Fischl
[fis...@nmr.mgh.harvard.edu]
Sent: Thursday, October 06, 2016 4:13 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] mris_divide_parcellation
Hi Fahimeh
you can also give mris_divide_parcellation a "splitfile" :
rst, a splitfile can be specified as the fourt
freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Bruce Fischl
> [fis...@nmr.mgh.harvard.edu]
> Sent: Friday, September 16, 2016 6:31 PM
> To: Freesurfer support list
> Subject: Re: [Freesurfer] mris_divide_parcellation
>
> how would you like them divided? You can also use
>
...@nmr.mgh.harvard.edu] on behalf of Bruce Fischl
[fis...@nmr.mgh.harvard.edu]
Sent: Friday, September 16, 2016 6:31 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] mris_divide_parcellation
how would you like them divided? You can also use
mris_make_face_parcellation to make units of approximately equal
how would you like them divided? You can also use
mris_make_face_parcellation to make units of approximately equal area
(either in the individual or in the group)
On Fri, 16 Sep 2016, Mamashli,
Fahimeh wrote:
Dear Freesurfer group,
I am going to divide a brain parcellation into divisions
Dear Freesurfer group,
I am going to divide a brain parcellation into divisions using
mris_divide_parcellation. As far as I know from the help comment, this function
"divides one or more parcellations into divisions perpendicular to the long
axis of the label". Is there any other program that
The name of which label?
On 07/02/2014 02:00 PM, Corinna Bauer wrote:
Whereby the label name is derived from which, the GM labels? i.e.
lh.rostralmiddlefrontal_div3
On Wed, Jul 2, 2014 at 11:45 AM, Bruce Fischl
fis...@nmr.mgh.harvard.edu mailto:fis...@nmr.mgh.harvard.edu wrote:
yes,
the new white matter divided labels. I was not able to extract the labels
using the matching grey matter names, but was able to do so using the label
number seen in the tools from tkmedit. Seeing as there are over 100 labels,
is there a more efficient way?
On Mon, Jul 7, 2014 at 12:08 PM,
Right, this is going to be a problem. One of the things you can do is to
use the --ctab option of mri_annotation2label to create a colortable,
something like
mri_annotation2label --ctab new.lh.ctab --s subject --hemi lh
--annotation newannot --outdir junk
You can do this for both hemis,
great, thanks! I'll give that a try and let you know how it goes.
On Mon, Jul 7, 2014 at 12:50 PM, Douglas N Greve gr...@nmr.mgh.harvard.edu
wrote:
Right, this is going to be a problem. One of the things you can do is to
use the --ctab option of mri_annotation2label to create a colortable,
Doug, that worked very well, thanks.
mri_aparc2aseg --s ${subject} --labelwm --hypo-as-wm --rip-unknown
--volmask --wmparc-dmax 2 --o ${subj_dir}/mri/wmdivided.nii --annot
aparc.split
mri_annotation2label --ctab new.rh.ctab --subject ${subject} --hemi rh
--annotation aparc.split --outdir
Hi Bruce,
I am trying to do just that using the following command line:
mri_aparc2aseg --s ${subject} --labelwm --hypo-as-wm --rip-unknown
--volmask --o ${subj_dir}/mri/wmdivided --annot aparc.split
After the slice labeling, I get the following:
Used brute-force search on 872 voxels
Fixing
Hi Corinna
you need to give some output extension so it knows what file type to write
(e.g. .mgz, .nii, .nii.gz. mgh, ...)
cheers
Bruce
On Wed, 2 Jul 2014, Corinna Bauer wrote:
Hi Bruce,
I am trying to do just that using the following command line:
mri_aparc2aseg --s ${subject} --labelwm
And then for breaking the individual labels up, would mri_extract_label be
the best option?
On Wed, Jul 2, 2014 at 11:01 AM, Bruce Fischl fis...@nmr.mgh.harvard.edu
wrote:
Hi Corinna
you need to give some output extension so it knows what file type to write
(e.g. .mgz, .nii, .nii.gz. mgh,
yes, or mri_binarize --match
cheers
Bruce
On Wed, 2 Jul 2014, Corinna Bauer wrote:
And then for breaking the individual labels up, would mri_extract_label be
the best option?
On Wed, Jul 2, 2014 at 11:01 AM, Bruce Fischl fis...@nmr.mgh.harvard.edu
wrote:
Hi Corinna
you need to
Whereby the label name is derived from which, the GM labels? i.e.
lh.rostralmiddlefrontal_div3
On Wed, Jul 2, 2014 at 11:45 AM, Bruce Fischl fis...@nmr.mgh.harvard.edu
wrote:
yes, or mri_binarize --match
cheers
Bruce
On Wed, 2 Jul 2014, Corinna Bauer wrote:
And then for breaking the
I figured it out. Thanks for your help!
On Wed, Jul 2, 2014 at 2:00 PM, Corinna Bauer corinna...@gmail.com wrote:
Whereby the label name is derived from which, the GM labels? i.e.
lh.rostralmiddlefrontal_div3
On Wed, Jul 2, 2014 at 11:45 AM, Bruce Fischl fis...@nmr.mgh.harvard.edu
wrote:
yes
On Wed, 2 Jul 2014, Corinna Bauer wrote:
Whereby the label name is derived from which, the GM labels? i.e.
lh.rostralmiddlefrontal_div3
On Wed, Jul 2, 2014 at 11:45 AM, Bruce Fischl fis...@nmr.mgh.harvard.edu
wrote:
yes, or mri_binarize --match
cheers
Bruce
On
hello,
I was wondering if it was possible to use mris_divide_parcellation on white
matter labels.
Thanks,
Corinna
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The information
Hi Corinna
not really, as that is a surface-based utility. You could divide the
cortical labels and then recrate the wmparc from it, which might do what
you want.
cheers
Bruce
On Tue, 1 Jul 2014, Corinna
Bauer wrote:
hello,
I was wondering if it was possible to use
For creating corresponding wm segmentations to the rois derived from
mris_divide_parcellation, should mri_aparc2wmseg be used or should I follow
the steps outlined in this posting
https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2010-February/013471.html?
Thanks
Corinna
On Wed, Apr 9,
Use mri_aparc2aseg with the --labelwm option. Look in the recon-all.log
file for an example command line that generates wmparc.mgz
doug
On 04/10/2014 09:52 AM, Corinna Bauer wrote:
For creating corresponding wm segmentations to the rois derived from
mris_divide_parcellation, should
Hi Doug,
Following the example in recon-all.log, I tried this: mri_aparc2aseg --s
FGH_09112013 --labelwm --hypo-as-wm --rip-unknown --volmask --o
mri/wmdivided.mgz --annot aparc.split
and received and mgh Write error.mghWrite(mri/wmdivided.mgz, -1): could not
open file
On Thu, Apr 10, 2014
no, I was in subjects_dir. Updated the command to this and it works now.
thanks.
mri_aparc2aseg --s FGH_09112013 --labelwm --hypo-as-wm --rip-unknown
--volmask --o FGH_09112013/mri/wmdivided.mgz --annot aparc.split
On Thu, Apr 10, 2014 at 11:24 AM, Douglas N Greve gr...@nmr.mgh.harvard.edu
In the mri_extract_label, there is a label number. Where would I find this
for the new labels?
i.e. mri_extract_label ${subj_dir}/mri/aparc+aseg.mgz 2035
${subj_dir}/hardi_labels/ctx-rh-insula.nii
On Tue, Apr 8, 2014 at 10:50 PM, Douglas Greve gr...@nmr.mgh.harvard.eduwrote:
yep, exactly
$FREESURFER_HOME/FreeSurferColorLUT.txt
cheers
Bruce
On Wed, 9 Apr 2014, Corinna Bauer
wrote:
In the mri_extract_label, there is a label number. Where would I find this
for the new labels?
i.e. mri_extract_label ${subj_dir}/mri/aparc+aseg.mgz 2035
It looks like the FreeSurferColorLUT.txt does not contain the label number
for the newly created labels (divided from the desikan atlas).
On Wed, Apr 9, 2014 at 9:53 AM, Bruce Fischl fis...@nmr.mgh.harvard.eduwrote:
$FREESURFER_HOME/FreeSurferColorLUT.txt
cheers
Bruce
On Wed, 9 Apr 2014,
Should I make up my own LUT for the new ROIs that specifies some colour and
label number?
On Wed, Apr 9, 2014 at 10:00 AM, Corinna Bauer corinna...@gmail.com wrote:
It looks like the FreeSurferColorLUT.txt does not contain the label number
for the newly created labels (divided from the
oh, those should be embedded in the .annot file it creates
On Wed, 9 Apr
2014, Corinna Bauer wrote:
It looks like the FreeSurferColorLUT.txt does not contain the label number
for the newly created labels (divided from the desikan atlas).
On Wed, Apr 9, 2014 at 9:53 AM, Bruce Fischl
you'll need to figure it out from the volume itself by loading the seg
with both -seg and -aux. When you find the label you want, click on it
and the aux value in the control window will tell you what the id is
doug
On 04/09/2014 09:41 AM, Corinna Bauer wrote:
In the mri_extract_label, there
Perfect. Thanks!
On Wed, Apr 9, 2014 at 10:22 AM, Douglas N Greve
gr...@nmr.mgh.harvard.eduwrote:
you'll need to figure it out from the volume itself by loading the seg
with both -seg and -aux. When you find the label you want, click on it
and the aux value in the control window will tell
Hello all,
I am planning to use mris_divide_parcellation to split the Desikan atlas
into smaller ROIs, but will need the new ROIs to be consistent between
subjects.
Can I achieve this if I register each subject to fsaverage space and then
apply the inverse transform to the divided parcellations
Exactly what you have described won't work very well because it would be
in the volume. I would divide up the parcellations in fsaverage space
like you've done, then map the parcellation to each subject using
mri_surf2surf (--sval-annot, see example 6)
doug
On 04/08/2014 04:54 PM, Corinna
Hi Doug,
After I have the labels then in each subject's T1 space, I will need to
then put them into diffusion and resting state space.
I already have scripts that put the parcellations into subject-specific
diffusion/resting state space (using bbregister, tkregister2, mri_vol2vol
(using the
yep, exactly
On 4/8/14 6:00 PM, Corinna Bauer wrote:
Hi Doug,
After I have the labels then in each subject's T1 space, I will need
to then put them into diffusion and resting state space.
I already have scripts that put the parcellations into
subject-specific diffusion/resting state space
Hi Bruce,
Thanks for your reply. This makes sense. One remaining question is which
surface is used to compute the eigen-axis, is it the white surface?
Best,
Martin
On 02/03/14 15:27, Bruce Fischl wrote:
Hi Christian and Martin
mris_divide_parcellation finds the primary eigen-axis of the
Thanks a lot Bruce! Using the sphere surface was what I was missing.
Christian
On Feb 4, 2014, at 12:16, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote:
it's the ?h.sphere so that folding isn't an issue
On Tue, 4 Feb 2014, Martin Luessi wrote:
Hi Bruce,
Thanks for your reply. This
Hi Christian and Martin
mris_divide_parcellation finds the primary eigen-axis of the parcellation
along the cortical surface, then splits it up into as many units as
specified (either enough to get it under the area threshold, or
explicitly specifed in a split file)
cheers
Bruce
p.s. the
...@nmr.mgh.harvard.edu]
Sent: Wednesday, May 29, 2013 8:41 PM
To: Tina Jeon
Subject: Re: [Freesurfer] mris_divide_parcellation color table error
Sure
On May 29, 2013, at 9:36 PM, Tina Jeon tina.j...@utsouthwestern.edu wrote:
The colors are visually different by a shade then loop every 4 or so colors.
I
Yes it worked. Thank you that is exactly what I needed.
Tina
-Original Message-
From: Bruce Fischl [mailto:fis...@nmr.mgh.harvard.edu]
Sent: Thursday, May 30, 2013 12:36 PM
To: freesurfer@nmr.mgh.harvard.edu
Cc: Tina Jeon
Subject: Re: [Freesurfer] mris_divide_parcellation color table
Hi Tina
Did you try visualizing it in tksurfer?
Bruce
On May 29, 2013, at 7:22 PM, Tina Jeon tina.j...@utsouthwestern.edu wrote:
Hello freesurfers,
I am trying to create a figure similar to the Hagmann et al 2008 paper with
998 rois overlaid onto the surface, however, I am finding that
Yes same result as with freeview.
Sent from my iPhone
On May 29, 2013, at 7:46 PM, Bruce Fischl
fis...@nmr.mgh.harvard.edumailto:fis...@nmr.mgh.harvard.edu wrote:
Hi Tina
Did you try visualizing it in tksurfer?
Bruce
On May 29, 2013, at 7:22 PM, Tina Jeon
hmmm, I haven't run that code in a long time. Are the colors different
but not visually so? That is, do the rgb values differ by 1 or 2 or
something like that? Or are they actualy identical?
On Thu, 30 May 2013, Tina Jeon wrote:
Yes same result as with freeview.
Sent from my iPhone
On May
Dear all,
I'm using mris_divide_parcellation to subdivide cortical regions into
smaller regions and I've some questions about such process.
I would like to transform my new annot file to labelled surface and
labelled cortical volume.
For the former, there's a 'simple' way to transform annot file
Hi Freesurfer users,
Does anyone have a method to divide aseg.mgz volumetric regions along a
longitudinal axis?
Or a simple split after finding a center of mass of an ROI?
I found that mris_divide_parcellation only splits up regions from the
surface based segmentation as found in the desikan
Hi Mario,
I don't think we've ever written such a thing but it would be pretty
straightfoward in matlab.
sorry
Bruce
On Tue, 24 Apr 2012, Mario Ortega wrote:
Hi Freesurfer users,
Does anyone have a method to divide aseg.mgz volumetric regions along a
longitudinal axis?
Or a simple split
Thank you Bruce, the parcellation looks good, as you say, I think that it
doesn't affect me.
yolanda
2012/2/7 Bruce Fischl fis...@nmr.mgh.harvard.edu
Hi Yolanda
does the resulting parcellation look ok? I think that's a small bug that
may not have any effect on you (there will just be extra,
Dear Freesurfer experts,
I have a question regarding mris_divide_parcellation. I have created a file
containing the parcels from aparc.annot that I want to split and I have run
the following command. Why is Freesurfer allocating 36 additional units?
When I open the new annotation file
Hi Yolanda
does the resulting parcellation look ok? I think that's a small bug that
may not have any effect on you (there will just be extra, unused color
table entries)
Bruce
On Tue, 7 Feb 2012, Yolanda Vives wrote:
Dear Freesurfer experts,
I have a question regarding
Dear FS Team,
I used mris_divide_parcellation to create a new parcelation with smaller
regions, but all these regions seem to have a different size. I am interested
to get smaller cortical parcellated regions, but all of them with the same
area. How can I get it? Could I decide the area size?
I'm surprised that the divisions are not roughly equal in area. How much
different are they? You can also spec an area threshold instead of a
number of subdivisions, but that just keeps dividing until all
subdivisions are below that area. I don't think we have anything that
will divide them
Hi Jose,
I have another tool that we haven't released that will do this more
closely. You can't do that with mris_divide_parcellation since the units
don't start with equal area (or multiples thereof)
cheers,
Bruce
On Thu, 19 Feb 2009, Jose
Luis Cantero Lorente wrote:
Dear FS Team,
I
Hi Jürgen,
turns out this was a display but in tksurfer, which I fixed. It would
stop displaying after the 3000th annotation unit. If you tell us what
os/hardware you are running on we can send you a new version.
cheers,
Bruce
On Sat, 17 Jan
2009, Jürgen Hänggi wrote:
Dear FS experts
Dear FS experts
My former problem is solved. When loading the produced annot with the GUI,
the formerly reported problem disappear.
Regards
Juergen
--
Juergen Haenggi
Ph.D. (Dr. des.)
Division Neuropsychology
Institute of Psychology
Dear FS experts
Sorry, me again. If I divide the parcellations into areas of 100 mm2 only
the most posterior part of the parcellations will be divided. Only with a
threshold of about 500 mm2, the whole hemisphere's parcellations will be
divided.
Are there not enough labels resp. colors
Hi Jürgen,
the cmdline you gave will only divide units bigger than 100 mm^2. Is that
what you want?
cheers,
Bruce
On Sat, 17 Jan 2009, Jürgen Hänggi wrote:
Daer FS experts
When using the command:
mris_divide_parcellation Ego_Mean3_FineParc rh aparc.annot 100 rh_annot_100
Only some
Hi Jürgen,
it will pick a random (unique) color for each new parcellation unit.
cheers,
Bruce
On Sat, 17 Jan 2009, Jürgen Hänggi
wrote:
Dear FS experts
Sorry, me again. If I divide the parcellations into areas of 100 mm2 only
the most posterior part of the parcellations will be divided.
is for the PowerPC, macintel dir is for the new Intel
Macs.
Nick
On Thu, 2007-05-10 at 19:45 -0400, Catherine Hartley wrote:
From: Catherine Hartley [EMAIL PROTECTED]
Date: May 10, 2007 7:10:19 PM EDT
To: Doug Greve [EMAIL PROTECTED]
Subject: Re: [Freesurfer] mris_divide_parcellation
then i get: Exec
try
chmod a+x mris_divide_parcellation
Catherine Hartley wrote:
Thanks! However when i try to execute the command, i get a message
saying Permission denied. Any ideas?
Thanks,
Cate
On May 10, 2007, at 5:30 PM, Doug Greve wrote:
here you go ...
From: Catherine Hartley [EMAIL PROTECTED]
Date: May 10, 2007 7:10:19 PM EDT
To: Doug Greve [EMAIL PROTECTED]
Subject: Re: [Freesurfer] mris_divide_parcellation
then i get: Exec format error. Binary file not executable.
[catemac:/Applications] cate% cd freesurfer/bin
[catemac:/Applications
Hartley wrote:
From: Catherine Hartley [EMAIL PROTECTED]
Date: May 10, 2007 7:10:19 PM EDT
To: Doug Greve [EMAIL PROTECTED]
Subject: Re: [Freesurfer] mris_divide_parcellation
then i get: Exec format error. Binary file not executable.
[catemac:/Applications] cate% cd freesurfer/bin
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