Re: [Freesurfer] Convert FSL .nii ROI into FreeSurfer Label

A surface label or a volume label? On 10/25/2020 2:17 PM, Hua, Jessica wrote: External Email - Use Caution Hi FreeSurfer Experts, How can I convert a .nii ROI into a FreeSurfer label? I was able to convert the .nii into a .mgh file but could not figure out how to convert to a label

[Freesurfer] Convert FSL .nii ROI into FreeSurfer Label

External Email - Use Caution Hi FreeSurfer Experts, How can I convert a .nii ROI into a FreeSurfer label? I was able to convert the .nii into a .mgh file but could not figure out how to convert to a label file. Thank you, Jessica

Re: [Freesurfer] Label on fsaverage failure

External Email - Use Caution Dear Douglas and Bruce,on the same subject, I wanted to ask two questions:1. since the ROIs were obtained on 2mm voxels, is the command  $ mri_vol2surf --mov ROI_set1/LeftAngG.img --regheader MNI_1mm --interp nearest --hemi lh --out Left_AngG

Re: [Freesurfer] Label on fsaverage failure

On 7/15/2020 10:59 AM, Eleni Nikalexi wrote: External Email - Use Caution Dear Douglas and Bruce, on the same subject, I wanted to ask two questions: 1. since the ROIs were obtained on 2mm voxels, is the command $ mri_vol2surf --mov ROI_set1/LeftAngG.img--regheader MNI_1mm --interp

Re: [Freesurfer] label to surface

External Email - Use Caution Hi Doug, I'm using this command: mri_label2label --srclabel lh.fusiform.label --trglabel output.label --s sub01 --regmethod surface --hemi lh --outmask outmask.gii Best regards, Sam On Fri, Jul 10, 2020 at 9:48 PM Douglas N. Greve wrote: > what's yo

Re: [Freesurfer] label to surface

what's your mri_label2label command? On 7/10/2020 3:05 PM, Sam W wrote: External Email - Use Caution Hi Doug and Tim, I'm running probtrackx with freesurfer surfaces as seeds. However probtrackx requires a file that contains both the whole surface file (eg, lh.pial) as well as the ov

Re: [Freesurfer] label to surface

External Email - Use Caution Hi Doug and Tim, I'm running probtrackx with freesurfer surfaces as seeds. However probtrackx requires a file that contains both the whole surface file (eg, lh.pial) as well as the overlay (the scalar values associated with the vertices of the roi). I c

Re: [Freesurfer] label to surface

what do you mean merge with the pial? On 7/9/2020 8:07 PM, Sam W wrote: External Email - Use Caution It works great Doug, thanks a lot! Can I ask you a follow up question please? I created the overlay with mri_label2label using --outmask as you suggested, but now I'd like to merge th

Re: [Freesurfer] label to surface

External Email - Use Caution It should just work when displayed on the pial surface, the vertex indices are equivalent. Did you try it? Or what exactly do you mean by 'merging' with the pial surface? Tim > On July 10, 2020 at 2:07 AM Sam W wrote: > > > External Email

Re: [Freesurfer] label to surface

External Email - Use Caution It works great Doug, thanks a lot! Can I ask you a follow up question please? I created the overlay with mri_label2label using --outmask as you suggested, but now I'd like to merge that overlay with the pial surface (lh.pial). Is there a tool I can use

Re: [Freesurfer] label to surface

Use mri_label2label with the --outmask option On 7/8/2020 10:14 PM, Sam W wrote: External Email - Use Caution Hi, Is there a way to convert a label file into a surface/overlay? Thank you! Best regards, Sam ___ Freesurfer mailing list Freesur

[Freesurfer] label to surface

External Email - Use Caution Hi, Is there a way to convert a label file into a surface/overlay? Thank you! Best regards, Sam ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/free

Re: [Freesurfer] Label on fsaverage failure

It has to be loaded as an overlay to a surface, not a surface itself. On 7/3/2020 10:10 AM, Eleni Nikalexi wrote: External Email - Use Caution Dear Douglas, thank you very much for your help; I run the recon of MNI152_T1_1mm_brain.nii.gz (which I moved into a directory called MNI_1mm

Re: [Freesurfer] Label on fsaverage failure

Try running recon-all on the MNI152. Load the ROI onto the reconned MNI152; load the surfaces as well and make sure that the ROI intersects with the surface, then use #3 below with --regheader MNI152 instead of --reg tmp.dat. You can also specify --trgsubject fsaverage and mri_vol2surf will map

[Freesurfer] Label on fsaverage failure

External Email - Use Caution Dear Freesurfer developers, We have a series of MRI scans and we are trying to extract cortical thickness in certain regions of interest. The ROIs already exist - some are in .img and some in NIFTI format - and we want to tranform them into labels and

Re: [Freesurfer] Label created in the symmetric space

External Email - Use Caution It worked as intended. Thank you very much. On Tue, Oct 8, 2019 at 6:43 PM Greve, Douglas N.,Ph.D. < dgr...@mgh.harvard.edu> wrote: > In that case, run mris_preproc in the same way but don't include the > paired-diff. Concatenate the two groups togeth

Re: [Freesurfer] Label created in the symmetric space

In that case, run mris_preproc in the same way but don't include the paired-diff. Concatenate the two groups together to give you one file. Smooth as you did before. Now with that one file run mri_segstats --seg csdbase.sig.ocn.mgh --i youronefile.mgh --avgwf subject.hemi.cluster.dat --excludeid

Re: [Freesurfer] Label created in the symmetric space

External Email - Use Caution Aha, yes. That is what I want. The original thickness values. Greve, Douglas N.,Ph.D. schrieb am Di., 8. Okt. 2019, 17:36: > That all looks fine, I'm just not sure what problem you want me to > solve. You said that the values in the y.ocn.dat file we

Re: [Freesurfer] Label created in the symmetric space

That all looks fine, I'm just not sure what problem you want me to solve. You said that the values in the y.ocn.dat file were all negative, it has to be this way because you specified only negative values when you ran glmfit-sim (and negative values are possible because  you have computed left-

Re: [Freesurfer] Label created in the symmetric space

External Email - Use Caution I will try to go back a bit, just to be sure I did not make a mistake. I registered both hemispheres of every subject (affected and non-affected) with xhemi. Then for the left-affected subjects I ran: mris_preproc --target fsaverage_sym --hemi lh --xhe

Re: [Freesurfer] Label created in the symmetric space

The input has both positives and negatives, so is is not surprising that the y.ocn.dat also has positive and negative. Not sure what is going wrong here ... On 10/7/2019 5:48 PM, Jose Graterol wrote: External Email - Use Caution Ok, I uploaded it with the name "glmdir.jg.allsubjects.tar

Re: [Freesurfer] Label created in the symmetric space

External Email - Use Caution Ok, I uploaded it with the name "glmdir.jg.allsubjects.tar.gz". I had to log in as anonymous and not with my email, otherwise it would throw an error (503 Login with USER first. Login failed.). The mgh file is inside the gz file too. Thanks again for yo

Re: [Freesurfer] Label created in the symmetric space

ok, I still don't know what is going on. Can you upload the glmdir and the input to mri_glmfit (ie, the argument of the --y flag). You can upload it using these instructions: From the linux command line, Create the file you want to upload, eg, cd $SUBJECTS_DIR tar cvfz subject.tar.gz ./subject N

Re: [Freesurfer] Label created in the symmetric space

External Email - Use Caution Hi Douglas, thanks for you answer. I have attached the file to the email. On Mon, Oct 7, 2019 at 5:24 PM Greve, Douglas N.,Ph.D. < dgr...@mgh.harvard.edu> wrote: > Let's backup a moment. Can you send the y.ocn.dat file that has > problematic values?

Re: [Freesurfer] Label created in the symmetric space

Let's backup a moment. Can you send the y.ocn.dat file that has problematic values? On 10/4/2019 4:58 AM, Jose Graterol wrote: External Email - Use Caution Dear Freesurfer Experts, I would appreciate your help. I will explain first what I have done and where my problem is. I want to

[Freesurfer] Label created in the symmetric space

External Email - Use Caution Dear Freesurfer Experts, I would appreciate your help. I will explain first what I have done and where my problem is. I want to measure the cortical thickness in stroke patients. Therefore I followed Douglas' instructions provided in this link

Re: [Freesurfer] label to asc

The label file has much less info than the surface file (eg, does not have neighborhood relations). mri_label2vol requires that a full surface file be provided. It might not be obvious because it usually finds the surface based on the subject name. On 7/25/19 3:29 PM, Sam W. wrote: > >

Re: [Freesurfer] label to asc

External Email - Use Caution Thanks Bruce, that's helpful! I take it that it's not possible to create a surface file simply using the information in the label file then? The reason I'm confused is that "mris_convert lh.white lh.white.asc" will convert a surface file to asc. The con

Re: [Freesurfer] label to asc

Hi Sam they are not the same. A label is just a list of vertices in the surface (with some possibly voxel coordinates and also with a single value/vertex). It doesn't have to be ever vertex in the surface, and also contains no information about topology (e.g. which vertices are connected by an

Re: [Freesurfer] label to asc

External Email - Use Caution Thanks Bruce. Can I ask you a very basic question? What exactly is the difference between a surface and a label file? I thought the difference was that the label file is just a normal text file containing the vertices that are used to construct a surfac

Re: [Freesurfer] label to asc

Hi Sam the labels are already ascii cheers Bruce On Tue, 23 Jul 2019, Sam W. wrote: External Email - Use Caution Hi, Is it possible to convert a label file like rh.cuneus.label into asc? I tried mris_convert --label rh.cuneus.label ctx-rh-cuneus rh.white rh.cuneus.asc but g

[Freesurfer] label to asc

External Email - Use Caution Hi, Is it possible to convert a label file like rh.cuneus.label into asc? I tried mris_convert --label rh.cuneus.label ctx-rh-cuneus rh.white rh.cuneus.asc but got an error: ERROR: unknown file annot file type specified for output: rh.cuneus.asc Tha

Re: [Freesurfer] label a ROI

Hi Francesca sorry, not sure if this got answered, but you should be able to create surface-based ROIs and run the analysis on them. cheers Bruce On Wed, 5 Jun 2019, Francesca Pentimalli wrote: External Email - Use Caution Dear Bruce,  Thank you very much for answering!

Re: [Freesurfer] label a ROI

External Email - Use Caution Dear Bruce, Thank you very much for answering! We are doing a study on correlating dyslexia, at an early stage, with various factors in children. Specifically, our goal is to look at how the 12 regions of the brain, that I mentioned in the previous em

Re: [Freesurfer] label a ROI

Hi Francesca what analysis do you want to run? cheers Bruce On Wed, 5 Jun 2019, Francesca Pentimalli wrote: External Email - Use Caution Dear Freesurfer experts, I am trying to create a mask and run the analysis into it considering just the following anatomical regions:

[Freesurfer] label a ROI

External Email - Use Caution Dear Freesurfer experts, I am trying to create a mask and run the analysis into it considering just the following anatomical regions: (1) inferior frontal gyrus pars opercularis (IFGOp) (2) inferior frontal gyrus pars orbitalis (IFGOr) (3) infe

Re: [Freesurfer] Label numbers for thalamic nuclei

of ?? ? Reply-To: Freesurfer support list Date: Friday, 20 July 2018 at 08:17 To: "freesurfer@nmr.mgh.harvard.edu" Subject: [Freesurfer] Label numbers for thalamic nuclei External Email - Use Caution Dear Freesurfer Team, I have been using segmentation of thalamic nucle

[Freesurfer] Label numbers for thalamic nuclei

External Email - Use Caution Dear Freesurfer Team, I have been using segmentation of thalamic nuclei from the Freesurfer dev version(freesurfer-linux-centos7_x86_64-dev). I see some thalamus labels in FreeSurferColorLUT.txt(#8001-8014), but I can't find label numbers for 25 d

Re: [Freesurfer] Label numbers aparc.a2009s

Hi Jürgen the FreeSurferColorLUT.txt file lists all the labels that we might use, not all the ones that we do use in any given parcellation, so it will certainly have ones that are not in any single parcellation. cheers Bruce On Sat, 3 Jun 2017, Juergen Haenggi wrote: Dear FS experts I hav

Re: [Freesurfer] Label numbers aparc.a2009s

Dear FS experts Please ignore my former email. the tool I used did not show the whole intensity range. sorry Cheers Jürgen - University of Zurich Dr. Jürgen Hänggi, Ph.D. Department of Psycholog

[Freesurfer] Label numbers aparc.a2009s

Dear FS experts I have a question wrt the label numbers in FreeSurferColorLUT.txt compared with those in aparc.a2009s+aseg.mgz. I noticed that the last ctx (GM) label in FreeSurferColorLUT.txt file is 12175 ctx_rh_S_temporal_transverse whereas in the aparc.a2009s+aseg.mgz file, the highest in

Re: [Freesurfer] label file from freesurfer 5.3

Thank you so much for your help! -- Y.J. Daniel Yang, Ph.D. Assistant Research Professor Autism and Neurodevelopmental Disorders Institute The George Washington University and Children’s National Health System E-mail: daniely...@gwu.edu > On May 31, 2017, at 3:24 PM, B

Re: [Freesurfer] label file from freesurfer 5.3

sure. Easy enough to do in matlab. On Wed, 31 May 2017, Daniel Yang wrote: Thanks, Bruce! It works now. Is it possible I can convert all the negative values in the label to something like 1? Best, Daniel --  Y.J. Daniel Yang, Ph.D. Assistant Research Professor Autism and Neurodevelopmental Diso

Re: [Freesurfer] label file from freesurfer 5.3

Thanks, Bruce! It works now. Is it possible I can convert all the negative values in the label to something like 1? Best, Daniel -- Y.J. Daniel Yang, Ph.D. Assistant Research Professor Autism and Neurodevelopmental Disorders Institute The George Washington University and Children’s National Hea

Re: [Freesurfer] label file from freesurfer 5.3

Hi Daniel it's because the values in your label are all negative and the default threshold is 0. Set it to -20 or something and you will see the label cheers Bruce On Wed, 31 May 2017, Daniel Yang wrote: Thank you. I just sent it to your mailbox. --  Y.J. Daniel Yang, Ph.D. Assistant Resea

Re: [Freesurfer] label file from freesurfer 5.3

Thank you. I just sent it to your mailbox. -- Y.J. Daniel Yang, Ph.D. Assistant Research Professor Autism and Neurodevelopmental Disorders Institute The George Washington University and Children’s National Health System E-mail: daniely...@gwu.edu > On May 31, 2017, at

Re: [Freesurfer] label file from freesurfer 5.3

sure, but I'll need the subject as well (at least one surface) On Wed, 31 May 2017, Daniel Yang wrote: Good to know, then, it must be the way I interact with FS 6.0.0 that is wrong. It’s a surface label. Can I send you the label file to see if you could view that in FS 6.0.0’s freeview using

Re: [Freesurfer] label file from freesurfer 5.3

Good to know, then, it must be the way I interact with FS 6.0.0 that is wrong. It’s a surface label. Can I send you the label file to see if you could view that in FS 6.0.0’s freeview using command line? -- Y.J. Daniel Yang, Ph.D. Assistant Research Professor Autism and Neurodevelopmental Dis

Re: [Freesurfer] label file from freesurfer 5.3

no, the label format should be backwards compatible. Was it a surface or volume label? On Wed, 31 May 2017, Daniel Yang wrote: Dear FreeSurfer experts, When I tried to use FreeSurfer 6.0.0’s freeview to open a label file generated by FreeSurfer 5.3, I could not see anything. Is it incompatib

[Freesurfer] label file from freesurfer 5.3

Dear FreeSurfer experts, When I tried to use FreeSurfer 6.0.0’s freeview to open a label file generated by FreeSurfer 5.3, I could not see anything. Is it incompatibility issue going on here? Thanks, Daniel ___ Freesurfer mailing list Freesurfer@nmr

Re: [Freesurfer] label to vol

By a volume file, do you mean a binary mask inside of a volume? If so, you should run mri_vol2surf to convert it into a surface overlay (binary mask), then use mri_cor2label with the --surf option On 01/27/2017 05:08 AM, francesca bottino wrote: > > > Dear FS's experts, > I have this problem: >

[Freesurfer] label to vol

Dear FS's experts, I have this problem: I want transform a volume file .nii in surfaces files .label. I had tried the command cor2label but I don't know very well how to use it. Please help me. Tnks Da: freesurfer-boun...@nmr.mgh.harvard.edu per conto di freesu

Re: [Freesurfer] Label creation

ot work? > > Thanks > > Cris > > > > *From:* freesurfer-boun...@nmr.mgh.harvard.edu > [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas Greve > [gr...@nmr.mgh.harvard.edu] > *Sent:* Tuesday, December 13, 2016 4:50 PM > *To:* freesurfer@nmr.mgh.harvard.edu &

Re: [Freesurfer] Label creation

[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas Greve [gr...@nmr.mgh.harvard.edu] Sent: Tuesday, December 13, 2016 4:50 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Label creation Not that easy. I would do it by selecting a vertex that is close to the coordinate you

Re: [Freesurfer] Label creation

Not that easy. I would do it by selecting a vertex that is close to the coordinate you want, then 1. Create a surface overlay with all vertices = 0 except your chosen vertex mri_volsynth --template $FREESURFER_HOME/fsaverage/surf/lh.thickness --delta vertexno 0 0 0 --o delta.mgh 2. Smooth

[Freesurfer] Label creation

Hi Freesurfer's experts Is there an easy way to create automatically a circular label with a radius centered on a vertex with predifined RAS/Tailarach coordinates on the fsaverage surface? Thanks Cris ___ Freesurfer mailing list Freesurfer@nmr.mgh.ha

Re: [Freesurfer] label analysis

Use mris_anatomical_stats On 8/18/16 9:53 AM, Raffaele Dubbioso wrote: Dear Freesurfer team, I'm working on structural data analysis using Fressurfer. I have drawn my own labels and now I'd like to get data like thickness, curvature, folding index in the same way that I usually get when I r

[Freesurfer] label analysis

Dear Freesurfer team, I'm working on structural data analysis using Fressurfer. I have drawn my own labels and now I'd like to get data like thickness, curvature, folding index in the same way that I usually get when I run the aparc.stat function. Can you please help me how to solve this problem?

Re: [Freesurfer] Label registeration

need more info, can't tell what you are trying to do. try sending some command lines On 04/22/2016 06:29 AM, Mohamed Abdelhack wrote: > Dear all, > > I have been trying so far to export Freesurfer labels into a volume > created by SPM > > I tried to coregister the anatomical data from Freesurfer

[Freesurfer] Solved! Re: MatrixMultiply: m2 is null error, trying to convert MNI152 ROI to FreeSurfer label

half of Douglas N Greve [gr...@nmr.mgh.harvard.edu<mailto:gr...@nmr.mgh.harvard.edu>] Sent: Wednesday, April 20, 2016 11:13 AM To: freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] MatrixMultiply: m2 is null error, trying to convert MNI152 ROI to FreeSurf

[Freesurfer] Label registeration

Dear all, I have been trying so far to export Freesurfer labels into a volume created by SPM I tried to coregister the anatomical data from Freesurfer and SPM and use the registeration file to turn my label file into volume but the resulting output just goes outside the brain. Has anyone tried t

Re: [Freesurfer] MatrixMultiply: m2 is null error, trying to convert MNI152 ROI to FreeSurfer label

ions... >>> % 0 nonzero vertices found >>> >>> label stat field identically zero - setting to 1 >>> 12304 unassigned vertices in label - building spatial LUT... >>> assigning vertex numbers to label... >>&g

Re: [Freesurfer] MatrixMultiply: m2 is null error, trying to convert MNI152 ROI to FreeSurfer label

ubject: Re: [Freesurfer] MatrixMultiply: m2 is null error, trying to convert MNI152 ROI to FreeSurfer label what is your tksurfer command line? Can you send all the terminal output from tksurfer? Does it work in freeview? On 04/13/2016 11:20 AM, DeCross, Stephanie N. wrote: Hi, I’m trying to ta

Re: [Freesurfer] MatrixMultiply: m2 is null error, trying to convert MNI152 ROI to FreeSurfer label

1 > 12304 unassigned vertices in label - building spatial LUT... > assigning vertex numbers to label... > MatrixMultiply: m2 is null! > > > Thanks, > Stephanie > > > From: freesurfer-boun...@nmr.mgh.harvard.edu > [freesurfer-bo

Re: [Freesurfer] MatrixMultiply: m2 is null error, trying to convert MNI152 ROI to FreeSurfer label

edu] on behalf of Douglas N Greve [gr...@nmr.mgh.harvard.edu] Sent: Wednesday, April 13, 2016 5:10 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] MatrixMultiply: m2 is null error, trying to convert MNI152 ROI to FreeSurfer label what is your tksurfer command line? Can you send

Re: [Freesurfer] MatrixMultiply: m2 is null error, trying to convert MNI152 ROI to FreeSurfer label

what is your tksurfer command line? Can you send all the terminal output from tksurfer? Does it work in freeview? On 04/13/2016 11:20 AM, DeCross, Stephanie N. wrote: > Hi, > > I’m trying to take an ROI in MNI152 volume space and make it into a > cortical surface label, for visualization purpose

[Freesurfer] MatrixMultiply: m2 is null error, trying to convert MNI152 ROI to FreeSurfer label

Hi, I’m trying to take an ROI in MNI152 volume space and make it into a cortical surface label, for visualization purposes. With my input being the lh thresholded, binarized MNI152 nii.gz label (when I visualize it, it looks as it should in fslview), I ran: mri_vol2vol -- mov -- targ $SUBJE

Re: [Freesurfer] Label or Overlay of Surface files

Hi Saeed lh.sulc and lh.curv are scalar overlays, not surfaces. The surfaces are e.g. lh.inflated, lh.white, lh.pial, etc cheers Bruce On Fri, 14 Aug 2015, Saeed Mahdizadeh Bakhshmand wrote: Hello, I am trying to load surface overlays in 3D Slicer on top of surface meshes (e.g. lh.Inf

Re: [Freesurfer] Label or Overlay of Surface files

SOLVED. On Fri, Aug 14, 2015 at 4:08 PM, Saeed Mahdizadeh Bakhshmand < saeedbakhshm...@gmail.com> wrote: > Hello, > > I am trying to load surface overlays in 3D Slicer on top of surface meshes > (e.g. lh.Inflated), > but surface overlays somehow don't load properly into 3D slicer, I am > trying r

Re: [Freesurfer] Label or Overlay of Surface files

Hello, I am trying to load surface overlays in 3D Slicer on top of surface meshes (e.g. lh.Inflated), but surface overlays somehow don't load properly into 3D slicer, I am trying right surface files (lh.sulc , lh.curve e.g.)? On Fri, Aug 7, 2015 at 10:14 AM, Saeed Mahdizadeh Bakhshmand < saeedbak

Re: [Freesurfer] Label or Overlay of Surface files

Hi Lee, Perfect, Thanks. Saeed On Thu, Aug 6, 2015 at 5:15 PM, Lee Tirrell wrote: > Hi Saeed, > > You can run either of the following commands to overlay the ?h.sulc or > ?h.curv file: > > tksurfer subject hemisphere surface -snap -sulc > tksurfer subject hemisphere surface -snap -curv > >

Re: [Freesurfer] Label or Overlay of Surface files

Hi Saeed, You can run either of the following commands to overlay the ?h.sulc or ?h.curv file: tksurfer subject hemisphere surface -snap   -sulc tksurfer subject hemisphere surface -snap   -curv Best, Lee On Thu, 6 Aug 2015, Saeed Mahdizadeh Bakhshmand wrote: I used it as this:tksurfer sub

Re: [Freesurfer] Label or Overlay of Surface files

I used it as this: tksurfer subject hemisphere surface -snap -overlay And it adds a* gray scale* version of sulcus map to the plain gray, How can I activate colors? Thanks, Saeed On Thu, Aug 6, 2015 at 4:20 PM, Bruce Fischl wrote: > load them as "curvature" files > > cheers > Bruce > > > On

Re: [Freesurfer] Label or Overlay of Surface files

load them as "curvature" files cheers Bruce On Thu, 6 Aug 2015, Saeed Mahdizadeh Bakhshmand wrote: And are they treated as label files (e.g. lh.aparc.annot ) in the label directory? And how they can be added to the tksurfer snapshot procedure? On Thu, Aug 6, 2015 at 4:04 PM, Bruce Fischl w

Re: [Freesurfer] Label or Overlay of Surface files

And are they treated as label files (e.g. lh.aparc.annot ) in the label directory? And how they can be added to the tksurfer snapshot procedure? On Thu, Aug 6, 2015 at 4:04 PM, Bruce Fischl wrote: > no, the scalar overlays are stored separately (e.g. lh.curv, lh.sulc, > etc...) > > On Thu, 6 Aug

Re: [Freesurfer] Label or Overlay of Surface files

no, the scalar overlays are stored separately (e.g. lh.curv, lh.sulc, etc...) On Thu, 6 Aug 2015, Saeed Mahdizadeh Bakhshmand wrote: Hello, Is scalar overlay information embedded into surface file itself? When I open them in freeview they are loaded with color overlays (sulcus/gyrus), but when

[Freesurfer] Label or Overlay of Surface files

Hello, Is scalar overlay information embedded into surface file itself? When I open them in freeview they are loaded with color overlays (sulcus/gyrus), but when I load same models into 3D slicer or take a snapshot in tksurfer, they are plain gray. Thanks, Saeed __

Re: [Freesurfer] Label to Nii Conversion

You can use mri_label2label and use the --outmask option. If you are going to use mri_segstats to do the extraction, you can skip the mri_label2label step and specify the label with --slabel (and add --id 1 otherwise it will give you two ROI results, one in the label, the other outside the labe

[Freesurfer] Label to Nii Conversion

I have a label file on the surface, but want to be able to use it to extract surface data that is already in nifti format (dimensions: [2737 1 6]). Is there a way to convert a label to nifti? Best Regards, Donald McLaren = D.G. McLaren, Ph.D. Research Fellow, Department of Neurolo

Re: [Freesurfer] label

Hi Fabrizio the strange error message is a bug in our reporting (which I just fixed), but it isn't the source of your problem. Does the cortex.label file exist? Note that you are specifying the right hemi label file for the left hemi stats, which is almost certainly wrong. I also don't think y

[Freesurfer] label

Dear FreeSurfers, I need to extract mean thickness from a manually defined label which is now in subjid/label (named mpfc.label) I tried with mris_anatomical_stats using the -l flag but here is what I got iMac-di-Mac:label fabriziopiras$ mris_anatomical_stats -l subjid/label/rh.cortex.label -b

Re: [Freesurfer] label to surf (.mgh file)

boun...@nmr.mgh.harvard.edu > [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve > [gr...@nmr.mgh.harvard.edu] > Sent: Thursday, 7 August 2014 8:16 AM > To: freesurfer@nmr.mgh.harvard.edu > Subject: Re: [Freesurfer] label to surf (.mgh file) > > Hi Sara,

Re: [Freesurfer] label to surf (.mgh file)

an this be correct? Thanks, Sarah From: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve [gr...@nmr.mgh.harvard.edu] Sent: Thursday, 7 August 2014 8:16 AM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer]

Re: [Freesurfer] label to surf (.mgh file)

Hi Sara, I'm not sure what you are trying to do. Are you doing a volume or surface-based analysis? If surface based, why do you need to convert it into the volume? doug On 08/05/2014 11:48 PM, Sarah Whittle wrote: > Hi, > > I would like to create an overlay from a number of labels from the sta

[Freesurfer] label to surf (.mgh file)

Hi, I would like to create an overlay from a number of labels from the standard 2005 aparc in order to perform an fdr correction of a significance map using a mask to restrict the search space. I would like to do this with fsaverage. As far as I can tell, there is no label or annotation to surf

Re: [Freesurfer] .label files for subcortical structures

...@nmr.mgh.harvard.edu] Sent: Tuesday, August 05, 2014 6:04 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] .label files for subcortical structures You can use mri_cor2label. The output coordinates will be "tkregister-style" RAS, which is probably not useful to you. Check

Re: [Freesurfer] .label files for subcortical structures

You can use mri_cor2label. The output coordinates will be "tkregister-style" RAS, which is probably not useful to you. Check out https://surfer.nmr.mgh.harvard.edu/fswiki/CoordinateSystems For how to convert to other coordinate systems doug On 08/05/2014 11:30 AM, Krieger, Donald N. wrote: > >

[Freesurfer] .label files for subcortical structures

Hi Everyone, What tool(s) are used to extract the vectors for subcortical labels? What I need are the RAS coordinates for the cerebellum, basal ganglia, etc. Is there something for extracting them from aseg.mgz ? Or is there something for generating a .annot file so that mri_annotation2label may

[Freesurfer] label from volume on decimated surface

Hello Freesurfer experts, I want to project a label from a volume on a decimated surface. Normally I do something like this to generate a label from the volume: mri_vol2surf --src subjects/foobar/mri/aparc+aseg.mgz --regheader foobar --hemi lh --surf pial --out test.mgh mri_cor2label --i test.mgh

Re: [Freesurfer] [Label] Extract coordinate of Corpus Callossum

Hi Thomas, no, all the values are in individual subject space. cheers Bruce On Mon, 17 Mar 2014, Thomas PAUL wrote: Okay thank you Bruce for your quick answer. I have one more question. I went through the whole ReconAllTable, and I can't find the answer: Based on what I read, I think that

Re: [Freesurfer] [Label] Extract coordinate of Corpus Callossum

Okay thank you Bruce for your quick answer. I have one more question. I went through the whole ReconAllTable, and I can't find the answer: Based on what I read, I think that all the volumes created by freesurfer (all the outputs) have had the Tailarach transform applied to them? So when I have ext

Re: [Freesurfer] [Label] Extract coordinate of Corpus Callossum

yes On Sat, 15 Mar 2014, Thomas PAUL wrote: Thank you Bruce for your help, it works. I didn't noticed that mri_extract_label existed.  So just to be sure, the output volume is not a mask, right? If I want to convert it to a mask, I use mri_binarize ? Thomas Paul. On Fri, Mar 14, 2014 at 2:51 P

Re: [Freesurfer] [Label] Extract coordinate of Corpus Callossum

Thank you Bruce for your help, it works. I didn't noticed that mri_extract_label existed. So just to be sure, the output volume is not a mask, right? If I want to convert it to a mask, I use mri_binarize ? Thomas Paul. On Fri, Mar 14, 2014 at 2:51 PM, Bruce Fischl wrote: > Hi Thomas > > you are

Re: [Freesurfer] [Label] Extract coordinate of Corpus Callossum

Hi Thomas you are probably better off getting it right out of the aseg.mgz. The cc labels in it are: #define CC_Posterior 251 #define CC_Mid_Posterior 252 #define CC_Central253 #define CC_Mid_Anterior 254 #define CC_Anterior 255 so you should just be able to run mri_extr

[Freesurfer] [Label] Extract coordinate of Corpus Callossum

Dear FreeSurfer experts, I've been using FreeSurfer for 2 months now, and I have a question on how to proceed to do the following thing: My goal is to obtain the CRS coordinates of the corpus callossum. Here is what I was thinking to do, based on what I read: 1. Annotation to segmentation: m

Re: [Freesurfer] label to curv .mgh

Not sure. What do you mean by "not getting there"? You can also use mri_label2label with the --outmask option doug On 12/05/2013 02:47 PM, Gregory Kirk wrote: > > hello, trying to convert a medial wall label to a curv format .mgh file > > running > > mris_convert --label lh.Medial_wall.label lh.

[Freesurfer] label to curv .mgh

hello, trying to convert a medial wall label to a curv format .mgh file running mris_convert --label lh.Medial_wall.label lh.white foo.mgh tried a few things but not getting there, what does it want ? thank You ___ Freesurfer mailing list Freesurfe

Re: [Freesurfer] .label versus .thresh.label

Ok great! Thanks for the quick responses, and for your help. Best, Krista On Sun, Nov 17, 2013 at 1:26 PM, Bruce Fischl wrote: > no, those are whole-brain parcellations so ever vertex is already assigned > the most likely label for it > > > cheers > Bruce > On Sun, 17 Nov 2013, krista kelly wro

Re: [Freesurfer] .label versus .thresh.label

no, those are whole-brain parcellations so ever vertex is already assigned the most likely label for it cheers Bruce On Sun, 17 Nov 2013, krista kelly wrote: Ok perfect. Just one last question, how would I use the thresholded option for the annotations (i.e. aparc.DKTatlas40.annot, aparc2009

Re: [Freesurfer] .label versus .thresh.label

Ok perfect. Just one last question, how would I use the thresholded option for the annotations (i.e. aparc.DKTatlas40.annot, aparc2009s.annot) when doing whole brain analyses? Thanks! On Sun, Nov 17, 2013 at 1:20 PM, Bruce Fischl wrote: > for most purposes, yes > > Bruce > On Sun, 17 Nov 2013,

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