Freesurfer September 2014

freesurfer@nmr.mgh.harvard.edu

120 participants
164 discussions

Brainmap Ontology
by Thomas Yeo 26 Sep '14

26 Sep '14

Dear FreeSurfer List, I like to introduce you to a new set of reference brain networks (cognitive components) estimated from 10,449 experiments and 83 behavioral tasks from the BrainMap database, which can be downloaded here: https://surfer.nmr.mgh.harvard.edu/fswiki/BrainmapOntology_Yeo2015. The networks will be incorporated in some future version of FreeSurfer. Since these networks are estimated from (meta-analytic) task data, they are meant to complement (not replace) the current resting-state networks in FreeSurfer (https://surfer.nmr.mgh.harvard.edu/fswiki/CorticalParcellation_Yeo2011) Cheers, Thomas

1 0

Re: [Freesurfer] possible to use freesurfer segmentations to get mean values for anatomic structures from other sequences
by Douglas Greve 25 Sep '14

25 Sep '14

Hi Sal, yes you can. Use bbregister to register the lowb image to the anatomical. This creates a registration matrix. Use mri_vol2vol and the registration to map the ADC map to the anatomical, then use mri_segstats to extract the values doug ps. Please post questions to the FS list instead of us directly so that others can benefit and it gets archived. thanks! On 5/25/13 1:03 PM, Salil Soman wrote: > Dear Dr. Greve, > > Is it possible to register a nonstructural MR sequences (e.g. an ADC > map) with the aseg.mgz file (or aparc+aseg.mgz file, etc) and then, > using the segmentation from the aseg (or aparc+aseg) file to output a > mean ADC value for each anatomic area segmented? > > Thank you for your time and consideration. > > Best wishes, > > Sal > > Salil Soman, MD, MS

3 11

Re: [Freesurfer] A question about spherical registration
by Reza Rajimehr 25 Sep '14

25 Sep '14

Thank you Doug for your comprehensive response. This looks clear, and I am going to try it out. Just one question for now: In step 1 (create a template from a single subject), I do not yet have "sphere.reg". Should I write "--surf-reg sphere"? make_average_surface --subjects $subjectlist[1] \ --out iter00 --template-only --surf-reg sphere Reza Hi Reza, I think that this should work. doug set subjectlist = (subject1 subject2 ...) 1. Create a template from a single subject make_average_surface --subjects $subjectlist[1] \ --out iter00 --template-only --surf-reg sphere.reg 2. Register each subject to this template, including first subject. Each of these may take 30 min, so, if you have a lot of subjects, you may want to submit each job to the cluster. foreach subject ($subjectlist) # Create subject/surf/iter00.sphere.reg, --no-annot for monkey surfreg --s $subject --t iter00 --no-annot end 3. Create a new template from all subjects using the new registration make_average_surface --subjects $subjectlist \ --out iter01 --template-only --surf-reg iter00.sphere.reg 4. Register each subject to this new template foreach subject ($subjectlist) # Create subject/surf/iter01.sphere.reg, --no-annot for monkey surfreg --s $subject --t iter01 --no-annot end 5. Return to step 3. Iterate 4 or 5 times to remove the dependence on the first subject. When using mri_surf2surf or mris_preproc, spec --surfreg iterXX.sphere.reg. For mris_preproc also spec --targ iterXX On 09/19/2014 10:24 AM, Reza Rajimehr wrote: > Hi, > > I have a question about spherical registration, and I couldn't find a > relevant answer in the mailing list. > > I have two subjects S1 and S2 with corresponding functionals. I want to > show the functionals of each subject on the surfaces of the third subject > S3. I have .sphere files for S1, S2, and S3, but I don't have .sphere.reg > files yet because these are monkey subjects and I did not want to register > them to the buckner40.tif template. Since my goal is not group averaging, > and it is just to map functionals to the same-subject anatomicals and then > to the target-subject anatomicals, I was thinking of one of the following > solutions: > > 1) Convert sphere of S3 to a template .tif file, then use mris_register to > register spheres of S1, S2, and S3 to that template and generate > sphere.reg for all the subjects. Not sure if mris_make_template works for > one subject though. > > 2) Make a template from "S1 and S2" through the procedure described at > https://surfer.nmr.mgh.harvard.edu/fswiki/SurfaceRegAndTemplates#Creatingar…. > Then register S1, S2, and S3 to that template and generate sphere.reg for > all the subjects. > > Which approach is recommended? > > BTW, I do not know of a monkey template that is based on the surfaces from > a large group of monkeys. > > Thanks for any advice, > Reza

2 1

Question about Longitudinal LME Modeling
by Karishma Smart 25 Sep '14

25 Sep '14

Dear Freesurfers, If I am planning to do a longitudinal analysis, I understand that the LME Model is probably the most appropriate choice. However, it says on the website that it is for univariate and mass-univariate analyses. I would need a longitudinal model that can handle *multivariate* statistics (a longitudinal study using multi-modal imaging + covariates). Can the LME model do this? If not, is there another way to do this in FreeSurfer? Thanks! Karishma -- Karishma Smart B.A. Biological Sciences Cornell University Class of 2013 Boston University School of Graduate Medical Sciences Class of 2015

1 0

A question about spherical registration
by Reza Rajimehr 25 Sep '14

25 Sep '14

Hi, I have a question about spherical registration, and I couldn't find a relevant answer in the mailing list. I have two subjects S1 and S2 with corresponding functionals. I want to show the functionals of each subject on the surfaces of the third subject S3. I have .sphere files for S1, S2, and S3, but I don't have .sphere.reg files yet because these are monkey subjects and I did not want to register them to the buckner40.tif template. Since my goal is not group averaging, and it is just to map functionals to the same-subject anatomicals and then to the target-subject anatomicals, I was thinking of one of the following solutions: 1) Convert sphere of S3 to a template .tif file, then use mris_register to register spheres of S1, S2, and S3 to that template and generate sphere.reg for all the subjects. Not sure if mris_make_template works for one subject though. 2) Make a template from "S1 and S2" through the procedure described at https://surfer.nmr.mgh.harvard.edu/fswiki/SurfaceRegAndTemplates#Creatingar…. Then register S1, S2, and S3 to that template and generate sphere.reg for all the subjects. Which approach is recommended? BTW, I do not know of a monkey template that is based on the surfaces from a large group of monkeys. Thanks for any advice, Reza

2 1

MNI Coordinates
by Venkataraman, Archana 25 Sep '14

25 Sep '14

Hi Freesurfer experts, I have a set of RAS coordinates in the Freesurfer fsaverage space. What is the easiest way to transform them to MNI152 space? Thanks. - Archana

2 3

FreeSurfer Labels for MNI template
by Ray Razlighi 25 Sep '14

25 Sep '14

Dear All, Is there any way I can get the Desikan-Killiany cortical and subcortical labels on MNI152 template. I know I can get a rough estimate using the linear transformation matrix "mni152.register.dat". I also find that the subject cvs_avg35 is non-linearly registered to MNI152 and given in the cvs_avg35_inMNI152 directory. But non of them are accurate enough for my purpose. I tried hopelessly to run the FreeSurfer on the MNI152 template itself and it failed. Any other suggestion is greatly appreciated. Best -- Ray Razlighi, Ph.D. Assistant Professor Division of Cognitive Neuroscience Department of Neurology Columbia University Alt: razlighi(a)gmail.com Office Phone: 212-342-1352 Office Fax: 212-342-1838

2 1

how to extract the individual cortical thickness or volume value of significant cluster after RFT correction
by wang kangcheng 24 Sep '14

24 Sep '14

Dear experts I have question regarding extracting the individual cortical volume value of significant cluster after RFT correction. I have 209 subjects in an analysis and G_pariet_inf-Angular showing significant correction with score of autism after RFT correction using command of mri_surfrft_jlbr in Matlab, how do I export individual subjects cortical volume values for significant regions ? In addition, I did not analyze it using QDEC and just use command following reference (https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis)Thank you and hope for responses. With best Regards,kangcheng Wang

2 3

Help on DTI pre-processing
by Gabriel Gonzalez Escamilla 24 Sep '14

24 Sep '14

2 1

Reporting of Significant Clusters
by Chris Wertz 24 Sep '14

24 Sep '14

Hi Freesurfers, I am curious about why in QDEC, when you correct for multiple comparisons and it spits out significant clusters with their cluster-wise p-values and annotations and then click on find clusters and go to max, it changes the annotation and coordinates of the previous output? I guess more importantly which cluster's annotation is more indicative of the centeroid of the significant cluster. For example after using the Monte Carlo Null-Z simulation I get a cluster that is labeled as the Pericalcarine and when I click on find clusters and go to max that same cluster is now deemed Precuneus? Thanks, Chris

1 0

← Newer
1
2
3
4
5
6
7
...
17
Older →

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 September 2014