Dear Bruce,
Reading the doc for read_annotation, it suggests that label entry
values should correspond to the colortable.table(:,5) indices. I wanted to
use it on Desikan annotation atlas and find annotation scout names for
selected cortical points:
[vertices, label, colortable] = read_annotati
oblem does the other issue
> cause? It may be that there are just some items in the color table that
> are not represented in the annotation
> doug
>
> On 03/05/2015 09:05 PM, Octavian Lie wrote:
> > Dear Bruce,
> >
> > Reading the doc for read_annotation, it su
Dear All,
Our MPRAGE and T2 SPACE FLAIR sequences are acquired at times during two
different scans, and the MPRAGE seq further gets reoriented in a pipeline
upstream of the Freesurfer step.
For best results, does the FLAIR volume have to be reoriented (and
resliced) in a rigid registration to the
Dear All,
We use freesurfer in an automatic routine mainly for brain extraction/
parcellation schemes. I want to upgrade from 5.2 to 5.3 on a linux (ubuntu,
64bit) computer, but without surprises.
So:
1. When extracting files/installing freesurfer tar.gz, would the update
override the 5.2 files i
Dear All,
I need to export a T1.mgz and N points (Nx3 coordinates .mat file) of the
same volume in SPM12b. N are actually intracranial electrodes.
For this, I save T1.mgz as .nii prior to import into SPM.
Should I use volume index, volume RAS or surface RAS coordinates for N?
What other transform
Dear All,
I have ubuntu 12.4, and downloaded/installed the dev (12/19/2013) version
of Freesurfer (I used previously version 5.1). Installation was uneventful,
including getting the return to command
> source $FREESURFER_HOME/SetUpFreeSurfer.csh
FREESURFER_HOME /usr/local/fs5.3/freesurfer
FSFA
Thank you,
Octavian
On Fri, Dec 20, 2013 at 2:44 PM, Octavian Lie wrote:
> Dear All,
>
> I have ubuntu 12.4, and downloaded/installed the dev (12/19/2013) version
> of Freesurfer (I used previously version 5.1). Installation was uneventful,
> including getting the return to comma
Dear All,
I downloaded/installed freesurfer-Linux-centos6_x86_64-dev version
(12/19/2013) on my ubuntu 12.04 using tcsh, also fixed missing libnetcdf
libraries missing in my distro, here is fs home directory:
FREESURFER_HOME /usr/local/fs5.3/freesurfer
FSFAST_HOME /usr/local/fs5.3/freesur
Dear All,
I have recently upgraded freesurfer (dev version 12/19/2013 centos6,
86X64) on my ubuntu 12.04 box, I previously used v 5.1(centos 4).
I fixed all other issues that I posted about (libnetcdf
missing,.tcshrc editing), now all seems to go well, including testing,
except
when I load tksur
Dear all,
I tried to run a subject's T1 starting with the dicom convert step (until
now, I used .nii volumes as imput, after dicom conversion in spm; I would
like to be able to use the dicom convert in freesurfer, since I have a
-T2pial step to refine pias afterwards, and it's easier this way).
I
solved, thank you,
Octavian
On Fri, Dec 20, 2013 at 2:44 PM, Octavian Lie wrote:
> Dear All,
>
> I have ubuntu 12.4, and downloaded/installed the dev (12/19/2013) version
> of Freesurfer (I used previously version 5.1). Installation was uneventful,
> including getting the re
solved, thank you,
Octavian
On Sat, Dec 21, 2013 at 11:55 AM, Octavian Lie wrote:
> Dear All,
>
> I downloaded/installed freesurfer-Linux-centos6_x86_64-dev version
> (12/19/2013) on my ubuntu 12.04 using tcsh, also fixed missing libnetcdf
> libraries missing in my distro,
Dear All,
I plan starting running the -FLAIRpial flag for pial refinement, after
recently upgrading freesurfer to dev (12/19/2013), centos6 86X64 build. I
installed the new fs according to the wiki guidelines.
I read on the forum that FSL_DIR has to be set up, and FSL has to be
installed for bbreg
Dear All,
We recently implemented pial correction using T2 space FLAIR with
freesurfer v 5.3, mostly successfully. We use 2-3 MPRAGE (sagittal + axial
and/or coronal) volumes as 001.mgz, 002/003.mgz for the motion correction
step in recon-all pipeline.
The typical times for acquiring space FLAIR i
t have a
> ton of experience with it, but 1 has seemed ok (not sure if we've ever tried
> two)
> Bruce
>
>
>
> On Thu, 2 Jan 2014, Octavian Lie wrote:
>
>> Dear Bruce,
>>
>> Thank you. We used one vs 2 NSA T2 space FLAIR sequences, without a
>> c
Dear All,
1. I need to erode the ?h.pial surfaces be exactly 3 mm, then
2. I need to downsample each of the eroded surfaces to 7500 vertices each, then
(3. Merge the downsampled surfaces (whether or not an intermediary
voxelizing step is involved))
I would appreciate any help with command syntax
applicable to this surface too,
Octavian
On Wed, Jan 8, 2014 at 11:54 AM, Bruce Fischl
wrote:
> can you cc the list? I don't know what you mean by "merge"
>
> On Wed, 8 Jan 2014, Octavian Lie wrote:
>
>> Thank you,
>>
>> I want to merge the pial eroded (of w
Dear All
I reoriented a volume on exporting to analyze format for an application
mri_convert -i path to file/T1.mgz --out_orientation PSR -o path to
file/T1reoriented.mgz
mri_convert -ot analyze -i path to file/T1reoriented.mgz -o path to
file/T1reorientedPSR.img
I need to reorient from the com
Dear All,
I ran recon-all and generated a brain.mgz and say, lh.pial.
I converted brain.mgz to brain.nii, imported the latter to matlab/spm and
realigned it to rbrain.nii, generating a transform matrix
M=rbrain.reorient.mat.
if MM is the header for rbrain.nii, the header O for the original brain.n
Dear All,
Among T2 FLAIR, eT2W FLAIR sense, T2, which sequence should be preferably
used as auxiliary for pial definition?
Does Freesurfer take care of coregistration between these and the MPRAGE?
What would be the command line (Linux Ubuntu) if I want to use SPM
generated nifti DICOM concatenatio
Dear all,
I need to transform my electrode FS volume index coordinates stored in a
.mat file (see attached) in surface RAS coordinates. Do you know of any
matlab code that could be shared to accomplish this and generate another
.mat with RAS coordinates?
Thank you,
Octavian Lie.
trodes.mat
Dear all,
I need to transform my electrode FS volume index coordinates stored in a
.mat file in surface RAS coordinates. Do you know of any matlab code that
could be shared to accomplish this and generate another .mat with RAS
coordinates?
Thank you,
Octavian Lie.
*To follow up and simplify for
Dear all,
I need to mark the cortical extent of a lesion (intersection of the lesion
and pial surface, where "lesion" represent a epilepsy related resection).
After the pial labeling of the resection, I need to register the labeled
surface to the fsaverage.
I completed recon-all routine on the pos
Actually, the white matter is affected too within the resection bed.
Just to make sure, using mri_label2label with surface option to pass a
label from subject 1 to subject 2 is equivalent to registering that label
to fsaverage via sphere.reg for that subject, then transferring the label
from fs av
Dear all,
I need to measure the distance between 2 points on the same hemisphere for
subject A, in the common surface space as I have to compare it with the
distance between other 2 points for subjects B, C...
I used
mris_pmake --subject A --hemi rh --surface0 sphere.reg --curv0 sulc --curv1
sulc
?dpial.ribbon.mgz and rCT head volumes for
normalization?
Also, that all patient volumes are 1mm and MNI template is 2 mm (I need
this specific one) is an issue during normalization?
Thank you,
Octavian Lie.
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Sorry,
I do not seem to see the light.
I have a point in volume index coordinates [128.9 172 62.9 1] and need to
obtain the surface/vertex RAS coordinates (not volume RAS).
matlab path
/usr/local/freesurfer/subjects/subjid/mri
if I type
tkrRAS = Torig*[128.9 172 62.9 1]'
it tells me Torig undefi
applications. Also,
if the surface can be created in MNE just on the right side that will solve
it.
Help much appreciated,
Octavian Lie.
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The
it into surface as lh.bem then run
> tksurfer on it
>
> On Thu, 1 Nov 2012, octavian lie wrote:
>
> Thank you for your quick prompt, how do I pull the inner skull surface
>> into tksurfer, given it is in /bem and not in /surf, and
>> does not have a lh or rh option?
&
Dear Bruce,
One last question. I saved the cut surface as rh.inner-skull-surface
(original was rh.sub_inner_skull_surface) as a patch, but when trying to
see it in tksurfer, I get the following error message:
tksurfer sub rh inner-skull-surface
subject is sub
hemi is rh
surface is inner-skull-surf
Dear Bruce,
Thank you for your assist.
I see the difference between patch and surface, but I would need to get he
cut surface in matlab. I do not know how to set the ripflag=1 for x<0.
Here is the code I use to upload surfaces in Matlab:
function [vertex_coords, faces] = read_surf(fname)
%QUAD_F
Dear All,
I have 2 coregistered MR volume (pre and postresective MRI) sets
for several epilepsy patients. I need to extract the resection volume (VOI=
pre - postresection volume) as a set of voxel coordinates. Can I do this in
freesurfer? Ideally I would avoid manual delineation slice by slice as i
Dear Bruce,
>>
>
If I use freeview slice by slice to mark the resection boundaries and I
mark a set of vertices on each slide, how should I save those? Do I have to
create a set of labels, each on one slide, and then combine them, or how?
I thank you for your thoughts,
Octavian.
>
> The informat
Dear All,
Excuse the basic nature of these quetions. I coregistered 2 analyze volumes
in SPM (pre and post resection MR scans for same patient) with cost
function masking. I imported the preresection scan in Freesurfer, and
processed it with recon -all.
1) What transform matrices should I multiply
Dear All,
I have created a volume of interest in itksnap and imported it in FS
as a .mgz volume filled binary mask. How can I:
1. export it from FS in matlab and generate a .mat array containing
only the volume pixels within the volume (intensity 1) ?
2. Is there a way to generate a 3D surface me
Dear Douglas,
Thank you very much for your input.
1. I generated the ind matrix as per your script, but what I wanted is to
get a matrix with the RAS coordinates for the pixels indexed in ind. Is
there a way to do this?
Thank you,
Octavian
___
Freesur
Dear All,
A simple issue of precedence. In the recon-all pipeline, wm edits take
precedence to pial edits.
If there are both wm and pial defects, should one apply edits sequentially,
say on brainmask.mgz (first wm edits, rerun recon-all say recon-all
-autorecon2 -wm, then do pial edits, rerun reco
Dear All,
In FS6.0.0, this flag is added to manually adjust watershed threshold
instead of its automatic calculation. I went back to the original paper by
Segonne et al, and I could identify the prefllooding height h and the post
watershed threshold t. I assume the flag refers to the latter.
Since
gt; And I don't think you want to edit the wm.mgz for wm edits. Probably you
> should edit brain.finalsurfs.mgz for both wm and pial. Can someone who has
> done more recent recons than I have confirm this?
>
> cheers
> Bruce
>
>
>
> On Thu, 9 Mar 2017, Octavian L
Can anybody comment on the new dura_thresh flag? See below,
Many thanks,
Octavian.
-- Forwarded message --
From: Octavian Lie
Date: Sat, Mar 11, 2017 at 9:28 AM
Subject: -dura_thresh
To: "freesurfer@nmr.mgh.harvard.edu"
Dear All,
In FS6.0.0, this flag is added t
Hello Bruce,
I think this ties to one of my previous questions. Most of the volumes I
processed need both wm and pial edits (typically deleting incorrectly added
voxels for both). More recently, I was editing wm.mgz for wm and
brainmask.mgz for pial. From the wiki, if changes are made for both wm/
Dear All,
I am stuck. Several brains I segment need both wm and pial edits, typically
deleting incorrectly incorporated voxels, such as dural voxels for pia, and
basal temporal hyperintensity artifact or bright dural voxels included due
to partial volume effects for wm.
I edited brainmask.mgz or
gt; Bruce
>
>
>
> On Fri, 31 Mar 2017, Octavian Lie wrote:
>
> Dear All,
>>
>> I am stuck. Several brains I segment need both wm and pial edits,
>> typically
>> deleting incorrectly incorporated voxels, such as dural voxels for pia,
>> and
>> basa
Dear Bruce,
>
> I just transferred subject r02.tar.gz.
>
> Again, wm.mgz edits (all deleted voxels, no additions) are not
> incorporated on reruns using any of the
> recon-all -autorecon-wm -aitorecon3
> recon-all -autorecon2 -autorecon3
> recon-all -make all
>
> For example, the complete command l
Hi there,
I have a similar problem not using longitudinal stream, just a routine
recon-all analyses, this with several processed subjects, Here is my
message sent several days ago.
Thanks,
Octavian.
Dear Bruce,
I just transferred subject r02.tar.gz.
Again, wm.mgz edits (all deleted voxels, no a
Dear All,
I wanted to know if there is any take on the issue of white matter edits
(specifically deleting unwanted voxels from wm.mgz). I sent a subject a
week ago for your review. It seems this is a problem that I had with
several scans, and by the message list, I am not the only one.
Recent user
From: Octavian Lie
Date: Sun, Apr 2, 2017 at 7:59 PM
Subject: wm edits not incorporated
To: octavian lie
Dear Bruce,
I just transferred subject r02.tar.gz.
Again, wm.mgz edits (all deleted voxels, no additions) are not incorporated
on reruns using any of the
recon-all -autorecon-wm -aitorecon3
xtent with how FS 5.3 was reacting, although I did not look at this
> systematically. There may be a reason that manual editing is just part of
> the story during rerun and does not automatically override the recon
> stream, but I do not know it.
> Octavian
>
>
>
>
> -
Dear All,
With FS6, -parallel -openmp x can really speed things up. I inherited code
from prior versions using -usegpu flag for GPU/CUDA (not supported more
recently). Is the latter redundant or affecting in any way the -parallel
-openmp x performance, should we take it out, please advise.
Thank
Dear All,
this is very basic. I have Analyze volumes, and I was suggested to use
-notal-check to bypass the 3rd recon step. I wanted to make sure skipping
the T registration step would not have the potential to mess up the
spherical registration in autorecon3 in any way on a case by case basis. I
dangerous format as it doesn't contain direction cosine info
>> and hence even if it looks right you may have left/right swapped and not
>> know it.
>>
>> I don't think the spherical stuff needs tal, so if it runs through
>> without it you are fine.
>>
Dear all,
I am editing recon-all segmentation results in freeview using the recon
edit function.
1. Is there a way to complement the toggle between the brainmask.mgz and
T1.mgz, especially at the end of pial editing, before resubmitting the
saved brainmask volume to recon-all? It would be nice to
g. For 2, usuually I'll do a little cluster ofr 3-4
> together in an area, then a big space to the next cluster, but probably
> even only 1 would be fine. 2-5mm is much denser than the cluster spacing
> needs to be. For 3, yes that is fine
>
>
> On Fri, 7 Nov 2014, Octavian Lie
ect we will take a look
> Cheers
> Bruce
>
>
>
> > On Nov 9, 2014, at 10:40 PM, Octavian Lie
> wrote:
> >
> > Dear all,
> >
> > 1. in the attached there is a gyrus that does not incorporated into
> surfaces, whatever I do (wm edits/topological d
, Nov 10, 2014 at 11:09 AM, Bruce Fischl
wrote:
> try changing the local dir to /usr/local/fs5.3/freesurfer/subjects and just
> putting the file without a path
>
> cheers
> Bruce
>
>
> On Mon, 10 Nov 2014, Octavian Lie wrote:
>
> > Thank you, Bruce
> >
> &g
Dear all,
Is there a way to generate random or seed-based whole cortical (surface) or
brain (volumetric) parcellations in freesurfer or plugins, generating n
equal area (volume) scouts, where the user can select the n?
Thank you,
Octavian
___
Freesurfer
Dear All,
I tried to get an outer pial surface on a previously processed pt subjid,
and I got the following error.
(recon-all was running another subject in a separate window, for what's
worth)
Please advise,
Octavian
recon-all -localGI -s subjid
WARNING: tcsh v6.17.06 has an exit code bug! Ple
/local/MATLAB/R2012b does not help when calling getmatlab
Please advise,
Thank you,
Octavian
-- Forwarded message --
From: Octavian Lie
Date: Mon, Nov 17, 2014 at 8:11 AM
Subject: outer pial error
To: "freesurfer@nmr.mgh.harvard.edu"
Dear All,
I tried to ge
Solved it, thank you
-- Forwarded message --
From: Octavian Lie
Date: Mon, Nov 17, 2014 at 8:11 AM
Subject: outer pial error
To: "freesurfer@nmr.mgh.harvard.edu"
Dear All,
I tried to get an outer pial surface on a previously processed pt subjid,
and I got the follo
Dear all,
After running the recon-all on a subject, I needed to create a 'pial'
surface to include the hippocampi, which are not included well in the pial
reconstruction. So I generated a mask and used it to mask brain.mgz.
1. All well, except that in both the mask and the masked brain volume
(re
It looks like there is only gray matter (int 42), similar to cortical
ribbon gray, no white matter in that gyrus in aseg, both in the original
recon, and after painting gyral centers in brainmask.
Octavian
On Tue, Nov 25, 2014 at 7:51 AM, Octavian Lie
wrote:
> Dear Bruce,
>
> I am not
I tried, here is the command:
mris_make_surfaces -cover_seg mri/aseg.mgz subjid lh
and the last 5 lines of the run:
...
smoothing surface for 5 iterations...
repositioning cortical surface to gray/csf boundary.
smoothing T1 volume with sigma = 2.000
creating distance transform volume from segmen
Dear All,
I am in the process of getting a powerful linux laptop to run Freesurfer.
Can I run Freesurfer on a 11.10 version of Ubuntu 64 bit ? Are there any
incompatibilities between the latest Freesurfer version and Ubuntu? Is
there any configuration issues and solution particular to my situation
Thank you for the info, can you share what freesurfer version you have that
happens to work well with ubuntu 11.10?
Octavian
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The info
this problem, or alternatively, do you suggest a specific
T1 protocol (TE/TR) to dim the dura a bit?
Thank you,
Octavian Lie.
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The
hat allows one to identify dura
>> by
>> it's short T2*. They might be able to give it to you depending on your
>> scanner and relationship with Siemens. Otherwise it can be difficult, as
>> lenghtening your TE to reduce the dura signal also reduced gray/white
>
Dear Bruce & FreeSurfers,
I ran freesurfer (86x64_64 centos version 5.1.0) on my new linux box
(Ubuntu 11.10 64 bit, NVIDIA GEforce GTX 580, no CUDA for now) using
recon-all -all; it went on for 8 hours, I got the message (Recon complete
without errors) in the log.txt file in my subject directory.
, 2012 at 6:46 PM, octavian lie wrote:
> Dear Bruce & FreeSurfers,
>
> I ran freesurfer (86x64_64 centos version 5.1.0) on my new linux box
> (Ubuntu 11.10 64 bit, NVIDIA GEforce GTX 580, no CUDA for now) using
> recon-all -all; it went on for 8 hours, I got the message (Recon
Dear All,
I am using a pipeline for electrode coregistration including freesurfer for
pial surface generation, run by default recon-all -all and mris_volmask
with --save_distance option. The FS files ?h.dpial.ribbon.mgz are the sole
FS output. They are converted in the pipeline to nii.gz files usi
Dear All,
I am increasingly fascinated by freesurfer.
Here is a rookie issue: I use a source imaging program that is rather
simple-minded in its MRI processing steps. To be able to use the inverse
solution tools of that program, I need to use 2 volumes:
- a head MRI to be used to electrode coregis
Dear All,
>
> I processed a MR brain after temporal lobe resection. While brainmask.mgz,
> and brain.mgz include the temporal remnant (correctly), the calculated pial
> surface excludes it (see attached). How, and at what step can I edit the
> image so that the pial surface (red line) is inclusive
External Email - Use Caution
Dear All, I recently changed from ubuntu 16.04 to 18.04 LTS, then
reinstalled Freesurfer.
As opposed to prior behavior, freeview image manipulation (mainly
mouse-based rotations) are exceedingly choppy and slow. The screen
briefly freezes after moving t
> Andrew
>
>
> From: freesurfer-boun...@nmr.mgh.harvard.edu
> on behalf of Octavian Lie
>
> Sent: Monday, February 10, 2020 9:32 AM
> To: freesurfer@nmr.mgh.harvard.edu
> Subject: [Freesurfer] freeview slow/choppy
>
> External Email - Us
External Email - Use Caution
Dear All,
I need to register:
1. T1.mgz to a T1 postresection volume (no contrast), with large
resection. Which one should I use, mri_robust_register, or bbregister,
if the latter, which is the better initiator (nmi, spm, fsl)?
2. T1.mgz to a 3D FLAIR
> an inter-modal similarity function, but you can also tell bbregister it is
> a T2 and it should do a good job (and implicitly register to the T1 since
> it is already aligned with the surface).
>
> 3. I'm not sure what you mean - can you explain further?
>
> cheers
>
but you can also tell bbregister it is
> a T2 and it should do a good job (and implicitly register to the T1 since
> it is already aligned with the surface).
>
> 3. I'm not sure what you mean - can you explain further?
>
> cheers
> Bruce
>
>
>
> On Sun,
> 23 F
External Email - Use Caution
Dear All,
Is there a way to kill a recon-all run on linux via ssh/putty. Ctrl+C is
not working, obviously, and it is not easy to figure out which process
encodes the recon-all runs with commands such as ps aux, top etc. One gross
way may be removing t
External Email - Use Caution
Dear All,
I have seen bbregister command lines using --o option to get the final
output (say a .nii vol), and others where bbregister is used to get an lta
transform, which is used in a follow-up step (mri_convert with -ns 1 (no
scale), and -rl orig.mg
0/2020 12:55 PM, Octavian Lie wrote:
>
> External Email - Use Caution
>
> Dear All,
>
> I have seen bbregister command lines using --o option to get the final
> output (say a .nii vol), and others where bbregister is used to get an lta
> transform, which is used in a
External Email - Use Caution
Dear All,
I ran recon-all on the 1st run using the -T2pial flag. After wm.mgz edits,
when running
recon-all autorecon2-wm -autorecon3 -T2pial volT2.mgz
it throws an error ~ 'flag volT2.mgz not recognized'. When reruning
recon-all as above, do we need t
to specify
> the T2 volume (eg, -T2 /path/to/T2.mgz). To apply the T2 to the pial use
> -T2pial (without any arguments)
>
> On 5/2/2020 7:55 PM, Octavian Lie wrote:
>
> External Email - Use Caution
> Dear All,
>
> I ran recon-all on the 1st run using the -T2pial fl
External Email - Use Caution
Dear All,
These are probably rookie questions.
1. I can read an .annot file with read_annotation.m, is there a way to
write one? (for example read it to matlab, modify, and save, or create a
combined (lh+rh) aparc.annot file etc.
2. On the same line,
:* freesurfer-boun...@nmr.mgh.harvard.edu <
> freesurfer-boun...@nmr.mgh.harvard.edu> *On Behalf Of *Octavian Lie
> *Sent:* Friday, January 8, 2021 11:59 AM
> *To:* Freesurfer support list
> *Subject:* Re: [Freesurfer] write .annot files
>
>
>
> *External Email
s,annotnames,annotfile);
> % clear mri
> % mri.vol = surfoverlay;
> % MRIwrite(mri,'vals.mgh');
> %
> % Run this command from a linux shell:
> % tksurferfv fsaverage lh inflated -aparc -ov vals.mgh -fminmax .01 1
> %
>
>
>
> On 1/6/2021 10:11 AM, Octavian Lie
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