[Freesurfer] Creation of V1 mask in volume

2017-10-17 Thread Florence Campana
Dear freesurfer experts, I am trying to create a V1 mask in volume, based on the V1 label, in fsaverage space. I use the following command: mri_label2vol --label /Applications/freesurfer/subjects/fsaverage/label/rh.V1.label --temp /Applications/freesurfer/subjects/fsaverage/mri/orig.mgz --hemi

Re: [Freesurfer] Problem flipping a label into other hemisphere

2017-10-17 Thread Neuro Lists
Hi, The one I tested with in the last couple of messages is just the standard bert subject after having done: cd ${SUBJECTS_DIR}/bert cd surf mris_left_right_register lh.sphere rh.sphere lh.sphere.left_right rh.sphere.left_right And then running: cd ../label mris_apply_reg --src-label

Re: [Freesurfer] Problem flipping a label into other hemisphere

2017-10-17 Thread Douglas N Greve
Is this fsaverage or one of your own subjects? On 10/17/2017 02:18 PM, Neuro Lists wrote: > Hi Doug, > Thanks a lot for looking into it. Unfortunately it's still not working > though. > > See here: > https://imgur.com/a/lxXUH > > Thanks again! > > On Mon, Oct 16, 2017 at 12:31 PM, Douglas

[Freesurfer] Advice on covariates in qdec or mri_glmfit

2017-10-17 Thread Jeff Crawford
Hello everyone. I am having trouble understanding the statistical effects of a covariate versus a nuisance factor in freesurfer and I would appreciate some advice. I want to run a correlation between cortical volume and the measurement of an enzyme while covarying for ETICV. In qdec, I select

[Freesurfer] Yeo atlas FreeSurfer

2017-10-17 Thread Martin Juneja
Hi experts, I am using Yeo atlas (7 networks) in my analysis. Where can I find name of all the regions involved in each of these 7 networks in Yeo atlas? Thanks. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu

Re: [Freesurfer] Skull-stripped data submitted on FreeSurfer version 6.0.0

2017-10-17 Thread Duran, Tugce
I think that is the issue. Freesurfer thinks there is brainstem in the skull-stripped image. That’s why it labels whatever gray matter it sees as brain stem. We’ll add the brain stem to the data and run it like that. Thanks! Tugce On 10/17/17, 1:28 PM,

Re: [Freesurfer] Problem flipping a label into other hemisphere

2017-10-17 Thread Neuro Lists
Hi Doug, Thanks a lot for looking into it. Unfortunately it's still not working though. See here: https://imgur.com/a/lxXUH Thanks again! On Mon, Oct 16, 2017 at 12:31 PM, Douglas Greve wrote: > Sorry, try this > > mris_apply_reg --src-label lh.BA45.label --trg

Re: [Freesurfer] Skull-stripped data submitted on FreeSurfer version 6.0.0

2017-10-17 Thread Douglas N Greve
Copy it before you run recon-all and copy it to brainmask.mgz (not to auto). If there is no brainstem, then I think it will fail On 10/17/2017 12:55 PM, Duran, Tugce wrote: > Do you mean after –autorecon1 –noskullstrip done we copy T1.mgz to > brainmask.auto.mgz and a link from

Re: [Freesurfer] Skull-stripped data submitted on FreeSurfer version 6.0.0

2017-10-17 Thread Duran, Tugce
Do you mean after –autorecon1 –noskullstrip done we copy T1.mgz to brainmask.auto.mgz and a link from brainmask.auto.mgz to brainmask.mgz? Because I also did that and saw some cerebral cortex labeled as brain stem. There is no brain-stem in my skull-stripped data. Tugce dur...@iupui.edu On

Re: [Freesurfer] Skull-stripped data submitted on FreeSurfer version 6.0.0

2017-10-17 Thread Douglas N Greve
No, but I think if you copy it to brainmask.mgz that it will then use that On 10/17/2017 12:28 PM, Duran, Tugce wrote: > Is there a flag like –noskullstrip where we can skip brain-stem > parcellation/labeling? > > Tugce > > On 10/17/17, 12:07 PM, "freesurfer-boun...@nmr.mgh.harvard.edu on

Re: [Freesurfer] Skull-stripped data submitted on FreeSurfer version 6.0.0

2017-10-17 Thread Duran, Tugce
Is there a flag like –noskullstrip where we can skip brain-stem parcellation/labeling? Tugce On 10/17/17, 12:07 PM, "freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Douglas N Greve" wrote: if they look

Re: [Freesurfer] lta_convert does not produce ITK transforms that are correctly applied by antsApplyTransforms

2017-10-17 Thread Christopher Markiewicz
Hi Martin, I've uploaded a .tgz file with a T1w volume, BOLD volume, and a valid LTA file. https://gate.nmr.mgh.harvard.edu/filedrop2/?g=7f71pykmv7p Chris From: freesurfer-boun...@nmr.mgh.harvard.edu on behalf of

Re: [Freesurfer] Skull-stripped data submitted on FreeSurfer version 6.0.0

2017-10-17 Thread Douglas N Greve
if they look ok, then I think they are ok On 10/17/2017 12:05 PM, Duran, Tugce wrote: > That is exaclty right! But how did freesurfer respond to that, performing the > skull stripping to skull-stripped data? > Should I trust the results since they looked okay? > > Tugce > > > dur...@iupui.edu

Re: [Freesurfer] Skull-stripped data submitted on FreeSurfer version 6.0.0

2017-10-17 Thread Duran, Tugce
That is exaclty right! But how did freesurfer respond to that, performing the skull stripping to skull-stripped data? Should I trust the results since they looked okay? Tugce dur...@iupui.edu On 10/17/17, 12:00 PM, "freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Douglas N Greve"

Re: [Freesurfer] Skull-stripped data submitted on FreeSurfer version 6.0.0

2017-10-17 Thread Douglas N Greve
if you put -all AFTER the -noskullstrip, then it would have performed the skull stripping On 10/17/2017 10:44 AM, Duran, Tugce wrote: > > Dear FreeSurfer Team, > > I have recently submitted my skull-stripped data into FreeSurfer v6. > Since this is a separate process than the default recon-all

[Freesurfer] Fwd: cortical/subcortical volume based analysis

2017-10-17 Thread miracle ozzoude
-- Forwarded message -- From: miracle ozzoude Date: Sat, Oct 14, 2017 at 3:32 PM Subject: Re: [Freesurfer] cortical/subcortical volume based analysis To: Freesurfer support list Hello Bruce, Thank you for the response. I

[Freesurfer] Fwd: running cross sectional analysis on .long outputs only

2017-10-17 Thread Garret O'Connell
Hello FreeSurfer experts, I am trying to do a cross-sectional baseline analysis from the outputs of the longitudinal processing stream, following the advice on a previous question's thread: https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2016- March/044681.html >From my reading of the

[Freesurfer] Skull-stripped data submitted on FreeSurfer version 6.0.0

2017-10-17 Thread Duran, Tugce
Dear FreeSurfer Team, I have recently submitted my skull-stripped data into FreeSurfer v6. Since this is a separate process than the default recon-all –all, I followed the recommended steps that are posted on the FSwiki website, here is the link for it:

Re: [Freesurfer] lta_convert does not produce ITK transforms that are correctly applied by antsApplyTransforms

2017-10-17 Thread Martin Reuter
Hi Chris, thanks, can you send the images and the exact commands. We have had success in the past, could be that you have a special case (e.g. maybe we never tested registration across different resolutions or whatever?). Thanks, Martin https://gate.nmr.mgh.harvard.edu/filedrop2/

[Freesurfer] Selecting OS for image analysis

2017-10-17 Thread Ramesh Babu
Dear Experts, I have purchased a new pc. I want to use for MRI and EEG analysis by using MATLAB, FSL, SPM, Fresurfer etc,. Which OS is suitable to handle these software? I have NVIDIA graphics card 610 in my system. I am using Ubuntu in another systm and little bit of experience in cent os.