Hi Anna
The DK atlas (or DKT?) gets written into the aparc+aseg.mgz volume, but the DKT
parts of it only consist of cortex. The subcortical labels are the normal ones
(caudate, putamen, etc...)
Cheers
Bruce
From: Arkhipova Anna, MUDr.
Sent: Monday, January 29, 2024 10:21 AM
To: Fischl, Bruce
Maybe you can give us more details about what you are trying to do? Generate an
fMRI time-series that is the average response in each cortical parcel? And
subcortical structure? The subcortical segmentation is not Talairach, although
I'm not sure that is relevant. Generating the average time ser
Hi Anna
Parcellation is more than just format conversion - you need to map it onto the
details of an individual subject's anatomy. In addition, the DKT atlas is only
cortical. If you want subcortical regions in addition you should run recon-all
as it will produce both.
Cheers
Bruce
From: Arkh
vard.edu
on behalf of priya padma
Sent: Wednesday, October 26, 2022 9:36 PM
To: Freesurfer support list
Subject: [Freesurfer] conversion of .stats to .csv
External Email - Use Caution
Dear Team,
I would like to convert the .stats files that are being generated in the stats
folder as a
External Email - Use Caution
Dear Team,
I would like to convert the .stats files that are being generated in the
stats folder as an output from recon-all to csv file or excel file. Is
there any way to convert .stats to .csv or .excel format? any help on
this would be much apprecia
On 2/10/2020 11:20 AM, Christian O'Reilly, Dr wrote:
External Email - Use Caution
Hi,
How can I convert a LTA file type 0 (LINEAR_VOX_TO_VOX) to a type 1
(LINEAR_RAS_TO_RAS)?
Use lta_convert
Also, given a volume x.nii.gz and a file y.lta, how do I obtaijn
z.nii.gz as the origina
External Email - Use Caution
Hi,
How can I convert a LTA file type 0 (LINEAR_VOX_TO_VOX) to a type 1
(LINEAR_RAS_TO_RAS)?
Also, given a volume x.nii.gz and a file y.lta, how do I obtaijn z.nii.gz as
the original volume x.nii.gz transformed according to y.lta? I tried with
mri_
Please send the command line and full terminal output. Also, please include the
previous emails
doug
On 12/19/2019 4:28 AM, Marina Fernández wrote:
External Email - Use Caution
Thanks Doug.
I created the surface with the command line that I sent you (mri_vol2surf ...)
and then, I run
External Email - Use Caution
Thanks Doug.
I created the surface with the command line that I sent you (mri_vol2surf
...) and then, I run that command that you sent me (tkregisterfv...) but I
have the following error when freeview is trying to load the file: 'Failed
to load MRI /
It is right if the register.dat maps 4d_inputBOLD.nii to the conformed
subject anatomical space. You can check this with
tkregisterfv --mov 4d_inputBOLD.nii' --reg 'register.dat'
On 12/18/19 10:23 AM, Marina Fernández wrote:
>
> External Email - Use Caution
>
> Thank you Doug/Bruce.
>
>
External Email - Use Caution
Thank you Doug/Bruce.
We would like to project our AFNI preprocessed EPI scans (T1-registration,
motion correction, linear regression, but unsmoothed) to Freesurfer
cortical surfaces in order to obtain one file containing 250 (number of
dynamics) EPI-c
Hi Marina
yes, mri_vol2surf will sample volumes onto the surface. You will need to
register them first (we typically use Doug Greve's bbregister for this).
What preprocessing did you do? For cortical data we don't recommend
smoothing in the volume - you are much better off sampling to the surf
Yes, use mri_vol2surf. Make sure to use --projfrac 0.5 to sample in the middle
of cortex. Run it with --help to get examples.
On 12/17/2019 11:16 AM, Marina Fernández wrote:
External Email - Use Caution
Dear experts,
I’ve done the fMRI preprocessing and now I would like to convert each f
External Email - Use Caution
Dear experts,
I’ve done the fMRI preprocessing and now I would like to convert each file
(that contains 250 volumes) to surface.
Is it correct to use the function mri_vol2surf? Should I use any specific
flag because they are 4D files? What is the best
, March 27, 2019 10:34:28 AM
To: Iglesias Gonzalez, Eugenio; Freesurfer support list
Subject: Re: [Freesurfer] Conversion of thalamic nuclei labels
ATTENTION: This email came from an external source. Do not open attachments or
click on links from unknown senders or unexpected emails.
External
them as
ROIs?
Da: freesurfer-boun...@nmr.mgh.harvard.edu
per conto di Sanchez, Juan (NYSPI)
Inviato: mercoledì 27 marzo 2019 15:17:41
A: Iglesias Gonzalez, Eugenio; Freesurfer support list
Oggetto: Re: [Freesurfer] Conversion of thalamic nuclei l
From: Sanchez, Juan (NYSPI)
Sent: Wednesday, March 27, 2019 10:15:18 AM
To: Iglesias Gonzalez, Eugenio; Freesurfer support list
Subject: Re: [Freesurfer] Conversion of thalamic nuclei labels
We have run the thalamic and amyhip segmentation scripts on HCP data and were
convert the segmented
, Eugenio; Freesurfer support list
Subject: Re: [Freesurfer] Conversion of thalamic nuclei labels
ATTENTION: This email came from an external source. Do not open attachments or
click on links from unknown senders or unexpected emails.
External Email - Use Caution
Hi Eugenio,
Yes, when I
Laboratory (CSAIL)
Massachusetts Institute of Technology
Lecturer on Radiology
Harvard Medical School
http://www.jeiglesias.com
From: Valentina Mancini
Date: Wednesday, 27 March 2019 at 10:08
To: "Iglesias Gonzalez, Eugenio" , Freesurfer support
list
Subject: Re: [Freesurfer] Con
visualize
the different subnuclei in SPM/Conn.
Best,
Valentina
Da: Iglesias Gonzalez, Eugenio
Inviato: mercoledì 27 marzo 2019 14:55:00
A: Freesurfer support list
Cc: Valentina Mancini
Oggetto: Re: [Freesurfer] Conversion of thalamic nuclei labels
Hi Valent
External Email - Use Caution
Hi Valentina,
I've never used FSLeyes but I suspect you'd need a lookup table to visualize
the nuclei properly. Do you see different pixel values when you move your
cursor over the different areas of the thalamus in FSLeyes?
Cheers,
/Eugenio
--
Juan
and your full command line for conversion?
On Wed, 27 Mar 2019, Iglesias
Gonzalez, Eugenio wrote:
External Email - Use Caution
Dear Valentina
Resolution should not be affected by MRI_convert. Can you please send us an
example/screen capture?
Cheers
Eugenio
Sent from mobile,
External Email - Use Caution
Dear Valentina
Resolution should not be affected by MRI_convert. Can you please send us an
example/screen capture?
Cheers
Eugenio
Sent from mobile, please excuse brevity and typos
From: Valentina Mancini
Sent: Wednes
External Email - Use Caution
Dear all,
I ran the thalamic segmentation implemented in FreeSurfer and, according to
visual inspection, I got nice results with a good delineation of all the nuclei.
Then, I wanted to use the label of the thalamic nuclei to select an ROI in the
MG
Try lta_convert
On 12/11/2018 03:46 PM, Jane Tseng wrote:
>
> External Email - Use Caution
>
> Dear Freesurfer experts,
>
> I was wondering if there is any way to convert the .dat file output
> from spmregister (generated using Freesurfer version 5.3) to a .lta
> file? Thank you!
>
> Be
External Email - Use Caution
Dear Freesurfer experts,
I was wondering if there is any way to convert the .dat file output from
spmregister (generated using Freesurfer version 5.3) to a .lta file? Thank
you!
Best wishes,
Jane
___
Freesur
Yes, I agree. Going to the volume irreversibly reduces the resolution and
would have to be very highres to have a hope of representing more than
two compartments.
cheers
Bruce
On Tue, 20 Nov 2018, ts...@rcmd.org wrote:
External Email - Use Caution
As you said, you can load FreeSurfe
External Email - Use Caution
As you said, you can load FreeSurfer data (both the surface files and volume
data) with the respective nibabel functions, i.e., read_geometry and
read_morph_data. The ?h.pial and ?h.white files are surface meshes, so
read_geometry would apply.
I'm n
Hi Inês
nibabel should be able to read freesurfer images directly (thanks to Satra!
I think):
http://nipy.org/nibabel/reference/nibabel.freesurfer.html
cheers
Bruce
On Tue, 20 Nov
2018, Borges Pereira Ines Isabel wrote:
External Email - Use Caution
Dear FreeSurfer deve
External Email - Use Caution
Dear FreeSurfer developers,
I am trying to segment the cortex of my subjects into multiple layers and am
trying several approaches.
I have tried the command "mris_expand -thickness lh.white 0.5 lh.graymid" and
it works perfectly.
I am also interested
no we don't, sorry
On 10/24/2013 07:26 AM, std...@virgilio.it wrote:
> Hi list,
>
> there is a way to convert niifty or .par/.rec in DICOM?
>
> Thank you very much,
>
>
> Stefano
>
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https
Hi list,
there is a way to convert niifty or .par/.rec in DICOM?
Thank you very much,
Stefano ___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is in
@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] Conversion question
Hi Panos
yes, mri_convert will do this with -odt int
cheers
Bruce
On Fri, 27 Sep 2013,
pfot...@nmr.mgh.harvard.edu wrote:
> Hi FS Community,
>
> I was wondering whether there is a way to convert a FLOAT type niftii file
&g
Hi Panos
yes, mri_convert will do this with -odt int
cheers
Bruce
On Fri, 27 Sep 2013,
pfot...@nmr.mgh.harvard.edu wrote:
> Hi FS Community,
>
> I was wondering whether there is a way to convert a FLOAT type niftii file
> to an INT type niftii file.
> Thanks in advance!
>
> Best,
> Panos
>
Hi FS Community,
I was wondering whether there is a way to convert a FLOAT type niftii file
to an INT type niftii file.
Thanks in advance!
Best,
Panos
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/li
mri_convert dicomfile file.mgz
where dicomfile is a single file from the series (it will find the rest)
On 9/7/13 3:28 AM, swathy p.s wrote:
How do i convert dicom into mgz files.
tried using recon-all
what does subject id refer to and what is its significance.
__
subject id is the identifier you pick for that subject. It is arbirtary but
needs to be unique (at least in that SUBJECTS_DIR). recon-all will read
dicom fine and create .mgz files from it. Try it and if it fails send us
your full command line and screen output and we will tell you what was
in
How do i convert dicom into mgz files.
tried using recon-all
what does subject id refer to and what is its significance.
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The informat
Anna, if you need to get it back into the native anatomical space, see
http://surfer.nmr.mgh.harvard.edu/fswiki/FsAnat-to-NativeAnat
You can use nii as the output format instead of mgz
doug
On 5/31/13 7:23 AM, Anna Josefson wrote:
Dear FreeSurfer users!
I am new to Freesurfer, and I have s
use mri_convertcheck this
linkhttps://surfer.nmr.mgh.harvard.edu/pub/docs/html/mri_convert.help.xml.html
Azeez Adebimpe
Date: Fri, 31 May 2013 13:23:20 +0200
From: anna.b.josef...@gmail.com
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] Conversion
Dear FreeSurfer users!
I am new
Dear FreeSurfer users!
I am new to Freesurfer, and I have succesfully managed to run recon-all on
my data, for every subject.
Now I plan to use the output - some of the different cortical and
subcortical brain structures as ROI's in my SPM analyses.
Then I would have to convert from freesurfer
To: Tina Jeon
Cc: Freesurfer@nmr.mgh.harvard.edu
Subject: RE: [Freesurfer] conversion from ascii to surface
something is wrong as there should be no vertex indices > 12721
On Fri, 17 May
2013, Tina Jeon wrote:
I created the ascii file directly from amira, which from what I
understand is 0 ba
: [Freesurfer] conversion from ascii to surface
something is wrong as there should be no vertex indices > 12721
On Fri, 17 May
2013, Tina Jeon wrote:
> I created the ascii file directly from amira, which from what I
understand is 0 based.
>
> -Original Message-
> From: Bruce Fis
May 17, 2013 9:15 AM
To: Tina Jeon
Cc: Freesurfer@nmr.mgh.harvard.edu
Subject: RE: [Freesurfer] conversion from ascii to surface
Hi Tina
how did you create the ascii file? The problem is that some of the faces
contain vertex numbers that are you of range. Note that the vertex indices
in the f
I created the ascii file directly from amira, which from what I understand is 0
based.
-Original Message-
From: Bruce Fischl [mailto:fis...@nmr.mgh.harvard.edu]
Sent: Friday, May 17, 2013 9:15 AM
To: Tina Jeon
Cc: Freesurfer@nmr.mgh.harvard.edu
Subject: RE: [Freesurfer] conversion from
...@nmr.mgh.harvard.edu]
Sent: Friday, May 17, 2013 8:57 AM
To: Tina Jeon
Cc: Freesurfer@nmr.mgh.harvard.edu
Subject: RE: [Freesurfer] conversion from ascii to surface
Hi Tina
can you send me the ascii file? Note that we assume in many places that the
surface files start with a hemisphere specifier, so your
13 5:49 PM
To: Tina Jeon
Cc: Freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] conversion from ascii to surface
Hi Tina
try mris_convert
cheers
Bruce
On Thu, 16 May 2013, Tina Jeon wrote:
Dear Doug, Nick, and all,
I am trying to convert a surface from Amira to freesurfer in order to
PM
To: Tina Jeon
Cc: Freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] conversion from ascii to surface
Hi Tina
try mris_convert
cheers
Bruce
On Thu, 16 May 2013, Tina Jeon wrote:
>
> Dear Doug, Nick, and all,
>
>
>
> I am trying to convert a surface from Amira to f
Hi Tina
try mris_convert
cheers
Bruce
On Thu, 16 May 2013, Tina Jeon wrote:
Dear Doug, Nick, and all,
I am trying to convert a surface from Amira to freesurfer in order to
visualize a parcellated neonate brain. I have the freesurfer ascii files
(white/pial) and need to convert those into
Dear Doug, Nick, and all,
I am trying to convert a surface from Amira to freesurfer in order to visualize
a parcellated neonate brain. I have the freesurfer ascii files (white/pial) and
need to convert those into surfaces that can be read by tksurfer.
Do you have any suggestions for how I could
FYI
-- Forwarded message --
Date: Tue, 7 Feb 2012 09:15:37 -0500
From: Ziad Saad
To: Bruce Fischl
Subject: Re: [Freesurfer] Conversion of an mgh file to nii
I just realized my post got rejected from the message list since I I am not a
subscriber. Could you throw it up there
Hey Doug and Bruce,
I believe that was the enlightenment I so desperately needed :).
Thank you very much for your continuous effort and prompt responses. Your
support is greatly appreciated!!!
Keep up the good work,
Omer Tal
> you could do the same if you sampled your test.nii into the volume.
you could do the same if you sampled your test.nii into the volume. At
the moment it's a surface overlay, so as Doug points out no volume loader
will know what to do with it. You need the surface geometry/topology to
properly display it. If you want to sample it into the volume I think you
want
that's why I asked if you are using SUMA, which knows about surfaces and
overlays. The standard AFNI stuff won't know what to do with it, but SUMA
should
Bruce
On Mon, 6 Feb 2012, Douglas N Greve wrote:
> It won't make sense to load it into fslview. This is a surface, and fslview
> is a volu
It won't make sense to load it into fslview. This is a surface, and
fslview is a volume viewer. This may be the problem that you are running
into with AFNI. If you want to map the surface back to the volume, use
mri_vol2surf.
doug
Omer Tal wrote:
> Hey Doug,
>
> I apologize, maybe I wasn't clea
Hey Bruce,
Maybe I can give more background information to help explain what I am
trying to do here.
I have a subject which I have both MEG and fMRI data on. When I
reconstructed my subject, I chose a dipole as a seed location and used it
for my MEG analysis. Now I want to use the same location a
Ziad: any idea why Omer can open this file in tksurfer but not afni? Omer:
I don't think you'll be able to load it in FSL since it's essentially a
surface. Can you give us details about how you are trying to load it in
AFNI? Are you using SUMA?
On Mon,
6 Feb 2012, Omer Tal wrote:
> Sorry, tha
Hey Doug,
I apologize, maybe I wasn't clear enough.
It DOESNT work in FSL. That would be enough for me if it did. It loads w/
out erroring out and quitting (as it did before the improper reshape), but
it is obviously not a proper image anymore as it lost its three dimensions
and nothing is displa
It appears to be working for both FS and FSL. If it is working in FS
and FSL and not in AFNI, then there's not much we can do about it. The
AFNI developers don't know about our tools, and we don't know about
theirs. I suggest you send the file to the AFNI developers and ask why
it does not loa
Sorry, that was the wrong error description (for the AFNI portion).
It just says cannot open dataset test.nii
Well, if it doesn't work on FSL or AFNI, I would guess it is the
conversion process from FreeSurfer. I don't think anyone on AFNI knows
mri_convert or mri_sruf2surf.
Honestly just trying
It sounds like it is doing the right thing. The geometry is going to be
bogus because it is a surface. You should post to the AFNI list.
doug
Omer Tal wrote:
> Hey Bruce,
>
> So the mgh file loads fine in tksurfer (shows proper map) for the given
> subject, and so does its corresponding mgz (crea
Hey Bruce,
So the mgh file loads fine in tksurfer (shows proper map) for the given
subject, and so does its corresponding mgz (created from mri_convert).
In FSL there is no physical error, but when loading in the nii file, the X
location is in ~786XX instead of the typical -128 to 128 or somethin
does it load ok in freesurfer (in tksurfer)? What error do you get in
AFNI/FSL? If it
On Mon, 6 Feb 2012, Omer Tal wrote:
> Hey Doug,
>
> Here is what I type it the terminal and what pops back at me. The error
> shows up later when trying to load (either though AFNI or FSL).
>
> mri_surf2surf --
Hey Doug,
Here is what I type it the terminal and what pops back at me. The error
shows up later when trying to load (either though AFNI or FSL).
mri_surf2surf --sval test.mgh --tval test.nii --reshape-factor 241 --s
23 --hemi lh
srcsubject = 23
srcval = test.mgh
srctype=
trgsubj
what's your command line and terminal output?
Omer Tal wrote:
> Tried both, but neither gave a proper nii image.
>
> Any other ideas?
>
> Omer Tal
>
>
>> That particular number factors to 241 and 653, so use one of those as
>> the reshape factor to surf2surf.
>> doug
>>
>> Omer Tal wrote:
>>
Tried both, but neither gave a proper nii image.
Any other ideas?
Omer Tal
> That particular number factors to 241 and 653, so use one of those as
> the reshape factor to surf2surf.
> doug
>
> Omer Tal wrote:
>> Hey Doug,
>>
>> I believe for this patient/hemisphere the number of vertices is 157
My apologies for not pointing it out but that number is not a prime
number, and its largest factor (653) is smaller than 2^15...
Please advise.
Thank you very much for your time,
Omer Tal
> Hey Doug,
>
> I believe for this patient/hemisphere the number of vertices is 157373.
>
> What is the work
That particular number factors to 241 and 653, so use one of those as
the reshape factor to surf2surf.
doug
Omer Tal wrote:
> Hey Doug,
>
> I believe for this patient/hemisphere the number of vertices is 157373.
>
> What is the workaround in the case my number of vertices is unluckily a
> prime?
Hey Doug,
I believe for this patient/hemisphere the number of vertices is 157373.
What is the workaround in the case my number of vertices is unluckily a
prime?
Thank you,
Omer Tal
> Hi Omar, how many vertices? The reshape only works if the number is not
> prime (actually the largest prime fac
Hi Omar, how many vertices? The reshape only works if the number is not
prime (actually the largest prime factor has to be less than 2^15.
doug
Omer Tal wrote:
> Hey Bruce,
>
> Thank you for the prompt response.
>
> The line is as follows:
>
> mri_convert -it mgh -ot nii test.mgh test.nii.
>
> Si
Hey Bruce,
Thank you for the prompt response.
The line is as follows:
mri_convert -it mgh -ot nii test.mgh test.nii.
Since I do agree that the issue is arising from the NIFTI bit limit, i
tried doug's suggestion of
mri_surf2surf --sval test.mgh --tval test.nii --reshape-factor 6 --s
subject_na
Hi Omer
what file are you trying to convert? What is your entire command line
with output and what problems do you have? Nifti unfortunately only allows
16 bits for the width/height/depth/nframes, so surface overlays can't
usually fit as nvertices x 1 x 1 x nframes since nvertices > 2^16 (or 2^
Hey there,
I am trying to convert an mgh file I created into an nii volume so I can
load it in AFNI. I was trying to use mri_convert, which I have used
previously to make nii volumes from my aparc+aseg and it worked great, but
this time the resulting file is faulty.
I've noticed a previous thread
Hi Paolo,
I think you'll find this tutorial has what you are looking for:
https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Diffusion#ResamplingStructuralDataintheDiffusionSpace
Allison
On Tue, 10 Jan 2012, paolo wrote:
> Hi, i have a problem:
>
> i have a file aseg+aparc.mgz, generated by fre
Hi, i have a problem:
i have a file aseg+aparc.mgz, generated by freesurfer, and i would like
to visualize it with trackvis (i mostly need the aparc part). the
problem is, that if i just convert it to nifti, it seems to be in a
different reference frame.
i tried to read the freesurfer coordinate
uce Fischl [mailto:fis...@nmr.mgh.harvard.edu]
> Sent: Sunday, August 23, 2009 6:22 PM
> To:
> Cc:
> Subject: Re: [Freesurfer] Conversion of wmparc.mgz to Original
> Volume Space
> without Resampling
>
> It depends on the resolution.
>
>
>
> On Aug 23, 2009, at
The original image was 1mm isotropic. Does MRIConvert not interpolate the
image if it is not necessary?
Thanks,
Matt.
-Original Message-
From: Bruce Fischl [mailto:fis...@nmr.mgh.harvard.edu]
Sent: Sunday, August 23, 2009 6:22 PM
To:
Cc:
Subject: Re: [Freesurfer] Conversion of
ata was reordered. This should not require interpolation to undo,
> right?
>
> Thanks,
>
> Matt.
>
> -Original Message-
> From: Bruce Fischl [mailto:fis...@nmr.mgh.harvard.edu]
> Sent: Sunday, August 23, 2009 5:47 PM
> To: Matt Glasser
> Cc: freesurf
Fischl [mailto:fis...@nmr.mgh.harvard.edu]
Sent: Sunday, August 23, 2009 5:47 PM
To: Matt Glasser
Cc: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] Conversion of wmparc.mgz to Original Volume Space
without Resampling
Hi Matt,
you can give a -rl switch to "reslice like" a templa
Hi Matt,
you can give a -rl switch to "reslice like" a template
volume. For a parcellation you'll want -interp nearest (or something like
that) also.
cheers,
Bruce
On Sun, 23 Aug 2009, Matt Glasser wrote:
> I am curious about how to use mri_convert to convert wmparc.mgz back to the
> space th
I am curious about how to use mri_convert to convert wmparc.mgz back to the
space that the original nii.gz volume that I gave FreeSurfer was in without
resampling for further analysis with FSL. The volume I imported was
176x208x176, and oriented xorient: Left to Right, yorient: Posterior to
Anteri
su
Cc: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] conversion
Sorry, FS does not have anything to convert from par and rec files.
doug
Lindsay Nagamatsu wrote:
> Hi,
>
> The output files that I get from our scanner are .par and .rec files, but
> I am now using fsl and freesurfer t
Sorry, FS does not have anything to convert from par and rec files.
doug
Lindsay Nagamatsu wrote:
> Hi,
>
> The output files that I get from our scanner are .par and .rec files, but
> I am now using fsl and freesurfer to analyze my data. How can I convert my
> files into a Nifti format to be used
Hi,
The output files that I get from our scanner are .par and .rec files, but
I am now using fsl and freesurfer to analyze my data. How can I convert my
files into a Nifti format to be used by fsl and freesurfer? Is there a way
that freesurfer can do this?
Thank you,
Lindsay
--
Lindsay Nagamat
You should be able to use mri_convert for this.
mri_convert --in_type mgz --out_type analyze INPUT.mgz OUTPUT.img
http://surfer.nmr.mgh.harvard.edu/fswiki/mri_5fconvert
Thanks.
Mithra.
On Dec 10, 2007 2:54 PM, Anca-Larisa Sandu <[EMAIL PROTECTED]> wrote:
> I have a question about conversion
mri_convert file.mgz file.img
should do it
cheers,
Bruce
On Mon, 10 Dec 2007, Anca-Larisa Sandu wrote:
I have a question about conversions.
Is it possible to convert a file with the extension
".mgz" from Freesurfer to a file with the extension
".img", which can be read for example in SPM? If i
Try something like
mri_convert orig.mgz orig.img
Anca-Larisa Sandu wrote:
I have a question about conversions.
Is it possible to convert a file with the extension
".mgz" from Freesurfer to a file with the extension
".img", which can be read for example in SPM? If it is
possible how should I do
I have a question about conversions.
Is it possible to convert a file with the extension
".mgz" from Freesurfer to a file with the extension
".img", which can be read for example in SPM? If it is
possible how should I do this conversion?
Thank you in advance!
Anca Sandu
__
sorry, I don't think we've ever dealt with these MINC formats.
Bruce
On Fri, 13
Jul 2007, jorge luis wrote:
Hello all
I would like to convert a freesurfer triangular
surface (ASCII or binary) to Minc Line OBJ file
format. I know how to convert to Minc Polygons OBJ
file format, but it is not
Hello all
I would like to convert a freesurfer triangular
surface (ASCII or binary) to Minc Line OBJ file
format. I know how to convert to Minc Polygons OBJ
file format, but it is not useful for my application.
I need a conversion to the Lines OBJ format.
Any help is welcome
In advance thank you
can you send the exact screen output (with your command)?
On Thu, 30 Jun 2005, David Soscia wrote:
Hey guys,
After some help from Andy Bell, I was able to get one of my images
converted from .dcm format, up and running with the program. For some
reason now, I keep getting the same error messa
Hey guys,
After some help from Andy Bell, I was able to get one of my images
converted from .dcm format, up and running with the program. For some
reason now, I keep getting the same error message when trying to convert
some other files (in a different location to COR format). It keeps
saying "u
92 matches
Mail list logo
