ehalf of Wang, Ruopeng
Sent: Tuesday, November 1, 2022 1:26:43 PM
To: Freesurfer support list
Subject: [EXTERNAL] Re: [Freesurfer] Freesurfer labels vertices and not faces?
I’m not sure I get exactly what you wanted to do. But in freeview, surface
colors are assigned by vertices, not faces. I
f of Fischl, Bruce R.,PHD
mailto:bfis...@mgh.harvard.edu>>
Sent: Tuesday, November 1, 2022 11:49:23 AM
To: Freesurfer support list
Subject: [EXTERNAL] Re: [Freesurfer] Freesurfer labels vertices and not faces?
Hi Daniel
Can you clarify what you mean? The surfaces don’t have any values/vertex (e
ehalf Of Daniel Schwartz
Sent: Tuesday, November 1, 2022 3:05 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] Freesurfer labels vertices and not faces?
External Email - Use Caution
I'm trying to display, for example, an aparc.2009 on the pial surface. Because
of reasons,
Layton Aging and Alzheimer's Disease Center
OHSU
From: freesurfer-boun...@nmr.mgh.harvard.edu
on behalf of Fischl, Bruce R.,PHD
Sent: Tuesday, November 1, 2022 11:49:23 AM
To: Freesurfer support list
Subject: [EXTERNAL] Re: [Freesurfer] Freesurfer labels vertices and not faces?
On Behalf Of Daniel Schwartz
Sent: Tuesday, November 1, 2022 1:24 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] Freesurfer labels vertices and not faces?
External Email - Use Caution
Hi,
I've more of a general question. It seems to me that, if I use mris_convert (t
External Email - Use Caution
Hi,
I've more of a general question. It seems to me that, if I use mris_convert (to
convert to ascii) to take a closer look at, for example, rh.pial.asc, and an
annot2label, there are exactly enough rows to label each vertex of each
triangle, but no
...@nmr.mgh.harvard.edu
*On Behalf Of *Sam W
*Sent:* Friday, June 3, 2022 12:03 PM
*To:* Freesurfer support list
*Subject:* Re: [Freesurfer] labels in anatomical space
*External Email - Use Caution *
Hi Bruce,
I have my subject's T1 image that I use as input in my recon -all
call
: Friday, June 3, 2022 12:03 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] labels in anatomical space
External Email - Use Caution
Hi Bruce,
I have my subject's T1 image that I use as input in my recon -all call. But all
the output from freesurfer (eg, surfaces in
pHV-h9MQl8KE0DV-OrqsV7uQU_gxbaLIl7SQeLo9fLKXARb5PZ9X-IHyfQhf_PIcOb6l4jJqZME_CByZqGbYbpvpD3tYyXIg3Q5SZyGvjmG_QnzD_xw6Q/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FFsAnat-to-NativeAnat)
can I do
the same with freesurfer labels?
Best regards,
Sam
On Fri, Jun 3, 2022 at 4:59 PM Fischl, Bruce
wrote:
> The con
On Behalf Of Sam W
Sent: Friday, June 3, 2022 10:46 AM
To: Freesurfer support list
Subject: Re: [Freesurfer] labels in anatomical space
External Email - Use Caution
Hi Bruce,
Thanks for your help!
I got the label after running mri_annotation2label using the
label\lh.aparc.annot file on
t;
> Cheers
>
> Bruce
>
>
>
> *From:* freesurfer-boun...@nmr.mgh.harvard.edu <
> freesurfer-boun...@nmr.mgh.harvard.edu> *On Behalf Of *Sam W
> *Sent:* Friday, June 3, 2022 9:12 AM
> *To:* Freesurfer support list
> *Subject:* [Freesurfer] labels in anatomi
support list
Subject: [Freesurfer] labels in anatomical space
External Email - Use Caution
Hello!
I have a label in freesurfer space, and I would like it to be in anatomical
space. Is this possible?
Best regards,
Sam
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Hello!
I have a label in freesurfer space, and I would like it to be in anatomical
space. Is this possible?
Best regards,
Sam
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Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.har
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Hello Experts,
I am trying to isolate ROIs using labels #601-#628 however I am getting the
following output and it is the same for each label. Any idea what is wrong here?
Thanks for your help!
Akilas-MacBook-Air:B301001 akilasekar$ isolate_labels.
External Email - Use Caution
Hello, i used this code:
mri_vol2surf --src /home/neuroimage/fsl/FreeSurfer/AAL.nii --regheader MNI
--projfrac 0.5 --hemi lh --out /home/neuroimage/fsl/FreeSurfer/AAL-lh.mgh
Also i tried to map the AAL into the surface of fsaverage with:
mri_vol2surf -
This might be the way it is given that the AAL is volume-based and you are
trying to put it on the surface. What is your vol2surf command?
On 12/10/2020 6:59 AM, Alberto Del Cerro Leon wrote:
External Email - Use Caution
Hello Freesurfer team
With your help i obtained a AAL atlas on the
External Email - Use Caution
Dear Douglas,Thank you for the reply,The MDROI.nii is a set of ROIs, which I
want to transform in separate labels. So how can I extract the ROIs?? I already
tried:
mri_extract_label MDROI.nii 1 label1.mgz
but it extracts the labels according to the in
Your mri_vol2label command is fine (since these are surfaces)
On 8/7/2020 10:52 AM, Eleni Nikalexi wrote:
External Email - Use Caution
Dear Douglas,
Thank you for the reply,
The MDROI.nii is a set of ROIs, which I want to transform in separate
labels. So how can I extract the ROIs??
The hemi just refers to either lh or rh to load the proper surface. The
command have no idea what you are transferring to the surface.
Before the mri_vol2label stage, try loading surf.MDROI onto the surface
as an overlay and see if the ROIs are showing up in the right place
On 8/6/2020 11:4
External Email - Use Caution
Dear Freesurfer developers,We have a volume that assigns unique numerical
labels to each of the ROIs it contains, in NIFTI format. I want to register it
to MNI152 (1mm) space, so that I can map it on my subjects and use
mris_anatomical_stats.I have t
look in $FREESURFER_HOME/FreeSurferColorLUT.txt
eg,
8103 Left-AV 0 85 0 0
8104 Left-CeM 170 85 0 0
8105 Left-CL 0 170 0 0
8106 Left-CM 170 170 0 0
8108 Left-LD 170 255 0 0
8109 Left-LGN 0 0 127 0
8110 Left-LP 0 85 127 0
8111 Left-L-Sg 170 85 127 0
8112 Left-MDl 0 170 127 0
8113 Left-MDm 170 170 1
External Email - Use Caution
Hello Freesurfer Team,
I am running thalamic parcellation using freesurfer 7.1 and the program
(http://freesurfer.net/fswiki/ThalamicNuclei) is outputting thalamic labels
e.g. 8108, 8109, 8208 etc. I was wondering if you might point me towards a
dic
Try
mri_binarize --i seg.nii --replaceonly segno1 segno2 --o newseg.nii
which will merge segno1 into segno2
On 4/12/2019 6:54 AM, Vidal Maxime wrote:
> External Email - Use Caution
>
> Hello,
>
> I have a t1w.nii file and a segmentation.nii file. For the latter, I was
> wondering how I c
External Email - Use Caution
C5dyzZczzzvSent from my Samsung Galaxy smartphone.
Original message From: Vidal Maxime
Date: 12/04/2019 11:54 (GMT+00:00) To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] Labels in nii files External Email - Use
External Email - Use Caution
Hello,
I have a t1w.nii file and a segmentation.nii file. For the latter, I was
wondering how I could join labels together and create new labels.
Best,
Maxime
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Hi Katherine - If you mean the .trk format, that's not for storing labels, it's
for storing tractography streamlines (i.e., a bunch of curves that are stored
as sequences of x,y,z point coordinates). You can convert the FreeSurfer labels
to nifti volumes, and see if the software t
Hello Everyone,
I would like to use the FreeSurfer labels for fMRI and DTI in graph theory
analyses. I am attempting to use UMPC <https://github.com/jbrown81/umcp> to
generate the graphs, which requires that the diffusion tensor imaging be in
.dtk form. However, I have been struggling to g
Yes, same for cingulate. I don't really know what you are referring to
in terms of mixed structures. Maybe some subcortical structures are
thought of in this way
On 09/18/2017 05:52 PM, Benjamin Luerweg wrote:
> is that the same for the cingulate gyrus? or is cyng really a white and grey
> mat
is that the same for the cingulate gyrus? or is cyng really a white and grey
matter splitted structure?
> Am 18.09.2017 um 23:50 schrieb Douglas N Greve :
>
>
>
> On 09/18/2017 05:47 PM, Benjamin Luerweg wrote:
>>
>> *am i right that numbers out of the wmparc file of e.g. the insula
>>>
On 09/18/2017 05:47 PM, Benjamin Luerweg wrote:
>
> *am i right that numbers out of the wmparc file of e.g. the insula
> are just the volumes of the white matter part of e.g. the insula?
> *
*no, insula is a gray matter cortical structure. the insulaWM in the
wmparc file is just WM
am i right that numbers out of the wmparc file of e.g. the insula are just
the volumes of the white matter part of e.g. the insula?
would it be ok to add the volumes of the aparc file as the grey matter
volume.. to get the complete
volume of e.g. the insula?
kind reg
hey all!
ok.. sorry guys i detected a calculation mistake… !!
and the now calculated values seem to be close enough to be correct…
anyway… the brainsegvol - brainsegvolnotvent number is different to adding all
ventricle volumes number like —> 21782 and 20980 …
any idea why ?
which way of calc
Can you post the numbers for each item? Your first calculation is over
200 thousand mm3 (10x the 2nd calc) which suggests a math error
On 9/17/17 2:55 PM, Benjamin Luerweg wrote:
alright.. so far…BUT:
Ive tried to get the volume of the ventricle system by using two
different calculations.
alright.. so far…BUT:
Ive tried to get the volume of the ventricle system by using two different
calculations.
first of all i tried to get the volume by: brainsegvol - brainsegvolnotvent
than i tried to simply add all the seprate parts of the ventricle system (rh
lat ventricle + lh lat ventricl
yes, you can add the various components of the cc or cingulate to get total
volume
As for the CSF label, I think it's for bits of csf that can be seen or
inferred on a T1 in sulci and maybe inferior regions. You might want to
check the original CMA (Caviness, Kenndy, et al) papers, but I imagi
hey mr greve,
hey fs community,
what do you think about adding the volumes of seperated parts of one structure
to a complete volume?
e.g. the corpus callosum or also cingulate gyrus.
is it ok to get the complete volume value by just adding the volumes of the
seperated parts?
beside that, am
thx so far! really thank you.. do you know how to find out more about that
label?
what do you think about how to get any informations about a possible adding of
different structure parts to a „complete one“ for example the Corpus callosum
thing?
greets bl
> Am 14.09.2017 um 18:40 schrieb Dougl
On 09/13/2017 05:38 PM, Benjamin Luerweg wrote:
> dear mr. greve,
> dear fs community,
>
>
>
> *REGARDING CSF and CSFVol:*
>
> i still don’t understand the whole CSF and CSFVol thing.
> it seems to be impossible that CSFVol ist the volume of the CSF label
> because CSFVol is *bigger* than CSF.
>
dear mr. greve,
dear fs community,
REGARDING CSF and CSFVol:
i still don’t understand the whole CSF and CSFVol thing.
it seems to be impossible that CSFVol ist the volume of the CSF label because
CSFVol is bigger than CSF.
additional to this aspect the value of the CSF label is a volume itself
CSFVol is actually the volume of the CSF label (index 24)
3rd4th5thCSF is the volume of the 3rd, 4th, 5th ventricles plus the CSF
label
VentChorVol is the volume of choroird plexus, lateral ventricles, and
inferior lateral ventricles
BrainSegVolNotVent = BrainSegVol - VentChorVol - 3rd4th5t
Hey Mr. Greve,
thank your very much again!
if i understand you right, the inside the console shown up values can’t be
extracted into a separate file?
beside that, this values are of interest for me, so that i copied them to a
text file.
as you can see: Getting Brain Vol
On 09/12/2017 09:06 AM, Benjamin Luerweg wrote:
> dear mr. Greve,
> dear fs community,
>
> first of all thank you very much for helping me so far.
>
> what i don’t understand is the difference between the value *CSF*
> (within the aseg.stat) and the *CSFVol* which shows up inside
> the console w
dear mr. Greve,
dear fs community,
first of all thank you very much for helping me so far.
what i don’t understand is the difference between the value CSF (within the
aseg.stat) and the CSFVol which shows up inside
the console while processing the command to generate the aseg.stat file.
additi
On 09/11/2017 01:20 PM, Benjamin Luerweg wrote:
> dear fs community,
>
> as a kind of a freesurfer greenhorn i would kindly ask you to help me
> out with identifying the different labels used by freesurfer.
> after using mri segstats most of the labels seem to be describing
> thereselfs in prop
dear fs community,
as a kind of a freesurfer greenhorn i would kindly ask you to help me out with
identifying the different labels used by freesurfer.
after using mri segstats most of the labels seem to be describing thereselfs in
proper way.
what i don’t understand are for example the differen
What about volume? For surface, it
seems that it is ok.
On Tue, Aug 22, 2017 at 1:29 AM Douglas N Greve
wrote:
>
> whatever annotation you give it (eg, aparc). There are not separate
> labels for the inner and the outer. The distinction is in the xyz
> coordinates. If you don't give it a surface,
whatever annotation you give it (eg, aparc). There are not separate
labels for the inner and the outer. The distinction is in the xyz
coordinates. If you don't give it a surface, it will use the xyz coords
from the inner (white) surface. If you give it --surface pial, it will
use the xyz coord
And what labels does this mri_annotation2label give? Does it give the outer
cortical boundary as well?
On Tue, Aug 22, 2017 at 12:19 AM Douglas N Greve
wrote:
> when you run mri_annotation2label you can specify the surface
> (--surface). By default, it uses white, but you can specify pial instea
when you run mri_annotation2label you can specify the surface
(--surface). By default, it uses white, but you can specify pial instead
On 08/21/2017 11:33 AM, Fereshte wrote:
> Hello FreeSurfer developers,
> Is it possible to have the segmentation labels after the pial surface
> is done in Fre
Hello FreeSurfer developers,
Is it possible to have the segmentation labels after the pial surface is
done in FreeSurfer? I mean once you do the topology correction and expand
the inner cortical boundary to make the pial surface ; is it possible to
have the inner and outer cortical boundaries as la
One possibility is the header information. I looked at the header
information and they are not exactly the same between the template and
atlas. Perhaps you can try the following:
>> mri_convert --targ Template_T1_IXI555_MNI152.nii --mov
>> Yeo2011_17Networks_MNI152_FreeSurferConformed1mm_LiberalM
Hi,
I was using Mango and MriCron to view the results. But you are right
that in freeview it looks just fine :) I saved the yeo atlas image as
nifti and it is now looking well also on mango and MRIcroN. So I suppose
that the problem was with analyze format.
Thank you all for the help :)
Mat
The Yeo2011_17Networks_MNI152_FreeSurferConformed1mm_LiberalMask.nii.gz
comes from
http://surfer.nmr.mgh.harvard.edu/fswiki/CorticalParcellation_Yeo2011,
and the description says it is the FSL MNI152 1mm template interpolated
and intensity normalized into a 256 x 256 x 256 1mm-isotropic volume
From the names, it looks like both the seg vol and the template vol are both
in mni152. Where did
Yeo2011_17Networks_MNI152_FreeSurferConformed1mm_LiberalMask.nii.gz come from?
One thing you can try is to invert the registration by adding --invertmtx to
the command line.
On 8/2/16 8:18 AM, M
Hi Freesurfer experts,
I just started to use Freesurfer and I was wondering how can I convert
images from MNI305 which uses Freesurfer to MNI152 which is used by SPM.
We would like to get MNI152 template of Yeo parcelation
(http://surfer.nmr.mgh.harvard.edu/fswiki/CorticalParcellation_Yeo2011)
ok thanks Dr. Fischl. I will use tksurfer in the meantime.
best wishes
Trisanna
--
Ph.D. Candidate
McGill University
Integrated Program in Neuroscience
Psychology
On Wed, Apr 27, 2016 at 8:27 AM, Bruce Fischl
wrote:
> yes, I think that's true, although editing labels on the surface is on our
yes, I think that's true, although editing labels on the surface is on
our to-do list I believe
On Tue, 26 Apr 2016, Trisanna Sprung-Much wrote:
thanks Dr. Fischl - it seems to match well so I will continue to use this
method. It would be great if Ruopeng could eventually edit Freesurfer to
all
thanks Dr. Fischl - it seems to match well so I will continue to use this
method. It would be great if Ruopeng could eventually edit Freesurfer to
allow for thresholding .labels too.
On another note, is there a way to edit labels in Freeview in a similar
manner to doing so in tksurfer?* From what
yes, that sounds right. Does it look correct? That is, are areas 1/4
etc.. in the central sulcus and such?
On Mon, 25 Apr 2016, Trisanna
Sprung-Much wrote:
Not a problem, Dr. Fischl!
In the meantime, could you please confirm that I am opening up a
cytoarchitectonic probability map I have as .
Not a problem, Dr. Fischl!
In the meantime, could you please confirm that I am opening up a
cytoarchitectonic probability map I have as .mnc correctly?
I basically change it to a surface overlay.mgz using mri_vol2surf and then
open it as an overlay with a surface in Freeview. I can then change th
Hi Trisanna
yes, but Ruopeng is on vacation to it will be a while
Bruce
On Mon, 25 Apr 2016,
Trisanna Sprung-Much wrote:
Hi there
With regards to this email from March, I cannot seem to be able to change
thresholds of .labels in Freeview. Could this be added as an option?
best wishes
Tris
Hi there
With regards to this email from March,* I cannot seem to be able to change
thresholds of .labels in Freeview*. Could this be added as an option?
best wishes
Trisanna
--
Ph.D. Candidate
McGill University
Integrated Program in Neuroscience
Psychology
On Sun, Mar 13, 2016 at 1:45 PM, Br
Hello FS community,
I have made some custom labels based on retinotopy data and I wish to
export these as SPM ROIs so that I can use some specific tools.
I grouped the labels into an annotation file and I used mri_label2vol to
convert it into nifti, I then imported it into matlab and I get a volum
Hi Trisanna
1. the .thresh labels have been thresholded with a p-value threshold that
is "best" on our training set of manually/architectonically defined labels.
2. Hmmm, not sure, but we have stopped development on tksurfer. Can you try
this on freeview? I can't remember if freeview allows c
Hi there
I have two questions regarding using the labels with tksurfer:
1. What exactly has been done to change the .label (e.g. lh BA44.label) to
.thresh.label (e.g. lh BA44.thresh.label?
2. The instructions on this page
https://surfer.nmr.mgh.harvard.edu/fswiki/BrodmannAreaMaps
to overlay th
I ran the MNI152 average through recon-all and it seemed to do ok. You
can get it from here
ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mni152.tar.gz
I don't know what kind of accuracy you are looking for, but for cortex,
you should work strictly in the surface and avoid volum
Dear All,
Is there any way I can get the Desikan-Killiany cortical and subcortical
labels on MNI152 template. I know I can get a rough estimate using the
linear transformation matrix "mni152.register.dat". I also find that the
subject cvs_avg35 is non-linearly registered to MNI152 and given in the
Don't use FreeSurferColorLUT.txt, you need to create your own color
table whose format is like FreeSurferColorLUT.txt
doug
On 06/20/2014 03:49 AM, Karen Marie Sandø Ambrosen wrote:
> Hi Bruce,
>
> When I input all the labels in the mris_label2annot command I get the
> result shown in: H09_copy_
We do not have a way to resolve the overlapping problem. That is
something you will have to figure out. You should be able to keep the
colors the same by specifying the entries in the color table
doug
On 6/19/14 3:41 PM, Karen Marie Sandø Ambrosen wrote:
> Dear Freesurfer experts,
>
> I have m
Hi Karen
What do you mean the results don't look right? Can you send an image?
Cheers
Bruce
> On Jun 19, 2014, at 9:41 AM, Karen Marie Sandø Ambrosen wrote:
>
> Dear Freesurfer experts,
>
> I have made a parcellation of the white matter surface outside of
> freesurfer in volumes. I convert the
Dear Freesurfer experts,
I have made a parcellation of the white matter surface outside of
freesurfer in volumes. I convert the volume labels to surface labels. I
have now a lot of surface labels (~500 for each hemisphere) which I want
to concatenate to an annotation file for easier visualizati
Hi Tanya, that tutorial is inaccurate. The statement is true within
subject. Across subject, we can map a vertex to another subject, but it
is not necessarily 1-to-1. Can you point me to the tutorial page so I
can fix it?
doug
On 05/14/2014 02:54 PM, Tanya wrote:
> Hi Freesurfers,
> I'm confu
Hi Freesurfers,
I'm confused about surface vertices labels. One of the tutorial mentions
that: " There is a one-to-one correspondence between surfaces which allows
the user to cross-reference vertices from one surface to another (even
across subjects) and to the volume." So there is a map between v
Hi list,
I'd like to obtained .labels of thalami to use it in FSL.
How can I do it?
Thanks,
Stefano ___
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The information in this e-mai
Use mri_cor2label
On 04/28/2014 01:11 PM, std...@virgilio.it wrote:
> Hi list,
>
> I'd like to obtained .labels of thalami to use it in FSL.
>
> How can I do it?
>
> Thanks,
>
>
> Stefano
>
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.
Try it with --thmin 0.5
doug
On 10/15/2013 11:34 AM, maria estanqueiro wrote:
> Dear all,
>
> I need the center coordinates of the anatomical labels from the
> desikan and destrieux atlases.
>
> I saw a similar post a while ago in which it was recommended the
> following:
>
> #1 Convert the a
Dear all,
I need the center coordinates of the anatomical labels from the desikan and
destrieux atlases.
I saw a similar post a while ago in which it was recommended the following:
#1 Convert the annotation to a set of labels. This is for the
Desikan atlas, but you can spec the destrieux in
On Fri, 26 Jul 2013, LAOUCHEDI
MAKHLOUF wrote:
Hi
i used freesurfer labels
in a study
and i want
to identify
primary areas
>> like V1/M1, the
>> stronger the correspondence is. We do supply
>> some explicit
>> estimates of Brodmann areas, have you looked
>> at them?
>>
>> Bruce
&
ronger the correspondence is. We do supply
some explicit
estimates of Brodmann areas, have you looked
at them?
Bruce
On Fri, 26 Jul 2013, LAOUCHEDI MAKHLOUF wrote:
Hi
i used
: LAOUCHEDI MAKHLOUF
Cc : "freesurfer@nmr.mgh.harvard.edu"
Envoyé le : Vendredi 26 juillet 2013 15h33
Objet : Re: [Freesurfer] correspondance between broadmann areas and
freesurfer labels
Hi Laouchedi
that is a big research question! The answer is a qualified yes, but it
depends strong
areas exist ?
Thanks
De : Bruce Fischl
À : LAOUCHEDI MAKHLOUF
Cc : "freesurfer@nmr.mgh.harvard.edu"
Envoyé le : Vendredi 26 juillet 2013 15h33
Objet : Re: [Freesurfer] correspondance between broadmann areas and freesurfer
labels
Hi Laouchedi
tha
dence is. We do supply
some explicit
estimates of Brodmann areas, have you looked
at them?
Bruce
On Fri, 26 Jul 2013, LAOUCHEDI MAKHLOUF wrote:
Hi
i used freesurfer l
ry areas like V1/M1, the
>> stronger the correspondence is. We do supply some explicit
>> estimates of Brodmann areas, have you looked at them?
>>
>> Bruce
>>
>>
>> On Fri, 26 Jul 2013, LAOUCHEDI MAKHLOUF wrote:
>>
>>
is. We do supply some explicit
estimates of Brodmann areas, have you looked at them?
Bruce
On Fri, 26 Jul 2013, LAOUCHEDI MAKHLOUF wrote:
Hi
i used freesurfer labels in a study and i want
to identify the broadmann
areas
you mean. In general we find that the
> closer you are to primary areas like V1/M1, the stronger the correspondence
> is. We do supply some explicit estimates of Brodmann areas, have you looked
> at them?
>
> Bruce
>
>
> On Fri, 26 Jul 2013, LAOUCHEDI MAKHLOUF wrote:
>
> Hi
, have you looked
at them?
Bruce
On Fri, 26 Jul 2013, LAOUCHEDI MAKHLOUF
wrote:
Hi
i used freesurfer labels in a study and i want to identify the broadmann
areas corresponding to some labels, is there any correspondence between the
two ?
Thanks
Hi
i used freesurfer labels in a study and i want to identify the broadmann
areas corresponding to some labels, is there any correspondence between the two
?
Thanks
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On 05/08/2013 05:24 PM, Tudor Popescu wrote:
> Sorry, one more iteration:
>
> 1) Command "mri_annotation2label --subject 01 --hemi lh --aparc.a2009s
> --outdir $SUBJECTS_DIR/01/myLabelsDestrieux" doesn't recognise the
> aparc.2009s flag (I tried a few other variations with no luck)!
The syntax i
Sorry, one more iteration:
1) Command "mri_annotation2label --subject 01 --hemi lh --aparc.a2009s
--outdir $SUBJECTS_DIR/01/myLabelsDestrieux" doesn't recognise the
aparc.2009s flag (I tried a few other variations with no luck)!
1') Assuming the above command works and I get .label files correspo
On 05/08/2013 01:28 PM, Tudor Popescu wrote:
>
> 2) ..and when would you use a surface mask versus a surface label?
>
> It is just a matter of convenience.
>
> Sorry, I meant I don't really understand what the difference is
> between a label and a mask, and in which circumstances each
> 2) ..and when would you use a surface mask versus a surface label?
>>
> It is just a matter of convenience.
Sorry, I meant I don't really understand what the difference is between a
label and a mask, and in which circumstances each should be used. I tried
finding an answer on the wiki but no luc
On 05/08/2013 12:02 PM, Tudor Popescu wrote:
> Thanks Doug. Follow-ups below
>
> 2) ..and when would you use a surface mask versus a surface label?
It is just a matter of convenience.
>
> 3) (it seems you skipped over this one:) )
Sorry:) what are you going to do with the ROI?
>
> 4) This opens up
Thanks Doug. Follow-ups below
2) ..and when would you use a surface mask versus a surface label?
3) (it seems you skipped over this one:) )
4) This opens up a coronal slice rather than a 3D image as in the picture I
linked to. Do I need to do anything else in tkmedit after it opens? (I
tried pre
On 05/08/2013 11:43 AM, Tudor Popescu wrote:
> Hello all,
>
> I have some more burning questions, for which I thank you in advance!!
>
> 1) I expected that "mri_annotation2label --subject 01 --hemi lh
> --outdir $SUBJECTS_DIR/myLabels" would give me labels corresponding to
> structures of the st
Hello all,
I have some more burning questions, for which I thank you in advance!!
1) I expected that "mri_annotation2label --subject 01 --hemi lh --outdir
$SUBJECTS_DIR/myLabels" would give me labels corresponding to structures of
the standard FreeSurfer atlas (Destrieux), instead it produced lab
v5.0.0 is too old. I'd suggest grabbing the current 5.1.0 build and
then just using the 'mri_annotation2label' from that.
On Thu Feb 28 12:17:02 2013, Sudhin A. Shah wrote:
> freesurfer-Linux-centos4_x86_64-stable-pub-v5.0.0
>
>
> On Feb 28, 2013, at 12:12 PM, Rudolph Pienaar wrote:
>
>> It loo
freesurfer-Linux-centos4_x86_64-stable-pub-v5.0.0
On Feb 28, 2013, at 12:12 PM, Rudolph Pienaar wrote:
> It looks like you might be running a too-old version of
> mri_annotation2label. What FS build/version are you running?
>
>
> On Thu Feb 28 11:36:50 2013, Sudhin A. Shah wrote:
>> Hi I got
It looks like you might be running a too-old version of
mri_annotation2label. What FS build/version are you running?
On Thu Feb 28 11:36:50 2013, Sudhin A. Shah wrote:
> Hi I got an error -lobesStrict unknown. I am running mri_annotation2label
> version stable5.
>
> Is there a workaround?
>
> O
Hi I got an error -lobesStrict unknown. I am running mri_annotation2label
version stable5.
Is there a workaround?
On Feb 28, 2013, at 10:47 AM, Rudolph Pienaar wrote:
> After a conventional FS run you can do the following:
>
> $>mri_annotation2label --subject --hemi --lobesStrict
> .lobesSt
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