Freesurfer

freesurfer@nmr.mgh.harvard.edu

3 participants
30135 discussions

QDEC ANALYSIS
by Walton, Matt 08 Apr '14

08 Apr '14

Hello Freesurfer experts. I am trying to run a QDEC analysis on some MRI data I have. I want to see if thickness is correlated with language scores I have for each subject, while accounting for differences in age, and gender. I would like to select the gender as a fixed variable, and both the age and language scores as continuous variables, however the QDEC GUI will not allow me to select more than one continuous variable at a time (from what I've read on the website/mailing list I should be able to select up to two. Any idea of what might be wrong here, and how I can fix it. Thanks So much, Matthew Walton

2 1

Export freesurfer data
by ye tian 08 Apr '14

08 Apr '14

Dear Freesurfers, I would like to do some customized model fitting for cortical thickness. Is there a way to export freesurfer data into R or simply as a text? Thank you very much! Sincerely, Ye

3 7

restrain range when calculating subcortical volumes, such as hippocampus
by Yu(余)Qijing(奇静) 08 Apr '14

08 Apr '14

Hi, I am wondering how can I get the volume of hippocampus within a certain range? Given that the most anterior and posterior part of hippocampus may be more susceptible to errors because of other structures like amygdala and fornix, so I am wondering if the measurement would be more reliable if the most anterior and posterior parts of it are excluded. For example, calculate the volume of hippocampus without the most anterior and posterior 4 slices? I guess I could calculate manually, by summing the product of area of hippocampus on every specific slice and the distance between slices. But where can I get the information about the area on every slice? And what is the distance between the two slices (if for the coronal view)? Does it depend on the original DICOM files, or does Freesurfer do some re-slicing during the reconstruction? Thank you very much! Best, QJ

1 0

Rat cortex Parcellation
by Craig, Michael 08 Apr '14

08 Apr '14

Hello, I have a question regarding the parcellation of the rat cortex. I am interested in parcellating the cortex into distinct regions using an atlas and then finding grey matter volumes for each region. I realize that Freesurfer is primarily meant to be used on human subjects, but is it possible to replace the MNI atlas with a rat atlas (like the LONI rat atlas) during the parcellation step? Thanks for your time and help. best wishes, Mike

2 1

Extract seed from resting state networks mask (Yeo and Buckner maps)
by Celine Louapre 08 Apr '14

08 Apr '14

Hi Freesurfer team I am running a functional connectivity analysis on resting state data, and I would like to use as seed the precuneus/posterior cingulate region as seen on fsaverage/label/${hemi}.Yeo2011_17Networks_N1000.annot. However, this region is part of the label 17Networks_16 comprising other regions. Is it possible to isolate this specific portion of the label to create a seed region for the connectivity analysis ? I tried to do it on tksurfer, drawing a path around the region but then I could not figure out how to extract this part of the label. Thank you very much for your help Best Celine -- Celine Louapre, MD-PhD Research Fellow at Massachusetts General Hospital Department of Radiology, MGH Building 149, Room 2301 13th Street Charlestown, MA 02129

2 1

Longitudinal Analysis Questions
by pfotiad＠nmr.mgh.harvard.edu 08 Apr '14

08 Apr '14

Hi FS community, I am using FS 5.3 to do a longitudinal analysis on some data of mine. I have manually edited some of the reconstructed scans (i.e. addition of control points and white voxels) where the reconstruction was not as precise: 1) Is the base template created from the recon-all -base command in the wiki preserving those edits or do I need to reapply them in the base template? I know that this has been answered for previous versions of FS but I was wondering whether anything has changed in more recent versions. 2) Is it ok to run the longitudinal analysis described in the wiki when my subjects have an unequal number of timepoints (i.e. one person has 3 different timepoints, whereas another one has five) or should they all have the same number of timepoints? Thanks in advance! Best, Panos

2 4

failed templates from longitudinal base step
by L. Koenders 08 Apr '14

08 Apr '14

Dear FreeSurfer people, I have a question regarding the longitudinal pipeline, because something goes very wrong with my output. A short summary of my project: I have 3Tesla data from two timepoints, consisting of 50 people, so 100 scans in total. I have two groups, a control and an experimental group (cannabis users). In FS v5.3.0, I ran all scans through the Cross pipeline, and made brainmask.mgz pial edits where necessary. So far so good. Subsequently, I ran all the scans (all the edited scans) through the Base pipeline. This is when I ran into troubles, because only 2 templates (out of the whole group) turned out all right. The surfaces of all other scans are skipping gyri (for an example see attachment template_surfs). The scans that turned out allright were the very first and very last one of my subjects, which i find suspicous. I could of course try editing all the templates using control points, however I have this feeling that something else is going wrong with the registration of baseline and follow up scan. Do you know if this is a common error, and if I can do anything to fix it? I hope you can help me! Thanks & best regards, Laura Koenders ________________________________ AMC Disclaimer : http://www.amc.nl/disclaimer ________________________________

2 1

PhD studentships, University of Trento, Italy
by Jorge Jovicich 08 Apr '14

08 Apr '14

Dear All, our PhD program (attached brochure) is recruiting (as am I). Please feel free to forward / share in circles. Relevant details: -The CIMeC has been ranked as best cog. neuro center in Italy. -Its faculty has 6 European Research Council starting grants, and 1 advanced grant. -The 3-year program is in English (Nov. 1, 2014- Oct. 31, 2017) -Application deadline: Tuesday May 13, 2014, 16.00 Central European Summer Time. -Topics: http://www.unitn.it/en/drcimec/32957/30th-cycle-topics-2014-call Jorge Jovicich -- Jorge Jovicich, Ph.D. MR Lab Coordinator Center for Mind Brain Sciences University of Trento, Via delle Regole, 101 38100 Mattarello (TN) Italy Telephone: +39-0461-28 3064 Fax: +39-0461-28-3066 Email: jorge.jovicich(a)unitn.it http://www.cimec.unitn.it/ http://polorovereto.unitn.it/~jovicich

1 0

Fw:Re: Re: questions about ROI analysis
by Rujing Zha 08 Apr '14

08 Apr '14

Hi FS experts and others, I completed the mri_annotation2label and mri_label2label(which used mask created from the mri_binarize), but the result is the same as that without mask.Here are my codes: ==================================================================================== mri_binarize --i *.ocn.mgh --match 1 --o cluster1.mgh mri_annotation2label --subject fsaverage --hemi rh --outdir $SUBJECTS_DIR/fsaverage/label mri_label2label --srclabel $SUBJECTS_DIR/fsaverage/label/rh.superiofrontal.label --srcsubject fsaverage --trgsubject test --regmethod volume --srcmask cluster1.mgh 1 bfloat ==================================================================================== Last step used the mask, but its result is just tha same as that without mask. I also checked the mask file which doesnot have any problem. Thanks. All the best. Rujing Zha -------- 转发邮件信息 -------- 发件人：charujing123 <charujing123(a)163.com> 发送日期：2014-02-27 09:46:23 收件人："freesurfer(a)nmr.mgh.harvard.edu" <freesurfer(a)nmr.mgh.harvard.edu> 主题：Re: Re: [Freesurfer] questions about ROI analysis Thanks doug, All the best. Rujing Zha 2014-02-27 charujing123 发件人：Douglas N Greve <greve(a)nmr.mgh.harvard.edu> 发送时间：2014-02-27 01:49 主题：Re: [Freesurfer] questions about ROI analysis 收件人："freesurfer"<freesurfer(a)nmr.mgh.harvard.edu> 抄送： On 02/25/2014 08:34 PM, charujing123 wrote: > Hidoug, > Thanks doug. > For 1st question,I want to reduce the search space of vertex-wise > analysis to a cluster. Extract the cluster that you want from the ocn to create a mask, eg, to get cluster2 mri_binarize --i ocn.mgh --match 2 --o cluster2.mgh The run mri_glmfit with --mask cluster2.mgh Then run mri_glmfit-sim with simulation > For 2nd question, i try freeview as tksurfer cannot work. However this > website cannot be logged > in:http://surfer.nmr.mgh.harvard.edu/fswiki/FreeviewGuide/FreeviewTools/Roi…. try http://surfer.nmr.mgh.harvard.edu/fswiki/FreeviewGuide > Thanks. > All the best. > Rujing Zha > 2014-02-26 > ------------------------------------------------------------------------ > charujing123 > ------------------------------------------------------------------------ > *发件人：*Douglas Greve <greve(a)nmr.mgh.harvard.edu> > *发送时间：*2014-02-25 23:46 > *主题：*Re: [Freesurfer] questions about ROI analysis > *收件人：*"freesurfer"<freesurfer(a)nmr.mgh.harvard.edu> > *抄送：* > > On 2/25/14 10:09 AM, Rujing Zha wrote: >> Hi FS experts and others, >> I have done two group thickness difference analysis based on whole >> brain. Now I want to do correlation analysis between specific ROI >> thickness and behavior score. I searched roi in the FS website, but I >> cannot distinguish the volume ROI and surface ROI very clearly. So I >> have some questions as below: >> 1,As I get some clusters in the two group t-test,I want to use one of >> these clusters to correlate thickness with behavior score. How to >> generate this mask and how to use this mask in the mri_glmfit and >> mri_glmfit-sim? > Do you mean you want to reduce the search space of a vertex-wise > analysis to a cluster or that you want to compute the mean thickness > within the cluster and correlate with your behavioral score? >> 2,If I want to draw ROI manually or set ROI according previous >> studies, how to create this ROI mask. > tksurfer can draw a label (as can freeview I think) > >> Any detailed information will be highly appreaciated. >> Thanks. >> All the best. >> Rujing Zha >> >> >> >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer(a)nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- 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: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.

1 0

NHP surface reconstruction in FS5.3
by S.V.Shepherd [work] 07 Apr '14

07 Apr '14

Greetings, I've been reconstructing a surface in an NHP using a Kolster T1 scan and FS5.3. It went very well, at first, but I've hit a wall. I have trouble in occipital (due to poor signal strength/constrast) and some typical-with-NHP problems in ACC and OFC. I think there are three related questions. 1) I lose parts of the ACC near the genu of the corpus callosum. I have attached a screen shot -- the white matter and gray matter both look decent. I wondered if the corpus callosum might be handled specially, and if differences between human and nhp callosi might prevent the ACC from growing normally? 2) In trying to deal with this, I greyed out the ACA, which was bright and potentially confounding. I wasn't sure how to do this in brain.finalsurfs.manedit, since my understanding is that only 1s (nonbrain) and 255s (wm) were preserved. I tried brain, which got overwritten, but ultimately succeeded by editing brainmask and rerunning -autorecon2-wm. Is there a way to repain gray matter in brain.finalsurfs.manedit? Alternately, if I continue editing brainmask (or equivalent) directly, should I be darkening or lightening the gray matter in the excluded section of the ACC? I would assume lighten -- but in the OFC, some gray matter (not shown) appears to be excluded for being too bright. 3) In some places I've specified wm (e.g. in the ACC, here) but it hasn't stuck. I assume this is because autorecon isn't convinced by the wm specification after looking at brain.finalsurfs -- how might I (gently!) override this? Thanks very much for your time and patience. stephen [image: Inline image 2][image: Inline image 1] *stephen v. shepherd phd* The Rockefeller University / 1230 York Avenue / New York NY 10065-6307 USA // 212.327.7620

2 1

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