Freesurfer February 2016

freesurfer@nmr.mgh.harvard.edu

123 participants
179 discussions

Hippocampal subfield segmentation in FS 6.0
by Sarah Lancaster 17 Feb '16

17 Feb '16

Hi all, We are running hippocampal subfield segmentations on about 300 subjects. We initially ran recon-all using FreeSurfer 5.3, but we used the new FreeSurfer 6.0 method for the hippocampal subfields. Will this cause problems in our analysis? Should we run them through recon-all again with 6.0? Thanks, Sarah Sarah Lancaster Research Assistant Duke-UNC Brain Imaging and Analysis Center Mental Illness Research, Education and Clinical Center Durham VA Medical Center sarah.lancaster(a)dm.duke.edu 919-286-0411 x7660

2 1

R: Re: v.6.0 Permissions Error
by Grafe,Brendan P. (BIDMC - Neurology) 17 Feb '16

17 Feb '16

Hello Doug, I tried rerunning the -base creation step without any luck. It appears that this process is reliant on the removed file: ERROR: cannot find /usr/local/freesurfer/stable6/average/RB_all_2016-02-11.gca -Brendan ------------------------------ Message: 21 Date: Tue, 16 Feb 2016 16:40:43 -0500 From: Douglas N Greve <greve(a)nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] v.6.0 Permissions Error To: freesurfer(a)nmr.mgh.harvard.edu Message-ID: <56C3975B.60401(a)nmr.mgh.harvard.edu> Content-Type: text/plain; charset=windows-1252; format=flowed ok, try now On 02/16/2016 04:38 PM, Grafe,Brendan P. (BIDMC - Neurology) wrote: > > Hello all, > > I am in the middle of a FreeSurfer v.6.0 longitudinal analysis, > running on the Martinos cluster, and I received an error today during > the (-base) template creation step regarding a file > that the pipeline calls upon: > > GCAread(/usr/local/freesurfer/stable6/average/RB_all_2016-02-11.gca): > could not open file > > I noticed that permissions access to this file are limited at present > to the greve group and that the file was last modified earlier today. > I'm unfamiliar with this component's functionality, but am assuming > access to it is necessary for template creation. Would this simply be > the issue? ----------------------------- Brendan P. Grafe MSc Clinical Research Assistant Berenson-Allen Center for Noninvasive Brain Stimulation Beth Israel Deaconess Medical Center 330 Brookline Avenue Boston, MA 02215 Tel: 617-667-0256 Fax: 617-975-5322 ________________________________ This message is intended for the use of the person(s) to whom it may be addressed. It may contain information that is privileged, confidential, or otherwise protected from disclosure under applicable law. If you are not the intended recipient, any dissemination, distribution, copying, or use of this information is prohibited. If you have received this message in error, please permanently delete it and immediately notify the sender. Thank you.

2 1

I: R: R: R: Re: To use a ROI.label as seed in FS-FAST
by stdp82＠virgilio.it 16 Feb '16

16 Feb '16

1 0

v.6.0 Permissions Error
by Grafe,Brendan P. (BIDMC - Neurology) 16 Feb '16

16 Feb '16

Hello all, I am in the middle of a FreeSurfer v.6.0 longitudinal analysis, running on the Martinos cluster, and I received an error today during the (-base) template creation step regarding a file that the pipeline calls upon: GCAread(/usr/local/freesurfer/stable6/average/RB_all_2016-02-11.gca): could not open file I noticed that permissions access to this file are limited at present to the greve group and that the file was last modified earlier today. I'm unfamiliar with this component's functionality, but am assuming access to it is necessary for template creation. Would this simply be the issue? Preemptive thanks, Brendan Grafe ----------------------------- Brendan P. Grafe MSc Clinical Research Assistant Berenson-Allen Center for Noninvasive Brain Stimulation Beth Israel Deaconess Medical Center 330 Brookline Avenue Boston, MA 02215 Tel: 617-667-0256 Fax: 617-975-5322 ________________________________ This message is intended for the use of the person(s) to whom it may be addressed. It may contain information that is privileged, confidential, or otherwise protected from disclosure under applicable law. If you are not the intended recipient, any dissemination, distribution, copying, or use of this information is prohibited. If you have received this message in error, please permanently delete it and immediately notify the sender. Thank you.

2 1

tkregister visualization issue
by Philip Brandner 16 Feb '16

16 Feb '16

Dear Freesurfer team, I encountered a visualization error with tkregister-sess after trying to look at the overlays of my 1st level analysis in a standard fMRI block designed localizer. tkregister loads without errors (menu plus window) but only very faint and small colored dots are visible, no inflated hemisphere as a surface no significant overlay of the contrast, nothing. It might seem like a specific problem with my setup, because from another computer in the lab the surface is visible (but no overlay). *Here is the terminal output during tkregiter-sess:* -bash-3.2$ tksurfer-sess -s NC211pre/ -analysis face.object.sm5.lh -c face-vs-object Surface fsaverage lh Map Surface fsaverage lh $Id: tksurfer-sess,v 1.16.2.2 2012/11/19 22:35:56 greve Exp $ Linux wiener 2.6.18-407.el5 #1 SMP Fri Oct 16 12:04:40 EDT 2015 x86_64 x86_64 x86_64 GNU/Linux Tue Feb 9 11:51:24 EST 2016 /Freiwald/lab_files/opt/freesurfer-Linux-centos4_x86_64-stable-pub-v5.3.0-full/bin/tksurfer list face-vs-object con/map face-vs-object /Freiwald/cpressl/imaging/tle/NC211pre/bold/face.object.sm5.lh/face-vs-object/sig.nii maplist /Freiwald/cpressl/imaging/tle/NC211pre/bold/face.object.sm5.lh/face-vs-object/sig.nii mri_concat /Freiwald/cpressl/imaging/tle/NC211pre/bold/face.object.sm5.lh/face-vs-object/sig.nii --o /Freiwald/cpressl/imaging/tle/NC211pre/bold/face.object.sm5.lh/tksconcat.nii ninputs = 1 Checking inputs nframestot = 1 Allocing output Done allocing nframes = 1 Writing to /Freiwald/cpressl/imaging/tle/NC211pre/bold/face.object.sm5.lh/tksconcat.nii cd /Freiwald/cpressl/imaging/tle setenv SUBJECTS_DIR /Freiwald/cpressl/imaging/tle/ tksurfer fsaverage lh inflated -overlay /Freiwald/cpressl/imaging/tle/NC211pre/bold/face.object.sm5.lh/tksconcat.nii -label-outline -colscalebarflag 1 -annot aparc -fthresh 2 -fmid 3.00000000000000000000 -fslope .50000000000000000000 Contrasts 0 face-vs-object setting colscalebarflag to 1 setting fthresh to 2.0000 setting fmid to 3.0000 setting fslope to 0.5000 subject is fsaverage hemi is lh surface is inflated surfer: current subjects dir: /Freiwald/cpressl/imaging/tle/ surfer: not in "scripts" dir ==> using cwd for session root surfer: session root data dir ($session) set to: surfer: /Freiwald/cpressl/imaging/tle checking for nofix files in 'inflated' Reading image info (/Freiwald/cpressl/imaging/tle//fsaverage) Reading /Freiwald/cpressl/imaging/tle//fsaverage/mri/orig.mgz surfer: Reading header info from /Freiwald/cpressl/imaging/tle//fsaverage/mri/orig.mgz surfer: vertices=163842, faces=327680 tkmedit: Trying to open /Freiwald/cpressl/imaging/tle/NC211pre/bold/face.object.sm5.lh/tksconcat.dat surfer: Interpreting overlay volume /Freiwald/cpressl/imaging/tle/NC211pre/bold/face.object.sm5.lh/tksconcat.nii as encoded scalar volume. surfer: curvature read: min=-0.673989 max=0.540227 reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt) Found embedded color table in annotation. 13887 vertices did not have an annotation! surfer: double buffered window surfer: tkoInitWindow(fsaverage) surfer: using interface /Freiwald/lab_files/opt/freesurfer-Linux-centos4_x86_64-stable-pub-v5.3.0-full/tktools/tksurfer.tcl Reading /Freiwald/lab_files/opt/freesurfer-Linux-centos4_x86_64-stable-pub-v5.3.0-full/tktools/tkm_common.tcl Reading /Freiwald/lab_files/opt/freesurfer-Linux-centos4_x86_64-stable-pub-v5.3.0-full/tktools/tkm_wrappers.tcl Reading /Freiwald/lab_files/opt/freesurfer-Linux-centos4_x86_64-stable-pub-v5.3.0-full/lib/tcl/fsgdfPlot.tcl Reading /Freiwald/lab_files/opt/freesurfer-Linux-centos4_x86_64-stable-pub-v5.3.0-full/tktools/tkUtils.tcl Successfully parsed tksurfer.tcl reading white matter vertex locations... % Please let me know if you have encountered this before and whether you might have a solution for this issue. Best regards, Philip Brandner

2 1

mri_annotation2label
by Worker, Amanda 16 Feb '16

16 Feb '16

Hi All, I am trying to run a vertex-wise analysis on a pre-defined ROI - the caudal anterior cingulate label as defined by the Desikan atlas. I have used mri_annotation2label to get these labels for each subjects ./label directory. I assumed that as these labels were created in fsaverage space, it would be ok to get these labels for each subject without further sampling to fsaverage? If not, how can I do this? I have also tried to run mri_glmfit, using --label instead of --cortex, but I don't have the label 'lh.caudalanteriorcingulate.label' in standardised space, only in each subjects directory. How can I specify that this is the label I'd like to confine my analysis to (this might be answered by the first question). Thanks in advance, Amanda

2 1

Fwd: Specifying color table file
by Faeze Vedaei 16 Feb '16

16 Feb '16

Hi Freesurfer experts, In order to using mris_label2annot command to create annot files, I've got an error: need to specify color table file. Does anyone know how can I create and specify color table file? In advance, I'd appreciate your consideration and time. Bests, Faezeh Vedaei

3 2

Re: [Freesurfer] comparison between two hemisphere in single
by Ashkan Faghiri 16 Feb '16

16 Feb '16

Thank you Douglas for your reply. I have perforemed surfreg --s subj1 --t fsaverage_sym --lh surfreg --s subj1--t fsaverage_sym --lh --xhemi mris_preproc --target fsaverage_sym --hemi lh --xhemi --paired-diff --srcsurfreg fsaverage_sym.sphere.reg --meas thickness --out lh.lh-rh.thickness.sm00.mgh --s subj1 for my *one* subject. as I understand "lh.lh-rh.thickness.sm00.mgh" file is the difference between the two hemisphere of my one subject (it's dimension is 163842 x 1 x 1). so I should check if these values are significantly different than zero, right? but DOF of this vector is 0 so mri_glmfit returns "ERROR: DOF = 0". which is correct I think. I believe I can't do this procedure for single subject. I want to check if there is thickening or thinning between two hemisphere for one subject. what should I do exactly? Regards, Ashkan -- -- Ashkan Faghiri MSc student of Bioelectrical Engineering Department of Electrical Engineering Sharif University of Technology

2 1

How to convert a surface label to .nii
by Afzal, Afsana 16 Feb '16

16 Feb '16

Hi, How can I convert a surface .label file to a .nii format? I'm using mri_label2label in the following way but the output is always in .label not .nii: mri_label2label --srclabel dlpfc-lh.label --outmask dlpfc-lh_mask.nii --s fsaverage --trglabel dlpfc-lh_mask.nii --regmethod surface --hemi lh Thanks for your help, Afsana ______________________________ Afsana Afzal Clinical Research Coordinator Massachusetts General Hospital Division of Neurotherapeutics Department of Psychiatry: Neurosciences 149 13th St, Room 2612 Charlestown, MA 02129 Phone: 617-643-5129 Fax: 617-726-4078

3 3

fwhm issue with mri_glm-sim
by Domenico Zacà 16 Feb '16

16 Feb '16

Dear FS team, I am running a surface based analysis on GWR on a group of 203 subjects. I generated left and right GWR maps, smoothed with a Gaussian kernel of FWHM 15 mm. However when I try to run the multiple comparisons correction analysis (mri_glmfit-sim --glmdir lh.w-g.pct_aesint.15.glmdir --cache 2 pos --cwp 0.05 --2spaces) I get the following error message: fwhm = 46.240061 ERROR: cannot find /opt/freesurfer/freesurfer-stable5/average/mult-comp-cor/fsaverage/lh/cortex/fwhm46/pos/th20/mc-z.csd Any idea how to get around this? Thanks Domenico Zacà, PhD MR Lab Research Fellow Center for Mind/Brain Sciences University of Trento, Italy Via delle Regole, 101 38100 Mattarello (TN) Italy Telephone: +39-0461-28 3069 Fax: +39-0461-28-3066 Email: domenico.zaca(a)unitn.it MRI Methods Group: http://r.unitn.it/en/cimec/mri

2 1

← Newer
1
...
8
9
10
11
12
13
14
...
18
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 2016