that what you use and whether you use it it
depends again on the question you are actually asking. There are some
very good and smart threads on this if you search. Mike Harms I seem to
recall
Carl Schwartz
>>>>>>>>>>>>>>>>>>>>>>
ing cluster, is not a biased metric.
best,
carl
>>>>>>>>>>>>
no, the vertex index is essentially arbitrary and you can't use it to
compare left and right. Doug had some tools for this, but I'm not sure
whether they are ready for primetime yet.
cheer
Hi Jeff - read the thread below starting with my Sept 8 2008 email.
Bruce - what is the status on the insula label for aparc?
carl
> Hello all,
>
> Thank you for your quick replies to my previous posts. One more
question. I am wondering what the difference is and if I should
As far as the first, This happens sometimes when you make your own average
subject. You just need to inflate it more. I will try to dig up an old
email I have on the commands.
As for the second, just click the redraW BUTTON
CARL SCHWARTZ
On 2/17/09 12:44 PM, "Devdutta W" wr
below worked for us
carl schwartz
-- Forwarded message --
From: Bruce Fischl
Date: Fri, Sep 5, 2008 at 1:26 PM
Subject: Re: more inflation
To: Doug Greve
two things:
1. use -n , where the default is 10 (try 20)
2. -dist , where the default l is 0.1 (try something smaller
Hi Lars,
In the interim you might want to take a look at thread below about this
issue where I discuss some admittedly imperfect approaches pending doug's
tool
carl schwartz
On 3/11/09 3:32 PM, "Douglas N Greve" wrote:
Not yet. I have some experimental software to do this but
?
While it looks like tal check not not automatically output the value of
the atlas_transform_error term,
Is the z score that DOES appear (automatically) in the log file the same z
score that Avi mentions below, that compares the atlas_transform_error
term to the training set?
Thanks!
Carl
List readers - here is a helpful clarification from Avi on my question to
Nick. Thx Avi!
carl
-- Forwarded Message
From: Avi Snyder
Reply-To: Avi Snyder
Date: Fri, 24 Apr 2009 01:37:50 -0400
To: , "Schwartz, Carl R.E."
Cc: ,
Conversation: Question about Tal QC logs
Subject: Re
at times have more
detail though I have never asked Doug if this will always work
correctly.
If others have discovered pros and cons in other regions, please share.
Best,
Carl
Carl E. Schwartz, M.D.
Harvard Medical School
Director, Developmental Neuroimaging & Psychopathology Labora
that
bias would seem to be absent for the contralateral label.
Carl
--
Carl E. Schwartz, M.D.
Harvard Medical School
Director, Developmental Neuroimaging & Psychopathology Laboratory
Psychiatric Neuroscience Program
Massachusetts General Hospital
tel 617-726-8965
fax 617-726-4078
On 12/2/0
tners site?
At home I can access the site as a guest…but when I download the
snowleopard build and it is only 167 MB which doesn't seem correct.
Thanks for your help with this,
Carl
--
<<•>>~<>~<<•>>~<>~<<•>>~<>~<<•>>
tvVxX ] [ argument ... ].
I thought about installing the new build but I don't see a snowleopard
verson?
I hope you are going to keep supporting snowleopard...any thoughts on why
the recon-all you sent doesn't run with
the freesurfer-Darwin-snowleopard-i686-dev-20150507 installation?
Thanks!
n *
*Using the suffix name: *
* subfieldAnalysis_T1_v1.0*
*And writing them to: *
* test_no-T1.txt *
*vermisii:RBrain carlanderson$ *
Hope this helps,
Carl
--
<<•>>~<>~<<•>>~<>~<<•>>~<>~<<•>>~<>~<<•>>~<&g
our dataset, or is it ok with 0.57x0.57 in plane resolution and
thinner slices? We are not planning on performing manual segmentation on the
dataset and thus want the settings to be optimal for the Freesurfer
segmentation.
What about number of averages?
Best regards,
Carl Pintzka
Dear Freesurfer,
When trying to start qdec I get the following error:
dyld: Library not loaded: /opt/X11/lib/libGLU.1.dylib
Referenced from: /Applications/freesurfer/bin/qdec.bin
Reason: image not found
Trace/BPT trap
Any suggestions for a work around?
Thanks,
Carl
LinkedIn
Carl Anderson souhaite se connecter à vous sur LinkedIn :
--
Je vous invite à faire partie de mon réseau professionnel en ligne sur le site
LinkedIn.
Accepter l'invitation de Carl Anderson
http://www.linkedin.
Dear FreeSurfers,
Anyone out there know of a list of talairach coordinates for FreeSurfer
cortical regions (MNI? I suppose)?
Thanks!
Carl
--
<<•>>~<>~<<•>>~<>~<<•>>~<>~<<•>>~<>~<<•>>~<>~<<•>>
25mb limit for
gmail (could I drop the file somewhere?)
Could the T2 values need to be in a special format?
Thanks very much for your help.
Carl
On Thu, Dec 30, 2010 at 6:06 PM, Nick Schmansky mailto:ni...@nmr.mgh.harvard.edu>> wrote:
mri_segstats, for example:
mri_segstats --se
--surf fsaverage lh --cortex --glmdir
ELS_CON_June26_contrast_one
2. The FSGD file (if using one)
3. And the design matrix above
--
<<•>>~<>~<<•>>~<>~<<•>>~<>~<<•>>~<>~<<•>>~<>~<<•>>~<&g
Hi Andrew,
Looks like only 3 lines.
I'll see if I can locate a back up.
Thanks,
Carl
On Wed, Nov 15, 2017 at 3:06 PM, Hoopes, Andrew
wrote:
> Hi Carl,
>
> How many lines of text exist in your license file?
>
> Andrew
>
> On Nov 9, 2017, at 8:18 AM, Carl Anderson wro
ORMAT nii.gz
SUBJECTS_DIR /Applications/freesurfer/subjects
MNI_DIR /Applications/freesurfer/mni
FSL_DIR /usr/local/fsl
could this be a bash vs tcsh problem as I am using bash?
--
<<•>>~<>~<<•>>~<>~<<•>>~<>~<<•>
Oh yes,
/Applications/freesurfer/subjects/bert/label/aparc.annot.ctab
On Tue, Mar 25, 2014 at 11:35 AM, Douglas N Greve wrote:
> does that file exist?
> On 03/25/2014 10:04 AM, Carl Anderson wrote:
> > Dear list,
> > I tried runing the example in mris_
No...I will try running it from lables
On Tue, Mar 25, 2014 at 6:04 PM, Douglas N Greve
wrote:
>
> does it exist in the same folder that you are running the command from?
>
> On 03/25/2014 05:15 PM, Carl Anderson wrote:
> > Oh yes,
> >
> > /Applications/
Hi Bruce,
Would it be possible to get a reprint? I no longer have Harvard Library
access.
Thanks,
Carl
On Tue, Dec 5, 2017 at 4:46 PM, Bruce Fischl
wrote:
> Hi All
>
> we just published a paper on 3D microscopic imaging of connectivity and
> architecture:
>
> https://www
Kind regards,
Carl
FreeSurfer version: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551
Platform: CentOS Stream 8
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The information
ate!
Kind regards,
Carl
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The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this
gards,
Carl
From: Trolle, Carl
Sent: 09 August 2022 12:37
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] Shift in cortical parcellation, issues with
previously suggested solution
Sorry, been trying to get this right for some time before getting back t
Hi, yes that’s correct, one of the sites gets us both axial and sagittal T1s at
1mm isotropic. Ok, after some discussion I think we’ll move along without using
averaged images.
Thank you for taking your time!
Kind regards,
Carl
___
Freesurfer
I'm sending what you asked for, otherwise I'll be happy to correct this.
Kind regards,
Carl
terminal
Description: terminal
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(mris_register and mris_ca_label) as
expert option files during recon-all to correct the incorrect parcellation of
the annot.aparc-file? If so, would that also require a later Freesurfer vesion
than what we’ve been using?
Kind regards,
Carl
___
Freesurfer
spot (please see attached). This
however seems to have caused the S_front_inf (yellow outline) to split into two.
Kind regards,
Carl
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to our situation. If we do find an interaction, would
that cluster then show up on the cluster summary in the glmdir-folder?
Thank you and sorry for all the questions, just wanting to make sure we are
doing this correctly.
Kind regards,
Carl Trolle
Research Fellow
Spaulding Neuroimaging Lab
Free
you for your time!
Kind regards,
Carl Trolle
Research fellow
Spaulding Neuroimaging Lab
Platform: linux-centos7_x86_64-7.1.1-20200723-8b40551
FreeSurfer version: 7.1.1
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FS permutation tutorial with
the output from above (after including the --eres-save flag in the mri_glmfit
command)?
Kind regards,
Carl
On 12/12/2022 6:14 PM, Trolle, Carl wrote:
> Thank you for the reply,
>
> 1. Once each participant's aparc has been broken and we'v
ectly?
Thanks!
--
<<•>>~<>~<<•>>~<>~<<•>>~<>~<<•>>~<>~<<•>>~<>~<<•>>~<>~<<•>>~<>~<<•>>
Carl M. Anderson, Ph.D. (mail stop 204)
Assistant Professor of Psychiatry,
Harvard Medical School &
The Neuroim
Well our primary reason for using this sequence is to better delineate the
amygdala.
On Wed, Feb 2, 2011 at 5:03 PM, Bruce Fischl wrote:
> what do you want to do with the echoes?
>
> On Wed, 2 Feb 2011, Douglas N Greve wrote:
>
> Hi Carl, you're probably better off takin
-z.negative --sim-sign neg --overwrite
With the same result.
Any suggestions?
Thanks!
--
<<•>>~<>~<<•>>~<>~<<•>>~<>~<<•>>~<>~<<•>>~<>~<<•>>~<>~<<•>>~<>~<<•>>
Ca
Thanks,
--
<<•>>~<>~<<•>>~<>~<<•>>~<>~<<•>>~<>~<<•>>~<>~<<•>>~<>~<<•>>~<>~<<•>>
Carl M. Anderson, Ph.D. (mail stop 204)
Assistant Professor of Psychiatry,
Har
) into your
$SUBJECTS_DIR"
My stupid question:
Could this be accomplished by creating subdirectories or links in
$SUBJECTS_DIR?
Thanks,
--
<<•>>~<>~<<•>>~<>~<<•>>~<>~<<•>>~<>~<<•>>~<>~<<•>>~<
!
<<•>>~<>~<<•>>~<>~<<•>>~<>~<<•>>~<>~<<•>>~<>~<<•>>~<>~<<•>>~<>~<<•>>
Carl M. Anderson, Ph.D. (mail stop 204)
Assistant Professor of Psychiatry,
Harvard Medical School &
The Neuroimaging Center,
Hi Lindsay,
I have run FS on Lion (10.7.2) on a MacBook Pro with excellent results.
Don't know about hypo&hyper.
Carl
On Wed, Nov 30, 2011 at 4:02 PM, Lindsay Ercole wrote:
> Has anyone else had problems installing FS 5.1 on a Mac running OS 10.7.2?
> (i.e. Lion)
>
> Al
Hi
Would it be possible to somehow download V4.2.0 for Tiger running on a
PowerPC Mac?
Thanks
---
Carl M. Anderson, Ph.D.
Assistant Professor of Psychiatry,
Harvard Medical School &
The Neural Imaging Center,
McLean Hospital 115 Mil
Dear all,
is there an anatomical description for the V5/MT label?
(Freesurfer Version 4.0.5)
Thank you in advance
Christoph
Christoph Schultz, MD
University of Jena
Department of Psychiatry
07743 Jena
Germany
Dr. C. Schultz
Universitätsklinik für Psychiatrie und Psychotherapie
Philosophenweg
ce Fischl 15.06.10 14.56 Uhr >>>
Hi Christoph,
the V5/MT label we distribute is based on the work of Karl Zilles and
Katrin Amunts who defined it histologically. I don't have the reference
handy, but it shouldn't be too hard to find.
cheers
Bruce
On Tue, 15 Jun 2010, Carl
Schult
something basic or something is completely wrong.
I can access the already created files but it doesn't let me run a recon-all
for some reason.
Thanks for your help!
Carl
--
Carl Dambkowski, MS
Research Assistant
Cerebral Localization Laboratory
Columbia University Medical Center
ts
MNI_DIR Desktop/local/freesurfer/mni
With no errors.
When I give the command:
echo $FREESURFER_HOME
I also get back:
Desktop/freesurfer
Any suggestions?
Thanks,
Carl
--
Carl Dambkowski
Research Assistant
Cerebral Localization Laboratory
Columbia University Medical Center
(212
Dear Freesufers,
How do I preprocess for freesurfer, heads collected headfirst prone
instead of the normal headfirst supine?
Thanks,
Carl
---
Carl M. Anderson, Ph.D.
Assistant Professor of Psychiatry,
Harvard Medical School &
The Brain Ima
Dear all,
I compared the mean curvature between two groups using the mri_glmfit
command and the Monte carlo simulation. Is there a possibility to
extract the smoothed average curvature values of the significant
clusters for all subjects?
Thank you in advance
Best regards
Christoph Schultz
Uni
Dear all,
for a vertex-wise comparison of the mean curvature is there a
possibility to change the signed curvature values from the preprocessed
curv.mgh to unsigned (absolute) values for the glm?
Thanks in advance,
Christoph
Universitätsklinikum Jena
Körperschaft des öffent
;>>
On Thursday 13 November 2008 08:23:08 Carl Schultz wrote:
> Dear all,
>
> for a vertex-wise comparison of the mean curvature is there a
> possibility to change the signed curvature values from the
preprocessed
> curv.mgh to unsigned (absolute) values for the glm?
>
The newest
Hi Bruce,
thank you very much. That' s what I looked for.
Best regards,
Christoph
>>> Bruce Fischl <[EMAIL PROTECTED]> 13.11.08 14.43 Uhr >>>
Hi Carl,
you could read them into matlab, take the absolute value, and write them
back out again if you want, then ru
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