[Freesurfer] error while performing recon-all for multiple datasets

Dear All, I want to run recon-all for multiple subjects. I named my sbjects as SZ01.nii, SZ02.nii etc. After setting the cd and environmanet variable, I ran using following for loop: for x in * do recon-all -i SZ*.nii -s $x -all done I got the following error: WHAT MIGHT BE THE REASON FOR THE

Re: [Freesurfer] How to calcutate Brain volume?

Dear All,   I went thru the link suggested by Mr. Cedric.https://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/2009-February/009600.html From that mail I understood how to create the label for multiple subjects. I already created a DLPFC for one individual. I want to know how to measure the

[Freesurfer] Problems with Saving Segmentation

Hello, I have troubles with saving my files, after I did some segmentation changes. I think this could be related to a problem, which I have, when I load the brainmask: libGL error: failed to load driver: nouveau libGL error: Try again with LIBGL_DEBUG=verbose for more details. This is

[Freesurfer] mri_segstats SNR calculation

Dear Freesurfers, After running the first tests of freesurfer 5.2, I found a file named $hemi.w-g.pct.stats on the stats folder. The last column of the file is a SNR calculation, i found on the help manual, that is required to add --snr to perform this calculation. I'm interested to know how

Re: [Freesurfer] Autoreg-sess and mri_surf2vol

Hi,  Sorry for the answer too late.  I tried the command to evaluate the RMS distance but I just get the difference between the 2 surfaces in terms of faces and vertices.  But I would compare my 2 surfaces by calculating the euler characteristic ( vertices-edges+ faces) .  Thank you so much

[Freesurfer] Thank you

Hi everyone, I would just say you thank you for the help you give to Freesurfer users. I use Freesurfer for my school project and I ended yesterday. I didn't know anything about Linux before and before segmentation software of cortical surface. I don't think I would did an so great job

[Freesurfer] autorecon2-cp error

Hi freesurfer, my autorecon2-cp after ctrl pts edits exited with this error message: CORRECTING DEFECT 0 (vertices=176788, convex hull=8149) Excessive topologic defect encountered: could not allocate -776253752 edges for retessellation Cannot allocate memory Could anyone help me with this,

Re: [Freesurfer] error while performing recon-all for multiple datasets

Hi Anupa you need to specify each input volume with -i if there are more than one. In your example you would need an inner loop of the form set inputs = () foreach vol (SZ*.nii) set input = ($inputs -i $vol) end recon-all $inputs ... cheers Bruce On Wed, 17 Apr 2013, Anupa AV wrote:

Re: [Freesurfer] autorecon2-cp error

Hi Claudia that defect is bigger than more cortical surfaces so something is dramatically wrong. Did you check any of the outputs (wm.mgz, filled.mgz, lh.orig, etc...)? cheers Bruce On Thu, 18 Apr 2013, Claudia Dacquino wrote: Hi freesurfer,  my autorecon2-cp after ctrl pts edits exited

Re: [Freesurfer] Hippo-subfields

Thank you for your answer, Juan. Yes, I want a surface of the whole hippocampus and I thought I had just obtained that using freeview and adding all hippo-subfield files. That resulted in the screenshot I previously attached. I just do not know how I can save the resultant surface. After I

Re: [Freesurfer] Hippo-subfields

I agree with Bruce. You can use MRIread.m to read in the data. Regarding the other question: first you need to combine the posteriors of all the subfields into a single posterior for the whole hippocampus. You can do that like this: mri_concat posterior_fimbria.mgz posterior_CA1.mgz ... --sum

Re: [Freesurfer] QDEC questions

Apologies for my previous long email; if anyone gets a chance to look over the questions I'd be really grateful! Many thanks indeed, Tudor On 16 April 2013 19:40, Tudor Popescu tud...@gmail.com wrote: Thanks Nick, (and thanks Doug too for the answer to question 2.) It must indeed have been a

Re: [Freesurfer] QDEC questions

Here's part 1. I'll write until I have to catch my shuttle, answer the rest tomorrow ... On 04/18/2013 05:27 PM, Tudor Popescu wrote: Apologies for my previous long email; if anyone gets a chance to look over the questions I'd be really grateful! Many thanks indeed, Tudor On 16 April

[Freesurfer] How to set the -retinotopy number in mkanalysis-sess due to different cycle time in the eccen and polar

Dear Doug, I want you could give me some guidances with my retinotopic analysis. Eccen run: TR 2 Ncycles 6, 64 sec per cycle, all scan 384 sec. Polar run: TR 2, then follow Ncycles 10, 32 sec per cycle, all scan 320 sec. I write the rtopy.par: stimtype polar diretion neg ncycles 10 and