Re: [Freesurfer] Freesurfer labels vertices and not faces?

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

Re: [Freesurfer] Freesurfer labels vertices and not faces?

fis...@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.g. scalar fields over the surface

Re: [Freesurfer] Freesurfer labels vertices and not faces?

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, I'd really

Re: [Freesurfer] Freesurfer labels vertices and not faces?

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? Hi Daniel Can you clarify what yo

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 (to convert

[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 (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

Re: [Freesurfer] labels in anatomical space

...@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

Re: [Freesurfer] labels in anatomical space

: 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 surf

Re: [Freesurfer] labels in anatomical space

-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 conformed sp

Re: [Freesurfer] labels in anatomical space

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

Re: [Freesurfer] labels in anatomical space

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 anatomical s

Re: [Freesurfer] labels in anatomical space

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 ___ Freesurfer mailing list

[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 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu

[Freesurfer] Labels #601-#628

External Email - Use Caution 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$

Re: [Freesurfer] labels in the surface {Disarmed}

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

Re: [Freesurfer] labels in the surface

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

Re: [Freesurfer] labels in .nii file

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

Re: [Freesurfer] labels in .nii file

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??

Re: [Freesurfer] labels in .nii file

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

[Freesurfer] labels in .nii file

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

Re: [Freesurfer] Labels from thalamic parcellation

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

[Freesurfer] Labels from thalamic parcellation

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

Re: [Freesurfer] Labels in nii files

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

Re: [Freesurfer] Labels in nii files

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

[Freesurfer] Labels in nii files

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 ___ Freesurfer mailing list

Re: [Freesurfer] FreeSurfer Labels To Diffusion Toolkit/TrackVis

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 that you're

[Freesurfer] FreeSurfer Labels To Diffusion Toolkit/TrackVis

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

Re: [Freesurfer] labels used by freesurfer

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 >

Re: [Freesurfer] labels used by freesurfer

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

Re: [Freesurfer] labels used by freesurfer

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

Re: [Freesurfer] labels used by freesurfer

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

Re: [Freesurfer] labels used by freesurfer

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

Re: [Freesurfer] labels used by freesurfer

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.

Re: [Freesurfer] labels used by freesurfer

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

Re: [Freesurfer] labels used by freesurfer

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

Re: [Freesurfer] labels used by freesurfer

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

Re: [Freesurfer] labels used by freesurfer

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

Re: [Freesurfer] labels used by freesurfer

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.

Re: [Freesurfer] labels used by freesurfer

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

Re: [Freesurfer] labels used by freesurfer

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 -

Re: [Freesurfer] labels used by freesurfer

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

Re: [Freesurfer] labels used by freesurfer

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

Re: [Freesurfer] labels used by freesurfer

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.

Re: [Freesurfer] labels used by freesurfer

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

[Freesurfer] labels used by freesurfer

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

Re: [Freesurfer] Labels from Pial surface

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

Re: [Freesurfer] Labels from Pial 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

Re: [Freesurfer] Labels from Pial surface

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

Re: [Freesurfer] Labels from Pial surface

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

[Freesurfer] Labels from Pial surface

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

Re: [Freesurfer] Labels to MNI152, SPM compatible

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 >>

Re: [Freesurfer] Labels to MNI152, SPM compatible

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 :)

Re: [Freesurfer] Labels to MNI152, SPM compatible

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

Re: [Freesurfer] Labels to MNI152, SPM compatible

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,

[Freesurfer] Labels to MNI152, SPM compatible

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)

Re: [Freesurfer] labels

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

Re: [Freesurfer] labels

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

Re: [Freesurfer] labels

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

Re: [Freesurfer] labels

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

Re: [Freesurfer] labels

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

Re: [Freesurfer] labels

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

Re: [Freesurfer] labels

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,

[Freesurfer] Export Freesurfer labels to SPM ROIs

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

[Freesurfer] labels

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

Re: [Freesurfer] FreeSurfer Labels for MNI template

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

[Freesurfer] FreeSurfer Labels for MNI template

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

Re: [Freesurfer] Labels to annotation

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:

Re: [Freesurfer] Labels to annotation

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

[Freesurfer] Labels to annotation

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

Re: [Freesurfer] Labels to annotation

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 k...@dtu.dk wrote: Dear Freesurfer experts, I have made a parcellation of the white matter surface outside of freesurfer in volumes. I

Re: [Freesurfer] labels of surface vertices

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

[Freesurfer] labels of surface vertices

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

Re: [Freesurfer] labels of thalami

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.edu

[Freesurfer] labels of thalami

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.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this

[Freesurfer] labels coordinates from atlases

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

Re: [Freesurfer] labels coordinates from atlases

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

[Freesurfer] correspondance between broadmann areas and freesurfer labels

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 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https

Re: [Freesurfer] correspondance between broadmann areas and freesurfer labels

, 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

Re: [Freesurfer] correspondance between broadmann areas and freesurfer labels

labels 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 i used freesurfer labels

Re: [Freesurfer] correspondance between broadmann areas and freesurfer labels

, 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     i used freesurfer labels in a study and i want to identify

Re: [Freesurfer] correspondance between broadmann areas and freesurfer labels

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 corresponding to some labels

Re: [Freesurfer] correspondance between broadmann areas and freesurfer labels

                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

Re: [Freesurfer] correspondance between broadmann areas and freesurfer labels

between broadmann areas and freesurfer labels Hi Laouchedi that is a big research question! The answer is a qualified yes, but it depends strongly on what labels 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

Re: [Freesurfer] correspondance between broadmann areas and freesurfer labels

...@nmr.mgh.harvard.edu À : LAOUCHEDI MAKHLOUF laouma...@yahoo.fr Cc : freesurfer@nmr.mgh.harvard.edu 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

Re: [Freesurfer] correspondance between broadmann areas and freesurfer labels

:             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

Re: [Freesurfer] correspondance between broadmann areas and freesurfer labels

, 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

Re: [Freesurfer] correspondance between broadmann areas and freesurfer labels

?                   Bruce                   On Fri, 26 Jul 2013, LAOUCHEDI MAKHLOUF wrote:                         Hi                             i used freesurfer labels in a study             and i want

Re: [Freesurfer] Labels and parcellations

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 is

[Freesurfer] Labels and parcellations

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

Re: [Freesurfer] Labels and parcellations

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 standard

Re: [Freesurfer] Labels and parcellations

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

Re: [Freesurfer] Labels and parcellations

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 a

Re: [Freesurfer] Labels and parcellations

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 luck..

Re: [Freesurfer] Labels and parcellations

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

[Freesurfer] labels to lobes

Hello, Is there a lookup table I can use to convert free surfer labels to lobes? Either label nos (1006, 2006 etc) or label names (ctx-rh-superiorfrontal)? I have 86 labels and want an easy way to differentiate them into the corresponding lobes. Thanks, S

Re: [Freesurfer] labels to lobes

Also, is there a way to associate these labels with motor/auditory/visual cortices? Or do I have to use the specific parcellations? On Feb 28, 2013, at 9:25 AM, Sudhin A. Shah sut2...@med.cornell.edu wrote: Hello, Is there a lookup table I can use to convert free surfer labels to lobes?

Re: [Freesurfer] labels to lobes

After a conventional FS run you can do the following: $mri_annotation2label --subject subj --hemi hemi --lobesStrict hemi.lobesStrict.annot Which will create an annotation file hemi.lobesStrict.annot containing the lobar labels. To extract these into their own individual label files, do

Re: [Freesurfer] labels to lobes

Thank you! Is there something similar to assign labels to functional cortices eg. motor, visual, auditory? Thanks S On Feb 28, 2013, at 10:47 AM, Rudolph Pienaar wrote: After a conventional FS run you can do the following: $mri_annotation2label --subject subj --hemi hemi --lobesStrict

Re: [Freesurfer] labels to lobes

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 subj --hemi hemi --lobesStrict

Re: [Freesurfer] labels to lobes

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? On Feb

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