Freesurfer February 2012

freesurfer@nmr.mgh.harvard.edu

124 participants
199 discussions

Extraction of vertex identifiers from a significant cluster
by Florsek 14 Feb '12

14 Feb '12

Dear all, We have performed a cluster analysis in Qdec and found a significant vertex-cluster after correction for multiple testing using the Monte Carlo simulation. Now, we would like to extract the (unique) identifiers of all vertices that form the significant cluster. We then would like to look up the spatial information (x, y, z) of these vertices. Our final aim is to map the vertices to an atlas which is different from that of Desikan. Is this a way suitable to achieve our aim? Many thanks for your help in advance! Best regards, Florian -- Florian Siedek Doctoral Scientist Institute of Human Genetics Department of Genomics Life& Brain Center University of Bonn Sigmund-Freud-Strasse 25 D-53127 Bonn Germany Email: florsek(a)gmail.com

2 1

(no subject)
by Meryem Ayse Yucel 14 Feb '12

14 Feb '12

Hi, I am trying to use selxavg3-sess function and getting this error. Below is the error I get. I actually have this fingertap.par file but freesurfer somehow does not see it. Any help would be appreciated. Thanks! Meryem Yucel PMI Lab Extension format = nii.gz ERROR: opening /autofs/space/moe_002/users/mayucel/PROJECT/Subject20/bold/001/fingertap No such file or directory ??? Output argument "partype" (and maybe others) not assigned during call to "/usr/local/freesurfer/stable5_1_0/fsfast/toolbox/fast_ldpar4.m (fast_ldpar4)". Error in ==> fast_ldpar4 at 45 par4 = []; Error in ==> flac_customize at 121 [par partype] = fast_ldpar4(parpath); Error in ==> fast_selxavg3 at 65 flac0 = flac_customize(flac0);

2 1

Re: [Freesurfer] Clusters locations
by Douglas N Greve 14 Feb '12

14 Feb '12

Antonella Kis wrote: > Hi Doug, > > 1) I would like to report the MNI coordinates and also a more exactly > region I mean if possible tto find exactly where in the > Left-Cerebral-White-Matter and Right-Cerebral-White-Matter my cluster > is located. What do you me by "exactly where"? The nearest cortical label? The fiber bundle? > > 2)Can you please tell me if for the mean diffusivity I should use the > simulation with the perm (as I use for the FA due to the fact that is > not so Gaussian) option or it is OK to use the grf option. I think you can use GRF for this as it corresponds to a normal contrast in a GLM. Note that the permutation is the stronger (but more conservative) test. > > > 3) Can you please explain what exactly means for my clusters if I hit > the positive sign under DISPLAY in Qdec? I mean if I compare the > cortical thickness between two classes: controls vs. Patients and > I am not interested in the sex or age differences just differences > between the two classes will positive mean clusters where cortical > thickness graeter in Class 1 than Class2 (Class1>Class2)? > > I have C = +1 -1 and my Class 1 = controls while Class2 = PAtients. Positive is Controls > Patients doug > > > THANKS YOU. > Antonella > ------------------------------------------------------------------------ > *From:* Douglas Greve <greve(a)nmr.mgh.harvard.edu> > *To:* Antonella Kis <atorok9(a)yahoo.com>; free surfer > <freesurfer(a)nmr.mgh.harvard.edu> > *Sent:* Tuesday, February 14, 2012 9:59 AM > *Subject:* Re: [Freesurfer] Clusters locations > > Hi Antonella, what level of detail do you want? I think that most > people are reporting MNI coordinates. > doug > > On 2/13/12 2:44 PM, Antonella Kis wrote: >> Hi Doug, >> >> I will be very grateful if you give me some directions regarding how >> I can get my clusters location ( my output is too general telling me >> just Left-Cerebral-White-Matter and Right-Cerebral-White-Matter) and >> the coordinates (MNI) when I run the: >> >> mri_volcluster --in GroupAnalysis_pos.glmdir/contrast/sig.mgh --mask >> GroupAnalysis_pos.glmdir/mask.mgh --no-fixmni --cwsig >> GroupAnalysis_pos.glmdir/contrast/permcsd.sig.cluster.mgh --sum >> GroupAnalysis_pos.glmdir/contrast/permcsd.sig.cluster.summary --ocn >> GroupAnalysis_pos.glmdir/contrast/permcsd.sig.ocn.mgh --cwpvalthresh >> .09 --seg cvs_avg35 aseg.mgz --csdpdf >> GroupAnalysis_pos.glmdir/contrast/permcsd.pdf.dat --csd >> GroupAnalysis_pos.glmdir/csd/permcsd.j001-contrast.csd --vwsig >> GroupAnalysis_pos.glmdir/contrast/permcsd.sig.voxel.mgh >> >> and >> >> >> mri_segstats --seg permcsd.sig.ocn.mgh --exclude 0 --i >> /media/2Tra/Antonella_2011/DTI_FS/GLM_CVS/GroupAnalysis-FA-MASKED.ANAT+CVS-to-avg35.nii.gz >> --avgwf fa.avg.dat --sum permcsd.sig.cluster.summary >> >> >> Thank you. >> Antonella > > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu <mailto:Freesurfer@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. > > -- 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

mri_volcluster register.dat question
by Huiting Liu 14 Feb '12

14 Feb '12

Hello all, I'm trying to run mri_volcluster on our third-level functional data and one of the required flagged arguments is the register.dat file. Our data preprocessing/registration was done in FSL, not Freesurfer, so we don't have this particular file. Is there anything we can do to get around this or do we need to run tkregister first in order to use mri_volcluster? Thanks for your time. -Huiting

2 1

mri_vol2surf
by Klein, Holger 14 Feb '12

14 Feb '12

Dear FreeSurfers, To get a better view on the pial surface of the Heschl' Gyri I used the command mri_vol2surf after having created the suitable label with (label2vol). My goal is to get My Command was: *mri_vol2surf --src pf_lh_vol.mgz --hemi lh --srcreg register.dat --out_type paint --o A1surf-lh.w* The output file was created without any error, but loading the file in freeview or tksurfer an error occured: *command: tksurfer WH lh A1surf-lh.w * * * *subject is WH* *hemi is lh* *surface is A1surf-lh.w* *surfer: current subjects dir: /Volumes/Macintosh/Freesurfer/Kontrollen/A1_Wilts_Heide* *surfer: not in "scripts" dir ==> using cwd for session root* *surfer: session root data dir ($session) set to:* *surfer: /freesurfer/Kontrollen/A1_Wilts_Heide* *checking for nofix files in 'A1surf-lh.w'* *Reading image info (/Volumes/Macintosh/Freesurfer/Kontrollen/A1_Wilts_Heide/WH)* *Reading /Volumes/Macintosh/Freesurfer/Kontrollen/A1_Wilts_Heide/WH/mri/orig.mgz* *surfer: Reading header info from /Volumes/Macintosh/Freesurfer/Kontrollen/A1_Wilts_Heide/WH/mri/orig.mgz* *ERROR: MRISread: file '/Volumes/Macintosh/Freesurfer/Kontrollen/A1_Wilts_Heide/WH/surf/lh.A1surf-lh.w' has 0 vertices!* *Probably trying to use a scalar data file as a surface!* * * Any help would be greatly appreciated. Thanks in advance Holger

1 0

Re: [Freesurfer] Clusters locations
by Douglas Greve 14 Feb '12

14 Feb '12

Hi Antonella, what level of detail do you want? I think that most people are reporting MNI coordinates. doug On 2/13/12 2:44 PM, Antonella Kis wrote: > Hi Doug, > > I will be very grateful if you give me some directions regarding how I > can get my clusters location ( my output is too general telling me > just Left-Cerebral-White-Matter and Right-Cerebral-White-Matter) and > the coordinates (MNI) when I run the: > > mri_volcluster --in GroupAnalysis_pos.glmdir/contrast/sig.mgh --mask > GroupAnalysis_pos.glmdir/mask.mgh --no-fixmni --cwsig > GroupAnalysis_pos.glmdir/contrast/permcsd.sig.cluster.mgh --sum > GroupAnalysis_pos.glmdir/contrast/permcsd.sig.cluster.summary --ocn > GroupAnalysis_pos.glmdir/contrast/permcsd.sig.ocn.mgh --cwpvalthresh > .09 --seg cvs_avg35 aseg.mgz --csdpdf > GroupAnalysis_pos.glmdir/contrast/permcsd.pdf.dat --csd > GroupAnalysis_pos.glmdir/csd/permcsd.j001-contrast.csd --vwsig > GroupAnalysis_pos.glmdir/contrast/permcsd.sig.voxel.mgh > > and > > > mri_segstats --seg permcsd.sig.ocn.mgh --exclude 0 --i > /media/2Tra/Antonella_2011/DTI_FS/GLM_CVS/GroupAnalysis-FA-MASKED.ANAT+CVS-to-avg35.nii.gz > --avgwf fa.avg.dat --sum permcsd.sig.cluster.summary > > > Thank you. > Antonella

1 0

reference for corpus callosum segmentation
by Kelsi Hirai 13 Feb '12

13 Feb '12

Hi freesurfers, We are using the segmentation of the corpus callosum into the Anterior, Mid Anterior, Central, Mid Posterior, and Posterior sections that are labeled in the freesurfer aparc+aseg file. However, some of the labeling is not correct in subjects post-stroke, so we need to manually draw some of the regions. What are the divisions based on? Is there a reference paper that describes the segmentation in more detail? Thank you! Kelsi

2 1

RD radial diffusivity and AD axial diffusivity
by Antonella Kis 13 Feb '12

13 Feb '12

Dear All, I would like to know how I can get the RD radial diffusivity and AD axial diffusivity after I was running dt_recon. I can see my mean diffusivity adc.nii and a file called radialdiff.nii but I am not sure which one is the AD and Rd. Can you please tell me the name of this files AD and RD as an output from the dt_recon? Thank you. Antonella

2 1

Question regading paired samples t-test
by Maren Strenziok 13 Feb '12

13 Feb '12

Hi, I want to set up a paired samples t-test to look at pre-post differences in cortical thickness in a group of subjects that underwent cognitive training. I could not get any information on this from the internet other then the suggestion to use the --paired -t flag. This, however, didn't work. I tried to build an fsgd file based on how I would set up the test in FSL, but that didn't work either. Any instructions on how to build the correct matrix and contrast files or an example would be highly appreciated. Thanks, Maren Maren Strenziok, Ph.D., Psychologische Psychotherapeutin (PTG) Postdoctoral Fellow, Arch Lab Department of Psychology 2071B David King Hall George Mason University MS 3F5, 4400 University Drive Fairfax, VA 22030-4444 Phone: 301-318-8912 Email: mstrenzi(a)gmu.edu

1 0

mris_make_face_parcellation
by Franz Liem 13 Feb '12

13 Feb '12

Dear Freesurfers, I have some questions regarding mris_make_face_parcellation (and possibly found one error in the .tri file). (I am working with freesurfer-Darwin-leopard-i686-stable-pub-v5.1.0). I would like to make a high res parcellation of several subjects and used ic3.tri. Parcels should correspond across subjects. I computed mris_make_face_parcellation ../surf/lh.sphere $FREESURFER_HOME/lib/bem/ic3.tri ./lh.ic3.annot 1. It seems not to make a difference whether I choose .sphere or .sphere.reg as input, the resulting parcellations are identical (i checked by comparing vertex label values in matlab; .inflated deviates a bit, but not substantially). According to Bruce (http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg18509.html) "You want to use either ?h.sphere if you want it to be uniform in subject space or ?h.sphere.reg if you want the parcels to correspond across subjects" Could anybody tell me how the parcellation is performed exactly? I thought it was performed on the input surf (the input surf is parcellated into (e.g.) 642 equally sized parcels), which should lead to different results at .sphere and .sphere.reg, shouldn't it? Alternatively, would it be better to mris_make_face_parcellation the fsaverage and mri_surf2surf the high res parcellation onto each subject to get cross-subject correspondency (I tried this. It didn't look that great with this command: mri_surf2surf --srcsubject fsaverage --sval-annot ic3.annot --trgsubject subject1 --tval ic3s03.annot --hemi lh )? To recap, what is the best strategy to arrive with cross-subject-corresponing parcellations? Performing mris_make_face_parcellation with ?h.sphere.reg for each subject individually? 2. There seems to be duplicate structNames/annotationValues when applying mris_make_face_parcellation with ic3.tri In fsaverage at least the following labelnames are given to two spatially separated labels. ic3.tri_vertex_25 (cluster 1 around vertex 41132, cluster 2 around vertex 157199) ic3.tri_vertex_42 (cluster 1 around vertex 137845, cluster 2 around vertex 155417) How come? Thanks for you help, Franz

2 2

← Newer
1
...
10
11
12
13
14
15
16
...
20
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 February 2012