[Freesurfer] Mean baseline Cth for each subject in a cluster obtained from a spc analysis

2018-03-12 Thread Fred Sampedro
Dear Freesurfer Experts, I ran a longitudinal Cth analysis and found a cluster with significant spc differences between two groups. It was easy to obtain the mean spc values in that cluster for all the subjects. However, I would also like to have a spreedsheet with the baseline mean Cth values

[Freesurfer] TRACULA -stat coord output file

2018-03-12 Thread Carissa Nicole Weis
Hello, Are the contents of the *.coords.mean.txt file generated from the trac-all -stat command, the average MNI coordinates along the tract across subjects? Or average coordinates in native space? Thanks! Carissa ___ Freesurfer mailing list

Re: [Freesurfer] hew hippocampal and amygdala subfields

2018-03-12 Thread Hoopes, Andrew
Hi Thomas, I have a feeling this issue has been fixed in recent updates, but I’ll need some more info to troubleshoot. Can you send the buildstamp (using the bugr command) for this FS dev version as well as the platform and version of the system you're running it on? thanks Andrew On March

[Freesurfer] FreeSurfer Error Edit Sequence

2018-03-12 Thread David S Lee
Hello Experts, Do you suggest FreeSurfer users to *strictly* follow the *error edit sequence* (Brain Mask --> WM --> GM --> Control Points) listed here (link below)? https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/TroubleshootingData If not, can users follow this sequence instead: Brain

Re: [Freesurfer] Negative areas in mris_sphere, dark in freeview

2018-03-12 Thread Bruce Fischl
Hi Chris we have c code for doing this but no binary that calls it in the way you need. This is the code: int MRISevertSurface(MRI_SURFACE *mris) { int v0, fno; FACE *face; for (fno = 0; fno < mris->nfaces; fno++) { face = >faces[fno]; if (face->ripflag) continue; v0 =

Re: [Freesurfer] TRACULA -stat coord output file

2018-03-12 Thread Yendiki, Anastasia
Hi Carissa – These are MNI coordinates. These mean paths are created only for visualizing group results. However the actual FA, etc measures that are used for group analyses are generated in each subject’s native space. Best, a.y From:

Re: [Freesurfer] FreeSurfer Error Edit Sequence

2018-03-12 Thread Boyd, Emma
Hi David, Please see my response here: https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg57251.html Best Emma From: freesurfer-boun...@nmr.mgh.harvard.edu on behalf of David S Lee

Re: [Freesurfer] Eliminate variable which is the same for all patients from FreeSurfer's Design Matrix

2018-03-12 Thread Douglas N. Greve
Yes, let's say you have 4 groups (eg, gender and sequence) and one covariate (BDI score). If you use a DODS model, then you will have 8 regressors (4 intercepts and 4 slopes). To test for an effect of covariate regressing out the group, then you would have [0 0  0 0 .25 .25 .25 .25] The +0.25

[Freesurfer] mri_vol2surf - what register.dat file to use?

2018-03-12 Thread Charlotte Grosse Wiesmann
Hi Doug, I was trying to map my volume mask from my study-specific average subject template space to the surface (still in my average subject template space) with mri_vol2surf as you suggested below. How d I get the correct register.dat file do do this? I have tried bbregister but am not sure

Re: [Freesurfer] Negative areas in mris_sphere, dark in freeview

2018-03-12 Thread Chris Adamson
So I think I have fixed it. When I swapped the volume used for geometry to radiological from neurological everything worked. -Original Message- From: freesurfer-boun...@nmr.mgh.harvard.edu On Behalf Of Bruce Fischl Sent: Tuesday, 13 March 2018

[Freesurfer] running -hippo-subfields with both T1 and T2 using FS 6.0

2018-03-12 Thread Alexopoulos, Dimitrios
I need a clarification with the command to run for generating the hippo subfields on 6.0 using both a T1 mprage and T2 space (both 1mm isotropic). I'd like to run the entire recon-all -all surface and hippo subfields processing stream. Would this be the correct command: recon-all -s subject

Re: [Freesurfer] Negative areas in mris_sphere, dark in freeview

2018-03-12 Thread Chris Adamson
I had already done this, it had no effect. -Original Message- From: freesurfer-boun...@nmr.mgh.harvard.edu On Behalf Of Bruce Fischl Sent: Tuesday, 13 March 2018 12:39 AM To: Freesurfer support list Subject: Re:

Re: [Freesurfer] Eliminate variable which is the same for all patients from FreeSurfer's Design Matrix

2018-03-12 Thread Kai Ohmstedt
Hi Douglas, thank you for the explanation of the contrasts, this helped a lot! All the best, Kai 2018-03-12 18:20 GMT+01:00 Douglas N. Greve : > Yes, let's say you have 4 groups (eg, gender and sequence) and one > covariate (BDI score). If you use a DODS model, then

Re: [Freesurfer] Negative areas in mris_sphere, dark in freeview

2018-03-12 Thread Bruce Fischl
hmmm, then maybe it is something else? If you email me a surface I'll see if I can find time to take a look. You can also take a look at the surface normal calculation and see if your faces are pointing inwards. I think mris_convert -n will write them out cheers Bruce On Mon, 12 Mar 2018,