the
longitudinal difference between T1 and T2.
Ple
Hi list,
I'm not sure that the files reported below are correct to assess the
longitudinal difference between T1 and T2.Please, could you check it? The
result which I have obtained bu running mri_glmfit is too strange.ThanksBest
regardsStefano
1) PAIRWISE.fsgd file---GroupDescrip
Thanks for that Doug!
Cheers,
*Dr Kevin Aquino*
Research fellow,
Sir Peter Mansfield Magnetic Resonance Center, The University of
Nottingham.
Honorary Research Fellow
School of Physics, Faculty of Science, University of Sydney
*E* kevin.aqu...@nottingham.ac.uk, aqu...@physics.usyd.edu.au | *W*
selxavg uses scenario #1, which corresponds to the 2nd image below, ie,
all the task regressors are in a single column and not pulled out on a
run-by-run basis. The nuisance regressors are specific to each run.
>
On 08/16/2017 08:24 PM, Kevin Aquino wrote:
> Thanks for that Doug,
>
> [I was ho
Thanks for that Doug,
[I was hoping i could do the parametric modulation in the contrast weights
-- SPM style of doing this after the betas were fit].
Regarding the X.mat question, sorry I wasn't clear. I can see it has the
nuisance regressors and constant terms, but is that x.mat used to estimat
It has the design matrix plus a lot of other stuff in it. For parametric
modulation, have you seen this page
https://surfer.nmr.mgh.harvard.edu/fswiki/FsFastParametricModulation
On 08/15/2017 09:52 PM, Kevin Aquino wrote:
> Dear all,
>
> I have a question regarding the output from selxavg3-sess.
Dear all,
I have a question regarding the output from selxavg3-sess. I noticed that
within an analysis there is a X.mat that looks like a design matrix --
however is this used at any stage of the analysis? The help message in
selxavg3-sess reads:
"This program will construct the design matrix f
@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] FS-FAST (preproc-sess)
What was your preproc-sess command and what folder are you running it from? And
did you use 3-digit, zero-padded strings as your run folder?
On 05/23/2017 09:17 AM, Alshikho, Mohamad J. wrote:
>
> Hi Doug,
>
> I wan
What was your preproc-sess command and what folder are you running it
from? And did you use 3-digit, zero-padded strings as your run folder?
On 05/23/2017 09:17 AM, Alshikho, Mohamad J. wrote:
>
> Hi Doug,
>
> I want to analyze rsfMRI data using FS-FAST. Kindly, I have question
> regarding the
Hi Doug,
I want to analyze rsfMRI data using FS-FAST. Kindly, I have question regarding
the command “ preproc-sess / Freesurfer v6”
In order to begin the analysis, I followed the steps as in FS-FAST wiki. First,
I organized the tree folders for the project as
“study_folder/session_ID/bold/run”.
Not much has changed outwardly. It uses the FS-generated brainmask
instead of running a skull stripping program on the functionals, and it
supports CVS (combined-volume-surface) registration for subcortical
analysis. Note sure what you mean by the second question.
On 02/06/2017 07:54 AM, std..
Hi list,I wonder which are the main changes in FS-FAST 6.0?The links used in
previous version are still useful?
ThanksStefano
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The in
PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] FS-FAST "If: Expression Syntax" Error
Check the contents of
/autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr00978/subjectname
It may have the subjectname repeated 3 times
On 07/18/2016 05:45 PM, Hibert, Matt
.mgh.harvard.edu] on behalf of Douglas N Greve
> [gr...@nmr.mgh.harvard.edu]
> Sent: Monday, July 18, 2016 5:23 PM
> To: freesurfer@nmr.mgh.harvard.edu
> Subject: Re: [Freesurfer] FS-FAST "If: Expression Syntax" Error
>
> Can you run the command below and send me dng.log?
...@nmr.mgh.harvard.edu
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve
[gr...@nmr.mgh.harvard.edu]
Sent: Monday, July 18, 2016 5:23 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] FS-FAST "If: Expression Syntax" Error
Can you run the command below a
Can you run the command below and send me dng.log?
register-sess -debug -s nmr00978 -d
/autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects -fsd sycabs -dof 6
-per-run -nolog -update |& tee dng.log
On 07/14/2016 02:51 PM, Hibert, Matthew Louis wrote:
> Hi All,
> I'm running into an error analy
Hi All,
I'm running into an error analyzing some fMRI data with FS-FAST in Freesurfer
version 5.3. The analysis runs fine until it gets to the register-sess part,
which quits before actually starting to do any registration. The last line of
the log file, attached, is "if: Expression syntax", b
Hi,I'm wondering whether the FS-FAST performed bandpass filtering.
Stefano___
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The information in this e-mail is intended only for the per
I think it may be our fcseed-config command line
fcseed-config -segid 1 -seg $SUBJECTS_DIR/Subj/mri/MRS_MASK.mgz -fsd
rest -mean -cfg MRS_MASK.config –overwrite
It should be -seg MRS_MASK.mgz
They way you have it, fcseed will use the segmentation for Subj for all
subjects, which is why it work
96
Normal
0
14
false
false
false
IT
X-NONE
X-NONE
Hi list,I'd like to performed FS-FAST using a ROI as seed.Should I use
fcseed-config? Thus, what should I put instead of -segid?Thanks and regards.
Stefano ___
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No, sorry. You can run tkregister-sess and it will show each one
sequentially. This is a good idea and it may be possible with the
transition to freeview.
doug
On 6/10/15 7:16 PM, sabin khadka wrote:
Hi all- Is there a command we can have screenshots (similar to one
employed in fsl) of fucnti
Hi all- Is there a command we can have screenshots (similar to one employed in
fsl) of fucntional--> structural registration in FSFAST to visually check the
registration on top of the BBR cost?
Cheers,
Sabin Khadka
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Frees
Some steps are volume-based and some are surface-based. Motion
correction is voxel based. Slice-timing correction is done in the
volume. It then gets sampled onto the surface where surface-based
smoothing is done. The GLM analysis is done on the surface. I often use
voxel and vertex interchang
Hi all,
I am seeking a little clarification regarding fMRI analyses with FS-FAST.
In the documentation and supplied PowerPoint presentations there are many
references to niftis, and statements like "Performs GLM fit at each voxel".
Given this, for the cortex, would I be correct in the assertion t
Hi,
I'm performing FS-FAST for functional connectivity analysis.I have performed
all step for cortical labels.Now, I'd like to perform the analysis for
subcortical structure.Which are the correct lines?
Using preproc-sess -s Sess01 -fwhm 5 -surface fsaverage lhrh -mni305 -fsd rest
-per-run for e
Thanks very much.
Xiaomin
> On Apr 13, 2015, at 9:43 AM, Douglas Greve wrote:
>
> Use the (undocumented) -trgsubject flag
>
>> On 4/6/15 9:10 AM, Xiaomin Yue wrote:
>> Hi All,
>>
>> I generated a group averaged surface using make_average_surface
>> successfully. Currently, I like to proce
Use the (undocumented) -trgsubject flag
On 4/6/15 9:10 AM, Xiaomin Yue wrote:
Hi All,
I generated a group averaged surface using make_average_surface
successfully. Currently, I like to process the fMRI data using this
group surface, instead of fsaverage, using the fs-fast pipeline. For
do
Hi All,
I generated a group averaged surface using make_average_surface successfully.
Currently, I like to process the fMRI data using this group surface, instead of
fsaverage, using the fs-fast pipeline. For doing so, I need to run
rawfunc2surf-sess with a parameter where I can input this gr
It depends on how long your event is. For most designs where the events
are on the order of seconds it should not make much of a difference. For
very short events, I'm not sure.
On 03/27/2015 04:13 PM, dgw wrote:
> Hi,
>
> How does event length/duration contribute to an FS-FAST analysis. Will
>
Hi,
How does event length/duration contribute to an FS-FAST analysis. Will
I produce different results, if I specify an event length of 1 second
versus an event length of 0.1 seconds? Most importantly, if yes, how
will they differ?
The reason I am asking is formerly I would use the actual duratio
Yes, look in fsnr.nii.gz
On 03/26/2015 03:53 PM, dgw wrote:
> Hi,
>
> Does FS-FAST perform any temporal SNR calculations on data?
>
> If so, how.
>
> Thanks,
> Dan
> ___
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> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.ha
Hi,
Does FS-FAST perform any temporal SNR calculations on data?
If so, how.
Thanks,
Dan
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The information in this e-mail is intended
Hello,
I am attempting to preprocess resting-state data using the preproc-sess
script
“preproc-sess -s subject -fsd rest -stc siemens -surface fsaverage lhrh
-mni305 -fwhm 4 -per–run”
The processing stops shortly after the “register-sess” command (does not
complete) and the last line is “Miss
On 12/19/2014 08:44 AM, std...@virgilio.it wrote:
> Dear FreeSurfer staff,
>
> I'd like to use FS-FAST but I have some difficulties.
> I have 3 runs of resting state.
>
> 1-Which is the more correct way to concatenate these runs?
I'm not sure what you mean. You don't need to concatenate them prior
Dear FreeSurfer staff,
I'd like to use FS-FAST but I have some difficulties.I have 3 runs of resting
state.
1-Which is the more correct way to concatenate these runs?2-Is this data
hierarchy corrected?
$FUNCIONAL_DATA (i.e. project) ---> Subj1 (i.e. Sess01) --->rest (i.e. bold) +
txt file --->
yes
On 10/23/2014 02:48 PM, dgw wrote:
> If I have events which precede the first MR volume, can I input
> negative values in my par file?
>
> I understand my power, and the advantage of doing this will be
> minimal, but I wanted to inquire if FS-FAST is capable of handling
> this case.
>
> Thanks,
If I have events which precede the first MR volume, can I input
negative values in my par file?
I understand my power, and the advantage of doing this will be
minimal, but I wanted to inquire if FS-FAST is capable of handling
this case.
Thanks,
Dan
___
Hi all,
When running a functional analysis and comparing two experimental
conditions, we observed that there are some voxels/vertices where both
condition A and condition B have a positive % signal change from baseline,
and condition A has greater activity than condition B.
In other regions, both
Hi Ronny
you should have run
recon-all -autorecon2-wm -subjid subj007 -autorecon3
at this point you should be fine running -make all. It should retain all
your manual edits
cheers
Bruce
On Fri, 7 Jun 2013,
preci...@nmr.mgh.harvard.edu wrote:
> Thanks Doug,
> I did make some manual edits to
On 06/07/2013 02:24 PM, preci...@nmr.mgh.harvard.edu wrote:
> Thanks Doug,
> I did make some manual edits to wm.mgz and brainmask.mgz then reran the
> subject a couple times using:
> recon-all -autorecon2-wm -subjid subj007
>
> Shouldn't -autorecon2-wm run through -autorecon2 and -autorecon3?
No,
Thanks Doug,
I did make some manual edits to wm.mgz and brainmask.mgz then reran the
subject a couple times using:
recon-all -autorecon2-wm -subjid subj007
Shouldn't -autorecon2-wm run through -autorecon2 and -autorecon3?
Will running 'recon-all -make all -s subj007' do away with my manual edits?
Hi Ronny, there is a dimension mismatch which usually means that the
surfaces for that subject are out of synch, ie, it has not been run
through to the end. This often happens when a subject is run all the way
through, then edited and re-run but the re-run only runs autorecon1 and
autorecon2 b
I am having an issue when running the preprocess script in fs-fast. It
failed once and I tried something and ran the script again and it failed
the same way. The command I ran is:
preproc-sess -s subj007 -fsd bold -stc siemens -surface fsaverage lhrh
-mni305 -fwhm 5 -per-run
Below is the part whe
You can do that, but you'll need to change the paradigm file to reflect
the new timing.
doug
On 04/10/2013 01:57 PM, preci...@nmr.mgh.harvard.edu wrote:
> If anything I was thinking of removing the first two time points, as those
> are going to get nixed anyway. I was hoping it wouldn't come to th
If anything I was thinking of removing the first two time points, as those
are going to get nixed anyway. I was hoping it wouldn't come to that but i
f that's the only way...
-Ronny
> Hi Ronny, the time point used to as the template is hard-coded to be the
> middle time point. If this is just the
Hi Ronny, the time point used to as the template is hard-coded to be the
middle time point. If this is just the case for one subject, a silly but
simple solution is to remove the last two time points from the time
series. This will cause the "middle" time point to shift to an earlier
time point
One of my subjects exhibited motion during the middle time point of one
the functional scans. FS-FAST then reads all other time points as having a
significant amount of motion because the subject was out of place during
the point that is marked as the origin. Is there some way that I can set a
diff
Oh, yes, I was thinking you were starting at 1 not 0. Sorry about that.
doug
On 03/21/2013 12:45 PM, preci...@nmr.mgh.harvard.edu wrote:
> So, to clarify I got the number of the acquisitions that I want to exclude
> from an fs-fast output file: fmcpr.dat in .../project/session/bold/008/
>
> This
Hi Ronny,
On 03/20/2013 05:57 PM, preci...@nmr.mgh.harvard.edu wrote:
> Hello all,
> I am starting to run some analysis using fs-fast and I had a few basic
> questions that I couldn't find answers on the wiki/tutorial.
>
> 1) Format of files for mkanalysis-sess -tpexclude tpexclude.dat
> What is t
Hello all,
I am starting to run some analysis using fs-fast and I had a few basic
questions that I couldn't find answers on the wiki/tutorial.
1) Format of files for mkanalysis-sess -tpexclude tpexclude.dat
What is the format of the input file for -tpexclude? Is it simply a single
column of intege
Hi Chris, the problem is that you do not have FSLDIR defined. Assuming
you have FSL installed, then setenv FSLDIR /place/where/fsl/is/installed
doug
On 11/06/2012 09:09 PM, Chris McNorgan wrote:
> Hi Doug,
>
> Attached are two plain-text files: fslog2.txt contains the redirected
> terminal outp
:32:30 CST 2012
> preproc-sess done
>
>
> Date: Mon, 05 Nov 2012 21:44:23 -0500
> From: Douglas Greve
> Subject: Re: [Freesurfer] fs-fast preprocessing resting state
> To:freesurfer@nmr.mgh.harvard.edu
> Message-ID:<50987987.7010...@nmr.mgh.harvard.edu>
> Content-Type: te
at Tue Nov 6 16:32:30 CST 2012
preproc-sess done
Date: Mon, 05 Nov 2012 21:44:23 -0500
From: Douglas Greve
Subject: Re: [Freesurfer] fs-fast preprocessing resting state
To:freesurfer@nmr.mgh.harvard.edu
Message-ID:<50987987.7010...@nmr.mgh.harvard.edu>
Content-Type: text/plain; charset
yes, that is probably best
cheers
Bruce
On Tue, 6 Nov 2012, Javeria Ali Hashmi wrote:
Hi there
I am running a program to generate a patient group specific template from T1
brains. I need to know which of the Free Surfer outputs will be best for
creating a patient brain template. The T1 images n
Hi there
I am running a program to generate a patient group specific template from
T1 brains. I need to know which of the Free Surfer outputs will be best for
creating a patient brain template. The T1 images need to be cleaned for
skull, meninges and neck. My guess is brain.finalsurfs.mgz.
thanks
Hi Chris, it should have been done with preproc-sess. What was your
preproc-sess command line? At some point, I had it set up so that it
would go to the bold directory by default unless you used "-fsd rest".
Newer versions require you to specify the FSD specifically.
doug
On 11/5/12 9:38 PM,
Hello,
I'm getting started with freesurfer. I've played around with some of
the tutorial data for fs-fast
(http://surfer.nmr.mgh.harvard.edu/fswiki/FsFastTutorialV5.1) and was
able to follow along and successfully carry out the preprocessing
exercises (which sufficed for my purposes), which a
I don't know why it's not there. I'm copying it over now, but it might
take a half an hour. Try back in a while (making sure to refresh your
browser window).
doug
Verena Gramse wrote:
> Hi,
> I am trying to follow the FS-FAST tutorial but I cant find the required data
> for it under the links
Hi,
I am trying to follow the FS-FAST tutorial but I cant find the
required data for it under the links specified on the tutorial site:
ftp://surfer.nmr.mgh.harvard.edu/pub/data/fsfast-functional.tar.gz,
ftp://surfer.nmr.mgh.harvard.edu/pub/data/fsfast-tutorial.subjects.tar.gz
Could you tell me whe
, but the t-stats have a noticeably reduced magnitude
> >>> across the brain. Is there anything that may differ about FS-FAST's
> >>> implementation of the GLM, such that t-stats would differ?
> >>>
> >>>
> >> You might try turning off the
ly reduced magnitude
>>>> across the brain. Is there anything that may differ about FS-FAST's
>>>> implementation of the GLM, such that t-stats would differ?
>>>>
>>>>
>>>
>>> You might try turning off the whitening (--no-whiten I think).
>>>
t;>
>> You might try turning off the whitening (--no-whiten I think).
>>
>>> 3) I saw in a ppt presentation on FS-FAST that the option -hpf can be
>>> used to add a highpass temporal filter to the model. However, when I
>>> use th
ppt presentation on FS-FAST that the option -hpf can be
>> used to add a highpass temporal filter to the model. However, when I
>> use this option with mkanalysis-new, the script says that the flag
>> isn't recognized. Is there another way to add such a filter?
>
I
> use this option with mkanalysis-new, the script says that the flag
> isn't recognized. Is there another way to add such a filter?
>
It's in the 5.X version.
doug
> Thanks in advance for any help. Cheers,
>
> Ben
>
> On Mon, Sep 5, 2011 at 12:00 PM,
> wro
2011 13:15:51 -0400
From: Benjamin Matthew Deen
Subject: [Freesurfer] FS-FAST modeling question
To: "freesurfer@nmr.mgh.harvard.edu"
Message-ID:
Content-Type: text/plain; charset="us-ascii"
Hi,
I'm trying to run a model in fs-fast using no intensity normalization a
gt; Date: Sun, 4 Sep 2011 13:15:51 -0400
> From: Benjamin Matthew Deen
> Subject: [Freesurfer] FS-FAST modeling question
> To: "freesurfer@nmr.mgh.harvard.edu"
> Message-ID:
>
> Content-Type: text/plain; charset="us-ascii"
>
> Hi,
>
Hi,
I'm trying to run a model in fs-fast using no intensity normalization and no
autocorrelation correction, for the purpose of comparing results with other
software packages, and comparing results with/without autocorrelation
correction. However, I haven't been able to get this to work so far
In /usr/local/freesurfer/subjects/jason/brainmapper/jason-functional/bold/005,
is there a file called f.nii?
doug
Jason Connolly wrote:
> Dear freesurfer experts:
>
> I am new to fs-fast and I am currently running sfa-sess on some retinotopy
> data and I think the main error is "cannot determ
Dear freesurfer experts:
I am new to fs-fast and I am currently running sfa-sess on some retinotopy data
and I think the main error is "cannot determine format of 005/f"
I read in a previous post related to retinotopy that you need to add the full
path to the .nii files and then it will work.
It does not, I'm almost finished with the fix (trying to do that and
finish my ismrm poster:).
Francisco Robles wrote:
Hi Dr. Greve,
I am writting to ask you if Free Surfer version 4.3 solves the bug
with the mkanalysis GUI you have described us. Please let me know to
download this release.
Hi Dr. Greve,
I am writting to ask you if Free Surfer version 4.3 solves the bug with the
mkanalysis GUI you have described us. Please let me know to download this
release. Thankfully yours.
Francisco Robles
Instituto de Nacional de Neurología
México
__
IMPORTANT! PLEASE READ!
I am writing to let you know I have recently uncovered a bug in FSFAST.
While I don't expect the bug to have widespread effects, the places
where it does have an effect could be serious.
I have set up the following web page to document the bug and help track
what is
no, i'm using 4.1 stable. is the development version open to the
public? (i don't see anything here:
http://surfer.nmr.mgh.harvard.edu/pub/dist/dev-releases/)
Or a patch/some minor edits I can copy into preproc-sess?
Or a *not the easiest* way :)?
thanks again
Doug Greve wrote:
Oh, in that
Oh, in that case the easiest thing to do is to smooth the raw data on
the surface. If you have a development version of freesurfer, you can do
this with preproc-sess using the -surf-fwhm option
doug
Scott Gorlin wrote:
Thanks Doug, though I'm still a bit confused:
I'd like to see the smooth
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