Re: [Freesurfer] Question about editing topology errors

External Email - Use Caution Hi there, just following up on this. Thank you! ___ Trisanna Sprung-Much, PhD Research Associate Montreal Neurological Institute [Logo Description automatically generated] From: freesurfer-boun...@nmr.mgh.harvard.edu on

[Freesurfer] Question about editing topology errors

happy. Is there a way to add control points for the pial? Thank you! Trisanna Sprung-Much, PhD McGill University Montreal Neurological Institute -- ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman

Re: [Freesurfer] question about surface registration to an average surface

I’m not really sure what you are trying to do, but I guess you will want to make your own average. I think there is a new script for this, so someone else will have to comment Cheers Bruce From: freesurfer-boun...@nmr.mgh.harvard.edu On Behalf Of Trisanna Sprung-Much Sent: Saturday

Re: [Freesurfer] question about surface registration to an average surface

ubject: Re: [Freesurfer] question about surface registration to an average surface Oh, then no, that won’t work From: freesurfer-boun...@nmr.mgh.harvard.edu On Behalf Of Trisanna Sprung-Much Sent: Saturday, December 4, 2021 10:48 AM To: Freesurfer support list Subject: Re: [Freesurfer] ques

Re: [Freesurfer] question about surface registration to an average surface

ter that to our atlas using mris_register. You will need to create a bunch of files that we expect though like ?h.curv, ?h.sulc, etc… You might also need to specify a volume, but I expect any conformed one will be ok Cheers Bruce From: freesurfer-boun...@nmr.mgh.harvard.edu On Behalf Of Trisa

[Freesurfer] question about surface registration to an average surface

ure pattern best aligns with the template data.Here is the same convexity data, now plotted on the lh.sphere.reg surface. Similar pattern, but "stretched around". surfer.nmr.mgh.harvard.edu Thank you, Trisanna -- Trisanna Sprung-Much, PhD Research Associate McGill University Montr

Re: [Freesurfer] turning a surface label into 3d object

External Email - Use Caution thanks Doug - I will give this a try! Appreciate it. -- Trisanna Sprung-Much, PhD Research Associate McGill University Montreal Neurological Institute From: freesurfer-boun...@nmr.mgh.harvard.edu on behalf of

[Freesurfer] turning a surface label into 3d object

skeletons that can be extracted in BrainVisa? Many thanks~ Trisanna -- Trisanna Sprung-Much, PhD Research Associate McGill University Montreal Neurological Institute ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu

Re: [Freesurfer] mri_label2label issues

/lh.white.old Verify that the old surface overlays on the new volume Map the old labels onto the new volume with mris_apply_reg --src-label old/label/lh.your.label --streg newsubject/surf/lh.white.old newsubject/surf/lh.white --o newsubject/label/lh.your.label On 11/3/2021 10:17 AM, Trisanna Sprung-Much

Re: [Freesurfer] mri_label2label issues

image I attached) and it is creating the same issue with the labels when I use mri_label2label. Why would mri_label2label with registration method as surface be having this issue? How might I overcome this to avoid redrawing my labels? Thank you, Trisanna -- Trisanna Sprung-Much, PhD Research

Re: [Freesurfer] mri_label2label issues

External Email - Use Caution Hi there Just wanted to follow up on this as I am still dealing with this issue and would love to avoid having to edit all labels. Thank you! Trisanna -- Trisanna Sprung-Much, PhD Research Associate McGill University Montreal Neurological

Re: [Freesurfer] mri_label2label issues

with the labels when I use mri_label2label. Why would mri_label2label with registration method as surface be having this issue? How might I overcome this? Thank you, Trisanna -- Trisanna Sprung-Much, PhD Research Associate McGill University Montreal Neurological Institute

Re: [Freesurfer] Converting volume to annotation

Apologizes for the naive question, but can anyone share as to how I can ultimately create a surface atlas when I have the volume.nii atlas file? Was I wrong with mri_vol2label as my first step? I am using Freesurfer version 7.2.0. Thank you, Paul -- Trisanna Sprung-Much, PhD Researc

Re: [Freesurfer] FW: make_average_subject without Talairach transform

External Email - Use Caution Hi there Could I get some input on this? Thanks, Trisanna Sprung-Much Research Associate McGill University MD Anderson Cancer Centre -- From: on behalf of Trisanna Sprung-Much Reply-To: Freesurfer support list Date: Monday, April 26, 2021 at

[Freesurfer] FW: make_average_subject without Talairach transform

External Email - Use Caution Hi there Still hoping for some help on this. Trisanna -- From: on behalf of Trisanna Sprung-Much Reply-To: Freesurfer support list Date: Tuesday, April 20, 2021 at 10:50 AM To: Freesurfer support list Subject: Re: [Freesurfer

Re: [Freesurfer] make_average_subject without Talairach transform

... --- hemi= lh avg_surf_name = white canon_surf_name = sphere.reg out_sname = avgtest xform = 2GabrielApril15.xfm --- mris_average_surface failed Trisanna Sprung-Much Research

Re: [Freesurfer] make_average_subject without Talairach transform

rage_subject On 3/25/2021 11:33 AM, Trisanna Sprung-Much wrote: External Email - Use Caution External Email - Use Caution Hi Doug The scans were registered (6 parameter) to a common chimp template prior to input to recon-all. The surfaces have reconstructed nicely and match the inp

Re: [Freesurfer] make_average_subject without Talairach transform

External Email - Use Caution Ah, neat! Ok, will give this a go! Thanks a bunch Trisanna Sprung-Much Research Associate McGill University MD Anderson Cancer Centre -- From: on behalf of "Douglas N. Greve" Reply-To: Freesurfer support list Date: Thursday, March 25,

Re: [Freesurfer] make_average_subject without Talairach transform

ch transform If you don't have a transform, how will you align the subjects into a common space? On 3/25/2021 10:19 AM, Trisanna Sprung-Much wrote: External Email - Use Caution External Email - Use Caution Hi there I’d like to know if it is possible to create an average volum

Re: [Freesurfer] make_average_subject without Talairach transform

will try as you suggest Trisanna Sprung-Much Research Associate McGill University MD Anderson Cancer Centre -- From: on behalf of "Fischl, Bruce" Reply-To: Freesurfer support list Date: Thursday, March 25, 2021 at 10:59 AM To: Freesurfer support list Subject: Re: [

[Freesurfer] make_average_subject without Talairach transform

External Email - Use Caution Hi there I’d like to know if it is possible to create an average volume and average surface of several subjects without having to incorporate the Talairach transform and no transform at all. Thank you, Trisanna Sprung-Much Research Associate

Re: [Freesurfer] What exactly are the BA_exvivo.thresh label and annotation files?

e as possible to the average area of the > individual BA labels. I hope this makes sense. I hope this helps! Trisanna Sprung-Much Research Associate McGill University MD Anderson Cancer Centre -- On 2021-02-18, 3:27 AM, "freesurfer-boun...@nmr.mgh.harvard.edu on behalf of julienbesle&qu

Re: [Freesurfer] overlap/intersection of labels?

merge_labels that may help? Best, Trisanna Sprung-Much Research Associate McGill University MD Anderson Cancer Centre -- From: on behalf of "Dr. Cornelius Kronlage" Reply-To: Freesurfer support list Date: Tuesday, February 16, 2021 at 11:19 AM To: "'freesurfer@nmr.mgh.ha

Re: [Freesurfer] mincRead error

. Best, Trisanna Sprung-Much Research Associate McGill University MD Anderson Cancer Centre -- From: on behalf of "Hoopes, Andrew" Reply-To: Freesurfer support list Date: Wednesday, February 10, 2021 at 9:54 AM To: Freesurfer support list Subject: Re: [Freesurfer] mincRead error Ca

Re: [Freesurfer] HCP T1w scans on FreeSurfer 7.1

.R.white.native.surf.gii is invalid! I used mris_convert to get the .white to open Any idea why it wouldn't be able to open as a .gii? From: freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Trisanna Sprung-Much Sent: Tuesday, January 26, 2021 6:12

Re: [Freesurfer] HCP T1w scans on FreeSurfer 7.1

he data in ${StudyFolder}/${Subject}/T1w is also in MNI space, but after only a 6 DOF rigid registration (i.e. no changes in brain shape, just a similar brain orientation and AC at 0,0,0). What does “paint surfaces” mean anyhow? Matt. From: on behalf of Trisanna Sprung-Much Reply-To: Freesurf

Re: [Freesurfer] HCP T1w scans on FreeSurfer 7.1

External Email - Use Caution Thanks for this Matt. Just a question – is it called “MNINonlinear” because a non-linear registration was used to MNIspace? If this is the case, I would prefer to paint in the subject’s native space. Best, Trisanna Sprung-Much Research Associate

Re: [Freesurfer] HCP T1w scans on FreeSurfer 7.1

External Email - Use Caution Hi Bruce Thanks for your speedy response. This would be an immense time saver if this works. I will give this a go. Yes, you are correct about the blurring as well! Best Trisanna Sprung-Much Research Associate McGill University MD Anderson Cancer

Re: [Freesurfer] HCP T1w scans on FreeSurfer 7.1

directly on these? This would save us from having to re-run all HCP subjects with recon-all in 7.1…. Best, Trisanna Sprung-Much Research Associate McGill University MD Anderson Cancer Centre -- From: on behalf of "Glasser, Matthew" Reply-To: Freesurfer support list Date: Tuesday,

Re: [Freesurfer] HCP T1w scans on FreeSurfer 7.1

Re: [Freesurfer] HCP T1w scans on FreeSurfer 7.1 Why are you registering it to the MNI prior to FS analysis? On 1/26/2021 10:13 AM, Trisanna Sprung-Much wrote: External Email - Use Caution Hi Doug and Matt So the HCP scans are at 0.5mm resolution because they were originally

Re: [Freesurfer] HCP T1w scans on FreeSurfer 7.1

FS analysis? On 1/26/2021 10:13 AM, Trisanna Sprung-Much wrote: External Email - Use Caution Hi Doug and Matt So the HCP scans are at 0.5mm resolution because they were originally 0.7mm and have been registered to our 0.5mm MNI152 template, to avoid losing data by registering to the 1mm

Re: [Freesurfer] HCP T1w scans on FreeSurfer 7.1

reesurfer-boun...@nmr.mgh.harvard.edu> <mailto:freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Trisanna Sprung-Much <mailto:trisanna.sprung-m...@mail.mcgill.ca> Sent: Tuesday, January 19, 2021 6:05 PM To: Freesurfer support list <mailto:freesurfer@nmr.mgh.harvard.edu> Subject: [Frees

Re: [Freesurfer] HCP T1w scans on FreeSurfer 7.1

/Linux recon-all -s TEST2 exited with ERRORS at Thu Jan 21 08:13:06 EST 2021 Any advice would be greatly appreciated, Trisanna From: freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Trisanna Sprung-Much Sent: Tuesday, January 19, 2021 6:05 PM To

[Freesurfer] HCP T1w scans on FreeSurfer 7.1

External Email - Use Caution Hi there If I want to run some HCP subjects that are 0.5mm iso T1w scans (MPRAGE) in FreeSurfer 7.1, would I simply use the following flags, or am I missing something? -3T -MPRAGE -hires Do we need an expert file with version 7.1 to specify the nu

Re: [Freesurfer] making labels in Freeview/Freesurfer 7.1.1

labels in Freeview/Freesurfer 7.1.1 Yes, that should work Bruce From: freesurfer-boun...@nmr.mgh.harvard.edu On Behalf Of Trisanna Sprung-Much Sent: Monday, January 18, 2021 5:01 PM To: Freesurfer support list Subject: Re: [Freesurfer] making labels in Freeview/Freesurfer 7.1.1

Re: [Freesurfer] making labels in Freeview/Freesurfer 7.1.1

used it before. [cid:15CC1D35-3F5C-4946-A2BE-C6B73EBEC9EF@lan] On Jan 6, 2021, at 11:32 AM, Trisanna Sprung-Much mailto:trisanna.sprung-m...@mail.mcgill.ca>> wrote: External Email - Use Caution Hi there As a follow-up to my earlier email, I figured it out. I can create 1 label

Re: [Freesurfer] making labels in Freeview/Freesurfer 7.1.1

External Email - Use Caution Hi Ruopeng This makes a lot more sense! And I figured out how to erase parts and add parts to the same label. Many thanks! Trisanna Sprung-Much, PhD McGill University Montreal Neurological Institute -- From: on behalf of "Wang, Ruopeng&quo

[Freesurfer] making labels in Freeview/Freesurfer 7.1.1

External Email - Use Caution Hi there As a follow-up to my earlier email, I figured it out. I can create 1 label in an annotation and simply have to assign an "index" value before saving. Could you please confirm that this is the best way to go about create a new label on a sur

[Freesurfer] creating labels on surfaces with Freeview 7.1.1

External Email - Use Caution Hi there, I am looking for instructions on how to create/edit my own labels directly on surfaces using the latest version of Freesurfer/Freeview but I cannot seem to find this documentation. My understanding is that an annotation file has multiple l

Re: [Freesurfer] Fwd: vertex MNI305

ause the cursor is not exactly on the vertex, but close > enough so that the vertex number is shown. > > Best, > Ruopeng > > On 08/21/2018 10:10 AM, Trisanna Sprung-Much wrote: > > External Email - Use Caution > Hi there > > Doug can you please confirm? Br

[Freesurfer] Fwd: vertex MNI305

Psychology -- Forwarded message ----- From: Trisanna Sprung-Much Date: Thu, Jul 26, 2018 at 7:35 PM Subject: vertex MNI305 To: Freesurfer support list 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

Re: [Freesurfer] Fwd: vertex MNI305

me during Doug's vacation. I believe that those > coords in fsaverage are MNI ones, but he can confirm > > cheers > Bruce > > > On Tue, 31 Jul 2018, Trisanna Sprung-Much wrote: > > >> External Email - Use Caution >> >> Hi there >&g

Re: [Freesurfer] Fwd: vertex MNI305

is came during Doug's vacation. I believe that those > coords in fsaverage are MNI ones, but he can confirm > > cheers > Bruce > > > On Tue, 31 Jul 2018, Trisanna Sprung-Much wrote: > > >> External Email - Use Caution >> >> Hi there &

[Freesurfer] Fwd: vertex MNI305

External Email - Use Caution Hi there Still waiting for an answer to this! Thanks! Trisanna -- Ph.D. Candidate McGill University Integrated Program in Neuroscience Psychology -- Forwarded message -- From: Trisanna Sprung-Much Date: Thu, Jul 26, 2018 at 7:35 PM

[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 x,y

Re: [Freesurfer] recon-all exited with error

rew > > On Jan 19, 2018, at 10:12 AM, Trisanna Sprung-Much < > trisanna.sprung-m...@mail.mcgill.ca> wrote: > > > > thanks Andrew. I had seen that and will give it a go - just wanted to make > sure that my recipient email would be the FreeSurfer support list. > &g

Re: [Freesurfer] recon-all exited with error

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.mcgill.ca> wrote: > > &

Re: [Freesurfer] recon-all exited with error

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 subject th

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

Re: [Freesurfer] recon-all exited with error

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 > > > > -- > > Ph.D. CandidateMcGill University

Re: [Freesurfer] recon-all exited with error

el2label 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 > (seemed to get to the very end) and t

Re: [Freesurfer] Brodmann areas - exvivo labels

t;> individual size. >> >> Peace, >> >> Matt. >> >> From: on behalf of Trisanna >> Sprung-Much >> >> Reply-To: Freesurfer support list >> Date: Tuesday, October 3, 2017 at 7:36 PM >> To: Freesurfer support list >> Su

[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 surfac

Re: [Freesurfer] Mid point on Freeview

oint at which > red transitions to green (for positive and negative curvature) > > cheers > Bruce > On Thu, 13 > Jul 2017, Trisanna Sprung-Much wrote: > > > Hi there > > I have a question concerning viewing a surface in Freeview (FS 6.0): What > > does the &quo

Re: [Freesurfer] Switch FreeSurfer Desikan-Killiany atlas to Civet

I believe the cortical thickness measures are taken slightly differently. This paper might offer some insights. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4408913/ Trisanna -- Ph.D. Candidate McGill University Integrated Program in Neuroscience Psychology On Fri, Jul 14, 2017 at 8:29 AM, Ant

[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

Re: [Freesurfer] smoothing kernal

ay 24, 2017 at 5:08 PM, Douglas N Greve 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 volumes and have created surfa

[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 is

Re: [Freesurfer] probability maps

2.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 PM,

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 wrote: > what format is your map of p-values in? > On Mon, 15 May 2017, Trisanna > Sprung-Much wrote: > > > Hi Bruce > > I would not

Re: [Freesurfer] probability maps

tty 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 vertex > > coordinates of the ve

[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 -- Ph

Re: [Freesurfer] smoothing kernel

ity 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 > > > > Trisanna > > > >

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

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

in Neuroscience Psychology On Fri, Feb 24, 2017 at 9:45 AM, Bruce Fischl wrote: > Hi Trisanna > > are you sure you aren't running out of disk space? If not, what happens > when you run the mri_convert command directly on the command line? > > cheers > Bruce > On Th

[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 orig.mg

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 K

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 finished without any error? > Some

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 wrote: > Still in 305 > > > On 01/25/2017 06:21 PM, Trisanna Sprung-Much wrote: > > Me again, > > > > Are the fsave

[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 ___ Free

Re: [Freesurfer] Freeview in 6.0 - editing labels

u 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, 2017, at 11:48 AM, Trisanna Sprung-Much

[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 l

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

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 than what 5.3 required, as listed >> here >

[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

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

ut 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 carries over when I try to a

Re: [Freesurfer] mri_average vs mri_concat

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

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] mri_average vs mri_concat

in Neuroscience Psychology On Thu, Oct 6, 2016 at 11:30 AM, Douglas Greve 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: > > Overlays in .mgz format

Re: [Freesurfer] mri_average vs mri_concat

Overlays in .mgz format using mri_vol2surf -- Ph.D. Candidate McGill University Integrated Program in Neuroscience Psychology On Wed, Oct 5, 2016 at 5:56 PM, Douglas N Greve wrote: > what is a labeled vertex? What file format? mgz? annot? > > > On 10/05/2016 05:03 PM, Trisanna

Re: [Freesurfer] mri_average vs mri_concat

as N Greve 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 works without --keep-filetype... :p it

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 wrote: > Dear FreeSurfers, >

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 M

Re: [Freesurfer] Volume to Surface

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.harvard.edu] on behalf of Tri

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 12:41 PM > > *To:* Freesurfer support list > *Subject:* Re: [Free

Re: [Freesurfer] Volume to Surface

s > 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 Trisanna Sprung-Much > [trisanna.

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 M

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] Volume to Surf

Re: [Freesurfer] Volume to 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, September 30, 2016

Re: [Freesurfer] Volume to Surface

g 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, 2016 10:40 AM >

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 create an inflated >

Re: [Freesurfer] license.txt?

istration 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 > > cannot seem to get a

[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 Neur

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.m

Re: [Freesurfer] colour scale

thanks! -- Ph.D. Candidate McGill University Integrated Program in Neuroscience Psychology On Mon, Sep 12, 2016 at 7:24 PM, Ruopeng Wang wrote: > It appears you are running version 5.3. The upcoming 6.0 should fix it. > > On Sep 12, 2016, at 5:34 PM, Trisanna Sprung-Much < > tr

[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 Integrat

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 m

Re: [Freesurfer] Freesurfer 6.0?

n 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 subjects to create better s

[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 Unive

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