_
From: freesurfer-boun...@nmr.mgh.harvard.edu
on behalf of Lilla Zollei
Sent: Wednesday, April 22, 2020 3:02 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] Infant freesurfer
Yes, I would
?
_
From: freesurfer-boun...@nmr.mgh.harvard.edu
on behalf of Lilla Zollei
Sent: Wednesday, April 22, 2020 2:26 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] Infant freesurfer
Hi Colleen,
The manual editing option has not yet been
Hi Colleen,
The manual editing option has not yet been added to the pipeline.
Best, Lilla
On Wed, 22 Apr 2020, COLLEEN PLETCHER wrote:
>
> Hello. I am working with the infant Freesurfer pipeline. I have noticed that
> some of our subjects may need to be manually edited, and then run through t
Our default setting to run mrri_cvs_register on our cluster is to use
35gb.
Lilla
On Tue, 29 Oct 2019, Nader Razmara wrote:
Hi expertsI use freesurfer vm 5.3 on oracle vb 6 with 8 GB ram.
When i use mri_cvs_register as:
mri_cvs_register --mov subjid --mni or
mri_cvs_register --mov subjid -
Hi Stefano,
If you suspect that the error is due to the small deformation values, can
you try to use -odt float to specify the output data format?
Lilla
On Tue, 29 Oct 2019, Stefano Zappala wrote:
Hi there,
I am having problem reading the final_CVSmorph_toS131032017_Supine.m3z
transfor
Hi Anna,
See attached.
Lilla
On Fri, 25 Oct 2019, Crawford, Anna wrote:
External Email - Use Caution
Hello,
Just a quick question. We recently installed the new thalamus segmentation
subroutine. It’s really wonderful, and much promise to our work.
I can’t find a lookup
Hi All,
We are looking into replacing our old Wacom segmentation tablet and the
two options that I have found so far are the
* Wacom Cintiq Pro 32
and
* Microsoft Surface Studio 2
Neither of these are linux compatible, which has created some issues
in the past.
Are there any groups out th
Hi Dimitrios,
Agree with Burce. The youngest we have processed with the standard
pipeline was about 4.5yrs.
Lilla
On Wed, 18 Sep 2019, Bruce Fischl wrote:
Hi Dimitrios
it's kind of an empirical question. Lilla does have some newer tools you
might consider instead of things aren't as accura
"mri_aparc2aseg" should work.
Lilla
On Fri, 2 Aug 2019, Mahshid Fouladivanda wrote:
Dear Experts,
I have a neonate MRI Image which its parcellation file, surface files and the ribbon are
not created by freesurfer. I have created an annotation file for it using
"write_annotation". Now, fo
a cvs registration flag and not an infant_recon one.
Best, Lilla
>
> On Thu, Jul 11, 2019 at 3:26 PM Lilla Zollei
> wrote:
>
> Hi Mahmoud
>
> Currently the -i flag is not activated. I can add that in a bit.
>
> Can you create soft links to your
Hi Mahmoud
Currently the -i flag is not activated. I can add that in a bit.
Can you create soft links to your input images?
Lilla
On Thu, 11 Jul 2019, Mahmoud wrote:
>
> Hi all,
> I have my data organized in this way:
> study/sub/T1/data.nii.gz
>
> infantFS wants the input as study/sub/mpr
Hi Anna,
We have not tried the pipeline on 1.5T data, but you are welcome to
download the beta version and see how well it is doing.
https://surfer.nmr.mgh.harvard.edu/fswiki/infantFS
Lilla
On Thu, 11 Apr 2019, Crawford, Anna wrote:
>
> Hello,
>
>
> I was looking to use the Freesurfer infan
__
From: freesurfer-boun...@nmr.mgh.harvard.edu
on behalf of Lilla Zollei
Sent: Thursday, February 7, 2019 10:31 AM
To: Freesurfer support list
Subject: Re: [Freesurfer] applyMorph gives (1 1 1) coordinates
Hi Noam,
Maybe a I am a bit confused
Hi Noam,
Maybe a I am a bit confused but in the attached file I do not see the
(1 1 1) coordinate that correspond to invalid coordinate
locations. Is the file that you attached your
electrodes_morph_to_colin27.txt or is it the terminal output?
Lilla
On Thu, 7 Feb 2019, Peled, N
We are currently working on including cerebellar parcellation in the FS
recon pipeline, but this feature is not yet available. Independently, you
could import and use the SUIT ROIs, but we do not have a pipeline for
that.
On Thu, 15 Nov 2018, std...@virgilio.it wrote:
Is available the seg
/CoordinateSystems?
Thanks!
Noam
__
From: freesurfer-boun...@nmr.mgh.harvard.edu
on behalf of Lilla Zollei
Sent: Wednesday, August 1, 2018 2:33:19 PM
To: Freesurfer support list
Subject: Re: [Freesurfe
Hi Derek,
We do not use the standard FS pipeline for the analysis of the age group
of your interest. In general, we have seen it being successfully used
on subjects down to 4.5yrs of age, but 25 mo is quite young to be analyzed
by the adult template. I assume, without seeing your data, that yo
__
From: freesurfer-boun...@nmr.mgh.harvard.edu
on behalf of Lilla Zollei
Sent: Wednesday, August 1, 2018 8:35:49
Hi Noam,
Can you can use the --mni flag?
"Use the CVS atlas in MNI152 space as a target for registration (as
opposed to the default CVS template)"
Lilla
On Wed, 1 Aug 2018, Peled, Noam wrote:
I need to transfer one of our patient's electrodes locations (depth electrodes,
they aren't loc
Hi Kelli,
Our beta version is ready and I can set you up with it. Please, send me a
note directly and I can help you with that.
Lilla
On Sun, 8 Jul 2018, Dominick, Kelli wrote:
External Email - Use Caution
Hello Freesurfer Experts,
I am hoping to use Freesurfer in infa
Hi All,
Many of you might know Rahul personally from his time spent in Boston, at
the Martinos Center and on Freesurfer (eg.: 'Desikan-Killiany' cortical
atlas). The below is a great piece about his current struggles with ALS
(and amazing work productivity):
https://www.washingtonpost.com/ne
Hi Aicha.
We have a different processing stream for infants. It is not only the
skullstripping that will not work for your cases but much of the remaining
pipeline. We are getting ready to release that pipeline.
Lilla
On Fri, 12 Jan 2018, Dijkshoorn, A.B.C. (Aicha) wrote:
Dear free surfer
Hi David and Noam,
I have fixed a bug in applyMorph. If you have access to the dev version of
the code base that should be available to you in a day. If not, send and
email to the list and we can provide you with it. Here are the steps:
(1) Run mri_cvs_register command. As the applyMorph cod
The currently available FS pipeline does not work for newborn infant brain
MRI.
Lilla
On Tue, 2 Jan 2018, Ting Li wrote:
> Dear Stuff,
>
> Happy new year.
>
> Does Freesurfer work for new born baby MRI or not? If I want to use it for
> baby MRI, what should I pay attention to? Thanks a lot!
>
Hi Gianluca,
> I am working with data coming from two different versions of Freesurfer, v5.1
> and v6.
> As measurements looks different (an excerpt below from aseg.stats files), I
> am trying to see if that difference is statistically relevant.
> Could you anticipate something with this respe
pared to or just as a
common spatial coordinate space where you can do your comparison?
Best, Lilla
>
> From: freesurfer-boun...@nmr.mgh.harvard.edu
> [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Lilla Zollei
> [lzol...@nmr.mgh.harva
Hi Aicha,
We do have a pipeline and I am trying to get it released by the end of the
year.
You should be able to build your own template independent from the adults,
but you will not be able to just plug this new one in to the adult
processing pipeline.
Lilla
On Mon, 27 Nov 2017, Dijksho
Hi Chintan,
Can you send your snapshot again? I do not have access to the attachment.
Best, Lilla
On Mon, 13 Nov 2017, Mehta, Chintan wrote:
Dear FreeSurfer users,
I'm using FS 6.0. I registered MRI scans to the CVS-Avg35 template (mri_cvs_register) and
viewed output. While the nonlinear
The neonatal pipeline and its atlasesis not yet released. I am working on
it, so hopefully you do not need to wait long.
Lilla
On Thu, 21 Sep 2017, Paula Diniz wrote:
> Hi experts!
>
> I want to perform recon-all pipeline on newborn MRI data.
>
> How I can do this? Which atlas you recommend?
FYI
-- Forwarded message --
Date: Mon, 7 Aug 2017 12:54:29 +
From: Meritxell Bach Cuadra
To: Meritxell Bach Cuadra
Subject: Open position at Lausanne University Hospital: research and development
engineer
Dear colleague,
we are looking for a research and development e
Please, see attached or below for details.
Lilla
Postdoctoral Research Fellow Position in Infant Brain MRI analysis at the
A.A. Martinos Center, MGH and Harvard Medical School under Dr. Lilla
Zöllei
A postdoctoral fellow is recruited for an NIH funded project for
developing Freesurfer-compa
-- Forwarded message --
De: Cyril Poupon
Dear All,
please transfer this post-doc proposal to your post-docs or PhD students who
could be interested to apply for a post-doc in Tim Dyrby's lab in Denmark to
develop methods to probe brain tissue cytoarchitecture using diffusi
Hi Gianluca,
For your younger ages, this is the wiki that I would check:
https://surfer.nmr.mgh.harvard.edu/fswiki/ChildBrainManualEdits
We will look into the stats file.
Best, Lilla
On Tue, 11 Jul 2017, Gianluca Sforza wrote:
Hi Lilla,is there a range of age I should possibly take more car
Hi Jess,
Yes, there are. But currently we are focusing on the 0-2yrs age range.
Your age range of interest will come after that.
Lilla
On Thu, 13 Jul 2017, Jessica Reynolds wrote:
I am wondering whether there are still plans to implement a pediatric
atlas/template? I’m working with child
sy for me to understand the gap.
> many thanks
> Sarbani
>
> From: freesurfer-boun...@nmr.mgh.harvard.edu
> [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Lilla Zollei
> [lzol...@nmr.mgh.harvard.edu]
> Sent: 05 July 2017 22:32
> T
rcellation Statistics
>Cortical Ribbon Mask
>Cortical Parcellation mapping to Aseg
>
> BW
> S Das
> ________
> From: freesurfer-boun...@nmr.mgh.harvard.edu
> [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Lilla Zollei
> [lzol...@nmr.mgh.harvard.edu]
> Sent: 04 July 2
Hi S Das,
We are trying to release the infant pipeline by the end of the summer.
Lilla
On Tue, 4 Jul 2017, Das S. wrote:
> Dear Freesurfer expert,
> I want to perform recon-all pipeline on neonates data.Can I do so?
> I was going through some mail archives and there it is said that on T1 image
Hi Cris,
As long as your parcellation file gets resampled into the diffusion space,
you should not have any trouble reading it into TrackVis. When defining
ROIs you can just select individual label values afterwards.
Lilla
On Thu, 15 Jun 2017, Leyton Moscoso, Cristian Eduardo wrote:
Hi Free
Hi Jack,
We do not have such an automated option at the moment.
Lilla
On Thu, 25 May 2017, John Hettema wrote:
To FreeSurfer team,
I have child MRI data for which it would be best to use a pediatric
atlas/template for warping, alignment, and labeling. I am aware of the Haskins
Pediatric
Hi Cristian,
Can you send me the original mri_cvs_register command? When I apply the
m3z transform to your moving volume the result is not registered to the
target.
set morph = combined_toColin27_elreg_aseg.m3z
set targ = N27orig.mgz
set mov = TS076CDorig.mgz
set out = ${mov:r}.2.${targ}
Hi Cristian,
Can you upload your files for us?
https://gate.nmr.mgh.harvard.edu/filedrop2/
Lilla
On Tue, 28 Feb 2017, Donos, Cristian wrote:
Hi,
I was able to apply the morph using combined_toColin27_elreg_aseg.tm3d instead
of fullCSVmorph.tm3d.
The resulting coordinates are wrong, but it
[linkedin-logo_318-50643.jpg] [world-wide-web-icon-for-website.png]
On Mon, Feb 20, 2017 at 4:43 PM, Lilla Zollei
wrote:
Hi Bhavana,
We recommend to assign about 35GB of RAM on our cluster nodes for this
operation. I am not sure how that compares to your VB.
Lilla
That is the same. You shoudl be fine.
Lilla
On Mon, 20 Feb 2017, Magnús Ingvi wrote:
Hi!I am running mri_cvs_regsiter, on the cvs_avg35 space. In the dt_recon
tutorial ( https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Diffusion ),
the expected .m3z output file is called
combined_tocvs_
Hi Cristian,
The below error message indicates that your morph cannot be read. How much
memeory do you have on the machine where you are running this operation?
Lilla
On Fri, 10 Feb 2017, Donos, Cristian wrote:
Hi,
I have registered a patient’s MRI over the ColinN27 with mri_cvs_register
Hi Dong,
What is the age range that you are working with?
Lilla
On Mon, 20 Feb 2017, Martin Reuter wrote:
No, not that I know of.
Also I expect that it also depends on other factors (like image resolution,
quality, subject anatomy etc) .
Best, Martin
Am 15.02.2017 um 08:21 schrieb Don
to the function.
Regards,
Bhavana
[linkedin-logo_318-50643.jpg] [world-wide-web-icon-for-website.png]
On Mon, Feb 20, 2017 at 12:21 PM, Lilla Zollei
wrote:
Hi Bhavana,
How much memory are you allocating to this process?
Lilla
On Mon, 20 Feb 2017, Bhavana
Hi Bhavana,
How much memory are you allocating to this process?
Lilla
On Mon, 20 Feb 2017, Bhavana Ganesh wrote:
> Hi Developers,
>
> I'm receiving this error while I try to run mri_cvs_register. The same error
> was received when I reran the same even after increasing the memory allocated
Hi Stefano,
You can try to use the attached matlab file for reading the m3z file.
Lilla
On Mon, 30 Jan 2017, Stefano Zappalà wrote:
Dear FreeSurfer Developers,
I am trying to visualize and modify the output warp field (in .m3z) of a
mri_cv_registration call aimed at aligning a T1w scan to
but the results were not
great so I suspect that something is incorrect in the syntax and/or inputs.
Thanks for your help!
Doug
Douglas Merkitch
Neurological Sciences
Rush University Medical Center
Email: douglas_merki...@rush.edu
On Jan 26, 2017, at 8:42 AM, Lilla Zollei
wrote:
Hi
Hi Doug,
In order to compute and apply the inverse of an m3z transform you would
need to use the --inv-morph flag instead of the --m3z and reverse your
targ and mov inputs. With the current implementation of mri_vol2vol though
I do not think that you can specify the order of the transforms (w
Hi Stefano,
If you have the final_CVSmorph_toSynthF.m3z file you can use mri_vol2vol
dirctly to apply it to another volume. Look for examples in
mri_cvs_register --help.
We are moving away from using the tm3d file format.
Lilla
On Wed, 11 Jan 2017, Stefano Zappalà wrote:
Hello FreeSurfe
Hi Nazanin,
You need to run the full recon on your subject before you can use this
registration command.
Lilla
On Sat, 24 Dec 2016, N Saf wrote:
Dear Freesurfers,
I try to register my subject with cvs atlas in mni space I use this command
mri_cvs_register --mov subject.nii --mni
I got this
The manually segmented brains exist. They will not be part of FS 6.0,
but we are planning an independent release for them early next year.
Lilla
On Thu, 15 Dec 2016, Axelson, Eric D wrote:
I asked this last week with no response:
Does the infant brain atlas mentioned in this paper
http
Hi Bob,
We are moving towards only using m3z files and the only reason you still
see tm3d files in your output is that you are using the --nocleanup flag
so all intermediate results are kept in your output directory. So this
means that you will not need to use the applyMorph tool.
The two t
Hi Gajendra,
The recon stream exists in a beta version and will not make it to 6.0. I
am hoping to release the stream and the atlas though before the end of the
year.
Lilla
On Thu, 29 Sep 2016, GAJENDRA KATUWAL (RIT Student) wrote:
Hello FreeSurfer experts,
I am considering using Freesur
Hi Michael,
I want to compare two populations using CVS so I can cross-register multimodal
maps (e.g. ASL, FA, QSM) for volumetric comparisons.
I’ve gotten CVS to work very well registering one subject to another, it really
is impressive
However, using the --mni option, it doesn’t work so w
Hi Mahmoud,
At the below link you will find some suggestions / settings that we use
with our Cintiq tablet:
https://surfer.nmr.mgh.harvard.edu/fswiki/FreeviewGuide/FreeviewWorkingWithData/FreeviewSegmentations
"Segmenting using a Cintiq tablet or display"
Best, Lilla
On Tue, 22 Mar 2016, Ma
Hi Elijah,
Yes, it is.
Lilla
On Sun, 20 Mar 2016, Elijah Mak wrote:
Hi Freesurfer Community,
I am running mri_cvs_register for the spatial normalization and it seems to
work very nicely on my set of DTI data in subjects with substantial atrophy.
However, I can't seem to find the file
co
FYI: this is a great program for PhD students and postdocs.
-- Forwarded message --
Date: Wed, 20 Jan 2016 17:09:55 +0100
From: Christian ROUX
To: ROUX Christian
Subject: 12th International Summer School on Biomedical Imaging,
Abbaye de Saint Jacut, Brittany, France, June 1
Hi John,
In order to use bbregister you would first need to recon your data set as
the registration algorithm relies on surfaces. After that
Usage: bbregister --s --mov --reg --
Help: bbregister --help
Lilla
On Sun, 17 Jan 2016, John Anderson wrote:
Dear experts,
I wanted to regist
Hi Shani,
Sure. You can do
mri_cvs_register --help
and that should give you lots of information.
Alternatively you can also go to
https://surfer.nmr.mgh.harvard.edu/fswiki/mri_cvs_register
and read through the presentation that we give at the FS course:
http://surfer.nmr.mgh.harvard.edu/pu
Email: jplas...@asu.edu
> Phone: (480)861-7017
>
> On Fri, Jul 31, 2015 at 12:31 PM, Lilla Zollei
> wrote:
>
> Hi Jon,
>
> What is the exact command that you used for the below described
> conversion?
>
Hi Jon,
What is the exact command that you used for the below described
conversion?
Lilla
On Fri, 31 Jul 2015, Jonathan Plasencia wrote:
> I've converted the aseg.mgz file to .nii (need data in nii to do some further
> work on the data). However, the number of voxels for a given structure
>
t; Fischl [fis...@nmr.mgh.harvard.edu]
> Gesendet: Mittwoch, 24. Juni 2015 16:37
> An: Freesurfer support list
> Betreff: Re: [Freesurfer] Freesurfer tool for children's data
>
> Hi Kristina
>
> what age? It works reasonably well down to 7 or even 5. Younger than that
> i
Oh, I see you do not have a recon for your high res volume. Could you try
the below mri_vol2vol command with an additional -lta flag that has the
transform that you computed to align your lowres and high res volumes?
Lilla
On Wed, 6 May 2015, Celine Louapre wrote:
> Thank you Lilla for the sugg
Hi Celine,
The m3z morph encodes a sptial transformation between two particular
coordinate systems. When you use mri_vol2vol below, the original space is
not the same as for your input volume used to be and that is why the
volumes are not in correspondence.
Could you compute the registration
You can use createMorph:
createMorph --out $tm3d --template $template \
--subject $moving --in gcam $m3z
--Lilla
On Wed, 25 Feb 2015, Zachary Greenberg wrote:
I using mri_cvs_register and applyMorph on a linux server (
freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0)
and I wo
Hi Shaheen,
Freesurfer does not handle that age-range so it is not applicable for
neonates.
Send me an email and I will tell you what we are developing now that might
be appropriate for you.
Lilla
On Fri, 6 Feb 2015, Shaheen Ahmed wrote:
Hello,
I am using freesurfer for neonates but g
Hi Jeff,
Yes that is the very first step in the recon-all processing.
Lilla
On Thu, 5 Feb 2015, jwa...@nmr.mgh.harvard.edu wrote:
> Hello Freesurfer,
> My MPRAGE dimensions are 1x1x1.33. The output of recon-all appears to
> be 1x1x1, judging by the fact that the aseg.stats columns for voxel
>
Hi Zach,
You would call it like the following:
applyMorph --template $t --transform $m point_list $i $o linear
wheer t is the template volume, m is the tm3d morph file, i is the input o
is the output and "linear" refers to the type of interepolation.
Lilla
On Wed, 4 Feb 2015, Zachary Greenber
Hi Berdakh,
We do not have any publicly available processing stream that would work
for this age range. I do have some preliminary tools though, so if you are
interested send me an email with a bit more details about your dataset and
I can tell you whether I could help.
Lilla
On Tue, 27 Jan
Hi, Could you use a colormap for your aseg? It is really hard to see the
different ROIs on a grayscale image.
Thanks, Lilla
On Wed, 26 Nov 2014, Octavian Lie wrote:
Dear Lilla,
Here is a snapshot of the aseg volume, which rescues some gray matter not
included in the pia. I am not sure if t
Hi Octavian,
If you have an OK aseg volume, you could try to fit a
surface over it using mris_make_surfaces with the -cover_seg flag.
Lilla
On Tue, 25 Nov 2014, Bruce Fischl wrote:
>
>
> -- Forwarded message --
> Date: Tue, 25 Nov 2014 08:05:55 -0600
> From: Octavian Lie
> R
Hi Piotr,
There are several tutorials that describe our standard data processing
pipeline. You can start by looking at:
http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial
with "Introduction to Freesurfer" and "Analyzing the Individual Subject".
If you have any further questions, please, se
lso in the attached file you can find the log of this command.
Best regards,
Mohammadi-Nejad
On Monday, September 29, 2014 2:12 PM, Lilla Zollei
wrote:
Hi Mohammadi-Nejad,
Could you include the command that you submitted and the error message and
log file from when the process terminated?
Lilla
Hi Mohammadi-Nejad,
Could you include the command that you submitted and the error message and
log file from when the process terminated?
Lilla
On Mon, 29 Sep 2014, Ali-Reza Mohammadi-Nejad wrote:
Hi
I am trying to do an mri_cvs_register for two subjects analyzed with FS-5.1.0
on a 64-bit
Could you also send the log file along?
Thanks, Lilla
On Wed, 10 Sep 2014, bigben2...@web.de wrote:
> I'm using the version stable v5.3.0.
> Ben
>
>
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/li
Hi Ben,
What version of freesurfer are you using?
Lilla
On Wed, 10 Sep 2014, bigben2...@web.de wrote:
Hey everyone,
i have tried to run the mri_cvs_register command but it returned an error in
the second step. It returned:
"VolumeMorph load - failed to open input stream"
I have entere
Hi Rito.
It is not finding information about the gradient table that was used for
the acquisition. If you have that information you can use the below option
to manually include it
--b bvals bvecs
If you do not you could try using load_dicom in order to grab that
information.
Lilla
On Mon,
applyMorph, and subtract the initial
virtual 4d image. The Jacobian matrix can also be calculated through this
fields.
That is definitely one way of doing it.
Best, Lilla
On Wed, Aug 6, 2014 at 3:35 PM, Lilla Zollei
wrote:
Hi Andre,
The jacobian field is computed in the coordinate
] reg_IBSR_01_2_IBSR_02_brain.nii.gz
[icon_10_generic_list.png] jacobian.nii.gz
Regards,
Andre Santos Ribeiro
PhD Student, Imperial College London
On Tue, Aug 5, 2014 at 4:24 PM, Lilla Zollei
wrote:
Hi Andre,
What do you mean by they "do not seem to match voxel-wise"? Are they of
ke here?
Sorry for this question in advance.
Regards,
Andre Santos Ribeiro
PhD Student, Imperial College London
On Fri, Jul 11, 2014 at 4:11 PM, Lilla Zollei
wrote:
Hi,
First, in the mri_cvs_register I kept all the files and therefore the
"combined_toIBSR_02_elreg_after
Contact Caterina Mainero, M.D. (cater...@nmr.mgh.harvard.edu) if
interested!
>>>
A full-time Research Technologist (Assistant) position is available in the
field of Neuroimaging of Multiple Sclerosis (MS) at the A. A. Martinos
Center for Biomedical Imaging of Massachusetts General Hospital (MGH
Hi Carina,
You can use the -f option (instead of -v used for volumes) when you are
calling freeview from the commandline in order to display a surface and
then append :overlay=overlay_filename after the filename to identify the
overlay that you want to use. You will need to decide which hemi
ase out the tm3d format.
Lilla
On Fri, Jul 11, 2014 at 3:11 PM, Lilla Zollei
wrote:
Hi, You should use the final m3z file. The -tm3d flag just indicates that
the file was created by mri_cvs_register.
Lilla
On Fri, 11 Jul 2014, André Ribeiro wrote:
I got an er
AM, André Ribeiro wrote:
Thank you! Didn't realized that function existed.
Regards,
Andre Santos Ribeiro
On Thu, Jul 10, 2014 at 4:59 PM, Lilla Zollei
wrote:
Hi Andre
You can run:
mri_jacobian -tm3d <3d morph>
--Lilla
On Thu,
Hi Andre
You can run:
mri_jacobian -tm3d <3d morph>
--Lilla
On Thu, 10 Jul 2014, André Ribeiro wrote:
Dear Freesurfer Community,
How can I obtain the Jacobian of the deformation field estimated through
mri_cvs_register for further use like VBM analysis?
Regards,
Andre Santos Ribeiro
Hi Emily,
You will need to resample them in a common space before you do group
analysis.
Lilla
On Tue, 1 Jul 2014, ebell...@uwm.edu wrote:
> Hello,
>
> I was wondering if it is better to keep the FA results from a DTI analysis in
> diffusion space for group analysis or if you should warp them
Hi Francesco,
The FS recon stream is set up for adult image analysis. In the past we
have had success with analysing data sets of children, but below the age
of 4yrs the success rate really drops and the stream is not recommended.
We are working on a separate stream for that population, but it
From: freesurfer-boun...@nmr.mgh.harvard.edu
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Lilla Zollei
[lzol...@nmr.mgh.harvard.edu]
Sent: Friday, March 21, 2014 10:12 AM
To: Francesco Baldacchini
Cc: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer
in the process of creatig a pipeline for them, but it is not yet ready for
distribution.
Lilla
On Thu, 20 Mar 2014, Francesco Baldacchini wrote:
Hi Lilla,
They range from neonates to 6 years old,
Francesco
2014-03-19 19:21 GMT+01:00 Lilla Zollei :
Hi Francesco,
How old are
Hi Francesco,
How old are your subjects?
Lilla
On Wed, 19 Mar 2014, Francesco Baldacchini wrote:
I have some quality problems with my scans. I'm trying to run recon-all on
pediatric brain images but, given the low contrast between cortical regions and
the white matter, I do consistently ge
Doug, mris_convert does not read / write that information either.
On Sun, 9 Feb 2014, Bruce Fischl wrote:
> really? I didn't realize that as I don't use them much. Doug: do you have
> something like MRISread?
>
> On Sun, 9 Feb 2014, Lilla Zollei wrote:
>
>>
&
m, but I guess you will need to figure
> out how to get the right ras2vox matrix into them
> cheers
> Bruce
> On Sun, 9 Feb 2014, Lilla Zollei wrote:
>
>>
>> Hi,
>>
>> I have some FS-style surface files that were created using outside tools
>> (from M
Hi,
I have some FS-style surface files that were created using outside tools
(from McGill). Due to some recent changes in FreeView they do not display
properly though as the useRealRAS bit in the header is not set to 1. Do we
have any C / Matlab code that I could use to change that?
Thanks, L
ced at any step.
Lilla
On Tue, 28 Jan 2014, Lilla Zollei wrote:
>
> I would say that for 5-8 the atlas would probably work. Below 5 I would be
> skeptical. There is no alternate atlas at the moment, but we are working
> on it.
>
> -Lilla
>
> On Tue, 28 Jan 2014, Mher Ala
I would say that for 5-8 the atlas would probably work. Below 5 I would be
skeptical. There is no alternate atlas at the moment, but we are working
on it.
-Lilla
On Tue, 28 Jan 2014, Mher Alaverdyan wrote:
> They are 2 - 8 years old.
>
>
> On Tue, Jan 28, 2014 at 11:46 AM,
Hi,
What is the age range of your subjects?
Lilla
On Tue, 28 Jan 2014, Mher Alaverdyan wrote:
> Hi all,
> I just wanted to know if it is acceptable to use the Destrieux atlas in FS
> for parcellation of brain images of pre-adolescents. If not this atlas, then
> which would be a recommended a
mply like to convert each label in the MNC file to a new Freesurfer
> label file.
> Caspar
>
>
>
> 2014/1/6 Lilla Zollei
>
> Hi Caspar,
>
> One thing you can do, if you have the label correspondences between
> your lables and the FS ones, is to use mri_
Hi Caspar,
One thing you can do, if you have the label correspondences between your
lables and the FS ones, is to use mri_binarize with the --replace option
in your volumes.
--replace V1 V2 : replace voxels=V1 with V2
For label descriptions you can loook up
$FREESURFER_HOME/FreeSurferColorLU
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