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Hello, any chance I could get the pass code? I'm really hoping to start my
project soon, and I haven't been able to get Freesurfer running from
scratch.
On Fri, Jun 17, 2022 at 2:05 PM Ryan Johnson wrote:
> Good afternoon!
>
> I
External Email - Use Caution
Good afternoon!
I would like the pass code to unzip the FreeSurfer 7 VirtualBox VM.
Thank you,
Ryan Johnson
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Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu
u%2Ffswiki%2FUpdateFreeview
Best,
Ruopeng
On Mar 28, 2022, at 6:45 PM, Sam Buck Johnson
mailto:samjo...@stanford.edu>> wrote:
External Email - Use Caution
Dear Freesurfer Community,
I use Freeview to render 3D views of overlays on cortical surfaces. For my
current processi
happens to know that this
functionality is absolutely not available, I would certainly like to know that,
too.
Thanks in advance.
Sincerely,
Sam Johnson
Postdoctoral Scholar
Brain and Education Lab, Stanford University GSE
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ssage that prints
to terminal and the full error report, both below.
Any help/advice is much appreciated.
Sincerely,
Sam Johnson
Postdoctoral Scholar
Yeatman Brain and Education Lab, Stanford University GSE
-
# terminal error message:
(base) samjohns@DNab40bbcb 7.2.0 % freeview
/Applica
External Email - Use Caution
The release notes for 7.0.0 claim that the -make option is "Gone" from
recon-all. This option, however, is still available and does not seem to fail.
I am running several thousand data sets on a cluster through Freesurfer 7.1.0,
and periodically the
Great - that makes sense!
Thanks again for your help in resolving this.
Eli
From: Eli Johnson
Sent: Friday, 27 January 2017 4:59 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] Cortical volume from masked region
Hi Doug,
I was reading the fourth
sorry for wasting so much
time!). In that case, what does the fourth/highlighted column represent?
Many thanks
Eli
________
From: Eli Johnson
Sent: Friday, 27 January 2017 10:24 AM
To: Freesurfer support list
Subject: Re: [Freesurfer] Cortical volume from masked regi
e you sent these files to:
+ gr...@nmr.mgh.harvard.edu
In case you'd like to modify some of the above information, please use the link
below:
http://gate.nmr.mgh.harvard.edu/filedrop2/?g=7z2xk77v3ue
Cheers,
The Martinos Center Web Team
____
From: Eli Johnson
Sent:
Ok sure, I will do it tomorrow as I don't have access to the stats file right
now
Many thanks!
From: Eli Johnson
Sent: Thursday, 26 January 2017 6:22 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] Cortical volume from masked region
Hi Doug,
Y
>
> In looking at your mask, it covers only half (or less) of the brain.
> This would explain why the total volume you get from the mask is much
> lesss than the total gm volume reported in aseg.stats.
>
>
>> On 01/20/2017 12:08 PM, Eli Johnson wrote:
>>
>> *Hi D
t;
>
>> On 01/20/2017 12:08 PM, Eli Johnson wrote:
>>
>> *Hi Doug,*
>>
>> *
>> *
>>
>> *Thanks a lot for your help!*
>>
>> *
>> *
>>
>> *I have run these commands and they complete with no problems. I can
case you'd like to modify some of the above information, please use the link
below:
http://gate.nmr.mgh.harvard.edu/filedrop2/?g=ahht5qz16h5
Cheers,
The Martinos Center Web Team
From: Eli Johnson
Sent: Wednesday, 25 January 2017 9:55 AM
To: frees
Hi Doug,
Thank you - I have uploaded the files for you.
Eli
From: Eli Johnson
Sent: Friday, 20 January 2017 5:08 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: Cortical volume from masked region
Hi Doug,
Thanks a lot for your help!
I have run these
ry/author.html#49559>
I would probably map the mask to the surface,eg,
mri_vol2surf --regheadersubject --hemi lh --projfrac 0.5 --i
scan500_std/mri/500_lobes_1-in-fs.mgz --interp nearest --o lh.mask.mgz
The run
mri_segstats --seg lh.mask.mgz --id 1 --accumulate --i lh.volume --o
lh.vol.stats
Hi all,
I am trying to extract the volume from a FreeSurfer segmented scan within a
pre-registered mask region, but only within the cortex, and wanted to check my
command.
The mask is a binary mask (value of 1 across the mask) and is in the same space
as the orig.mgz file. It covers part of
Hi there,
I am trying to run a monte carlo correction on my average subject, using the
full mri-mcsim run with 1 iterations (and about 200 participants). This is
taking a long time, and the cluster I have access to has a limit of 72 hours
which isn't long enough to finish processing. Is the
not it was intentional and/or is beneficial
to run steps 12-14 on a case where no control points were added. Thanks.
Chad
From: Harms, Michael [mailto:mha...@wustl.edu]
Sent: Tuesday, February 04, 2014 11:44 AM
To: Johnson, Chad P; Freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer
ns which would argue against
starting at the fill stage following white matter edits. I can provide any
additional information if needed to help solve this problem and any information
that can be provided regarding this would be most helpful. Thanks.
Chad P. Johnson, Ph.D.
Postdoctora
the disk is full?
>
> On 11/27/2013 07:43 AM, Johnson, Eileanoir wrote:
>>
>> Hi there,
>>
>> I am currently trying to run freesurfer version 5.3.0 on a cluster
>> and am encountering an error when running recon-all.
>>
>> The error is:
>>
Dear FS
Can you please tell me what is the default template file used in the
recon-all script ?
thanks
--
Johnson J. GadElkarim
Research Assistant, Department of Psychiatry,
PhD Candidate, Dept. of Electrical & Computer Eng.,
University Of Illinois at Chicago
Mob: 312 - 376 - 7322
Email:
In mri_segstats command line generated from autorecon, I get an error that the
option "--euler" is unknown.
== /nfsscratch/PREDICT/opt/freesurfer-5.2-beta/freesurfer/bin/recon-all
3667 if( ( -e surf/lh.orig.nofix ) && ( -e surf/rh.orig.nofix
thanks it works now :)
On 04/12/2012 12:48 PM, Douglas N Greve wrote:
> Take the inverse
>
> On 04/12/2012 01:47 PM, Johnson wrote:
>> I do the transformation in Matlab, I found out that the matlab
>> *load_mgh* function returns the vox2ras matrix, where can I find the
>&g
I do the transformation in Matlab, I found out that the matlab
*load_mgh* function returns the vox2ras matrix, where can I find the
ras2vox matrix?
On 04/12/2012 12:11 PM, Bruce Fischl wrote:
yes
On Thu, 12 Apr 2012, Johnson wrote:
The vector coordinates will be in the voxel space
On 04/12
The vector coordinates will be in the voxel space
On 04/12/2012 11:54 AM, Bruce Fischl wrote:
> Hi Johnson
>
> it depends whether you are using the ras2vox or vox2ras. It should be:
>
> V_rawavg = M_ras2vox_rawavg * inv(M_ras2vox_aseg) * V_aseg
>
> Where the V_* are 4
t; On Apr 11, 2012, at 7:48 PM, Johnson wrote:
>>
>>> there are two transformation matrices one in aseg and one in rawavg, how do
>>> I use them ?
>>>
>>> On 04/11/2012 6:12 PM, Bruce Fischl wrote:
>>>> yes
>>>> On Wed, 11 Apr 2012, Joh
so to be clear about it, suppose T1 is the matrix in aseg and T2 is the
one in rawavg,
to transform from aseg to rawavg I will apply invert(T1)*T2
is that correct?
On 4/11/2012 8:12 PM, Bruce Fischl wrote:
> Invert one and compose it with the other
>
>
>
> On Apr 11, 2012, at 7
there are two transformation matrices one in aseg and one in rawavg, how
do I use them ?
On 04/11/2012 6:12 PM, Bruce Fischl wrote:
> yes
> On Wed, 11 Apr 2012, Johnson wrote:
>
>> great, so if I can read the header from the aseg file and the header from the
>> rawavg header
but since the aseg is
> derived from the rawavg that should be exactly correct
>
>
> On Wed, 11 Apr 2012, Johnson wrote:
>
>> And it exactly does that, does it register them together or use a pre-known
>> transformation matrix
>> On 04/11/2012 3:46 PM, Bruce Fischl wro
And it exactly does that, does it register them together or use a
pre-known transformation matrix
On 04/11/2012 3:46 PM, Bruce Fischl wrote:
> Hi Johnson
>
> I believe it resamples the aseg to have the same geometry as the
> original scan.
>
> cheers
> Bruce
> On Wed, 11
Hi
Can someone tell me please in*_details_*what does this line do?
mri_label2vol --seg aseg.mgz --temp rawavg.mgz --o aseg-in-rawavg.mgz
--regheader aseg.mgz
thanks
--
Johnson J. GadElkarim
Research Assistant, Department Of Psychiatry,
PhD Candidate, Department Of Electrical& Computer
ut the geometry in the
> header (--regheader) (assuming that the two volumes share a coordinate
> system).
> doug
>
> On 04/04/2012 01:48 PM, Johnson wrote:
>> Hi
>> Can anyone tell me please how mri_label2vol works, I know what it does,
>> but I need to know how it wor
Hi
Can anyone tell me please how mri_label2vol works, I know what it does,
but I need to know how it works to take the FS space to the original
anatomy space: does it do registration or does it use a transformation
matrix. If the latest which one, where can I find it?
regards
--
Johnson J
from my understanding, scanner coordinates (i.e. considering the
resolution of each voxel)
regards
JG
On 03/27/2012 6:14 PM, Douglas N Greve wrote:
> Hi Johnson, can you be more specific? scanner coordinates? voxel
> coordinates?
>
> On 03/27/2012 06:20 PM, Johnson wrote:
>> Th
;
>
>
>
> On 03/27/2012 04:10 PM, Johnson wrote:
>> Hi
>> I have the tracts in (x,y,z) format not as an nii file
>> regards
>> JG
>> On 03/27/2012 11:25 AM, Douglas N Greve wrote:
>>> Hi Johnson, try something like this:
>>>
>>> mr
OK
T1 space is the space acquired from the machine, original anatomical space
regards
JG
On 03/26/2012 2:25 PM, Bruce Fischl wrote:
> can you post to the list so others can answer? And can you clarify
> what you mean by "T1" space?
>
> On Mon, 26 Mar 2012, Johnson wrote:
should register to
> mri/brain.mgz. You can do this with bbregister, or with any affine
> registration tool of your choice.
>
> On Mon, 26 Mar 2012, Johnson wrote:
>
>> Hi
>> I found it in a 256x256x256 space while the T1 we use is in different
>> space, I f
--regheader aseg.mgz
what is the transformation used ?
JG
On 03/26/2012 12:24 PM, Anastasia Yendiki wrote:
>
> Hi Johnson - The aparc+aseg.mgz is in the same space as the T1 used as
> input to freesurfer.
>
> a.y
>
> On Mon, 26 Mar 2012, Johnson wrote:
>
>> Hi F
space, so
my question is: what is the transformation matrix that relates the T1
which I have used in freesurfer for parcellation and segmentation with
the aparc+aseg.mgz file produced by FS?
thanks
JG
On 3/19/2012 2:36 PM, Bruce Fischl wrote:
> Hi Johnson
>
> have you tried using bbreg
Hi
This is Johnson, I am researcher at univ. of IL at chicago, I have a
question regarding freesurfer:
What is the transformation matrix that relates the freesurfer aparc+aseg
space to the aparc+aseg-in-rawavg space,
I am asking this question for the following reason:
I have white matter fiber
Hi
This is Johnson, I am researcher at univ. of IL at chicago, I have a
question regarding freesurfer:
What is the transformation matrix that relates the freesurfer aparc+aseg
space to the aparc+aseg-in-rawavg space,
I am asking this question for the following reason:
I have white matter fiber
Sorry for the noise.
This was a bug in our distribution system where version 4.05 was being
installed in /opt/freesurfer-4.1.0. It is a bug on our end.
Thanks for helping us figure this out.
Hans
On 12/12/08 6:38 PM, "Greg Harris" wrote:
> Nick,
>
> We have yet another request regarding t
working again.
Hans
--
Hans J. Johnson, Ph.D.
[EMAIL PROTECTED]
278 GH
The University of Iowa
Iowa City, IA 52241
(319) 353 8587
Notice: This UI Health Care e-mail (including attachments) is covered by the
Electronic Communications Privacy Act, 18 U.S.C. 2510-2521, is confidential and
may
ESURFER_HOME/bin/recon-all.makefile
${make_flags}" which then calls the recon-all again. The problem is that
the nested call of recon-all from the makefile does not get the command line
flags for redirecting the log files.
You help is always appreciated.
Thanks,
Hans
--
Hans J. Johnson, Ph.D.
[EMAIL P
Hello,
Is there a way to apply a custom color scale to overlays in tksurfer. It
seems that the the only options are "Green Red; Heat; "Blue Red". I would
really like to make my own colors.
Any suggestions would be greatly appreciated.
Thanks,
Hans
--
Hans J. Johnso
Bruce,
I don't know who advised us to use mris_annot_to_segmentation, but based on
the helpful comments from the freesurfer team, we have moved to using
mri_aparc2aseg instead.
Thanks Doug!
Hans
--
Hans J. Johnson, Ph.D.
[EMAIL PROTECTED]
278 GH
The University of Iowa
Iowa City, IA
. We have been
playing with it to see if we can resurrect any useful information from it.
Our standard processing with freesurfer does include the cerebellum.
Regards,
Hans
--
Hans J. Johnson, Ph.D.
[EMAIL PROTECTED]
278 GH
The University of Iowa
Iowa City, IA 52241
(319) 353 8587
> From:
Nick and Bruce,
THANKS. No segfault now! We will investigate the processing steps in the
next few days, and get back to you with our findings.
Hans
--
Hans J. Johnson, Ph.D.
[EMAIL PROTECTED]
278 GH
The University of Iowa
Iowa City, IA 52241
(319) 353 8587
> From: Nick Schmansky <
bit linux" version of the code.
Again, thank you for the quick response.
Hans
--
Hans J. Johnson, Ph.D.
[EMAIL PROTECTED]
278 GH
The University of Iowa
Iowa City, IA 52241
(319) 353 8587
> From: Bruce Fischl <[EMAIL PROTECTED]>
> Date: Fri, 24 Aug 2007 10:26:03 -0400 (EDT)
> To
/tempFScase.tgz
cd tempFScase/
csh TESTME.csh
I am hoping that if this were run through a debugger that the problem is
going to be quite easy to fix. Will you please let us know if there is
anything that we can do to help address this issue?
Thanks,
Hans
--
Hans J. Johnson, Ph.D.
[EMAIL PROTECTED]
278 GH
Developers:
I am trying to convert a nifti formated image to the mgz format using
mri_convert, but there is an error stating that the time units are unknown.
Since there are only 3 dimension, the time dimension should not matter.
mri_convert -it nii -ic 128 128 128 -oc 128 128 128 -iid 1.0 0.0 0.
gt; 149 Thirteenth Street, Room 2301 Charlestown, MA 02129 USA
>
>
>
> On Wed, 2005-07-27 at 07:52 -0500, Hans Johnson wrote:
>> Hello Freesurfer Developers,
>>
>> We are at
Bruce Fischl" <[EMAIL PROTECTED]> wrote:
> Hi Nick,
>
> could you help Hans get stuff installed? Hans: didn't you guys already
> have a version running?
>
> thanks,
> Bruce
>
>
> On Wed, 27 Jul 2005, Hans Johnson wrote:
>
>> Hell
tware" "Please try installing again".
Your help and advise is greatly appreciated.
Thanks,
Hans J. Johnson, PhD
Director of Image Processing
The Department of Psychiatry,
The University of Iowa
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Hello,
We are tryying to convert some raw images from our GE LX scanner into cor format using "mri_convert" with plans to do inflation etc.
We have tried a number of ways (see below) to no avail. The program tells us it is "reading images from 001/I.001," but never comes back. If anyone has
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