Re: [Freesurfer] Autorecon 1 y autorecon 2

Hi Kelly, the analysis of your subject is failing at the point of registration to the Talairach space. Since the status of the registration is FAILED, I would certainly check the result and follow instructions on how to proceed, as explained on the following web-page: http://surfer.nmr.mgh.har

[Freesurfer] vertex wise correction for multiple comparisons using permutation

Dear Freesurfers, I'd like to correct for multiple comparisons vertex-wise instead of cluster-wise. Is it possible to do this using permutation (and not FDR)? I've seen in an e-mail from last year that the values of maximum statistic stored in the CSD file could be used for this purpose, and I'd b

Re: [Freesurfer] Creating a file with discrete locations with Freesurfer

Hi Andres, I'm not sure I understand. What discrete set of points are you talking about? A downsampling of the surface? If so, I think Matti (ccd) knows how to do this. cheers, Bruce On Wed, 3 Dec 2008, Andres Felipe Salazar Gomez wrote: Good evening freesurfer list, I need to create a te

Re: [Freesurfer] recon-all rerun

Hello, A clarification about this (based on my understanding/reading of the recon-all code) to help avoid any potential confusion about how the - clean-bm flag operates more generally: If you rerun the skull stripping without the -clean-bm flag, recon-all will preserve any edits previously made

Re: [Freesurfer] Creating a file with discrete locations with Freesurfer

Thank you Bruce, I want to do source localization based not on the cortex surface sources but on discrete sources located in specific places in deeper structures (brainstem). I will contact Matti then. Thanks again, -- Andrés > Hi Andres, > > I'm not sure I understand. What discrete set of poi

[Freesurfer] missing information in volume headers

Dear freesurfer gurus, I noticed something unusual in some of our data today. When the command mri_info was run on some of the orig.mgz volumes the values listed for echo time and flip angle in some of the scans were 0.00, even though there was a listing for repetition time. What could have c

Re: [Freesurfer] missing information in volume headers

It was likely converted thru an intermediate format that did not retain those values (eg, nifti or analyze) before being imported into freesurfer. Jared Price wrote: Dear freesurfer gurus, I noticed something unusual in some of our data today. When the command mri_info was run on some of the

Re: [Freesurfer] vertex wise correction for multiple comparisons using permutation

Yes, the max stat is stored in the CSD, and it's purpose is to enable voxel-wise correction, but I've never gotten around to it (and this is the 1st request:). You might be able to program something in matlab pretty quickly. You can use FS's load_csd.m to load the CSD file, and MRIread() to l

Re: [Freesurfer] missing information in volume headers

Hi Jared, if you converted it from a format that doesn't store this info (e.g. analyze). It won't change anything in the standard stream though Bruce On Thu, 4 Dec 2008, Jared Price wrote: Dear freesurfer gurus, I noticed something unusual in some of our data today. When the command mri_in

[Freesurfer] quick follow-up

Will missing header info affect the rebuild_gca_atlas script? I noticed it didn't like it if echo time, repetition time etc. didn't match. Also, I assume there is no difference, or minimal enough difference to ignore, in the 001.mgz file when converted from say nifti or straight from dicom.

Re: [Freesurfer] quick follow-up

it should be fine, although you may have to insert the info to disable the sanity check On Thu, 4 Dec 2008, Jared Price wrote: Will missing header info affect the rebuild_gca_atlas script? I noticed it didn't like it if echo time, repetition time etc. didn't match. Also, I assume there is no

[Freesurfer] stable3

Hello! I was just wondering if there is anything going on with the stable3 environment, or any changes currently being tweaked. The reason is that I have a script for analysis that sometimes says "ispl failed" which usually resolves itself if I wait a day or two, but hasnt resolved as of yet. T

Re: [Freesurfer] mri_ca_normalize infinite loop

Hi Mishkin if you put the subject on our site we'll take a look. cheers, Bruce On Thu, 4 Dec 2008, Mishkin Derakhshan wrote: Hi, I have one subject which seems to cause mri_ca_normalize to hang. I've checked and the registration to tal is okay, as is the brainmask. The subject in question do

[Freesurfer] a display problem

Hi Freesurfer expert, I just started to use freesurfer. I tried to follow the instruction to learn how to use "tksurfer". However, when I type "tksurfer bert lh inflated". Only a very small part of brain was showed (see the attachement). I do not know the reason. Could you please do me a favor and

[Freesurfer] questions about region-wise analysis data

Hi everyone, while the machine is busy crunching through our data set, i would like to prepare myself from the next step of the analysis, which is a region-wise analysis of the computed metrics by the freesurfer pipeline. Being a complete novice in the use of this software, i wou