Re: [Freesurfer] trac-all -path Segmentation fault

Hei Er det id 2 og 3 du har problemer med? Det ser ut som at du ikke har kjørt bedpostx på disse to idene og jeg ser at du ikke har kjørt trac-all -prep utifra logfilen . [/work/projects/nn9208k/subjects/LMR/dtitracula/2]: ls dlabel dmri dpath scripts [/work/projects/nn9208k/subjects/LMR/dti

[Freesurfer] hello experts

Hello experts. I have some question to you. I used SurfStat statistical tool to analyze the two group(control, patient) When i click the surf in fsaverage folder and then show up lh.pial and lh.pial_avg. What is the differences between lh.pial and lh.pial_avg ? lh.pial_avg means that real subj

[Freesurfer] tksurfer viewing issues

Hello, I too am having trouble with tksurfer displaying the surfaces upside down and back to front, but believing that they are correctly oriented (i.e. Talairach coordinates change in the wrong direction wrt to the surface but in the correct direction wrt the display window). I"m also running a C

Re: [Freesurfer] mgz file format

No, no PHI gets transferred into the mgz file. On 9/29/16 1:08 AM, prasser wrote: Hi, When using mri_convert to create 001.mgz from dicom that have *not* been anonymized does any patient, institution, study description etc information get transferred into the 001.mgz? Thanks. _

Re: [Freesurfer] REPOST cluster feature extraction from qdec output

Hi, Many thanks for your prompt reply Pr. Greve. I did : mri_glmfit --y /home/damien/bin/freesurfer/subjects/qdec/RH_Dys-CT_CSA_AgeGenderWRCSA/y.mgh --fsgd /home/damien/bin/freesurfer/subjects/qdec/RH_Dys-CT_CSA_AgeGenderWRCSA/qdec.fsgd dods --glmdir /home/damien/bin/freesurfer/subjects/qde

[Freesurfer] Freesurfer compliant pediatric brain template for pediatric brain segmentation using reconall

Hello FreeSurfer experts, I am considering using Freesurfer recon-all for segmentation of T1 brain MRIs of young subjects (1-4 years). I am planning to use a Freesurfer compliant pediatric template to maximize the segmentation accuracy. In the publication titled *A FreeSurfer-compliant consistent

Re: [Freesurfer] tksurfer viewing issues

Hi Paige we have stopped development and most support of tksurfer. Can you use freeview instead or is there still some functionality that you need that is unique to tksurfer? cheers Bruce On Thu, 29 Sep 2016, Paige Scalf wrote: > Hello, > > I too am having trouble with tksurfer displaying the

Re: [Freesurfer] Projecting processed 4D functional data to individual surfaces

I want to project to the native subject surfaces though, not fsaverage. If I use —trgsubject subjID would that work with the —icoorder flag? Alternatively I guess I could project to fsaverage and then use mri_surf2surf to move back to the subject surface, but that seems like a roundabout way t

Re: [Freesurfer] Projecting processed 4D functional data to individual surfaces

Hi Jared the icosahedra are only used to represent average space surface (fsaverage[4-7]), not individual subjects. cheers Bruce On Thu, 29 Sep 2016, Jared P Zimmerman wrote: I want to project to the native subject surfaces though, not fsaverage.  If I use —trgsubject subjID would that wor

Re: [Freesurfer] Projecting processed 4D functional data to individual surfaces

Ahh, thanks Bruce. Is there a way to downsample the subject meshes? -jared > On Sep 29, 2016, at 10:18 AM, Bruce Fischl wrote: > > Hi Jared > > the icosahedra are only used to represent average space surface > (fsaverage[4-7]), not individual subjects. > > cheers > Bruce > On Thu, 29 Sep 20

[Freesurfer] Demeaning of "group" covariate in LME models

Dear all, I am trying to perform a longitudinal statistic by using the LME mass univariate toolbox. I have two groups of subjects (each acquired 3 or 4 times over the follow-up), and I want to test whether atrophy progresses differently over time in these two groups. I followed the tutorial on

[Freesurfer] VM box installation error

Hi, I am a new user and trying to install Freesurfer using the virtualbox installation instructions (windows 7). I have created the virtual machine and can view the VB manager with the correct specific (general, system, display, etc) using the freesurfer image (freesurfer*.vdi). The FreeSur

Re: [Freesurfer] Longitudinal surface analysis of PET data

Dear Freesurfer's experts, Could you answer me about my last question with no response in the mail below ? When using cortical thickness in longitudinal analysis with LME, we used lh.thickness or rh.thickness from -long subject directories. These data followed particular processing steps includin

[Freesurfer] PET/MRI registration failed with bbregister or mri_coreg

Dear Freesurfer's experts, I would like to register PET image onto T1 anatomical. I used bbregister with the following command and it failed : *bbregister --s SUBJID --init-fsl --t2 --mov PET.nii.gz --reg Pet2T1.register.dof6.dat --lta Pet2T1.register.dof6.lta --init-reg-out Pet2T1.init.register.

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

Another bump. On 09/21/2016 04:18 PM, Joel Bruss wrote: > I have two subjects, subA and subB. subA has a binary ROI mask, native > space, that I'd like to place in subB's native space. Both subjects have > been run through all stages of recon, edited, etc. Is there a better or > easier way to ac

Re: [Freesurfer] Infalted/Label

I'll cc the list, which I should have done the first time. No, you didn't do anything wrong. This is what mri_label2label should do - sample these locations onto the surface you specify and fill in the vertex indices. Check the output of label2label and see if it has values >= 0 cheers Bruce On

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

The way you have it configured now, this is a volume-based ROI, so you need to use the volume-based reg method. This will map between the two subjects using the affine (12 dof) talairach registration which will not be as accurate as the surface-based registration. If this is a cortical ROI, I c

Re: [Freesurfer] Projecting processed 4D functional data to individual surfaces

I don't understand what you mean. When you use ico (when it used to work), it always went to fsaverage space. Do you want to decimate the native space surfaces? On 09/29/2016 10:15 AM, Jared P Zimmerman wrote: > I want to project to the native subject surfaces though, not > fsaverage. If I us

Re: [Freesurfer] Demeaning of "group" covariate in LME models

sorry, not sure I understand. Are you coding a catagorical variable as a continuous covariate? What tutorial are you referring to? On 09/29/2016 10:39 AM, Valsasina Paola wrote: > > Dear all, > > I am trying to perform a longitudinal statistic by using the LME mass > univariate toolbox. I have

Re: [Freesurfer] Infalted/Label

This is the output on label2label. The first colum of the created column is -1. mri_label2label --srcsubject segfs --srclabel /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/label/Testing1.label --trgsubject segfs --trglabel Testing1N.label --regmethod volume srclabel = /mnt/netScra

Re: [Freesurfer] REPOST cluster feature extraction from qdec output

1) Sorry, I don't understand what you are trying to do 2) Depends on what you are testing. If you are looking at the slopes of the covariates, then demeaning is not important. If you are looking at group differences, you should first look for a difference in the slopes. If there is no significa

Re: [Freesurfer] Infalted/Label

That is a volume-based label. Try using the --paint option to mri_label2label to convert it to a surface-based label (assuming it is actually on the surface). Run mri_label2label with --help to get an example On 09/29/2016 12:38 PM, Crawford, Anna wrote: > This is the output on label2label. The

Re: [Freesurfer] Infalted/Label

I added the --paint option which seemed to run successfully. I loaded it as a label on the inflated surface and it did not crash, but I do not see it anywhere on the surface. Does this just mean that I didn't actually draw it on the surface? As in, everything was done correct, the location of th

Re: [Freesurfer] Infalted/Label

Sounds like it. View the label on the volume while displaying the surfaces in the volume and see if they intersect On 09/29/2016 01:12 PM, Crawford, Anna wrote: > I added the --paint option which seemed to run successfully. I loaded it as a > label on the inflated surface and it did not crash,

Re: [Freesurfer] Infalted/Label

you can also look at the vertex index of the first entry in the label file and type that into the "cursor" field in freeview so it will go to that point. My guess is that it does intersect the surface, otherwise the label indices would have stayed -1 On Thu, 29 Sep 2016, Douglas N Greve wrote:

Re: [Freesurfer] Infalted/Label

It seems as though I did something else wrong. I am guessing it has to do with dmax (I used inflated as my surface) for the --paint option. I had tried 0,1, and dmax as the input to the option. The new label it created only had 1 entry of all zeros which is why I cannot find it on the surface or

Re: [Freesurfer] Infalted/Label

oh, don't use inflated! The sampling uses the surface to look up the location for the sampling. Use white most likely. The vertex index will allow you to see if on the inflated surface without doing anything else cheers Bruce On Thu, 29 Sep 2016, Crawford, Anna wrote: > It seems as though I di

Re: [Freesurfer] Re Re Re Re: Question regarding mri_convert

I looked at some structures and the absolute differences range from 8-35 mm^3. They are quite small but I was surprised to see any difference since they are the same scan. Thanks, Tamara Hi Tamara can you let us know how big the differences are? thanks Bruce On Wed, 28 Sep 2016, Douglas Greve

Re: [Freesurfer] Infalted/Label

i used dmax white. I now can see it on the inflated surface. Thank you for all your help in getting this working. Sorry, it took so long since I'm trying to figure all of this out still. The next step will be to take a volume that already has a selected region defined and projecting that region

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

Ah, I see. The ROI will be subject-dependent (I want to do this for multiple subjects) but the majority, if not all, should be cortical. Any help you'd be willing to provide would be much appreciated. On 09/29/2016 11:31 AM, Douglas N Greve wrote: > The way you have it configured now, this is a

Re: [Freesurfer] Infalted/Label

glad it worked out Bruce On Thu, 29 Sep 2016, Crawford, Anna wrote: > i used dmax white. I now can see it on the inflated surface. Thank you for > all your help in getting this working. Sorry, it took so long since I'm > trying to figure all of this out still. The next step will be to take a >

[Freesurfer] Cortical thickness using qdec (between scanners)

Hello FS experts, I have a data set of 20 subjects (patients) collected at location-1 with 3T Siemens scanner. Also, I have a set of age-matched 20 subjects (controls) collected at location-2 with 3T Siemens scanner. I am interested in comparing cortical thickness between controls and patients us

Re: [Freesurfer] Cortical thickness using qdec (between scanners)

Hi, Even if the two sites are the same Siemens model, you are going to have difficultly convincing people that any differences you find might not just be a site effect.  In my opinion, this falls into the “not possible at all” category. cheers, -MH --  Michael Harms, Ph

[Freesurfer] Training Tracula to add more pathways

Hi there, As a complete newbie to the Tracula tool, I have a questions about using it. Is it possible to train tracula to track additional pathways other than the 18 thats are already included? I was to track several pathways that are not included with Tracula. Best, Kris ___

Re: [Freesurfer] Projecting processed 4D functional data to individual surfaces

Yeah, I think I misunderstood what was happening with the ico registration. I thought it was using the ico to downsample the subject surface, but I see that this is an atlas space and I can do w/e calculations I need I this space and then register back to subject space after. Thanks for the h

Re: [Freesurfer] Repost: Error using LGI script despite making suggested chages to Matlab script.

Hi, Reposting. Thanks. On Tue, 27 Sep 2016 16:53:21 -0700 prasser wrote Hi, I'm looking to please get some help with -lgi. I'm using matlab R2015b and FS5.3 with recon-all -s subj_id -lgi on os x 10.11. Looking at the output, the first error occurs about here: