Re: [Freesurfer] error creating template (base) for longitudinal analysis

Hi Bente, so you did process subjectname_pre_nii and subjectname_post_dicom independently with freesurfer (recon-all)? You should have those directories in you subjects dir. I have never seen the error you are getting. Can you send me the full recon-all.log to see at what step it is failing? In

Re: [Freesurfer] Fixing Talairach.lta

To check it with tkregister2, you can: tkregister2 --mov $FREESURFER_HOME/average/RB_all_2008-03-26.gca \ --targ ../brainmask.mgz --lta-inv talairach.lta --reg talairach.lta.reg.dat \ --surfs --s $subject I don't have anyway to actually save the result at this time. doug Jeff Sadino wrote

Re: [Freesurfer] cvs_avg35

Hi Antonella, 1) Can you please help me find or get the the cvs_avg35/mri/norm.mgz? I saw online the same question was posted on June 2011 but there is no answer for the question online: http://www.opensubscriber.com/message/freesurfer@nmr.mgh.harvard.edu/15506607.html Have you run the cvs

Re: [Freesurfer] Fixing Talairach.lta

Hi Jeff, yes, you should be able to use the 5.1 talairach.lta with 5.0. Make sure you rerun everything forward from the talairach.lta step cheers Bruce On Thu, 17 Nov 2011, Jeff Sadino wrote: Hello, I have several subjects with bad surfaces in fs 5.0.0.  After checking their talairach.lta

Re: [Freesurfer] mri_surf2surf ico to ico

Hi Don, I found the problem (which is that it skips loading the target surface when the source and target subjects are the same; it now verifies that the ico order is also the same and loads the target surface if not). You can get the new version from here: ftp://surfer.nmr.mgh.harvard.edu/trans

[Freesurfer] Fixing Talairach.lta

Hello, I have several subjects with bad surfaces in fs 5.0.0. After checking their talairach.lta file, these transforms are all bad. I tried using tkregister2 to create a good talairach.lta file, but it just wasn't working. I tried rerunning these subjects in fs 5.1.0, and their talairach.lta f

Re: [Freesurfer] Motion in anatomical images

Hi Cynthia motion in 3D anatomical scans doesn't work the same way as in 2D functional scans since the data is being acquired in spatial frequency ("k-space"), not in space. There are sequences around that compensate for motion, including one recently developed at MGH by M Dylan Tisdall and And

[Freesurfer] Motion in anatomical images

Hello, I am wondering whether there is any way to compensate for motion in anatomical images (for the purposes of salvaging data for cortical thickness analysis)? If not, is there a general rule of thumb or some way to tell how much motion is too much for this type of analysis? Or is it more of

Re: [Freesurfer] mri_surf2surf ico to ico

My suggested work-around in my earlier email does not actually work. It outputs as ico7 even though my "average" subject is ico3. From: dhagle...@hotmail.com To: freesurfer@nmr.mgh.harvard.edu Date: Thu, 17 Nov 2011 11:52:22 -0800 Subject: [Freesurfer] mri_surf2surf ico to ico I am tryi

[Freesurfer] error creating template (base) for longitudinal analysis

Dear FS-experts, I'm doing a longitudinal comparison of cortical thickness and am therefore following the steps of the longitudinal stream on the freesurfer wiki. I've created templates for all of my subjects but one, for which I received an error message trying to create the template (or base)

[Freesurfer] mri_surf2surf ico to ico

I am trying to use mri_surf2surf to resample surface data in mgh format from ico4 to ico3. There is an apparent bug, however, in that the output file has the same dimensions as the input file despite srcicoorder = 4 and trgicoorder = 3. I am using ico for both srcsubject and trgsubject. This

Re: [Freesurfer] read_fscolorlut

thanks Don, I put your fix in Bruce On Thu, 17 Nov 2011, Don Hagler wrote: FYI, in version 5.1.0, FreeSurferColorLUT.txt has a space (" ") instead of an empty line at line 1189.  This causes the matlab funciton read_fscolorlut to throw an error. An easy fix is to change this line:     if(~isem

[Freesurfer] read_fscolorlut

FYI, in version 5.1.0, FreeSurferColorLUT.txt has a space (" ") instead of an empty line at line 1189. This causes the matlab funciton read_fscolorlut to throw an error. An easy fix is to change this line: if(~isempty(tline) & tline(1) ~= '#') break; end to this: if(~isempty(deblank(t

Re: [Freesurfer] Hippocampal Sub field segmentation

Hi All, There is a large variability between labs. An extensive effort has begun for produce a "Harmonized Protocol for Hippocampal Volumetry", see: http://www.hippocampal-protocol.net/SOPs/index.html This group has been working on this goal for a few years. Good resources at their site, par

Re: [Freesurfer] Hippocampal Sub field segmentation

Hi Joshua I'll cc Jean Augustinack and Stephan Heckers, who I know have opinions on this issue :) cheers Bruce On Thu, 17 Nov 2011, Joshua Lee wrote: There is great variability between the different segmentation protocols used by different research groups, and I think people are eager for

Re: [Freesurfer] Hippocampal Sub field segmentation

There is great variability between the different segmentation protocols used by different research groups, and I think people are eager for a standard to facilitate comparison and replication. By becoming part of Freesurfer, I suspect that your segmentation algorithm will become that standard. Luc

Re: [Freesurfer] Hippocampal Sub field segmentation

Hi Joshua, I'm not a neuroanatomist so I can't really answer that question. My aim has just been to replicate what a human expert has given us as segmentation examples on a number of different subjects. I know that different labs follow very different conventions for labeling the subfields manual

Re: [Freesurfer] Hippocampal Sub field segmentation

At least by my reading of the Duvernoy Human Hippocampus atlas, the most anterior and posterior extents of the hippocmapus (perhaps just a slice at the tips in most scans) are almost entirely composed of the CA1 subfield. Thoughts? Joshua - Joshua Lee Graduate Student Center for Mind and Brain & D

Re: [Freesurfer] Hippocampal Sub field segmentation

Thanks Koen. On Thu, Nov 17, 2011 at 6:14 AM, Koen Van Leemput wrote: > The answer is close to what Shashwath suggested, except that the > "Hippocampus" segmentation is really computed at the same time as all > the other subfields. For unfortunate reasons, the tail of the > hippocampus that is no

Re: [Freesurfer] Hippocampal Sub field segmentation

The answer is close to what Shashwath suggested, except that the "Hippocampus" segmentation is really computed at the same time as all the other subfields. For unfortunate reasons, the tail of the hippocampus that is not further subdivided in our manual training segmentations was called "Hippocampu

Re: [Freesurfer] Hippocampal Sub-Field Segmentation

Hi Allan and Joshua, The hippocampal subfield segmentation really just uses a few output files generated by the usual FreeSurfer volumetric stream, so the short answer is that it should be perfectly possible to use 5.1 to do hippocampal subfield segmentation on FreeSurfer results processed with 5.