Re: [Freesurfer] Calculate WM, GM and CSF volume

Hi Bruce, Yes, I would like to reduce the required calculation time, until desired results are available. Best regards, Iven -Ursprüngliche Nachricht- Von: Bruce Fischl [mailto:fis...@nmr.mgh.harvard.edu] Gesendet: Mittwoch, 20. Juli 2011 15:19 An: Fellhauer, Iven Cc:

[Freesurfer] Defining the Calcarine and distances from it in the Hinds et al. V1 label

Dear All, I've been trying out the automatic V1 labelling using the Hinds et al. (NeuroImage, 2008 vol. 39 (4) pp. 1585-99) and, as far as I can tell it seems to work pretty well on our anatomical scans (In general I'd be interested in the opinions/experiences of others who've tried it). I

Re: [Freesurfer] Pial Edits on Base Template

Hi Jeff, I think you'll have to run with -force. In the newer version 5.1, this is updated so that you don't have to anymore. And you might be right that deleting the folder is not a good idea since the edits were made in there. If you made edits in the cross and want to rerun the base, then

Re: [Freesurfer] Tracula with individual bvecs files

Hi Jürgen - There is no bvecslist option. Currently there is no support for multiple bvecs files in one configuration file but it's certainly something that can be added to the next release. For now you'd have to change the configuration file accordingly for each subject with a different

Re: [Freesurfer] Calculate WM, GM and CSF volume

Hi Iven we don't recommend that as many steps interact. For example, although we don't do it automatically now, we do have procedures for automatically correcting the aseg based on the subsequently created surfaces. cheers Bruce On Thu, 21 Jul 2011, Fellhauer, Iven wrote: Hi Bruce, Yes,

Re: [Freesurfer] Defining the Calcarine and distances from it in the Hinds et al. V1 label

Hi Krish, 1. What do you mean just the calcarine itself? Do you mean the fundus? mris_divide_parcellation can be used to chop the pericalcarine or V1 labels up along it's primary eigenaxis, which is a reasonable approximation to eccentricity. 2. You could draw occipital pole in fsaverage

Re: [Freesurfer] Cortical segmentation error

Hi Bruce, thanks for your explanation. I was thinking the the segmentation region is used to calculate cortical thickness, by the way, is it used for calculate something? such as the GM volumes? I want to know this to be sure if in some point I have to fix this. About the heterotopias, is a good

Re: [Freesurfer] dcm conversion to nii

Hi Antonella, for each acquisition you give mri_convert *one* dicom file in that series and it will figure out the rest. You will then have one volume file per series. Something like: mri_convert one .dcm file in the Ax_PD series) Ax_PD.nii.gz cheers Bruce On Thu, 21 Jul 2011, Antonella

Re: [Freesurfer] Cortical segmentation error

Hi Carolina, no, the aseg cortex/wm is not used for thickness or volume (it can be, but we don't recommend it). The surfaces are. As for the heterotopias, I don't really know what a good output would be. It depends what you want to do with them. I guess they should be gray matter, no?

[Freesurfer] literature about multiple comparison correction

Dear list, Could you please recommend the literature about multiple comparisons correction, especially about Monte-Carlo simulation. Thank you, Tanja. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu

Re: [Freesurfer] literature about multiple comparison correction

Check out hayasaka and nichols 2003. pdf below ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/hayasaka.2003.ni.1014.clustersize.pdf doug Tetiana Dadakova wrote: Dear list, Could you please recommend the literature about multiple comparisons correction, especially about

Re: [Freesurfer] literature about multiple comparison correction

That paper is great. Lazar also has a nice review of a number of approaches in her book: Lazar, N. The statistical analysis of functional MRI data. On 7/21/11 11:39 AM, Douglas N Greve wrote: Check out hayasaka and nichols 2003. pdf below

[Freesurfer] Segmentation Fault during mri_ca_normalize

Hi all, I was having consistent errors with two cases during mri_ca_normalize, and after using an updated version (mri_ca_normalize_centos), one case went through smoothly. I'm having trouble with the second case, however; it now repeatedly reports a segmentation fault partway through

Re: [Freesurfer] Segmentation Fault during mri_ca_normalize

Hi Tali can you email me the nu.mgz, the talairach.lta and the brainmask.mgz? I'll see if I can get it to happen and fix it. thanks Bruce On Thu, 21 Jul 2011, Tali Swisher wrote: Hi all, I was having consistent errors with two cases during mri_ca_normalize, and after using an updated

Re: [Freesurfer] Problem registering labels to native space

Quick update: this fix worked brilliantly. Many thanks for the help, J Richey -Original Message- From: Douglas N Greve [mailto:gr...@nmr.mgh.harvard.edu] Sent: Monday, July 18, 2011 5:20 PM To: John Richey Cc: 'Bruce Fischl'; 'freesurfer@nmr.mgh.harvard.edu' Subject: Re: [Freesurfer]

[Freesurfer] long_mris_slopes error

I received the follow error while running a set of subjects under 'long_mris_slopes,' and wasn't able to decipher the problem. It appears that mris_calc is not able to do the division for these files (dividing by 0 perhaps?). Any help appreciated, here's the command and tail end of

[Freesurfer] trac-all -bedp error

Hi, I run the trac-all bedp process and it comes up with the following errors: 56 slices processed 56 slices processed 57 slices processed Queuing post processing stage 58 slices processed For some reason the bedpostX process DOES NOT appear to have successfully completed. Please examine your

Re: [Freesurfer] trac-all -bedp error

Where is the data? On Thu, 21 Jul 2011, pho...@nmr.mgh.harvard.edu wrote: Hi, I run the trac-all bedp process and it comes up with the following errors: 56 slices processed 56 slices processed 57 slices processed Queuing post processing stage 58 slices processed For some reason the