Freesurfer

freesurfer@nmr.mgh.harvard.edu

30132 discussions

Re: [Freesurfer] question abt fsaverage_sym
by Douglas N Greve 10 Apr '12

10 Apr '12

On 04/10/2012 10:04 AM, Ritobrato Datta wrote: > Hi Doug, > > I am following up on the post below > > https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2012-February/022613… > > Question 1) How is the new fsaverage_sym different from the old one ? There was a small bug in the construction of the old one that caused the left hemi target to give slightly different results than the right hemi target. thus, if you did two different analyses, one targeting the lh and on targeting the rh, then they would give different results. Even now, you won't get exactly the same, but it will be very close. > > Question 2) The multiple comparison correction shud be untar'ed' to 'average' folder and not fsaverage_sym folder ? > > in the email you have the following - > ######## Untar fsaverage_sym.mcc.tar.gz into > $FREESURFER_HOME/average/mult-comp-cor/ > cd $FREESURFER_HOME/average/mult-comp-cor/ > tar xvfz fsaverage_sym.mcc.tar.gz > ######## Those instructions are correct. > > Question 3) Is there a mac version of mri_convert.linux I just put one there called mri_convert.macos. The uname from the machine it came from is: Darwin Kernel Version 9.8.0: Wed Jul 15 16:55:01 PDT 2009; root:xnu-1228.15.4~1/RELEASE_I386 i386 let me know if that does not work. doug > > Please let me know. > > Thanks > > Rito > > Ritobrato Datta, Ph.D. > Post Doctoral Researcher > Department of Neurology > University of Pennsylvania School of Medicine > 3rd Floor, Room 312 > 3710 Hamilton Walk (Goddard Laboratories) > Philadelphia, PA 19104-6241 > > -- Douglas N. Greve, Ph.D. MGH-NMR Center greve(a)nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html

1 0

Identifying meridia in retinotopic maps
by Greg Burgess 10 Apr '12

10 Apr '12

HI freesurfers, I have a few questions that were asked previously, but I don't seem to be able to find (or possibly understand) the answers. 1) I'm displaying polar and eccentricity maps using the rtview script. However, no color wheel appears, and I do not seem to be able to find an option to display it in the tksurfer menus. What colors correspond to the horizontal and vertical meridia? Is there a way to display the color wheel as a legend? 2) If, instead of using rtview, I display the heat maps in tksurfer, how do I know what values correspond to the horizontal and vertical meridia? 3) My fieldsign maps appear very speckled, like red and blue polka dots across all of cortex. However, as far as I can determine, the polar and eccentricity maps look reasonable. As suggested elsewhere, I've applied various amounts of smoothing in the fieldsign-sess call. More smoothing makes it look better, but even with 10mm of smoothing, it's unclear if the fieldsigns are correct. How can I track down the problems with the fieldsign maps? Thanks in advance! --Greg ____________________________________________________________________ Greg Burgess, Ph.D. Staff Scientist, Human Connectome Project Washington University School of Medicine Department of Anatomy and Neurobiology Email: burgessg(a)pcg.wustl.edu

2 1

How to let fsfast process the data not named f.nii.gz?
by Zhen Zonglei 10 Apr '12

10 Apr '12

My raw BOLD data is named func.nii.gz in each run directory. It preprocess-sess reported the ERROR: could not determine format for S0001/obj/004/f, even I provide the –i func option. Is there an easy way to let fsfast process the data not named f.nii.gz ? The version I used is FS 5.1. Thanks Zonglei

2 1

recon-all processing stages
by Ed Gronenschild 10 Apr '12

10 Apr '12

Hi I'm not sure but does the Talairach stage precede the nu-correct stage in version v5.1.0? If so, is there an option to switch these two stages? Cheers, Ed

1 0

mapping label from fsaverage LH to fsaverage RH
by Ritobrato Datta 10 Apr '12

10 Apr '12

Hi All, In the fig attached, I have an area of activation in the LH fsaverage. I have created a label from it. I am wondering if there is a way to map this label to the RH fsaverage surface ? Please let me know. Thanks Ri

1 0

Possible underestimation of eTIV ?
by Cheryl McCreary 09 Apr '12

09 Apr '12

Dear Freesurfer experts, I have recently processed a group of subjects and am interested in the eTIV and brain volume to estimate the brain parenchymal fraction. The values that eTIV from the asegstats seem to be underestimated. I understand that the eTIV is based on an atlas scaling factor determined from determinant of the affine transform to the Talairach atlas. Is the transform to Talairach space completed after the skull has been removed? If CSF surround the brain is missing from the brainmask, would this result in a smaller estimate of total intracranial volume? Our subject population is older with the presence of atrophy. Would you recommend manual editing of the brainmask and reprocessing to include CSF surrounding the brain to get a better representation of the intracranial volume? Thanks for your advice and any clarification of the method can offer. Regards, Cheryl

2 1

Middle Frontal Region
by Vina Goghari 09 Apr '12

09 Apr '12

Hi, Would anyone be able to share some papers that suggest different functions (or the reason for this differentiation) of the caudal and rostral middle frontal region as parcellated by FreeSurfer? Many thanks, Vina Goghari

2 1

Longitudinal Template Edits
by Tate, David Franklin 09 Apr '12

09 Apr '12

We have been using the version 5.1 to do some longitudinal processing on a Mac computer using Lion. Our template results have several areas that concern us and we are wondering the best approach for editing. We believe it is edit the pial surfaces in tkmedit. However, the tutorials are a bit confusing as they seem to contain slightly different steps and in neither place do they provide the kind of detail (i.e., which editing tool to use in tkmedit and if there are any configuration changes needed). We have posted the following screen captures. The first shows is from free view and shows that strange lines in the hippocampus. The last two show attempts at editing but in the posterior part of the brain in the inter hemispheric fissure. Any help would be greatly appreciated. Thanks, [cid:3A68F9FB-CA43-46B6-8D1B-8F0F42243677@v3.uthscsa.edu] [cid:4483FB3B-AB38-4350-973B-A800BD6FD3CA@v3.uthscsa.edu] [cid:220E38D7-5796-47E4-BDE5-DDB75CB6E2AE@v3.uthscsa.edu]

3 3

Reading/loading posterior_* files from hippocampal subfield segmentation
by Irwin, William 09 Apr '12

09 Apr '12

Hi- This is probably a question for Koen, but perhaps others could help me out. I want to read into Matlab the 'posterior_*.mgz' files generated by the subfield segmentation. I'm not exactly sure the format/content of these files, but in addition to any information (e.g., some coordinate reference), I'm assuming it contains the posterior probability (0 - 255, scaled) for each (sub) voxel for each of the regions/fields. I tried the obvious Matlab file (i.e., load_mgh.m), but that results in an error (the current Matlab directory contains the files and if I include the full path the same error obtains): >> [vol M] = load_mgh('hippoposterior_right_CA4-DG.mgz'); gzip: hippoposterior_right_CA4-DG.mgz.gz: No such file or directory ERROR: problem reading fname SWITCH expression must be a scalar or string constant. Error in load_mgh (line 156) switch type Given what I know (or think I know) about the procedure by which the subfields are labeled, it likely isn't surprising the genearl Matlab scripts don't properly deal with the posterior subfield files. My objective is to be able to evaluate the distribution of voxels values (posterior probabilities) which exist for each of the subfields/regions. Thanks, Wil

2 2

mpr2mni305 failed for 2 subjects.
by Zheng Hui 09 Apr '12

09 Apr '12

1 0

Jump to page:

2026

2025

2024

2023

2022

2021

2020

2019

2018

2017

2016

2015

2014

2013

2012

2011

2010

2009

2008

2007

2006

2005

2004

Freesurfer