Re: [Freesurfer] longitudinal processing, template and flags

Thanks Martin for your reply, I am agree with you on point 1. What would you say in the case that we are interested in rates of decline from baseline to 12 months, but besides 6 months follow-up we also have 24 months?. Here I see more conceptual problems. In an hypothetical context of severe

Re: [Freesurfer] Troubleshooting - uncertainty about adding control points

Hi Bruce, thanks for your answer! Am 30.01.2014 um 14:40 schrieb Bruce Fischl fis...@nmr.mgh.harvard.edu: Hi Janosch it's impossible to tell from a single slice whether those points should be added or not. The white matter in your image is *very* dark in these regions, do you know why?

Re: [Freesurfer] longitudinal processing, template and flags

Hi Daniel, I'd also include 24 month into both the processing and analysis. It is not really that we are trying to improve a registration here. We are trying to improve segmentation and surface placement of each time point. I'd aways use all data, except there are good reasons to drop (eg strong

Re: [Freesurfer] Longitudinal analysis within one group

Dear Doug and Martin, Thanks a lot. I just have one group including 20 subjects. The scans have been done in a range of 0.9 to 1.5 years difference (tp2-tp1). Is ooh if I use the instructions from Paired Analysis : https://surfer.nmr.mgh.harvard.edu/fswiki/PairedAnalysis ? Regards, Best regards,

Re: [Freesurfer] Troubleshooting - uncertainty about adding control points

Hi Janosch there should be some corrected subjects in the tutorial. The white matter surface shouldn follow the perceived boundary, although it may look wrong when it is when it is curving sharply out of plane. I don't have much experience with MDEFT, so I can't comment on the parameters

Re: [Freesurfer] Longitudinal analysis within one group

Given the different time distances, the best would be mixed effects models. The 2 stage model should also work as it incorporates time (but not different correlations according to time distance). Again I don't see what you are analyzing with only one group. There will always be thinning, and

Re: [Freesurfer] brainmask VS wm correction

Hi Elisa it's tough to tell from just the wm.mgz image. Are the voxels excluded from the pial brain or are they dura? What does the orig surface show? If the orig doesn't follow the wm.mgz and you think it should, that means there is a topological defect that was inaccurately corrected and

Re: [Freesurfer] bbregister and AFNI

On 01/30/2014 06:34 PM, Ajay Kurani wrote: Hi all, I used freesurfer to process my anatomical scans, followed by BBregister to align my resting state scan to the anatomical and finally afni to process the resting state fmri scans. After recon-all I used bbregister: * * *bbregister

Re: [Freesurfer] mri_convert - Scaling of Values

Hi Dan I think specifying -ns 1 will do the trick cheers Bruce On Fri, 31 Jan 2014, Daniel Carey wrote: Dear All, We have been using mri_convert to convert .nii format quantitative scans (specifically R1 volumes) into .mgz (float) format, so they can be used as input to mri_vol2surf.

[Freesurfer] mri_convert - Scaling of Values

Dear All, We have been using mri_convert to convert .nii format quantitative scans (specifically R1 volumes) into .mgz (float) format, so they can be used as input to mri_vol2surf. Inputting the .nii files to mri_vol2surf has produced an error in values in the output paint file, whereas this

Re: [Freesurfer] mri_convert - Scaling of Values

what is your mri_convert command line. Send the terminal output too. doug On 01/31/2014 12:14 PM, Daniel Carey wrote: Dear All, We have been using mri_convert to convert .nii format quantitative scans (specifically R1 volumes) into .mgz (float) format, so they can be used as input to

[Freesurfer] adding color scale to freeview

Dear Freesurfer Experts, Is there a way to create custom color scale - like “Heat”, “Jet”, etc - for use in Freeview? Thanks, Fred Lado Montefiore Medical Center ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu

Re: [Freesurfer] LGI ERROR: make_roi_paths did not complete successfully!

Hi Marie, Yes, I'm using matlab R3013a. In $FREESURFER_HOME/matlab folder I don't have a file called SearchProjectionOnPial.m. Should I create it and paste the updated function? Thanks for your help!! Wanda On 30 January 2014 15:09, Marie Schaer marie.sch...@unige.ch wrote: Hi Wanda,

[Freesurfer] Recon-all error

Hello, I am using recon-all, and it gives me error and exits and I cannot understand why. I would appreciate it if you give me a clue why it's not working. I've written a piece of script (recon.bash attached) to be copied to the subject's folder, and when run it should automatically go through

Re: [Freesurfer] Recon-all error

Emad, please run mri_converrt /Users/louispuybasset/Desktop/Zebouni_Fadi/T1/IM-0002-0001.dcm junk.mgh and send us the terminal output On 01/31/2014 03:28 PM, Emad Ahmadi wrote: Hello, I am using recon-all, and it gives me error and exits and I cannot understand why. I would appreciate it

Re: [Freesurfer] ERROR: dimension mismatch between y and X.

that looks like the right size. I am stumped. What version of FS are you using? Do you have access to other versions? On 01/31/2014 02:50 PM, Wanda Truong wrote: This is what I get: [Vinas-iMac:Wanda_SFS/qdec/Untitled] vinagoghari% ls -l y.mgh -rw-r--r-- 1 vinagoghari staff 1055844047 30

Re: [Freesurfer] LGI ERROR: make_roi_paths did not complete successfully!

Hi Wanda, You should have this function in $FREESURFER_HOME/matlab, the same way you should have compute_lgi.m and many other matlab functions there. Are you sure that you are looking at the correct location and / or that you didn't delete it? Marie On Jan 31, 2014, at 11:32 AM, Wanda