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 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 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 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
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 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
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
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
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
>
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 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 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 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
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 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
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 Jim,
Using the current FS recon pipeline with your data is indeed not feasible.
We are in the process of creating another pipeline geared towards that age
range.
Lilla
On Thu, 10 Oct 2013, Alexopoulos, Dimitrios wrote:
> Just wondering if anyone has attempted to process T1-mpr data for a
Hi Liv,
What you are asking for is quite ambitious. As you have noticed, most of
the image processing tools fail on the infant data sets as they are
usually of much lower SNR, they have changing GM/WM contarst, higher noise
and a much smaller anatomy. So it is not only a question of creating
Hi Tommi,
> I am preparing to CVS register 30+ subjects to improve FSL probabilistic
> tractography alignment across subjects. First, thanks for a really cool
> tool! Then, I have some questions:
>
> 1. mri_cvs_register step1 is spherical registration. However, I have
> already run FS5.3 recon-a
mri_robust_register --help
You would need to use the "--affine" flag.
Lilla
On Fri, 22 Nov 2013, Nathaniel Reynolds wrote:
> Hi all,
>
> I can't find any explanation of how to perform an affine registration with
> mdi_robust_register. Could someone please explain?
>
> Thanks,
> Nathaniel
> _
It is not checked in as of now to the FS distribution. I can send it to
you.
On Fri, 22 Nov 2013, Nathaniel Reynolds wrote:
> Hi again,
>
> Does anybody know about a function called "mri_mi"?
>
> I have someone else's script that seems to utilize it, but I can't seem to
> access it myself.
>
>
This is a bit delayed response (my apologies) to an earlier question to
the list:
The boost library is installed by default on CentOS platforms. If a user
gets the libboost error then they are using a different platform which
doesn't have boost installed by default. On RedHat systems libboost
Hi Andre,
I posted the below on Monday on the list:
The boost library is installed by default on CentOS platforms. If a user
gets the libboost error then they are using a different platform which
doesn't have boost installed by default. On RedHat systems libboost can be
installed by typing t
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
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,
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
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,
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
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
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
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:
>
>>
&
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
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
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
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
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
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
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 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
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 Martina,
What was the command that you ran when executing mri_cvs_register. The
default outpur directory is $SUBJECTS_DIR/$subject/cvs. The help alos
explains how you can change that directory.
--Lilla
On Thu, 21 Mar 2013, Bruce Fischl wrote:
> mri_vol2vol or mri_convert can apply the .m3
Hi Maish,
You can just go to
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
and unsubscribe your email address.
Lilla
On Wed, 27 Mar 2013, Dalwani, Manish wrote:
> Hello Admin,
>
> Please unsubscribe this email address.
>
> Regards,
> Manish
>
Hi Josh,
We do not yet have a publicly available atlas for that population. We are
working on it though and will announce it as soon as it is ready.
Lilla
On Tue, 2 Apr 2013, Joshua Lee wrote:
> The aseg has shown poor performance in my sample. Are there settings,
> atlases, etc, available t
Hi Daniel,
What operating system are you using?
Lilla
On Tue, 28 May 2013, Barron, Daniel S wrote:
Hello,
I am trying to perform an inter-subject registration using mri_cvs_register on
version 5.3.
When I ran mri_cvs_check, my feedback was I needed to find
"mri_cvs_register.settings.txt
ur
>>> $FREESURFER_HOME/bin directory:
>>>
>>> ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/patches/mris_resample
>>>
>>> Feel free to contact me if you have any additional questions/issues.
>>>
>>> -Zeke
>>>
>>>
HI,
A patch is now available for the "mris_resample : Command not found"
error you encountered.
Simply download the file from the following link and place it in your
$FREESURFER_HOME/bin directory:
ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/patches/mris_resample
--Lilla
On Thu, 6 J
Hi, Can you be more specific? What files / volumes do you want to
compute a group average of?
On Sun, 9 Jun 2013, Fernando Valle-Inclán wrote:
Hi freesurfers, After doing cvs registration, how can I make a group
average? Is fsaverage OK?
Thanks
_
m talking about "final_CVSmorphed_tocvs_avg35.norm.gz"Thanks for the
very prompt reply
F
2013/6/9 Lilla Zollei
Hi, Can you be more specific? What files / volumes do you want to compute
a group average of?
On Sun, 9 Jun 2013, Fernando Valle-Inclán wrote:
Hi freesurfers, After doing
Hi Marcel, You would ned at least twice as much. Also, is there a
specific reason for you to use the --m3d flag? That will result in writing
out uncompressed morph files which will take up a lot of space.
Lilla
On Tue, 9 Jul 2013, Marcel Falkiewicz wrote:
Dear FreeSurfers,
I'm trying to us
Hi,
What type of registration file do you have representing the diff2anat
transformation? With mri_vol2vol you can use many different types of
transformations, if you switch the --reg flag to --xfm, --fsl or --lta,
for example.
Lilla
On Mon, 8 Jul 2013, Hoptman, Matthew wrote:
Hi all,
diff2anat.bbr.mat
Matrix from regfile:
-0.001 0.972 -0.234 -3.311;
-0.001 0.234 0.972 69.949;
0.000 0.000 0.000 1.000;
0.000 0.000 0.000 0.000;
Best,
Matt
-Original Message-
From: Lilla Zollei [mailto:lzol...@nmr.mgh.harvard.edu]
Sent: Wednesday, July 10, 2013 6:07 PM
To
It should be in your $FREESURFER_HOME/subjects directory.
Lilla
On Sun, 28 Jul 2013, SHAHIN NASR wrote:
Hi, Would you tell me where I can find cvs_avg35 brain template.
--
Shahin Nasr
PhD in Cognitive Neuroscience
Martinos Imaging Center, MGH
Harvard Medical School
_
Hi Daniel,
You need to specify the full path to the target volume, the subject id
is not sufficient. It should be somthing like this:
$FREESURFER_HOME/subjects/cvs_avg35_inMNI152/mri/norm.mgz
Lilla
On Tue, 6 Aug 2013, Barron, Daniel S wrote:
> Hi Freesurfers (Lilla),
>
> I'm running v5.1.0 o
Hi Marcel,
First, you will find a lot of details about the usage of mri_cvs_register
if you use the --help flag in the terminal.
See detailed responses to your questions below:
I'm trying to use mri_cvs_register (whose registration accuracy is, by the
way, jaw-dropping) for EPI images. Ho
idea... Can you think of any solutions to this issue?
Best regards,
Marcel
2013/8/8 Lilla Zollei
Hi Marcel,
First, you will find a lot of details about the usage of mri_cvs_register
if you use the --help flag in the terminal.
See detailed responses to your questions below
Hi Cyrus,
You can run the following script:
compute_label_volumes.csh
It will list all the labels that are in your segmentation file (and also
tell you the number of voxels colored by this label and th etotal volume).
Lilla
On Tue, 5 Jun 2012, Sarosh, Cyrus wrote:
Hello,
I was hopin
Hi Daniel.
> i'm currently applying mri_cvs_register and I'm very happy with the nice
> results. Congratulation for this very clever approach. However, some data
> sets which I work on have still aseg.mgz which are not segmented
> appropriately. As far as I understand aseg.mgz is not redefined
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
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 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
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
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 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
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
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_
[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
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
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 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 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 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
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
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
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
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
-- 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
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
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
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?
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
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
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 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
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 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
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 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 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 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 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
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,
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
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
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
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
] 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
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
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,
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
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
>
>
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