[Freesurfer] surfaces from 0.5mm scan

Hi there My initial email didn't seem to have sent and so I am re-sending it: I would like to know if it is possible to create surfaces from a scan that is 0.5mm isotropic. I tried to run recon-all on our MNI 2009b atlas which is 0.5mm cubed and it crashed quite quickly afterwards. I wonder if

Re: [Freesurfer] surfaces from 0.5mm scan

g mris_make_surfaces > > cheers > Bruce > On Wed, 25 May 2016, Trisanna Sprung-Much wrote: > > > Hi there > > > > My initial email didn't seem to have sent and so I am re-sending it: > > > > I would like to know if it is possible to create surfaces from a s

[Freesurfer] concerting surface format

Hi there is there a way to convert .mesh (BrainVisa) to the Freesurfer surface format? mri_convert doesn't seem to do it. best wishes Trisanna -- Ph.D. Candidate McGill University Integrated Program in Neuroscience Psychology ___ Freesurfer mailing

Re: [Freesurfer] registering to fsaverage

, Bruce Fischl <fis...@nmr.mgh.harvard.edu> wrote: > Hi Trisanna > > you don't need to inflate the overlays. They can just use the existing > surface-based (sphere.reg) registration. > > cheers > Bruce > On Wed, 15 Jun 2016, Trisanna Sprung-Much wrote: > > Hi t

[Freesurfer] Fwd: concerting surface format

Hi there is there a way to convert .mesh (BrainVisa) to the Freesurfer surface format? mri_convert doesn't seem to do it. best wishes Trisanna -- Ph.D. Candidate McGill University Integrated Program in Neuroscience Psychology ___ Freesurfer mailing

[Freesurfer] registering to fsaverage

Hi there So I have sulcal labels from another software (.mnc format) from which I am trying to generate some probability maps. I was able to convert the .mnc to .mgz surface overlay using mri_vol2surf for my MRIs after running all MRIs in recon-all. So, now I have all my painted voxels as surface

Re: [Freesurfer] registering to fsaverage

Integrated Program in Neuroscience Psychology On Mon, Jun 20, 2016 at 9:27 AM, Bruce Fischl <fis...@nmr.mgh.harvard.edu> wrote: > yes, your last file on the command line should be the output file (the > average) > > cheers > Bruce > > > On Mon, 20 Jun 2016, Trisan

Re: [Freesurfer] registering to fsaverage

m in a week or two. > > As for this, if you overlays are mapped to fsaverage you can just use > mri_average to average them. > > cheers > Bruce > > > > On Sun, 19 Jun 2016, Trisanna Sprung-Much wrote: > > Hi Doug >> >> So all of my overlays for each subject have been

Re: [Freesurfer] registering to fsaverage

mgh.harvard.edu> wrote: > >> Try surf2surf with --mapmethod nnf >> >> On 06/15/2016 04:25 PM, Trisanna Sprung-Much wrote: >> > Hi Doug - yes they do actually, I was quite pleased. I did some trials >> > with other subjects and the mri_vol2surf all looks go

Re: [Freesurfer] registering to fsaverage

Fischl <fis...@nmr.mgh.harvard.edu> wrote: > Hi Trisanna > > the binaries that take mandatory command-line arguments (i.e. without a -- > or - in front of them) require all options to be given before the mandatory > arguments > > cheers > Bruce > > On Mon, 20

Re: [Freesurfer] registering to fsaverage

Program in Neuroscience Psychology On Wed, Jun 22, 2016 at 9:32 PM, Bruce Fischl <fis...@nmr.mgh.harvard.edu> wrote: > Hi Trisanna > > if you are using mri_average you can give it -p as the first argument and > it will compute a percent at the end > Bruce > On Wed, 22 Jun 20

Re: [Freesurfer] registering to fsaverage

properly > sample the labels onto the surface. Do the labels on subject 00350 > surfaces look ok? > > On 06/15/2016 04:00 PM, Trisanna Sprung-Much wrote: > > thanks Dr. Fischl > > > > So the command seems to have worked! I have copied what ran in my > &g

Re: [Freesurfer] registering to fsaverage

worked beautifully. Thank you! -- Ph.D. Candidate McGill University Integrated Program in Neuroscience Psychology On Wed, Jun 15, 2016 at 4:41 PM, Douglas N Greve <gr...@nmr.mgh.harvard.edu> wrote: > Try surf2surf with --mapmethod nnf > > On 06/15/2016 04:25 PM, Trisanna Sp

[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] mri_vol2surf after recon-all

e > argument to --reg. I'll need to figure out how to generate a .dat/.lta for > the 305. > > > > On 4/6/16 12:50 PM, Trisanna Sprung-Much wrote: > > Any ideas? > > Trisanna > > -- > Ph.D. Candidate > McGill University > Integrated Program in Neuroscience &g

[Freesurfer] mri_vol2surf after recon-all

Hi Freesurfer I have some labels (.mnc) that are painted voxels generated from a Montreal Neurological Institute software. I am trying to project the labels onto the surfaces generated from recon-all that I applied to the corresponding MRI volumes. *I used mri_vol2surf: * mri_vol2surf --src

Re: [Freesurfer] mri_vol2surf after recon-all

On Tue, Apr 5, 2016 at 6:34 PM, Bruce Fischl <fis...@nmr.mgh.harvard.edu> wrote: > Hi Trisanna > > what space are your labels in? > > cheers > Bruce > On Tue, 5 Apr 2016, Trisanna Sprung-Much > wrote: > > > Hi Freesurfer > > > > I have some l

Re: [Freesurfer] mri_vol2surf after recon-all

Any ideas? Trisanna -- Ph.D. Candidate McGill University Integrated Program in Neuroscience Psychology On Tue, Apr 5, 2016 at 9:37 PM, Trisanna Sprung-Much < trisanna.sprung-m...@mail.mcgill.ca> wrote: > Hi Dr. Fischl > > I have a mixture - some of the labels were painted in t

Re: [Freesurfer] mri_vol2surf after recon-all

in Neuroscience Psychology On Fri, Apr 8, 2016 at 12:47 PM, Douglas N Greve <gr...@nmr.mgh.harvard.edu> wrote: > > > On 04/07/2016 03:50 PM, Trisanna Sprung-Much wrote: > > thanks, Doug. I am still extremely confused, however. *Am I meant to > > run recon-all first? *I w

Re: [Freesurfer] tksurfer

Hi John I do not know anything about the error that you are getting but I was also having some problems with tksurfer and was told by Dr. Fischl that this viewer is no longer being updated and that it would be best to try freeview. Did you give this a go? best wishes Trisanna -- Ph.D.

Re: [Freesurfer] mri_vol2surf after recon-all

--mov icbm.nii.gz --s $subject --reg > $SUBJECTS_DIR/subject/transforms/icbm.reg.dat --dof 12 > --lta $SUBJECTS_DIR/subject/transforms/icbm.reg.lta > > This will use a linear (12 dof) registration which might not be > particularly accurate > > > On 04/08/2016 01:27 PM, Trisa

Re: [Freesurfer] labels

lopment on tksurfer. Can you > try this on freeview? I can't remember if freeview allows changing > thresholds in labels, but if not Ruopeng can add it to his list of feature > requests > > cheers > Bruce > > > > On Sat, 12 Mar 2016, Trisanna Sprung-Much wrote:

Re: [Freesurfer] labels

ion 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? >>

Re: [Freesurfer] labels

k 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 .mn

Re: [Freesurfer] labels

h 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 >> a

Re: [Freesurfer] mri_vol2surf after recon-all

ot; named identity.nofile and it will > assume that the transform is the identity. You can then use mri_vol2label > to sample the label onto the surface and visualize it with: > > freeview -f lh.inflated:label=lh.labels.label > > or some such > > cheers > Bruce > &g

[Freesurfer] identity.nofile

Hi All! Could someone please tell me how to run mri_vol2surf using identity.nofile as the transformation? I cannot find any documentation on identity.nofile Additionally, if my next step is to use the output of mri_vol2surf in mri_cor2label, which takes surface overlays OR volumes, what format

Re: [Freesurfer] identity.nofile

the label onto the surface and visualize it with: freeview -f lh.inflated:label=lh.labels.label or some such cheers Bruce On Thu, 14 Apr 2016, Trisanna Sprung-Much wrote: Hi there Just to reiterate my point above, when I open a surface created in Freesurfer with my labels.mgz (converted f

Re: [Freesurfer] identity.nofile

9/2016 03:05 PM, Trisanna Sprung-Much wrote: > > Hi Doug > > > > below is the email I had written last Friday. I thought it got lost in > > the mix. I was told by Bruce to use identity.nofile as the > > transformation since my labels and T1s are already in the same sp

Re: [Freesurfer] identity.nofile

each surface > > location). In freeview you can view it as: > > > > freeview -f lh.inflated:overlay=surfaceoverlay.mgz > > > > > > cheers > > Bruce > > > > On Tue, 19 Apr 2016, Trisanna Sprung-Much wrote: > > > >> Hi Doug >

Re: [Freesurfer] identity.nofile

provided function() line 0 in unknown directory unknown file [unset]: aborting job: application called MPI_Abort(MPI_COMM_WORLD, 59) - process 0 -- Ph.D. Candidate McGill University Integrated Program in Neuroscience Psychology On Tue, Apr 19, 2016 at 8:59 PM, Trisanna Sprung-Much

Re: [Freesurfer] identity.nofile

mi option. Ruopeng, can you add something to > freeview to handle this case more elegantly? > doug > > > > On 04/20/2016 10:42 AM, Trisanna Sprung-Much wrote: > > Hi Doug and Bruce > > > > *This what I get when I run the head command on the label:* > > >

Re: [Freesurfer] identity.nofile

line > below. That space should not be there, so if it was there when you ran the > command try again without the space. > > > On 4/19/16 9:19 PM, Trisanna Sprung-Much wrote: > > Hi Doug > > I tried again in the terminal and got this: > > * trisanna@kaplan:~$ freeview -f >

Re: [Freesurfer] identity.nofile

University Integrated Program in Neuroscience Psychology On Tue, Apr 19, 2016 at 4:15 PM, Trisanna Sprung-Much < trisanna.sprung-m...@mail.mcgill.ca> wrote: > many thanks - will give this a go! > > -- > Ph.D. Candidate > McGill University > Integrated Program in Neuroscience

Re: [Freesurfer] mri_vol2surf after recon-all

wrote: > > this is a known bug. Try this version instead > ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mni152reg > > On 04/13/2016 01:06 PM, Trisanna Sprung-Much wrote: > > Hi Doug > > > > So I tried running mni152reg and had the following error: > > >

Re: [Freesurfer] mri_vol2surf after recon-all

FREESURFER_HOME/sources.csh > > On 04/14/2016 10:31 AM, Trisanna Sprung-Much wrote: > > thanks, Doug. *Unfortunately, I got a different error this time:* > > > > trisanna@kaplan:~$ mni152reg --s icbm-102 > > /usr/local/freesurfer-5.3//sources.csh: No such file or directory. &

Re: [Freesurfer] identity.nofile

On Wed, Apr 20, 2016 at 12:00 PM, Douglas N Greve <gr...@nmr.mgh.harvard.edu > wrote: > nope, you need to give it just the name of the subject and the > hemisphere. Run it with --help for more info > > On 04/20/2016 11:35 AM, Trisanna Sprung-Much wrote: > > Hi Doug > &g

Re: [Freesurfer] Freesurfer 6.0?

k we'll have a beta version in two weeks, but that's > just a guess. > > doug > > > > On 7/25/16 4:01 PM, Trisanna Sprung-Much wrote: > > > Hi there > > Do we have a potential date for the Freesurfer 6.0 release? I was told I > would want to re-run all my subjec

Re: [Freesurfer] registering subject pial to fsaverage

The only thing you are doing with this command is to change the number > and identity of the vertices, the xyz will not change at all and so the > appearance of the surface will not change (much). > > On 07/21/2016 01:11 PM, Trisanna Sprung-Much wrote: > > Hi Doug > > > &g

Re: [Freesurfer] ROIs defined in MNI space and vol2surf

Hey there I think you just need to use "--regmethod subject" instead of specifying a registration .dat file. I had similar troubles a few months ago as my labels were made on the volume and I simply wanted to overlay them onto their surfaces in Freesurfer and didn't want any transformation to be

[Freesurfer] Freesurfer 6.0?

Hi there Do we have a potential date for the Freesurfer 6.0 release? I was told I would want to re-run all my subjects to create better surfaces using Freesurfer 6.0 and I am wondering if it really will improve surface extraction that much. Many thanks! Trisanna -- Ph.D. Candidate McGill

Re: [Freesurfer] registering subject pial to fsaverage

wrote: > I don't understand what you did or what the problem is. Can you elaborate? > > On 7/19/16 5:23 PM, Trisanna Sprung-Much wrote: > > Hi there > > I tested registering a subject's pial surface to fsaverage and compared > the original pial (from recon-all) with this regis

Re: [Freesurfer] registering to fsaverage

resolved? > doug > > On 06/30/2016 01:26 PM, Trisanna Sprung-Much wrote: > > Hi Bruce > > > > here is the output of my mri_vol2surf for a volumetric spam created in > > minc tools. When I then overlay this result in Freeview, it displays a > > Min of 127 and a Max

[Freesurfer] registering subject pial to fsaverage

Hi there I tested registering a subject's pial surface to fsaverage and compared the original pial (from recon-all) with this registered pial surface. It turns out that they are almost identical in nature, and I am wondering how this is possible if recon-all does not alter the input data. Below

Re: [Freesurfer] registering to fsaverage

any ideas? Thanks! Trisanna -- Ph.D. Candidate McGill University Integrated Program in Neuroscience Psychology On Wed, Jun 22, 2016 at 10:22 PM, Trisanna Sprung-Much < trisanna.sprung-m...@mail.mcgill.ca> wrote: > thanks Bruce - I had found that option for my fsaverage maps and

Re: [Freesurfer] registering to fsaverage

> On Jun 29, 2016, at 2:54 PM, Trisanna Sprung-Much < > trisanna.sprung-m...@mail.mcgill.ca> wrote: > > Hi Bruce > > I simply use > > mri_vol2surf --mov spam.mnc --output overlayspam.mgz --regheader subject > --hemi lh --surf pial > > Trisanna > > -- &

Re: [Freesurfer] registering to fsaverage

probability map? > > Bruce > > > > On Wed, 29 Jun 2016, Trisanna Sprung-Much wrote: > > Hi Bruce >> So, when I take a probability map formed using linear volumetric >> registration with minc tools and saved as .mnc and convert it to an >> overlay.mgz and open

Re: [Freesurfer] registering to fsaverage

wrote: > how do you create the overlay? > On Wed, 29 Jun 2016, Trisanna Sprung-Much wrote: > > Hi Bruce >> >> To create the spam I used minctools: >> >> mincaverage input.mnc output.mnc >> >> I blurred the spam using >> >> mincblur i

Re: [Freesurfer] registering to fsaverage

Integrated Program in Neuroscience Psychology On Sun, Jun 19, 2016 at 12:46 PM, Bruce Fischl <fis...@nmr.mgh.harvard.edu> wrote: > no problem. > > Bruce > On Sun, 19 Jun 2016, Trisanna Sprung-Much wrote: > > thanks Dr. Fischl - I think sometimes my emails don't get sent out on t

Re: [Freesurfer] registering to fsaverage

AM, Trisanna Sprung-Much < trisanna.sprung-m...@mail.mcgill.ca> wrote: > Hi Dr. Fischl > > I ran the following mri_average and consistently get this message. It > seems to be trying to read my output as one of the input volumes. If I > don't specify an output it re-writes my l

Re: [Freesurfer] How to check recon-all finished without any error

Try checking your recon all.log in your scripts folder of the subject. Trisanna -- Ph.D. Candidate McGill University Integrated Program in Neuroscience Psychology On Thu, Feb 2, 2017 at 1:52 PM, shi yao wang wrote: > Dear FS experts: > How to check recon-all

Re: [Freesurfer] license file not working

The .license that it comes with is not the same as the license.txt that you have to acquire. I was able to use an old license.txt from my Freesurfer 5.3 for 6.0. Best Trisanna -- Ph.D. Candidate McGill University Integrated Program in Neuroscience Psychology On Thu, Feb 2, 2017 at 3:21 PM, X

Re: [Freesurfer] Freesurfer 6.0 and ex-vivo T1

vo recon stream is > still a work in progress > > cheers > Bruce > On Tue, 24 Jan 2017, Trisanna Sprung-Much wrote: > > Hi there >> I am wondering if the Freesurfer 6.0 version is more flexible with the >> parameters used for ex-vivo scans other tha

[Freesurfer] Freesurfer 6.0 and ex-vivo T1

Hi there I am wondering if the Freesurfer 6.0 version is more flexible with the parameters used for ex-vivo scans other than what 5.3 required, as listed here https://surfer.nmr.mgh.harvard.edu/fswiki/ExVivo. We acquired some ex-vivo scans at 0.4mm iso but not with those above parameters. many

[Freesurfer] Freeview in 6.0 - editing labels

Hi there Does the 6.0 version of Freeview have a way to edit labels on surfaces similar to how tksurfer allowed us to do this? Thanks! Trisanna -- Ph.D. Candidate McGill University Integrated Program in Neuroscience Psychology ___ Freesurfer mailing

[Freesurfer] Freesurfer 6.0 and MNI template

Me again, Are the fsaverage volumetric coordinates in Freesurfer 6.0 still in MNI305 space or have they been updated to the MNI152 space? many thanks! Trisanna -- Ph.D. Candidate McGill University Integrated Program in Neuroscience Psychology ___

Re: [Freesurfer] Freesurfer 6.0 and MNI template

thanks Doug! -- Ph.D. Candidate McGill University Integrated Program in Neuroscience Psychology On Wed, Jan 25, 2017 at 6:27 PM, Douglas N Greve <gr...@nmr.mgh.harvard.edu> wrote: > Still in 305 > > > On 01/25/2017 06:21 PM, Trisanna Sprung-Much wrote: > > Me again, &

Re: [Freesurfer] Freeview in 6.0 - editing labels

t; which is a bug. But you can save it by “Save ROI as”. Sorry for the > inconveneince. > > In future update we plan to simply label editing by combining surface and > volume labels. Hopefully that will make label editing a lot easier. > > Best, > Ruopeng > > On Jan 25, 2

Re: [Freesurfer] recon-all error (6.0)

Bruce > On Thu, 23 Feb 2017, > Trisanna Sprung-Much wrote: > > > Hi All > > > > I am trying to run a subject in 6.0 (it ran perfectly well in 5.3) and > it stops when > > trying to transform to the "conformed" space. I get the following error > afte

[Freesurfer] recon-all error (6.0)

Hi All I am trying to run a subject in 6.0 (it ran perfectly well in 5.3) and it stops when trying to transform to the "conformed" space. I get the following error after about a minute. I have not seen this error before. mri_convert ./tmp.mri_nu_correct.mni.2860/nu1.mnc orig_nu.mgz --like

[Freesurfer] colour scale

Hi there is there a way to view a colour scale bar in Freeview rather than Tksurfer, for instance, for a probability map? I can alter the Min and Max by "Configure Overlay" but cannot seem to display the bar next to my surface. Many thanks Trisanna -- Ph.D. Candidate McGill University

Re: [Freesurfer] colour scale

how else would you suggest I generate a colour bar? tksurfer doesn't appear to be working for me either. Best Trisanna -- Ph.D. Candidate McGill University Integrated Program in Neuroscience Psychology On Mon, Sep 12, 2016 at 7:53 PM, Trisanna Sprung-Much < trisanna.sprung-m...@mail.mcgill

Re: [Freesurfer] colour scale

isanna > > -- > Ph.D. Candidate > McGill University > Integrated Program in Neuroscience > Psychology > > > On Mon, Sep 12, 2016 at 5:05 PM, Ruopeng Wang <rpw...@nmr.mgh.harvard.edu> > wrote: > >> There is a color bar button on the toolbar, or you can go to men

Re: [Freesurfer] license.txt?

e file. Also, it seems the > registration page is working: > >https://surfer.nmr.mgh.harvard.edu/registration.html > > On 09/23/2016 01:30 PM, Trisanna Sprung-Much wrote: > > Hi there > > > > I am installing Freesurfer on a Mac for the workshop next week and I

Re: [Freesurfer] group analysis

there is a tutorial with similar variables available here https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis Trisanna -- Ph.D. Candidate McGill University Integrated Program in Neuroscience Psychology On Wed, Oct 5, 2016 at 9:22 AM, charles laidi

Re: [Freesurfer] mri_average vs mri_concat

n 10/05/2016 05:03 PM, Trisanna Sprung-Much wrote: > > the source files are labelled vertices from 20 subjects: > > > > -T1s were labelled using an MNI software > > -Surfaces were created in FreeSurfer and surface overlays of the > > labels were created using mr

Re: [Freesurfer] mri_average vs mri_concat

in Neuroscience Psychology On Thu, Oct 6, 2016 at 11:30 AM, Douglas Greve <gr...@nmr.mgh.harvard.edu> wrote: > What are the pixel values in the mgz file? They should be binary, ie, 1=in > a label, 0 = out of label > > On 10/6/16 10:22 AM, Trisanna Sprung-Much wrote: > >

Re: [Freesurfer] mri_average vs mri_concat

as N Greve <gr...@nmr.mgh.harvard.edu> wrote: > what are the source files ("all files"). What data type, value range, > where did they come from? > > > On 10/05/2016 04:48 PM, Trisanna Sprung-Much wrote: > > Hi Doug > > > > So, of course now it w

[Freesurfer] license.txt?

Hi there I am installing Freesurfer on a Mac for the workshop next week and I cannot seem to get a license.txt because the page is no longer is accessible. However, it seems to be running fine without this file. Thoughts? Trisanna -- Ph.D. Candidate McGill University Integrated Program in

Re: [Freesurfer] Volume to Surface

-regmethod > > Anna > -- > *From:* freesurfer-boun...@nmr.mgh.harvard.edu [ > freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Trisanna Sprung-Much > [trisanna.sprung-m...@mail.mcgill.ca] > *Sent:* Friday, September 30, 2016 12:41 PM > > *To:* Freesurfer support list &

Re: [Freesurfer] Can I change the pial surface outline by the adding the control point?

Hi there To my understanding, if you want to edit the pial (push it outwards more) then you need to edit the white matter, as the pial is made from the white matter surface. You can do this by manually extending the white matter surface and re-running your surfaces. Trisanna -- Ph.D. Candidate

Re: [Freesurfer] Volume to Surface

read_register(): Success > Error reading inplaneres from /mnt/netScratch/crawforda/ > BrainStem/study11074/S2sdt/segfs/surf/lh.sphere.reg > -- > *From:* freesurfer-boun...@nmr.mgh.harvard.edu [ > freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Trisan

Re: [Freesurfer] Volume to Surface

not sure what the .w means. When I try to load it onto the surface, I > get an error: "Failed to load Surface overlay." > > Thank you, > Anna > -- > *From:* freesurfer-boun...@nmr.mgh.harvard.edu [ > freesurfer-boun...@nmr.mgh.h

Re: [Freesurfer] Volume to Surface

- > *From:* freesurfer-boun...@nmr.mgh.harvard.edu [ > freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Trisanna Sprung-Much > [trisanna.sprung-m...@mail.mcgill.ca] > *Sent:* Friday, September 30, 2016 11:04 AM > > *To:* Freesurfer support list > *Subject:* Re: [Freesurfer] Vo

Re: [Freesurfer] Warping an ROI from one subject to another

I think it might have to do with the format of your output file - perhaps try .mgz? This is what I used. Then open the surface and use the "overlay" option to overlay your ROI as a surface overlay. Trisanna -- Ph.D. Candidate McGill University Integrated Program in Neuroscience Psychology On

Re: [Freesurfer] Volume to Surface

You have to run recon-all to get the surfaces of a volume. Trisanna -- Ph.D. Candidate McGill University Integrated Program in Neuroscience Psychology On Fri, Sep 30, 2016 at 9:47 AM, Crawford, Anna wrote: > Hello, > > I am trying to take nay volume that is registered and

Re: [Freesurfer] Volume to Surface

t; created using recon-all. > > Anna > -- > *From:* freesurfer-boun...@nmr.mgh.harvard.edu [ > freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Trisanna Sprung-Much > [trisanna.sprung-m...@mail.mcgill.ca] > *Sent:* Friday, September 30, 20

Re: [Freesurfer] Volume to Surface

t; surface if that makes sense. > > Thank you, > Anna > -- > *From:* freesurfer-boun...@nmr.mgh.harvard.edu [ > freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Trisanna Sprung-Much > [trisanna.sprung-m...@mail.mcgill.ca] > *Sent:* Friday, Septemb

Re: [Freesurfer] mri_average vs mri_concat

not sure about mri_concat, but mri_average -noconform -p ... should do the > trick > > cheers > Bruce > On Wed, 19 Oct 2016, Trisanna Sprung-Much wrote: > > Something weird is happening with mri_vol2surf - even though the data >> looks great, the values are odd >> which ca

Re: [Freesurfer] mri_average vs mri_concat

in Neuroscience Psychology On Mon, Oct 17, 2016 at 5:21 PM, Trisanna Sprung-Much < trisanna.sprung-m...@mail.mcgill.ca> wrote: > Hi Doug > > *Here is what I ran:* > > *trisanna@kaplan:~$ mri_vol2surf --mov > /data-01/trisanna/freesurfer/icbm-113/label/label_aalf.mnc

Re: [Freesurfer] mri_average vs mri_concat

Does anyone know who wrote the script for mri_concat? I would really like to get this figured out. thanks Trisanna -- Ph.D. Candidate McGill University Integrated Program in Neuroscience Psychology On Fri, Oct 21, 2016 at 12:13 PM, Trisanna Sprung-Much < trisanna.sprung-m...@mail.mcgill

Re: [Freesurfer] mri_average vs mri_concat

Hi Doug Any thoughts on this? Trisanna -- Ph.D. Candidate McGill University Integrated Program in Neuroscience Psychology On Thu, Oct 6, 2016 at 10:37 PM, Trisanna Sprung-Much < trisanna.sprung-m...@mail.mcgill.ca> wrote: > Hi Doug > > So the pixel values are 0 and 1 *in th

Re: [Freesurfer] smoothing kernel

wrote: > what is a sulcal probability map? > On Thu, 30 Mar 2017, Trisanna Sprung-Much > wrote: > > > thanks, Bruce - that is what I am learning. And if it was to smooth data > > from a sulcal probability map? A FWHM of 10 seems pretty high > > best > > > &g

Re: [Freesurfer] smoothing kernel

thanks, Bruce - that is what I am learning. And if it was to smooth data from a sulcal probability map? A FWHM of 10 seems pretty high best Trisanna -- Ph.D. Candidate McGill University Integrated Program in Neuroscience Psychology On Thu, Mar 30, 2017 at 12:17 PM, Trisanna Sprung-Much

[Freesurfer] smoothing kernel

Hi there I am wondering whether there is an acceptable FWHM to use to smooth surface data (for instance, a probability map)? Many thanks Trisanna -- Ph.D. Candidate McGill University Integrated Program in Neuroscience Psychology ___ Freesurfer mailing

[Freesurfer] Mid point on Freeview

Hi there I have a question concerning viewing a surface in Freeview (FS 6.0): *What does the "mid point" variable refer to?* I can change it and it seems to change the shading within the sulci when I am looking at a white matter surface. Many thanks Trisanna -- Ph.D. Candidate McGill University

[Freesurfer] probability maps

Hi there I have generated some anatomical probabilistic maps as overlays on the fsaverage pial surface. Is there a way to automatically find the vertex coordinates of the vertex with the highest probability of overlap? Or does this have to be done manually in Freeview? Many thanks Trisanna --

Re: [Freesurfer] probability maps

wrote: > hmmm, should be pretty easy in matlab, no? > On Mon, 15 May 2017, Trisanna > Sprung-Much wrote: > > > Hi there > > I have generated some anatomical probabilistic maps as overlays on the > > fsaverage pial surface. Is there a way to automatically find the

Re: [Freesurfer] probability maps

Trisanna -- Ph.D. Candidate McGill University Integrated Program in Neuroscience Psychology On Mon, May 15, 2017 at 2:53 PM, Bruce Fischl <fis...@nmr.mgh.harvard.edu> wrote: > what format is your map of p-values in? > On Mon, 15 May 2017, Trisanna > Sprung-Much wrote: > > &

Re: [Freesurfer] probability maps

gt; b = MRIread('map2.mgz'); > > c = MRIread('map3.mgz'); > > d = (a.vol > thresh + b.vol > thresh + d.vol> thresh)/3; > > [mm ii] = max(d); > > Then the vertex number will be ii-1 (need to convert from 1-based to > 0-based) > > > > > On 5/15/17 3:34 P

Re: [Freesurfer] smoothing kernal

, 2017 at 5:08 PM, Douglas N Greve <gr...@nmr.mgh.harvard.edu> wrote: > not sure what you are trying to do or why you would want to smooth the > prob map > > > On 05/24/2017 05:03 PM, Trisanna Sprung-Much wrote: > > Hi there > > > > I labelled sulci in 40 T1 vo

[Freesurfer] smoothing kernal

Hi there I labelled sulci in 40 T1 volumes and have created surface overlays using mri_vol2surf and then registered these to fsaverage using mri_surf2surf. I want to generate a statistical probability map using mri_concat and then mris_fwhm for each sulcus. What is an acceptable FWHM to use? It

[Freesurfer] Brodmann areas - exvivo labels

Hi there If I wanted to compare some spatial probability maps of some sulci of interest with the Juelich Data provided by FreeSurfer, would it make more sense to use the unthresholded Brodmann areas or the .thresh ones? Based on my understanding of how the .thresh was created (by creating a

Re: [Freesurfer] Brodmann areas - exvivo labels

oup size approximately matched the >> individual size. >> >> Peace, >> >> Matt. >> >> From: <freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Trisanna >> Sprung-Much >> <trisanna.sprung-m...@mail.mcgill.ca> >> Reply-To:

Re: [Freesurfer] recon-all exited with error

vard.edu/fswiki/FtpFileExchange > On Tue, 16 Jan > 2018, Trisanna Sprung-Much > wrote: > > > Hi Bruce > > Thanks for the speedy reply. Should I attach it here or is there a place > I can upload it to? > > > > best > > Trisanna > > > > -- >

Re: [Freesurfer] recon-all exited with error

ear up this issue. > > best, > Andrew > > > On Jan 17, 2018, at 4:03 PM, Trisanna Sprung-Much < > trisanna.sprung-m...@mail.mcgill.ca> wrote: > > Sorry, Bruce. ignore my last email. Not sure what happened there. > > I now am trying to upload icbm-205.tar.gz (the

Re: [Freesurfer] recon-all exited with error

> hmmm, I've never seen label2label core dump before. Can you tar, gzip and > upload the entire subject dir? > On Tue, 16 Jan 2018, Trisanna Sprung-Much > wrote: > > > Hi there > > > > I ran Freesurfer 6.0 on a subject last night and it took about 12 hours > (seem

Re: [Freesurfer] recon-all exited with error

ss than 2GiB, I suggest sending your data via the > Martinos file drop (directions at the bottom of this page: > https://surfer.nmr.mgh.harvard.edu/fswiki/FtpFileExchange). > > best > Andrew > > On Jan 18, 2018, at 11:53 AM, Trisanna Sprung-Much < > trisanna.sprung-m...@mail.m

Re: [Freesurfer] recon-all exited with error

local: icbm-205.tar.gz remote: icbm-205.tar.gz 200 PORT command successful. Consider using PASV. 425 Failed to establish connection. -- Ph.D. Candidate McGill University Integrated Program in Neuroscience Psychology On Wed, Jan 17, 2018 at 2:01 PM, Trisanna Sprung-Much < trisanna

[Freesurfer] vertex MNI305

External Email - Use Caution Hi there This might be a very silly question but I actually cannot find the answer in the email archive: Assuming I have loaded a label onto fsaverage in Freeview and want to get the MNI305 coordinate of that labelled vertex, am I simply using the

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