port?
Best,
Yujing
From: freesurfer-boun...@nmr.mgh.harvard.edu
On Behalf Of Westin, Karin
Sent: Saturday, February 24, 2024 6:10 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] mris_convert reading surf.gii files?
External Email - Use Caution
Hi
I'm trying to cre
External Email - Use Caution
Hi
I'm trying to create an .annot file from a label.gii file using an HCP
fsavarage.surf.gii file (eg mris_convert --annot my_label.label.gii
fsaverage_template.L.surf.gii lh.my_annot.annot). However I keep getting the
error
** failed to open GIF
edu
On Behalf Of Lauri Tuominen
Sent: Friday, January 13, 2023 12:29 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] mris_convert to gifti
External Email - Use Caution
Dear Freesurfer experts,
A quick question. I am trying to convert my cortical thickness analysis result
External Email - Use Caution
Dear Freesurfer experts,
A quick question. I am trying to convert my cortical thickness analysis results
into a gifti file preferably combining left and right, like so:
mris_convert --combinesurfs lh.gamma.mgh rh.gamma.mgh both.gamma.gii
I get th
External Email - Use Caution
Dear Freesurfer Developers,
I must admit that I have not used Freesurfer for quite some time, i.e. I may be
a little rusty. I vaguely remember having the same issue a few years ago, but I
cannot find anything in the forum that seems to work for me.
Do you mean that the inflated is not somehow in line with the pial? They
are not supposed to be (and it is not clear what that would mean). The
white and pial look aligned
On 7/6/20 7:16 AM, Mason Wells wrote:
External Email - Use Caution
Hi Experts,
I am using mris_convert to conve
yup, sounds good. Good luck
Bruce
On Thu, 22 Aug 2019, Damion V Demeter wrote:
External Email - Use Caution
Hi Bruce,
I have been doing some investigating on our side and I believe the issue may
have to do with something in our environment. It appeared to happen across
system
External Email - Use Caution
Hi Bruce,
I have been doing some investigating on our side and I believe the issue
may have to do with something in our environment. It appeared to happen
across systems, but we are not experiencing the error on another system. I
am trying to identify
Hi Damion
you can upload them to our ftp
site
https://surfer.nmr.mgh.harvard.edu/fswiki/FtpFileExchange
cheers
Bruce
On
Sun, 18 Aug 2019, Damion V Demeter wrote:
External Email - Use Caution
Hi Bruce,
My apologizes, I just saw this reply because I didn't realize I had
External Email - Use Caution
Hi Bruce,
My apologizes, I just saw this reply because I didn't realize I had the
list on digest mode. I would very much appreciate your help! How/where
should I upload the files?
Thank you!
Damion
Hi Damion
if you upload the relevant files so that
Hi Damion
if you upload the relevant files so that we can replicate this we will
fix it
cheers
Bruce
On Wed, 14 Aug 2019, Damion V Demeter wrote:
External Email - Use Caution
I am having an issue processing some of my subjects through the HCP pipeline
and have no idea what
External Email - Use Caution
I am having an issue processing some of my subjects through the HCP
pipeline and have no idea what this error means. If anyone could help out,
I'd appreciate it! Here is all the info:
1. Some (not all) of my subjects are getting a segmentation fault er
External Email - Use Caution
Hi,
I am planning to convert an ASCII file to a gifti file using mris_convert.
I am using FreeSurfer 5.3 on Linux 9 stretch.
The ASCII file includes the vertex id , its MNI305 coordinates and p
value. Vertex id is 0-based, from 0 to 20483.
I used
Actually, you might be able to do it this way.
first, combine the surfaces with
mris_convert --combinesurfs lh.white rh.white lh+rh.white
next, combine the overlays in matlab, something like
lh = MRIread('lh.overlay.mgz');
rh = MRIread('rh.overlay.mgz');
lhrh = lh;
lhrh.vol = [lh.vol rh.vol];
Hi Joao, please remember to send to the list. We don't have anything to
merge two hemis together. Manybe the other software has this functionality.
On 1/2/18 11:11 AM, João V. Dornas wrote:
Hi Douglass,
thank you for your response.
I created two surfaces overlay files like this:
lh.mgz
rh.m
I'm not sure what that flag does, but you have to pass it surface files,
not mgz files
On 1/1/18 1:22 AM, João V. Dornas wrote:
Dear Friend,
I am trying to run this command using the last version of Freesurfer:
mris_convert --combinesurfs my-left-surface.mgz my-right-surface.mgz
lh.r
Dear Friend,
I am trying to run this command using the last version of Freesurfer:
mris_convert --combinesurfs my-left-surface.mgz my-right-surface.mgz
lh.rh.asc
But I receive this error:
No such file or directory
freadFloat: fread failed
The input data file are inside the root directory. I
Hi Ziad, yes, it's related to that. Thank you for the help!
Best
Francesca
2015-05-06 16:25 GMT+03:00 Ziad Saad :
> Hello folks,
>
> I am ccing all those on the thread because I am not sure my reply to the
> support list will get through.
>
> GIFTI is the way to go as Matt suggested and all of A
Hi Matt, I can answer only partially to your question. SUMA/afni in
general supports GIFTI format but I don't know if is it possible to
directly convert from GIFTI to .dset.
Usually I convert my annot file to .niml.roi with FSread_annot and
.niml.roi to .1D.dset with ROI2dataset.
Best
Francesca
Does SUMA support GIFTI and provide a utility to convert between its
formats and GIFTI? I was also wondering what a .dset was and how to get
it into GIFTI so it could be easily used across software platforms.
Thanks,
Matt.
On 5/5/15, 5:30 PM, "Bruce Fischl" wrote:
>sorry, I think this may be
sorry, I think this may be a question for the SUMA people - I don't know
what .dset format is. Are you going to do the masking within SUMA? I'll cc
Ziad so he can chime in.
cheers
Bruce
On Tue, 5 May 2015, Francesca Strappini wrote:
I'm trying to mask a time series dataset that I mapped to t
I'm trying to mask a time series dataset that I mapped to the surface in
SUMA (surface created with freesurfer and imported into SUMA). I think the
input should be in the .dset fomat (region mapped to the surface). The
problem is that when I save my label the annotation file has only a list of
vert
you can just create a label file I guess. What input does SUMA take?
On Tue,
5 May 2015, Francesca Strappini wrote:
Sorry, just to be clear, I meant how can I create a mask on the surface in
which at each vertex is assigned a value, 0 or 1.
I need to create this mask for exporting the freesurf
what are you trying to mask?
On Tue, 5 May 2015, Francesca Strappini wrote:
Thank you! Do you know which function should I use?
Best
Francesca
2015-05-05 15:30 GMT+03:00 Bruce Fischl :
yes, you can use a label for this (we use the ?h.cortex.label
for this purpose routinely to remov
Sorry, just to be clear, I meant how can I create a mask on the surface in
which at each vertex is assigned a value, 0 or 1.
I need to create this mask for exporting the freesurfer labels into SUMA
and ultimately to extract the time series from each vertex.
Thanks
Francesca
2015-05-05 16:06 GMT+0
Thank you! Do you know which function should I use?
Best
Francesca
2015-05-05 15:30 GMT+03:00 Bruce Fischl :
> yes, you can use a label for this (we use the ?h.cortex.label for this
> purpose routinely to remove non-cortical stuff)
>
> On Tue, 5 May 2015, Francesca Strappini wrote:
>
> Thank yo
yes, you can use a label for this (we use the ?h.cortex.label for this
purpose routinely to remove non-cortical stuff)
On Tue, 5 May 2015,
Francesca Strappini wrote:
Thank you so much! I understand what's the problem and I will make my custom
ctab file.
Last question, about the annot files, i
Thank you so much! I understand what's the problem and I will make my
custom ctab file.
Last question, about the annot files, is it possible with freesurfer to
create a mask with the annot or the label files in which the value 1 is
assigned to the region and 0 to the rest of the brain?
Thanks aga
Francesca,
I looked at the files you sent and replicated the problem. It is due to
creating your lh.EKppa.annot file using FreeSurferColorLUT.txt as the
colortable file. You should create your own colortable file, which is
simple to do, and create a new .annot file using that colortable (ie,
the
Francesca,
How was lh.EKppa.annot created? Is it a custom list of annotations?
Does it include an embedded colortable appropriate for those
annotations?
Can you send me the files 'lh.EKppa.annot' and 'lh.white'? I can try to
replicate the problem.
Also, can you run this:
mris_info lh.EKppa.an
Hi, sorry to bother, I'm re-posting this question just in case it got lost.
Thanks.
Hi,
I have a question about mris_convert. I've created some regions on the
surface and now I would like to make them directly readable into SUMA. I
ran this command but it ended with an error message.
mris_conver
Hi,
I have a question about mris_convert. I've created some regions on the
surface and now I would like to make them directly readable into SUMA. I
ran this command but it ended with an error message.
mris_convert --annot lh.EKppa.annot
/usr/local/freesurfer/subjects/EK/surf/lh.white lh.EKppa.ann
;>
>> From: freesurfer-boun...@nmr.mgh.harvard.edu
>> [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Zachary
>> Greenberg
>> Sent: Wednesday, March 04, 2015 7:05 PM
>> To: Freesurfer support list
>> Subject: Re: [Freesurfer] mris_convert lh.pial t
Of Zachary Greenberg
Sent: Wednesday, March 04, 2015 7:47 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] mris_convert lh.pial to lh.pial.asc coordinate shift
awesome! thanks a bunch Don.
-zack
On Wed, Mar 4, 2015 at 4:24 PM, Krieger, Donald N.
mailto:krieg...@upmc.edu>> wrote:
H
f Pittsburgh
>
>
>
> *From:* freesurfer-boun...@nmr.mgh.harvard.edu [mailto:
> freesurfer-boun...@nmr.mgh.harvard.edu] *On Behalf Of *Zachary Greenberg
> *Sent:* Wednesday, March 04, 2015 7:05 PM
> *To:* Freesurfer support list
> *Subject:* Re: [Freesurfer] mris_convert lh.pial to lh.pial.asc
>
half Of Zachary
Greenberg
Sent: Wednesday, March 04, 2015 7:05 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] mris_convert lh.pial to lh.pial.asc coordinate
shift
Thanks bruce. It will work out fine if I can just pull out that c_(ras)
array in a pipelined way to apply it to the asc
ment of Neurological Surgery
University of Pittsburgh
From: freesurfer-boun...@nmr.mgh.harvard.edu
[mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Zachary Greenberg
Sent: Wednesday, March 04, 2015 7:05 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] mris_convert lh.pial to lh.p
Thanks bruce. It will work out fine if I can just pull out that c_(ras)
array in a pipelined way to apply it to the ascii data.
I'm struggling a bit to achieve that though. I think because mris_info
outputs the tables of *_(ras) info in a strange way. For example, if I try
to cat the output of mri
Hi Zack
the ascii format I don't think supports the c_ras info, which is why you
see a shift
cheers
Bruce
On Wed, 4 Mar 2015, Zachary Greenberg wrote:
Ok I figured out that this shift corresponds to the c_(RAS) value in the
header of lh.pial, which you can get with 'mris_info lh.pial'
Altern
Ok I figured out that this shift corresponds to the c_(RAS) value in the
header of lh.pial, which you can get with 'mris_info lh.pial'
Alternatively you can get the first coordinate and subtract it from the
first coordinate of lh.pial.asc with 'mris_info lh.pial --v 0'
Is there a way I'm not thin
Hi all,
I discovered that converting the mesh data from freesurfer lh.pial format
to ascii (.asc) causes a shift in the coordinates of the mesh. You can see
this by overlaying the two surfaces in freeview, and looking at the
difference between the [0 0 0] surface RAS coordinate in lh.pial vs
lh.pi
Mike,
Hi, a new mris_convert I’ve posted to the ftp site corrects this problem. It
will now store the volume geometry info into two giiCoordSys structs, which an
updated freeview will be able to read. mris_convert is here:
ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/misc/linux-centos
Yes the HCP pipelines have to take care of this as well so that the
surfaces and volume align outside of FreeSurfer.
Peace,
Matt.
On 5/27/14, 8:35 AM, "Franz Liem" wrote:
>Hi Michael,
>
>I had a similar problem a while ago. Maybe this might help.
>http://www.mail-archive.com/freesurfer%40nmr.m
Hi Michael,
I had a similar problem a while ago. Maybe this might help.
http://www.mail-archive.com/freesurfer%40nmr.mgh.harvard.edu/msg31152.html
Best,
Franz
Am 23.05.2014 um 05:38 schrieb Harms, Michael:
>
> Hi,
> I converted a surface to GIFTI
> e.g.,
> mris_convert lh.white lh.white.gii
>
Hi,
I converted a surface to GIFTI
e.g.,
mris_convert lh.white lh.white.gii
lh.white and lh.white.gii align when they are both loaded in 'tkmedit'.
However, they do not align when loaded simultaneously in 'freeview'.
Of possible relevance: When I loaded lh.white.gii into 'freeview', I got
I think this is due to the fact that there is some geometry information
in our surface format that is probably not present in gii. Ruopeng, can
you verify?
doug
On 02/20/2014 05:11 PM, Karen Marie Sandø Ambrosen wrote:
> Hi again,
>
> When I convert a surface to .gii with mris_convert, it is sh
Hi again,
When I convert a surface to .gii with mris_convert, it is shifted
compared to the original surface when loaded into freeview (see previous
mail). Does anyone know how to solve this?
Best,
Karen
On 02/18/2014 10:01 AM, Karen Marie Sandø Ambrosen wrote:
> Hi Freesurfer experts,
>
> I a
Hi Freesurfer experts,
I am trying to run tracktography from freesurfer labels using
probtrackx2 in fsl. To convert the labels to surfaces I use the
label2surf command as recommended on the fslwiki. To use the label2surf
command I need to convert the surface, e.g. lh.white into a
fsl-compatibl
oops, sorry list, this was supposed to go to Pedro...
On 15/10/11 17:39, Anderson Winkler wrote:
Ah Pedro,
Se era isso que você precisava, poderia ter falado. Eu tenho isso
pronto, que pode ser chamado via linha de comandos. Foi usado no paper
que vc deve ter visto...
Abração,
Anderson
On 1
Ah Pedro,
Se era isso que você precisava, poderia ter falado. Eu tenho isso
pronto, que pode ser chamado via linha de comandos. Foi usado no paper
que vc deve ter visto...
Abração,
Anderson
On 15/10/11 13:09, Pedro Paulo de Magalhães Oliveira Junior wrote:
Michael,
Thanks for the hint.
Her
Michael,
Thanks for the hint.
Here's a program that converts the surface + annotation in a Stanford PLY
Object file
# Create ply
# Stanford Object format
from surfer import io as io_
surface = io_.read_geometry
('/Applications/freesurfer/subjects/bert/surf/lh.pial')
labels = io_.read_annot
('/A
Yes, but --seg in mri_annotation2label --subject bert --hemi lh --seg
saida.mgz produces a volume and not a surface.
-
Pedro Paulo de Magalhães Oliveira Junior
Netfilter & SpeedComm Telecom
-- www.netfilter.com.br
-- For mobile: ht
Have you tried using mri_annotation2label with the --seg output option?
doug
Michael Waskom wrote:
> If you know Python, you can likely do this pretty easily with tools
> from the PySurfer package: http://pysurfer.github.com/
>
> (Check out surfer.io.read_annotation).
>
> If you're just using th
Thanks.
It works as I wished.
from surfer import io as sIo
a = sIo.read_annot('label/lh.aparc.annot')
b = sIo.read_geometry('surf/lh.pial')
And now I can have each vertex labeled
-
Pedro Paulo de Magalhães Oliveira Junior
Netfil
If you know Python, you can likely do this pretty easily with tools from the
PySurfer package: http://pysurfer.github.com/
(Check out surfer.io.read_annotation).
If you're just using the io routines, you won't need the somewhat heavy
Mayavi visualization dependencies. You should be able to read
it wouldn't be that hard to put something together if you want to avoid
matlab. Spec out what you need and send me a sample, maybe on Bert
Bruce
On Sat, 8
Oct 2011, Pedro Paulo de Magalhães Oliveira Junior wrote:
Thanks.
I suppose I can't do this without matlab. Right?
-- iOS 5.0
Em 08/10
Thanks.
I suppose I can't do this without matlab. Right?
-- iOS 5.0
Em 08/10/2011, às 19:29, Bruce Fischl escreveu:
> there is a write_annotation.m file you can use
> On Sat, 8 Oct 2011, Anderson Winkler wrote:
>
>> ops, it seems the comments inside the dpxwrite.m no longer reflect what it
>>
there is a write_annotation.m file you can use
On Sat, 8 Oct 2011, Anderson
Winkler wrote:
ops, it seems the comments inside the dpxwrite.m no longer reflect what it
does. You probably don't need this, but anyway, the version attached is more
up-to-date.
Anderson
On 08/10/11 17:28, Anderson
ops, it seems the comments inside the dpxwrite.m no longer reflect what
it does. You probably don't need this, but anyway, the version attached
is more up-to-date.
Anderson
On 08/10/11 17:28, Anderson Winkler wrote:
Hi Pedro,
There is probably a way to do that using FS tools from the command
Hi Pedro,
There is probably a way to do that using FS tools from the command line,
but the attached script should do the same. The result is a
"data-per-vertex" file, which is the same as the .asc files from
mris_convert. There is no geometry input, hence the vertex coordinates
are all set to
I need to create a file where I have the parcellation value (structure name)
per vertex.
I've tried mris_convert --annot
/Applications/freesurfer/subjects/bert/label/lh.aparc.annot
/Applications/freesurfer/subjects/bert/surf/lh.pial parc.asc
But I get the error: ERROR: unknown file annot file typ
Hi Doug,
That version seems to do the trick! Thanks!
Emily
On 3/20/07, Doug Greve <[EMAIL PROTECTED]> wrote:
Sorry, fell thru the cracks the first time. Which version of freesurfer
are you using? The stable versions do not allow writing of mgh files
from mris_convert. I've put a new version h
Sorry, fell thru the cracks the first time. Which version of freesurfer
are you using? The stable versions do not allow writing of mgh files
from mris_convert. I've put a new version here:
ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mris_convert
See if that works
doug
Hi Freesurfer Community,
I sent this message to the mailinglist a little bit ago. It never
showed up in my mailbox, although it seems to have posted on the
mailinglist website. Anyway, on the chance that it didn't mail out
properly, I thought I'd resend it, as I still havent been able to
figure o
Hi,
I have a question about using mris_convert to convert .asc to .mgh. I
have a .mgh file I made with mri_vol2surf (target subject as
fsaverage). I convert it to .asc using this command:
mris_convert -c 010.onerun.space.intval.lh.fsave.mgh
/home/ecooper/subjects/fsaverage/surf/lh.white lh.010mg
On Friday 11 March 2005 13:24, Bruce Fischl wrote:
> the output surface has to have the extension .asc .
Thanks, that fixed it.
Cheers
--R
--
Rudolph Pienaar, M.Eng, D.Eng / email: [EMAIL PROTECTED]
MGH/MIT/HMS Athinoula A. Martinos Center for Biomedical Imaging
149 (2301) 13th Street, Charlest
Hi,
try "mris_convert input_surface output.asc".
This should work.
Florent
-
Florent Segonne
PhD Candidate
Stata Center 32-D430 CSAIL MIT
1 617 253 2986
http://people.csail.mit.edu/~fsegonne
-
On Fri, 11 Mar 2005, Rudolph Piena
Hi Rudolph,
the output surface has to have the extension .asc .
cheers,
Bruce
On Fri, 11 Mar 2005,
Rudolph Pienaar wrote:
> Hi all -
>
> I'd like to convert a FreeSurfer surface to ASCII format - essentially so
> that
> I can import it into say an external 3D viewer program.
>
> I understo
Hi all -
I'd like to convert a FreeSurfer surface to ASCII format - essentially so that
I can import it into say an external 3D viewer program.
I understood that 'mris_convert' converts a surface to ASCII. For a given
subject with say an inflated right hemisphere surface, I've tried called it
Converting pathces to ascii using mris_convert with
% mris_convert -p rh.temp.patch.flat rh.temp.patch.flat.asc
seems to give incorrect topology in the ascii patch (the
triangles are "messed up"). I loaded the asc patch
into tksurfer, and also converted it back to binary and
loaded it in tksurfe
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