External Email - Use Caution
Dear freesurfer,
Kindly send me the 7z file unlock password
Thank you
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Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information i
t city (Miami, FL) and
renewable for multiple years. Thanks!
Anthony
--
Anthony Steven Dick, Ph.D.
Associate Professor
Director, Cognitive Neuroscience Program and Graduate Certificate in Cognitive
Neuroscience
Florida International University MM Campus AHC4 454
Department of Psychology and Cent
/science/article/pii/S1361841515000171
Anthony
--
Anthony Steven Dick, Ph.D.
Associate Professor
Director, Cognitive Neuroscience Program and Graduate Certificate in Cognitive
Neuroscience
Florida International University MM Campus AHC4 454
Department of Psychology and Center for Children and
$50K plus benefits postdoc in Miami, FL, two years. Please take a look!
http://myweb.fiu.edu/adick/post-doctoral-fellow-positions/
--
Anthony Steven Dick, Ph.D.
Associate Professor
Director, Cognitive Neuroscience Program and Graduate Certificate in Cognitive
Neuroscience
Florida International
convert to
a single .nii file for input into Freesurfer. You may be able to skip the
Osirix step with what you have.
Anthony
On 6/7/17, 11:26 AM, "freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Emily
Rogers" wrote:
Do you have any recommendations for programs to convert t
, and that takes time.
However, I could tell you what files are in the MRI directory? Or provide other
information that might be helpful? If you know what files the segmentation
needs I could possibly just run those specific flags.
Anthony
From: on behalf of "Iglesias Gonzalez,
Eugenio&qu
–autorecon2 and –autorecon3 that
we could run so we don’t have to re-freesurf everything, or would it be better
to just run –all? In other words, what are the minimum files needed to get
hippocampal-subfields-T1 to run?
Thanks for any suggestions!
Anthony
—
Anthony Steven Dick, Ph.D.
Associate
Hello,
I got it running. I just deleted all old license files, resent the the
registration. When I got the email I created both a .license and a
license.txt in $Freesurfer_Home, and it worked. Just one of those things
I guess?
Anthony
On 2/3/17 12:34 PM, Z K wrote:
> Anthony,
>
>
Thanks Matt. I already tried it with a new registration, but it doesn't
hurt to try it again. That may be where the issue is. I'll post if that
turns out to be the problem. Thanks!
Anthony
On 2/2/17 6:28 PM, Matt Glasser wrote:
Like I said, they changed the format at some point a
encountered this issue and have been using Freesurfer for 11
years. If history is any guide, it will probably turn out to be
something stupid that I did :)
Anthony
On 2/2/17 3:40 PM, Trisanna Sprung-Much wrote:
The .license that it comes with is not the same as the license.txt
that you have
140 Feb 2 15:06 .license
[38c9862eb0b0:/Applications/freesurfer] adick%
Any ideas?
Thanks!
Anthony
--
Anthony Steven Dick, Ph.D.
Associate Professor
Director, Cognitive Neuroscience Program and Graduate Certificate in Cognitive
Neuroscience
Department of Psychology
Florida Internat
A recommendation: talk to a statistician about implementing an analysis
for missing data. There are a number of options that may be available to
you to allow a more straightforward and scientifically sound approach.
Anthony
On 1/19/17 10:15 AM, Greenberg, Jonathan wrote:
Dear FreeSurfer
/mattcieslak/easy_lausanne
Anthony
On 1/18/17 4:57 PM, Aya Kabbara wrote:
Thank you..
Actually, I realized that using tksurfer I can do a manual parcellation.
However, I need an automatic parcellation. Is there a way?
Get Outlook for Android <https://aka.ms/ghe
the sender and properly
dispose of the e-mail.
--
Anthony Steven Dick, Ph.D.
Associate Professor
Director, Cognitive Neuroscience Program and Graduate Certificate in Cognitive
Neuroscience
Department of Psychology
Florida International University Modesto A. Maidique Campus AHC4 454
11200 S.W. 8th
in both areas.
http://cn.fiu.edu/ and https://cscap.fiu.edu/
Anthony
On 10/28/16 6:54 PM, Bruce Fischl wrote:
> Hi All,
>
> just a note to say that if there are any faculty in clinical psychology
> programs looking for a grad student for next September, you would be
> extreme
Please distribute!
http://myweb.fiu.edu/adick/post-doctoral-fellow-positions/
--
Anthony Steven Dick, Ph.D.
Associate Professor
Director, Cognitive Neuroscience Program and Graduate Certificate in Cognitive
Neuroscience
Department of Psychology
Florida International University Modesto A
Dear colleagues--Please share widely, we are looking to hire
immediately. Thanks!
The S.E.L.F Regulation Laboratory (http://self-regulationlab.fiu.edu/;
PI Dr. Paulo Graziano, PhD) in collaboration with the Developmental
Cognitive Neuroscience Laboratory (http://dcn.fiu.edu; PI Dr. Anthony
Hello,
See the paper at this link: http://www.ncbi.nlm.nih.gov/pubmed/25086832
Anthony
> On 8/2/16 12:26 PM, Ritobrato Datta wrote:
>> Hello All,
>>
>> We are studying adolescents with HIV and are interested in
>> frontostriatal tracts (anything from frontal co
Hello,
This paper is very relevant to this issue:
Sanfilipo MP, Benedict RH, Zivadinov R, Bakshi R (2004) Correction for
intracranial volume in analysis of whole brain atrophy in multiple
sclerosis: the proportion vs. residual method. Neuroimage 22:1732–1743.
Anthony
On 6/10/16 9:34 AM
issue.
Anthony
On 5/25/16 10:34 AM, Alan Francis wrote:
Hi Imagers -
I am looking at the Uncinate fasciculus in a Cannabis use disorder
(CUD). I found that CUD subjects have significantly shorter tract
length and a significant group x side interaction in comparison with
controls. Have you
Hello Chiara,
I believe there is some precedent for using Freesurfer for group
analysis without warping:
http://onlinelibrary.wiley.com/doi/10.1002/hbm.20158/abstract
Anthony
On 2/15/16 1:08 PM, Chiara Bulgarelli wrote:
Dear All,
I would like to ask you for some advice about segmenting MRI
Another option is to open the files in OsiriX, and export to DICOM from
there. This does not, to my knowledge, have a batch option though.
Anthony
On 1/6/16 9:35 PM, Bruce Fischl wrote:
Hi John
Luca Marinelli (ccd) might be able to help you.
cheers
Bruce
On Thu, 7 Jan 2016, John Anderson
Dear Colleagues,
Please find below an advertisement for our Postdoctoral position at
Florida International University, Miami, FL. Details are also provided
in the attached pdf. Thank you!
Anthony
>>>
The Cognitive Neuroscience and Imaging Center at Florida International
University
Don, if that doesn't work, try the procedure outlined in this paper,
although it is rather involved:
http://www.architalbiol.org/index.php/aib/article/viewArticle/1221
Anthony
On 11/17/15 8:27 AM, Bruce Fischl wrote:
Hi Don
it's impossible to say. Certainly 6.0 will be your best
Hello Bruce,
I used the rebuild_gca_atlas.csh script (attached). I only commented out
the cluster configuration options. Otherwise the script is unchanged.
The process fails in the same place when we use one subject.
Thanks!
Anthony
On 10/13/15 12:07 PM, Bruce Fischl wrote:
and how did
ioned covariance matrices regularized
reading 'nu.mgz'...
freeing gibbs priors...done.
bounding unknown intensity as < 18.3 or > 695.1
Segmentation fault
So it appears to be a problem with the gca creation? However, mri_info
on both RB_all_2014-08-21.gca and RB_one_2015-10-13.gca look id
brains with a file called
seg_edited.mgz. If you don't get the error, then maybe it is a problem
with our local settings (although we get this error on multiple
different computers). Thanks for any help!
Anthony
On 7/20/15 2:30 PM, Anthony Dick wrote:
> Hello,
>
> I was wonderi
AFNI's @SUMA_Make_Spec_FS command will convert the aparc+aseg file for a
particular subject to BRIK/HEAD format, which can easily go to nifti.
This might get you what you want in a couple of easy steps.
Anthony
On 7/31/15 2:26 PM, Bruce Fischl wrote:
HI Pantea
our atlases contain a lot
Hello,
I was wondering if these got uploaded correctly. Please let me know if I
made a mistake and thanks,
Anthony
On 7/9/15 1:41 PM, Bruce Fischl wrote:
> sure
> On Thu, 9 Jul 2015, Anthony Dick wrote:
>
>> Hello Bruce,
>>
>> I am still getting this error after r
encounter, to varying degrees. I don't know
how Freesurfer deals with R1 maps and that may or may not make a difference.
So the short answer to your question is that you should check all of the
subjects.
Anthony
On 7/9/15 5:04 PM, O'Shea,Andrew wrote:
> I'm by no means an expe
Hello Bruce,
I am still getting this error after re-running autorecon1 in the newest
version of FS. Can I upload two brains and see what is the issue? I'm a
bit stumped on this one.
Anthony
On 5/26/15 12:21 PM, Bruce Fischl wrote:
> Hi Anthony
>
> sorry, I know you've poste
orms/talairach_one.lta'...
mri_read(): couldn't determine type of file
//subjects/4/mri/transforms/talairach_one.lta
mri_em_register: could not open input volume
//subjects/4/mri/transforms/talairach_one.lta.
--
Anthony Steven Dick, Ph.D.
Assistant Professor
Director, Cognitive Neu
Hello,
I just wanted to give this message a bump. Thanks!
Anthony
On 5/15/15 9:49 AM, Anthony Dick wrote:
> Hello,
>
> I have been stumped by this error I keep getting using the
> rebuild_gca_atlas.csh script. I am trying to build a cerebellar atlas,
> so I am wondering if the
/4/mri/transforms/talairach_one.lta'...
mri_read(): couldn't determine type of file
//subjects/4/mri/transforms/talairach_one.lta
mri_em_register: could not open input volume
//subjects/4/mri/transforms/talairach_one.lta.
--
Anthony Steven Dick, Ph.D.
Assistant Professor
Director, Cognitive Neu
We have the same problem using the same coil (GE 750; mainly occipital
pole), so any suggestions for how to correct this would be very helpful.
Thanks!
Anthony
On 1/5/15, 7:05 PM, Douglas Merkitch wrote:
Hello Freesurfer experts,
We have T1 data from a 3T GE 32-channel head coil that
nough
subjects would suggest "binning" them into smaller ages. This would be a
nice resource regardless, so hopefully this serves as a bump on the
subject number question.
Anthony
On 12/18/14, 2:43 PM, Jason Tourville wrote:
We are planning to generate a surface template from e
Wed Nov 5 23:58:13 EST 2014
For more details, see the log file
/Users/adick/Documents/013_new/scripts/recon-all.log
To report a problem, see
http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
On 11/5/14, 2:51 PM, Z K wrote:
> Hello Anthony,
>
> The problem isnt with the location of
for freesurfer/bin using the chmod command: chmod
-R a+x freesufer/bin/*
Not really sure what the issue is, but it seems to be related to the
upgrade to Yosemite.
Anthony
On 11/5/14, 1:39 PM, Martin Reuter wrote:
Hi Anthony,
wasnt the answer (by Mathew Riddle 10/23) to this to move Bert to a
?Hello,
I am encountering the exact same problem on Yosemite (10.10). The log file is
attached. Any ideas? I am pretty stumped.
Anthony
From: freesurfer-boun...@nmr.mgh.harvard.edu
on behalf of Matthew Riddle
Sent: Thursday, October 23, 2014 7:48 AM
To
Hello,
This shell script may do close to what you want it to do, so you could
modify it. It does it within AFNI using converted freesurfer surfaces.
http://faculty.fiu.edu/~adick/links/alphasurface.tcsh
If you see any errors please let me know.
Anthony
On 7/18/14, 12:39 PM, Douglas Greve
Hello Angela,
Have you tried just running the specific commands to get the output file
you need?
https://surfer.nmr.mgh.harvard.edu/fswiki/ReconAllDevTable
Anthony
On 7/7/14, 10:52 AM, angela.fav...@unipd.it wrote:
> Dear Freesurfer team
> I am sorry to bore you again with my problems,
-help to see the command line syntax. Look for
the relevant files in the SUMA folder. You can also edit the @SUMA
program to add any file you have newly created that is not a standard
freesurfer file.
Anthony
On 6/9/14, 11:15 AM, Tara Ann Miskovich wrote:
> Thank you Paul that is very help
-help to see the command line syntax. Look for
the relevant files in the SUMA folder. You can also edit the @SUMA
program to add any file you have newly created that is not a standard
freesurfer file.
Anthony
On 6/9/14, 11:15 AM, Tara Ann Miskovich wrote:
> Thank you Paul that is very help
Hello,
Can the Freesurfer software register two flatmaps that are not created
in Freesurfer? Would they just need to be converted? And which program
is appropriate?
Anthony
--
Anthony Steven Dick, Ph.D.
Assistant Professor
Director, Cognitive Neuroscience Program and Graduate Certificate in
rlay value (lower right of GUI if I recall).
Anthony
On 2/27/13 4:59 PM, Douglas N Greve wrote:
> You can load the segmentation as both a segmentation and an input volume
> in tkmedit, eg
>
> tkmedit subject orig.mgz -aux gmroi_volume.nii.gz -seg gmroi_volume.nii.gz
>
> You can then se
Hi Bruce,
Do you mean use the flags for the individual mri_normalize command from
the command line? If so, which parameters are best to modify in this
situation?
http://surfer.nmr.mgh.harvard.edu/fswiki/mri_normalize
Anthony
On 9/11/12 3:06 PM, Bruce Fischl wrote:
> Hi Anthony
>
>
Hello--was just thinking about upgrading to Mountain Lion. Am I to
assume freesurfer will not work if I do this?
Anthony
On 9/10/12 11:58 AM, Nick Schmansky wrote:
> Fidel,
>
> Sorry, but the GEMS tools are not built for our mac powerpc distribution.
> we no longer support that pla
lease contact the Partners Compliance HelpLine at
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Dir
Hi Bruce,
Can you point me somewhere in the right direction? Is there some example
I could start with? I don't use Matlab, although it seems similar to R
so I should be okay with learning the syntax, but I just need a place to
start.
Anthony
On 4/20/12 4:02 PM, Bruce Fischl wrote:
>
Thanks Bruce. What's the easiest way to "paste" those labels. Manually
through tkmedit, or through the command line?
Anthony
On 4/20/12 3:53 PM, Bruce Fischl wrote:
> HI Anthony
>
> I would make sure to include an entire brain labeling in the training
> set. You
., RB_all_withskull_2012-04-13.gca instead
of e.g., RB_all_withskull_2008-03-26.gca.
Basically, I want to apply the new cerebellar parcellation to existing
freesurfed brains.
Anthony
--
Anthony Steven Dick, Ph.D.
Assistant Professor
Department of Psychology
Florida International University
Modesto
redefine the data structure?
Anthony
--
Anthony Steven Dick, Ph.D.
Assistant Professor
Department of Psychology
Florida International University
Modesto A. Maidique Campus DM 296B
11200 S.W. 8th Street
Miami, FL 33199
Phone: 305-348-4202 (try this first)
Lab Phone: 305-348-9057 or 305-348-9055
Fax
Hello--was wondering if you guys have any ideas. I am a bit stumped.
Thanks for the help!
Anthony
On 4/4/12 4:50 PM, Anthony Dick wrote:
> No, but the conversion from the original .nii works...
>
> [miles:[PATH]] adick% mri_convert chuman_1.mgz junk.mgh
> mri_convert chuman_1.mgz ju
t;
> On 04/04/2012 12:29 PM, Anthony Dick wrote:
>> Hello Bruce,
>>
>> Sorry--just getting back to this project. The basic problem is that I am
>> trying to align a cerebellar parcellation with the underlay in tkmedit.
>> I was working on this with Doug, and his su
.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg21209.html).
Here is the information you requested.
Anthony
[miles:[PATH]] adick% mri_info chuman_1.mgz
Volume information for chuman_1.mgz
type: MGH
dimensions: 141 x 103 x 87
voxel sizes: 0.8083, 0.9715, 0.8214
Hello--I am giving this message a bump. Please let me know if there are
any suggestions. Thanks!
Anthony
On 2/15/12 1:43 PM, Anthony Dick wrote:
> Hello,
>
> I have run the following successfully, but when I have moved on to other
> brains I get:
>
> mri_label2vol --seg c
8GB RAM.
Anthony
--
Anthony Steven Dick, Ph.D.
Assistant Professor
Department of Psychology
Florida International University
Modesto A. Maidique Campus DM 296B
11200 S.W. 8th Street
Miami, FL 33199
Phone: 305-348-4202 (try this first)
Lab Phone: 305-348-9057 or 305-348-9055
Fax: 305-348-3879
Em
Hello Rashmi,
This is an AFNI issue. You'll have to read the SUMA manual and convert
your Freesurfer files to AFNI-readable surfaces using @SUMA_Make_Spec_FS
and other commands. There are too many steps to list here, but it is not
too difficult once you get the hang of it.
Anthony
On
That did the trick! Thanks very much!
Anthony
On 1/26/12 12:31 PM, Douglas N Greve wrote:
> OK, try running
> mri_label2vol --seg chuman_1_do.mgz --temp orig.mgz --regheader
> chuman_1_do.mgz --o chuman_1_do.conf.mgz
> Then load chuman_1_do.conf.mgz as a segmentation.
> doug
&
rom?
>
> Anthony Dick wrote:
>> Here is the command, in case I didn't run it right.
>>
>> adick% mri_convert chuman_1_do_shft.nii --in_like orig.mgz
>> chuman_1_do_shft_new.nii
>> mri_convert chuman_1_do_shft.nii --in_like orig.mgz
>> chuman_1_do_sh
AFNI.
Anthony
On 1/13/12 2:11 PM, Douglas N Greve wrote:
> Hi Anthony, how are you creating the parcellation? Are you generating
> it off the orig.mgz?
> doug
>
> Anthony Dick wrote:
>> Hello,
>>
>> I am trying to train a cerebellar atlas based on 20 manually
>
alignment.
However, loaded in AFNI the underlay and overlay of course align. Is
there a quick fix to get them in alignment?
Anthony
--
Anthony Steven Dick, Ph.D.
Assistant Professor
Department of Psychology
Florida International University
Modesto A. Maidique Campus DM 296B
11200 S.W. 8th Street
mpliance HelpLine
> at
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> error
> but does not contain patient information, please contact the sender and
> properly
> dispose of the e-mail.
>
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Assistant Professor
D
o simulation.
>>
>> Thank you,
>> Tanja.
>> ___
>> Freesurfer mailing list
>> Freesurfer@nmr.mgh.harvard.edu
>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>
>>
>>
--
Anthony Steven Dick, Ph.D.
Assistant Professor
Departme
be published yet (unless I missed it). Any added pathways should have
to meet the same standards.
Anthony
On 6/15/11 1:07 PM, Bruce Fischl wrote:
> Hi Anthony
>
> we included the tracts that we found that we could segment reliably,
> under the guidance of a trained neuroanatomist.
tates the application of tractography to large datasets".
This seems to me to be a horrible idea. Tractography is not at this
point a completely data driven procedure.
Anthony
On 6/15/11 12:44 PM, Anastasia Yendiki wrote:
>
> Hi Anthony - The labeling was done based on Wakana et
; Catani's arcuate fasciculus is based on one paper etc.). Is
it such a good idea to go automatically identifying white matter tracts
without saying how they are identified?
Anthony
On 6/15/11 12:07 PM, Seán Froudist Walsh wrote:
Hi Anastasia,
Thanks for getting back to me and well done o
>> figuring out a good way to do the cut.I have tried using the "Make
>> closed path" and "Custom fill" options in tksurfer, but am having
>> trouble getting those to make a clean cut right at y=26.
>>
>> I'd appreciate any suggestions!
>>
dy? I know Makris
and colleagues had done something similar to this, but I am not sure if
it has been developed for Freesurfer.
Anthony
--
Anthony Steven Dick, Ph.D.
Assistant Professor
Department of Psychology
Florida International University
Modesto A. Maidique Campus DM 296B
11200 S.W. 8th Street
if
it has been developed for Freesurfer.
Anthony
--
Anthony Steven Dick, Ph.D.
Assistant Professor
Department of Psychology
Florida International University
Modesto A. Maidique Campus DM 296B
11200 S.W. 8th Street
Miami, FL 33199
Phone: 305-348-4202 (try this first)
Lab Phone: 305-348-9057 or
Would this problem also apply for fMRI or diffusion weighted scanning?
On 12/20/10 10:41 AM, Bruce Fischl wrote:
> Hi Anthony,
>
> I don't think so. The problem is that the fundamental T1 contrast is
> different at 3T than att 1.5T, which results in systematic biases.
>
>
antly?
Always wondered about this.
Anthony
On 12/20/10 9:26 AM, Martin Reuter wrote:
> Hi Diederick,
>
> In a longitudinal study you need to ensure identical acquisition and
> processing, else you'll introduce a systematic bias.
> Some of my recent analyses indicate that even upd
Pruden) and the Developmental Cognitive Neuroscience Laboratory
(directed by Dr. Anthony Dick) at Florida International University needs
a highly capable, organized, and well-spoken individual to serve as a
full-time laboratory coordinator for both labs. We seek a recent college
graduate who has
mr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
> The information in this e-mail is intended only for the person to whom it is
> addressed. If you believe this e-mail was sent to you in error and the e-mail
> contains patient information, please contact the Partners Compliance HelpLi
is it possible to modify this procedure to
also output maximum cluster sizes in terms of number of nodes, rather
than area?
Can you please let me know if I am mistaken in any of these assumptions?
Thanks in advance.
Anthony
--
Anthony Steven Dick, Ph.D.
Post-Doctoral Fellow
Human Neuroscience
One way to do it is to convert the Freesurfer brains to AFNI readable
surfaces using AFNI's SUMA add-on (http://afni.nimh.nih.gov/afni/suma).
The steps are detailed in the documentation.
Anthony
Dickinson, Annelise (NIH/NIMH) [F] wrote:
> Hi all,
>
> Sorry if this is a REALLY
/structural equation modeling, EEG/MEG, TMS,
behavioral experimental methods, or neuroinformatics would also be
advantageous.
Applicants should email their CV and a statement of research interests
to Professor Steven Small (sm...@uchicago.edu).
--
Anthony Steven Dick, Ph.D.
Post-Doctoral Fellow
ld be intercepted, corrupted, lost,
>> destroyed, arrive late or incomplete, or contain viruses. The sender
>> therefore does not accept liability for any errors or omissions in the
>> contents of this message, which arise as a result of e-mail transmission.
>>
>>
/kwckol), but those papers
do not use Freesurfer. Anything with Freesurfer?
Anthony
--
Anthony Steven Dick, Ph.D.
Post-Doctoral Fellow
Human Neuroscience Laboratory
Department of Neurology
The University of Chicago
5841 S. Maryland Ave. MC-2030
Chicago, IL 60637
Phone: (773)-834-7770
Email: ad
Hi Seok-
Is there a compelling reason to combine the two hemispheres? Are you
trying to identify similar vertices in both hemispheres?
Anthony
p...@netfilter.com.br wrote:
I think Bruce or Douglas can explain better.
However, the reason for both hemispheres being separated is that you
Hi Bruce,
That would be great. I'm aware of the difficulty in putting partial volume
information into segmentation, but maybe it could help to achieve other useful
information as aseg.stats only provides the total volume for each label.
Thanks,
Anthony
--- On Thu, 5/3/09, Bruce Fischl
Hi Bruce,
Thanks a lot for your reply . Is there anyway that I can get a mask for a
certain class (e.g WM) after partial volume correction using FS ? Or is it
possible for you to provide more details of it so I can reproduce the
calculation to get the mask ?
Anthony
--- On Thu, 5/3/09, Bruce
Hi all,
In recon-all pipeline , mri_segstats runs with -pv mri/norm.mgz
option ,as written from
http://surfer.nmr.mgh.harvard.edu/fswiki/mri_segstats , it is used to
compensate partial voluming. I wonder what exactly does this do, as the volumes
given by aseg.stats are different from
aseg.mgz a
Hi Mike,
Thanks for your reply . I'll give it a try.
Anthony
--- On Tue, 13/1/09, Michael Harms wrote:
From: Michael Harms
Subject: Re: [Freesurfer] GM calculation?
To: slam_...@yahoo.com
Cc: freesurfer@nmr.mgh.harvard.edu
Date: Tuesday, 13 January, 2009, 9:28 PM
Hi Anthony,
For cor
en by aseg.mgz ?
Thanks
Anthony
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Hi all,
Recently I tried out longitudinal processing on my 1st time point subjects (
directly generated by recon-all, no post processing or manual editing involved)
. Then I ran asegstat2table for both 1st and 2nd time point subjects to compare
cortical WM and cortical cortex volumes. From what
Hi Bruce,
Thank you for your prompt reply ,guess I can only deal with GM an WM with
freesurfer for now. I read somewhere in our archive that you were considering
other approaches to compute sulcal CSF like using T2-images , will it be
available for distribution ?
Thanks,
Anthony
--- On Wed
Dear all,
Is there anyway to calculate CSF volume using freesurfer? I only know
freesurfer supports GM and WM calculation based on aseg.mgz and aseg.stats .
Thanks,
Anthony
New Email addresses available on Yahoo!
Get the Email name you've always wanted on the new @ymai
If you are just getting started, this is the best place.
http://surfer.nmr.mgh.harvard.edu/fswiki/RecommendedReconstruction
Once you have the basics the wiki is much more manageable. I think
manual is at the bottom of the list because functionality is at the top.
Anthony
Eliezer Kanal wrote
Hi Liat-
If you converted directly using mri_convert, you may run into some
problems. If so, I suggest using the program Ziad wrote
(@SUMA_Make_Spec_FS) which takes care of some of the freesurfer/AFNI
conversion problems automatically. See the AFNI posts on this issue.
Anthony
Doug Greve
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--
Anthony Steven Dick, Ph.D.
Post-Doctoral Fellow
Human Neuroscience Laboratory
Department of Neurology
The University of Chicago
5841 S
Hello-
Are there any plans to implement the cerebellum segmentation of Makris
et al. (2005; Neuroimage, 25) as an automated segmentation into part of
the freesurfer workflow?
Anthony
--
Anthony Steven Dick, Ph.D.
Post-Doctoral Fellow
Human Neuroscience Laboratory
Department of Neurology
The
hough
mri_convert in Freesurfer may do what you want (not sure if it preserves
the transformation though...
Anthony
Garrett McGrath wrote:
To the freesurfer people:
I would like to know if there is a way to generate a new volume
file from the original volume file using the matrix of transforma
Hi Graham-
The link below has a step-by-step method of editing labels in
Freesurfer. It may be of some use.
http://www.ci.uchicago.edu/wiki/bin/view/HNL/EditROI
Please let me know if it makes things any easier.
Anthony
Bruce Fischl wrote:
Hi Graham,
is this on an individual subject or on
I have been able to run it with --no-symlink (the flag has to go last),
but I get errors like this:
mris_make_average_surface: could not read surface file
/Volumes/data/NL-GCS/subjects/freesurfer_3.0.1/GCS_adults/--no-symlink/surf/rh.sphere.reg
Thanks.
Anthony
Furlong, Carolyn wrote:
Hi
t;writing Gaussian curvature to ./rh.white_avg.K...done.
>writing mean curvature to ./rh.white_avg.H...done.
>reading group avg surface area 1032 cm^2 from file
and ended with this error.
>ln: rh.sphere: Operation not supported
Any ideas?
Thanks.
--
Anthony Steven Dick, Ph.D.
Post-Doctoral
File->Label->Load Color Table).
3). After editing the current aparc.annot, open View->Windows->Labels.
You will need to relabel the newly created label using the Labels
window. If you don't do this, the parcellation will not save the changes.
Anthony
Goldman, Aaron (NIH/NIMH) [C]
Does anyone have any other ideas about why it would just be appearing
now?
We know it was not a problem in the past. Additionally, we have recently
tried a very old freesurfed brain (over 2 years old), and it comes out
pretty good.
Any ideas?
Thanks.
Anthony
--
Anthony Steven Dick, Ph.D.
Hi Nick-
Yes, I am. If tksurfer would still work on an Intel, then this appears
to be the problem. Will wait for a new release. Thanks.
Anthony
Nick Schmansky wrote:
Anthony,
Are you using a new Intel-processor based Mac? If so, we don't
support that just yet. The 'X Error&#
d not found.
tcsh: gcc: Command not found.
FSL_DIR /Applications/freesurfer/fsl
Any help at all would be most appreciated.
Thanks,
Anthony
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