Re: [Freesurfer] Fwd: Inflated and Spherical Morphing --- Step by step surfaces

Ok, but how about the mophing process? Isn't inflated brain transformed to the sphere directly? Is there a middle step that is hidden (e.g. inflatted to the brain flat maps and spreading these maps over the sphere)? I want to generate a contineous transformation video from WM to inflated and inflat

Re: [Freesurfer] Fwd: Inflated and Spherical Morphing --- Step by step surfaces

yes, because it is unfolding on the sphere to recover metric properties. -w 1 gives you every iteration. You will need to show curvature or you won't see anything On Thu, 6 Aug 2015, Saeed Mahdizadeh Bakhshmand wrote: > Hello, > What are your suggested values for w and n in mris_sphere? I set

[Freesurfer] Announcing PySurfer version 0.6

Hello everyone, We are pleased to announce the 0.6 release of PySurfer , a Python library for visualizing MRI and MEG data. Changes in this version include: - Simplified the selection of parameters that customize the visualization - Enhanced plotting of Freesurfer mor

Re: [Freesurfer] Fwd: Inflated and Spherical Morphing --- Step by step surfaces

Hello, What are your suggested values for *w* and *n* in *mris_sphere*? I set *w* to 5 and all of the iterations are spheres! Thanks, Saeed On Wed, Aug 5, 2015 at 1:06 PM, Bruce Fischl wrote: > Hi Saeed > > if you specify -w to mris_inflate or mris_sphere it will save snapshots > of the proce

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] mkanalysis-sess, timewindow

The second number in the psdwin parameter is set as 40 in the flac_ev_parse.m for 'spmhrf', 'gamma', 'fslgamma'. It seems that timewindow has no effect on hrf? why is psdwin 40? Thanks, Xiaomin From: yu...@hotmail.com To: freesurfer@nmr.mgh.harvard.edu Date: Thu, 6 Aug 2015 15:17:04 -0400 Su

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

[Freesurfer] FSFAST

Hi all,If I understand correctly, preproc-sess command takes mid point of EPI image as reference and make template and calculate motion parameters. I could not figure if I could use different image as reference, is it possible? Cheers, Sabin Khadka___

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] (no subject)

Hello, Thank you for the report. Can you please provide a simplified context of how this came about... meaning, does the crash ONLY occur when you alter the contents of a file? Does the crash ever occur during a normal recon? Many files in freesurfer are read on a bite-wise basis and if the co

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] how to obtain sulcal depth in a given region for a specific subject

Thanks so much for your help!! - Daniel On 8/6/15, 3:06 PM, "freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Bruce Fischl" wrote: >ignore grayvol, the other two will be the mean and standard deviation of >the sulc > >cheers >Bruce >On Thu, 6 Aug 2015, Yang, Daniel wrote: > >> Hi Bruce, >> >

Re: [Freesurfer] Weird Freesurfer results

Thanks, Dr. Fischl. Original image and recon: + brainmask.mgz (1.27 MiB) < http://gate.nmr.mgh.harvard.edu/filedrop2/?p=agy57k1qjyh> + lh.pial (4.33 MiB) < http://gate.nmr.mgh.harvard.edu/filedrop2/?p=1k79w4nsitw> + lh.white (4.33 MiB) < http://gate.nmr.mgh.harvard.edu/filedrop2/?p=90gq0da66ar>

Re: [Freesurfer] mkanalysis-sess, timewindow

Hi, Doug, Thanks for your response. Here is my command: mkanalysis-sess -fsd bold -paradigm xy_mky_category_eye_weights.par -event-related -refeventdur 1 -timewindow 10 -TER 2 -no-inorm -delay 0 -polyfit 3 -gammafit 0 8 -gammaexp 0.3 -nuisreg mcprextreg 3 -nuisreg eye_movTR_xy 2 -nuisreg fsl_

Re: [Freesurfer] mkanalysis-sess, timewindow

if it is useful, i can upload the Xtmp.mat file. thanks, Xiaomin > Date: Thu, 6 Aug 2015 10:36:50 -0400 > From: gr...@nmr.mgh.harvard.edu > To: freesurfer@nmr.mgh.harvard.edu > Subject: Re: [Freesurfer] mkanalysis-sess, timewindow > > it would be helpful to have your mkanalysis-sess command >

Re: [Freesurfer] Changing Color Labels

use nearest neighbor interpolation. Also, probabaly better to use mri_label2vol instead On 08/06/2015 02:17 PM, Owais Syed wrote: > Hi freesurfer experts! > > Sorry if this is a basic question, but I have a manual parcellations > for the cortex of the temporal lobe. The problem is that since my

Re: [Freesurfer] how to obtain sulcal depth in a given region for a specific subject

ignore grayvol, the other two will be the mean and standard deviation of the sulc cheers Bruce On Thu, 6 Aug 2015, Yang, Daniel wrote: > Hi Bruce, > > Thanks so much! From the output of mris_anatomical_stats, I can see that > it affects the following three variables: > > GrayVol ThickAvg ThickSt

Re: [Freesurfer] how to obtain sulcal depth in a given region for a specific subject

Hi Bruce, Thanks so much! From the output of mris_anatomical_stats, I can see that it affects the following three variables: GrayVol ThickAvg ThickStd When sulc is used instead of thickness, do you know what the meaning of these three variables is changed to? Many thanks, Daniel On 8/6/15, 1:3

[Freesurfer] Changing Color Labels

Hi freesurfer experts! Sorry if this is a basic question, but I have a manual parcellations for the cortex of the temporal lobe. The problem is that since my voxel size is <0.38, 0.38, 0.38>, I converted it to 1 mm voxel size (which I did using mri_convert -c) so that I can compare it to, but the

Re: [Freesurfer] wm parcellation freesurfer

That was it! (and yes, we were trying to have freesurfer do an autoparcellation for higher resolution MRI, but the full reconstruction unfortunately keeps failing on processes like skull strip). But for now, we will use the 1 mm reconstruction. Thank you for the help! Owais On Mon, Aug 3, 2015 at

Re: [Freesurfer] Fornix Segmentation

Yes, I was able to locate that file. Thank again! Don't know how I managed to miss it the first time! Regards,Maryam On Thursday, August 6, 2015 1:35 PM, Bruce Fischl wrote: does it not say "writing fornix to mri/fornix.mgz" and write out a separate file? The other thing you cou

Re: [Freesurfer] Weird Freesurfer results

Hi Brent if you upload the subjects and point us at the specific locations you expect to see effects and the ones you don't we will take a look cheers Bruce On Thu, 6 Aug 2015, Brent Womble wrote: So I'm making changes to the intensity values in a specific area (a sphere or several slices

Re: [Freesurfer] how to obtain sulcal depth in a given region for a specific subject

sure, you can use mris_anatomical_stats with the label (-l) and specify sulc instead of thickness on the command line Bruce On Thu, 6 Aug 2015, Yang, Daniel wrote: > Dear FreeSurfer Experts, > > Is there a way to obtain sulcal depth in a given region (label) for a > particular subject? > > Man

Re: [Freesurfer] Fornix Segmentation

does it not say "writing fornix to mri/fornix.mgz" and write out a separate file? The other thing you could consider is using tracula for this, which I think will work even in the absence of diffusion data. cheers Bruce On Thu, 6 Aug 2015, Syeda Maryam wrote: > Hi Bruce, > > Thanks so much

[Freesurfer] how to obtain sulcal depth in a given region for a specific subject

Dear FreeSurfer Experts, Is there a way to obtain sulcal depth in a given region (label) for a particular subject? Many thanks! Daniel ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurf

Re: [Freesurfer] Fornix Segmentation

Hi Bruce, Thanks so much for getting back to me on this! Yes, I have tried mri_cc with -f and I am able to view part of the fornix along with the corpus callosum when I call up the appropriate labels. However, I don't seem to be able to visualize the two structures separately. Is it possible to

Re: [Freesurfer] Fornix Segmentation

Hi Maryam try specifying -f on the mri_cc command line (as the first option) cheers Bruce On Thu, 6 Aug 2015, Syeda Maryam wrote: > Hi everyone, > > So I've been going through the list trying to see if someone has encountered > the same problem as me with regards to segmentation of the fornix

[Freesurfer] Fornix Segmentation

Hi everyone, So I've been going through the list trying to see if someone has encountered the same problem as me with regards to segmentation of the fornix but have not found a solution as yet. I'm a grad student and still relatively new to freesurfer. My research group is using freesurfer to s

Re: [Freesurfer] mkanalysis-sess, timewindow

it would be helpful to have your mkanalysis-sess command On 08/05/2015 04:17 PM, Xiaomin Yue wrote: > Hi, > > I set timewindow to 10 in the mkanalysis-sess. When I loaded Xtmp.mat > in to maltlab, then plot(flac.ev(2).Xirf), the size of the > flac.ev(2).Xirf is 20 points, which is corrected bec

Re: [Freesurfer] mri_convert IMA to MGZ

On 08/05/2015 04:24 PM, Borzello, Mia wrote: > Hi freesurfers, > > I want to localize electrode locations from a NHP CT scan, am i able > to do that with tkmedit without coregistering first? I don't need all > the parcellations of a specific atlas, just the RAS coordinates. Yes > > Also, the CT

Re: [Freesurfer] ID-swapping freesurfer data?

We don't have tools to explicitly change those strings. You can read them into matlab as Bruce suggests. You can also convert them to nifti and then back to mgz. On 08/05/2015 05:07 PM, Nate Vack wrote: > Thanks! > > One complication I'm seeing is that when I uncompress, say, an .mgz > file, th