Re: [Freesurfer] Skullstrip error issue

Hi Rashmi, I assume you've read the skullstrip wiki page, but I've included it below just in case. Have you tried different watershed thresholds? Also, you do not need to include the -clean-bm flag every time. You can run the skullstrip step once with the -clean-bm to start from scratch, and

Re: [Freesurfer] Freesurfer and FSL

I'm not sure about this, but probably the doctors use the same methods for left-hippocampus and right-hippocampus. The softwares, FSL and Freesurfer, don't have a different away to operate in either hippocampus. Do you agree? That way of operating confuses me on how to interpret the differences

Re: [Freesurfer] Freesurfer and FSL

Hi Ana yes, our Neuron (2002) and NeuroImage (2004) papers describe the techniques. cheers Bruce On Wed, 3 Oct 2012, Ana Arruda wrote: I'm not sure about this, but probably the doctors use the same methods for left-hippocampus and right-hippocampus. The softwares,  FSL and Freesurfer, don't

[Freesurfer] cortical parcellation question

Dear experts, I have a couple of questions regarding the cortical parcellation atlas that is used in Freesurfer: 1) I would like to know if it is possible to obtain the Desikan-Killiany atlas in 3D analyze/nifti format. With each region of the brain assigned a discrete integer number (for

Re: [Freesurfer] cortical parcellation question

Hi Daniel, 1. Do you mean the atlas or the parcellation of your subjects? We cannot distribute the individual subjects in the atlas as the data was collected under an IRB long ago that didn't include this. The atlas itself (summary statistics derived from those subjects) is included in the

Re: [Freesurfer] Freesurfer and FSL

Thank you very much! About the previous question, do the softwares use the same criteria for each hippocampus? ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in

Re: [Freesurfer] Freesurfer and FSL

kind of. There are natural lateralizations in the brain that are taken into account. Not sure what is known about lateralizations of hippocampal subfield and white matter components though Bruce On Wed, 3 Oct 2012, Ana Arruda wrote: Thank you very much! About the previous question, do

Re: [Freesurfer] Freesurfer and FSL

I haven't gone so far. I've just done the simplest way. I've search the proper commands just to do the hippocampus segmentation, but not its subfields. All my analysis was made with the left and right-hippocampus volumes from the *aseg.stats *file. ___

Re: [Freesurfer] Freesurfer and FSL

Hi Ana the point is that even if you aren't segmenting individual structures, if some are not in your manual protocol but are in ours, then lateralization in them will cause lateralization differences in the degree of overlap between the two cheers Bruce On Wed, 3 Oct 2012, Ana Arruda

Re: [Freesurfer] Freesurfer and FSL

Yes, you're right. But in that case, these changes would be quite similar for right-hippocampus too. Based on my analysis and literature, Freesurfer has more accurate measures than FSL. The doctors are quite conservative about boundaries so that measures are the smallest between Freesurfer and

[Freesurfer] long_mris_slopes error

Dear Freesurfer Experts, While performing the long_mris_slopes cmd, we receive an error: --- SUBJECT pls_pd_base00 Running Within-Subject GLM Writing ./tmp-pls_pd_base00_lh_thickness_Rx7HLs/X-long.mat ... mri_glmfit --y

[Freesurfer] Configuring freesurfer developer's environment on Ubuntu

Hello freesurfer users! I've got a brand new PC with Ubuntu 12.04 64-bit running and following the freesurfer developer's guide to set up a developer environment, I'm getting numerous undeclared function / undefined type errors during make. Seeing that the undeclared functions or variable types

Re: [Freesurfer] Configuring freesurfer developer's environment on Ubuntu

I am running the freesufer on ubuntu and working fine without any other configuration. I followed the configuration and it is simple http://mirko.windhoff.net/how_to/install_freesurfer_on_ubuntu azeez From: dkim...@cw.bc.ca To: freesurfer@nmr.mgh.harvard.edu Date: Wed, 3 Oct 2012 13:03:49

[Freesurfer] A question about downsmapling mulitple surfaces (white, pial, sphere) for registration

Hi, FreeSurfer experts Currently, I am planning to run tractography using wm surfaces as seed masks and pial surfaces as stop masks implemented in FSL. In order to make fibers go through one hemisphere to another, I need to remove the medial wall from both seed surfaces and the pial surfaces.

Re: [Freesurfer] long_mris_slopes error

Not sure. Maybe try the updated scripts From http://martinos.org/~mreuter/long/ Best Martin Alexandru Hanganu al.hang...@yahoo.ca wrote: Dear Freesurfer Experts, While performing the long_mris_slopes cmd, we receive an error: --- SUBJECT pls_pd_base00

[Freesurfer] mris_pmake options

Dear all, I need to measure the distance between 2 points on the same hemisphere for subject A, in the common surface space as I have to compare it with the distance between other 2 points for subjects B, C... I used mris_pmake --subject A --hemi rh --surface0 sphere.reg --curv0 sulc --curv1

[Freesurfer] is skull strip needed

if there is extra skull left after skull stripping but the pial surface is fine ( i.e. the left skull did not get included in the pial surface ) is it nessesary to adjust watershed parameters or manually remove it and reprocess the data set ? I am thinking it is not needed if it is not

[Freesurfer] subdividing consistently within aparc.annot

hi bruce, is there a way to divide consistently (same number of regions and one to one correspondence - obviously not the exact same areas) across subjects within aparc regions? cheers, satra ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu

Re: [Freesurfer] subdividing consistently within aparc.annot

Would the Lausanne2008 template from the connectome mapping toolkit not do the trick? http://nipy.sourceforge.net/nipype/users/examples/dmri_connectivity_advanced.html On 3 October 2012 23:18, Satrajit Ghosh sa...@mit.edu wrote: hi bruce, is there a way to divide consistently (same number

Re: [Freesurfer] More than two time-points in longitudinal base = Memory allocation error?

Liz, a 64bit build is in the works. in the meantime, you can get a version of mri_robust_register built for lion (64b) here: ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/misc/macos-lion/ Nick On Tue, 2012-10-02 at 12:12 -0400, Martin Reuter wrote: Hi Liz, I have no idea about

Re: [Freesurfer] subdividing consistently within aparc.annot

hi john, thanks. that's the idea, but what i want is that sub-division is done within regions that are either determined automatically through the freesurfer classifier or through manual parcellations. not a fixed template of parcels that's transferred via the spherical registration. cheers,

[Freesurfer] fixing the talairach.xfm

Hi, I have a few very basic clarification questions regarding the recon-all processing pipeline. I am currently following the instructions here: http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Talairach Near the end of the page, it instructs me to rerun the whole process using my new

Re: [Freesurfer] fixing the talairach.xfm

Hi Eric, the talairach.xfm will not be overwritten. When run recon-all the first time, it creates two files: talairach.auto.xfm and talairach.xfm, which have the same contents. When you edit the registration, it changes the talairach.xfm. When recon-all is run again, it sees that the

Re: [Freesurfer] cortical parcellation question

Thanks Bruce, When you say the atlas itself is included in the Freesurfer distribution, do you mean there is a 3D version of it available in the download? Also, I am not looking for the individual subjects' images, I just want a copy of the final atlas as a 3D image in analyze/nifti format.