[Freesurfer] Longitudinal edits on norm.mgz instead of brainmask

2020-05-17 Thread Elena Pozzi
External Email - Use Caution Dear experts, I have a longitudinal study with 2 time points and I created the base template following the longitudinal tutorial. I open the images to inspect the result and I made some edits to the base. However, I made the edits on the norm.mgz

Re: [Freesurfer] why fsaverage fold is a "link folder"

2020-05-17 Thread Bruce Fischl
because it is a folder we distribute that doesn't change for each study. You can certainly remove the link and cp -r it in from our distribution if you prefer. cheers Bruce On Sun, 17 May 2020, ZhangBo wrote: External Email - Use Caution Hi teams,  For recon-all in

Re: [Freesurfer] DTI and T1 AND T2 WEIGHTED IMAGES

2020-05-17 Thread Bruce Fischl
oh, then check out the bbregister help and see if you can get it working On Sun, 17 May 2020, Amar Shukla wrote: External Email - Use Caution yes  On Sun, May 17, 2020 at 8:54 PM Bruce Fischl wrote: sorry, I'm not sure I understand. bbregister will let you

Re: [Freesurfer] Group Analysis Covariates

2020-05-17 Thread Hua, Jessica
External Email - Use Caution Sure, attached are the files again and here is our previous correspondence: Original question: After running the permutation and finding significant clusters, I am trying to calculate the value for each participant for these significant clusters.

[Freesurfer] why fsaverage fold is a "link folder"

2020-05-17 Thread ZhangBo
External Email - Use Caution Hi teams, For recon-all in parallel, why fsaverage fold is a "link folder"? I run recon-all in one computer (Ubuntu), and copy the result to another computer for analysis. And error happened when I need to use data in fsaverage folder. Thanks

Re: [Freesurfer] DTI and T1 AND T2 WEIGHTED IMAGES

2020-05-17 Thread Amar Shukla
External Email - Use Caution Dear Sir, thank you, Sir, for your valuable advice, Can I register all the t2 types file with a Structural template, cross-registration we can do or not? On Mon, May 11, 2020 at 11:04 PM Douglas N. Greve wrote: > It is probably more up-to-date

Re: [Freesurfer] DTI and T1 AND T2 WEIGHTED IMAGES

2020-05-17 Thread Bruce Fischl
sorry, I'm not sure I understand. bbregister will let you register a T2 to the T1 of the same subject, is that what you want? cheers Bruce On Sun, 17 May 2020, Amar Shukla wrote: External Email - Use Caution Dear Sir, thank you, Sir, for your valuable advice, Can I

Re: [Freesurfer] DTI and T1 AND T2 WEIGHTED IMAGES

2020-05-17 Thread Amar Shukla
External Email - Use Caution yes On Sun, May 17, 2020 at 8:54 PM Bruce Fischl wrote: > sorry, I'm not sure I understand. bbregister will let you register a T2 > to the T1 of the same subject, is that what you want? > > cheers > Bruce > On Sun, 17 May 2020, > Amar Shukla wrote:

Re: [Freesurfer] vol2subfield single time course from multiple regions

2020-05-17 Thread Bruce Fischl
Hi Stefano --replaceonly takes two arguments - the label you want to replace and the one you want to replace it with cheers Bruce On Sun, 17 May 2020, std...@virgilio.it wrote: External Email - Use Caution just a kind reminder many thanks Il 15 maggio 2020 alle

Re: [Freesurfer] Longitudinal edits on norm.mgz instead of brainmask

2020-05-17 Thread Douglas Greve
Which edits did you make? Control points are not linked to a volume and will be applied appropriately. Or did you make edits meant to fix the mask? On 5/17/20 4:29 AM, Elena Pozzi wrote: > External Email - Use Caution > > Dear experts, > > I have a longitudinal study with 2 time points

Re: [Freesurfer] Group Analysis Covariates

2020-05-17 Thread Douglas Greve
And what is your new question? On 5/17/20 12:10 PM, Hua, Jessica wrote: External Email - Use Caution Sure, attached are the files again and here is our previous correspondence: Original question: After running the permutation and finding significant clusters, I am trying to

Re: [Freesurfer] vol2subfield single time course from multiple regions

2020-05-17 Thread stdp82
External Email - Use Caution just a kind reminder many thanks > Il 15 maggio 2020 alle 1.05 std...@virgilio.it ha scritto: > > mri_binarize --i $SUBJECTS_DIR/mri/ThalamicNuclei.v10.T1.mgz > --replaceonly 8204 --replaceonly 8205 --replaceonly 8206 --replaceonly 8217 >

Re: [Freesurfer] Longitudinal edits on norm.mgz instead of brainmask

2020-05-17 Thread Elena Pozzi
External Email - Use Caution Hi Douglas, I added some control points, but also and mostly made edits meant to fix the mask (e.g., deleted some voxels). ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu