[Freesurfer] wmfill problem

Hi surfers,   I experience a problem during the first step of the create surface routine : fill white matter. Specifically, the ponscall.dat file in mri/tmp is empty and at the start of step two (tessellate RH white matter) I'm asked to confirm that "the images in .../mri/filled/COR-0 cannot

Re: [Freesurfer] wmfill problem

you need to use the "volume scanner coords" in tkmedit, not the indices. On Thu, 22 Dec 2005, Sven Panis wrote: Hi surfers, I experience a problem during the first step of the create surface routine : fill white matter. Specifically, the ponscall.dat file in mri/tmp is empty and at the start

[Freesurfer] mri_ca_normalize

Hello, I am having a problem with the mri_ca_normalize step in autorecon2. When I run autorecon2 (in the dev version: recon-all-nmr -subjid avm004 -autorecon2 -nosubcortseg -hemi lh), it gives me a message that norm.mgz is missing, and it seems that the files are not being created (either in

[Freesurfer] Sulcal depth

Hi all, >From my understanding, ?h.sulc can be used to measure sulcal depth. I'm wandering if it is possible to use this to get the depth of a sulcus within an ROI, and if so, how you would extract the relevant measures, i.e.., would it be obtainable through mris_anatomical_stats? Thanks, Alex

Re: [Freesurfer] mri_ca_normalize

Hi Margo, you should be using the talairach.lta file created by mri_em_register (not the talairach.xfm that you have in your command line). cheers, Bruce On Thu, 22 Dec 2005, Margo McKenna Benoit wrote: Hello, I am having a problem with the mri_ca_normalize step in autorecon2. When I run

Re: [Freesurfer] Sulcal depth

not all that easily, although I guess we could write out something from mris_inflate that has the units of mm. On Fri, 23 Dec 2005, Fornito, Alexander wrote: Hi all, From my understanding, ?h.sulc can be used to measure sulcal depth. I'm wandering if it is possible to use this to get the dep

RE: [Freesurfer] Sulcal depth

As far as the cortical thickness of sulci is concerned, the program refers to the cortex in between two giry, right? Thanks, -francesca Francesca Bagnato, MD NIB-NINDS-NIH 10 Center Drive Building 10, Room 5B16 Bethesda, MD, 20892 USA ph #: 001-301-402.6391 fax #: 001-301-402.0373 -Original

RE: [Freesurfer] Sulcal depth

you mean in a parcellation unit? It's whatever the parcellation unit is defined to be. On Thu, 22 Dec 2005, Bagnato, Francesca (NIH/NINDS) [F] wrote: As far as the cortical thickness of sulci is concerned, the program refers to the cortex in between two giry, right? Thanks, -francesca Frances

RE: [Freesurfer] Sulcal depth

Yes, this is what I mean. Thanks, -francesca Francesca Bagnato, MD NIB-NINDS-NIH 10 Center Drive Building 10, Room 5B16 Bethesda, MD, 20892 USA ph #: 001-301-402.6391 fax #: 001-301-402.0373 -Original Message- From: Bruce Fischl [mailto:[EMAIL PROTECTED] Sent: Thursday, December 22, 200

RE: [Freesurfer] Sulcal depth

What it require a lot of work? What would be the odds of somehting like that happening in the near future? :) On another issue, if the .sulc file encodes dinsitguises between sulcal and gyral regions with positive and negative signs, is it possible to extract the thickness of sulcal and gyral r

Re: [Freesurfer] wmfill problem

actually, I think it needs to be talairach coords. The next version will use indicies (and so will be independent of the tal transform). doug > you need to use the "volume scanner coords" in tkmedit, not the indices. > > On Thu, 22 Dec 2005, Sven Panis wrote: > >> Hi surfers, >> >> I experience

RE: [Freesurfer] Sulcal depth

you might be able to use mri_segstats. Give it the thickness file as --in, and use the sulc as the mask and use a threshold of 0 (or close to 0). Note, you might have to convert the thickness and sulc from curv format to mgh (use mri_surf2surf). doug > What it require a lot of work? What would b

RE: [Freesurfer] Sulcal depth

sure, just sum them separately. Would be easy to do in matlab (we did it in our PNAS thickness paper) On Fri, 23 Dec 2005, Fornito, Alexander wrote: What it require a lot of work? What would be the odds of somehting like that happening in the near future? :) On another issue, if the .sulc fil

Re: [Freesurfer] wmfill problem

oh yeah, you're right. Unless no tal exists, in which case it's "volume scanner". On Thu, 22 Dec 2005 [EMAIL PROTECTED] wrote: actually, I think it needs to be talairach coords. The next version will use indicies (and so will be independent of the tal transform). doug you need to use the "

RE: [Freesurfer] Sulcal depth

Famous last words, but seems simple enough. Will give it a try. Would just like to clarify what the columns represent in curvature files after converting to ascii: The first volumn is the vertx id. The next three columns are the xyz co-ords. The rightmost column is the actual 'curvature value', e.

RE: [Freesurfer] Sulcal depth

I think they are volume RAS coords, with 0,0,0 at the center of the volume. I think we distribute a read_label.m or load_label.m that can read it into matlab. On Fri, 23 Dec 2005, Fornito, Alexander wrote: Famous last words, but seems simple enough. Will give it a try. Would just like to clar

RE: [Freesurfer] Sulcal depth

So, read_label could be used to load the label in, and then that could be used to pull out the relevant vertices from the .thickness and .sulc files? Also, is there a straightforward way of converting the final column in the .sulc file into mm (as in mm sulcal depth)? Alex Fornito M.Psych/PhD