Freesurfer

freesurfer@nmr.mgh.harvard.edu

30088 discussions

piping contrast enhanced MPRAGES
by Ritobrato Datta 03 Apr '12

03 Apr '12

Hi, Is it advisable to run recon-all on contrast enhanced T1 MPRAGEs ? Or is there a separate pipe to process such images ? If yes, is there a way to combine contrast enhanced and regular (non-contrast enhanced) MPRAGEs to increase SNR for purposes of morphometry ? I have attached a pic for reference. Thanks Ri

2 1

Problem with output size of segmented GM and WM files
by Fellhauer, Iven 03 Apr '12

03 Apr '12

Dear all, I followed the steps described here: http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg21266.html and here: https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2009-September/01178… to create GM and WM output files. The size of the input file is 176 x 256 x 256 (native space) but the output file has the size 256 x 256 x 256. Is it possible that the output size is equal to the input size? If it is possible how can I do this? Best regards, Iven

2 1

question about fsaverage
by Charlotte Bernard 03 Apr '12

03 Apr '12

Dear Freesurfer experts, I would like to know if it is necessary to have exactly the same number of subjects in my fsaverage and in my qdec.table.dat? If it is a problem how can I eliminate the subjects I don't study from the fsaverage? Thanks for all, Charlotte

2 1

Rejoindre mon réseau sur LinkedIn
by Max Gunther via LinkedIn 03 Apr '12

03 Apr '12

LinkedIn ------------ Max Gunther souhaite se connecter à vous sur LinkedIn : ------------------------------------------ Je vous invite à faire partie de mon réseau professionnel en ligne sur le site LinkedIn. Accepter l'invitation de Max Gunther http://www.linkedin.com/e/-qq80um-h0kxjfmi-1w/qaAr-Z_86TRZ5lXG-dA9kZQ49qSe5… Voir l'invitation de Max Gunther http://www.linkedin.com/e/-qq80um-h0kxjfmi-1w/qaAr-Z_86TRZ5lXG-dA9kZQ49qSe5… ------------------------------------------ Quel est l'intérêt de faire partie du réseau de Max Gunther ? Le réseau de Max Gunther développera votre propre réseau : Si vous acceptez l'invitation de Max Gunther, vous pourrez voir qui vous connaissez dans son réseau et demander à Max Gunther de vous présenter. Appartenir à un réseau est toujours un plus pour votre carrière. -- (c) 2012, LinkedIn Corporation

1 0

Re: [Freesurfer] white-gray contrast algorithm
by Douglas N Greve 02 Apr '12

02 Apr '12

why don't you use the gray/white contrast map that freesurfer produces? On 04/02/2012 04:24 PM, John Fredy wrote: > Dear Douglas and David, > > I am trying to know the gray-white contrast in images from epileptic > patients. In know that I can use the freesurfer surface to obtain the > coordinates for the interface between gray-white substance, but some > help is welcome because the paper that I read introduce elements like > use the data 0.5 before and 0.5 after the interface > > How I can convert the surface to voxel coordinates? > > How I can obtain the data (0.5 mm) out of the resolution of my images > (that is 1 mm)? > > Any interpolation suggestion? > > Exists some code that I can use > > Thanks in advance > > John Ochoa > Bioingeniería > Universidad de Antioquia > > On Mon, Apr 2, 2012 at 12:12 PM, Bruce Fischl > <fischl(a)nmr.mgh.harvard.edu <mailto:fischl@nmr.mgh.harvard.edu>> wrote: > > Hi John > > Doug and David (ccd) can point you in the right direction once you > are done with your surface recons > > cheers > Bruce > > > On Mon, 2 Apr 2012, John Fredy wrote: > > Dear Bruce, > I have interest in the tools that you mentioned > > Best > > John Ochoa > > On Sat, Mar 31, 2012 at 5:31 PM, Bruce Fischl > <fischl(a)nmr.mgh.harvard.edu <mailto:fischl@nmr.mgh.harvard.edu>> > wrote: > Hi John > > we can provide that for you if you download and install > FreeSurfer, then run recon-all on your data. We also provide > tools for computing gray/white contrast once recon-all > has been > run. > > cheers > Bruce > > On Sat, 31 Mar 2012, John Fredy wrote: > > Hello all, I am looking for a white-gray matter contrast > algorithm > > I see the publication: Individual Differences in Verbal > Abilities Associated > with Regional Blurring of the Left Gray and White Matter > Boundary > > http://www.ncbi.nlm.nih.gov/pubmed/22031871 > > But,how I can obtain the coordinates of the interface > between gray and white > matter? > > Thanks in advance > > > > > > > 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

2 1

Re: [Freesurfer] TRACULA exited with errors
by Anastasia Yendiki 02 Apr '12

02 Apr '12

Hi Carolina - The bvecs file that you're attaching has commas as the decimal separator. See this suggestion: http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg18395.html The input DWIs can be in a format other than dicom, but then some additional inputs must be specified, see: http://surfer.nmr.mgh.harvard.edu/fswiki/dmrirc Also, from http://surfer.nmr.mgh.harvard.edu/fswiki/Tracula: Note that, because TRACULA relies on the underlying anatomy as derived from the FreeSurfer cortical parcellation and subcortical segmentation, these need to be generated before running trac-all. This means that before you run trac-all you will have to analyze your subjects' anatomical images with recon-all and make sure that they have a good-quality mri/aparc+aseg.mgz. Hope this helps, a.y On Mon, 2 Apr 2012, Carolina Valencia wrote: > I have under dmri folder of Diff001 2 files bvals and bvecs without an order of columns, in the same folder I found files called > dwi_orig.mghdti.bvals andbvecs which have the rows and columns you said. I attached the files (I rename them to old in order to save > the correct ones) Regarding the question to process my own data. I have to recon-all my structural data and to have the orig DWI > dicoms in order to use trac-all, right? > > Thanks for the help! > > 2012/4/2 Anastasia Yendiki <ayendiki(a)nmr.mgh.harvard.edu> > > Hi Carolina - The bvecs and bvals in the tutorial data should have 3 lines and 1 line, respectively, with 70 entries in > each line. Is that not what you have? > > For different possibilities for inputs, please see the tracula wiki page, and particularly the link to the example dmrirc > file: > http://surfer.nmr.mgh.harvard.edu/fswiki/Tracula > > a.y > > On Mon, 2 Apr 2012, Carolina Valencia wrote: > > > Hi FS users > I'm trying to run TRACULA tutorial without sucess. After setting the dmrirc_single_subject and run the first > command step trac-all > -prep -c $TUTORIAL_DATA/diffusion_tutorial/scripts/dmrirc_single_subject > It exited with ERRORS, related to bvecs and bvals which is weird because I downloaded the data via wget and > chech the size. > > #@# Tensor fit lun abr 2 13:23:46 COT 2012 > dtifit -k /home/cvalencia/freesurfer/subjects/tracula_tutorial//diffusion_tutorial/Diff001/dmri/dwi.nii.gz -m > /home/cvalencia/freesurfer/subjects/tracula_tutorial//diffusion_tutorial/Diff001/dlabel/diff/aparc+aseg_mask.bbr.nii.gz > -r > /home/cvalencia/freesurfer/subjects/tracula_tutorial//diffusion_tutorial/Diff001/dmri/bvecs -b > /home/cvalencia/freesurfer/subjects/tracula_tutorial//diffusion_tutorial/Diff001/dmri/bvals -o > /home/cvalencia/freesurfer/subjects/tracula_tutorial//diffusion_tutorial/Diff001/dmri/dtifit > Error: bvecs and bvals don't have the same number of entries > Linux cvalencia-Precision-WorkStation-T3400 2.6.35-32-generic-pae #67-Ubuntu SMP Mon Mar 5 21:23:19 UTC 2012 > i686 GNU/Linux > > trac-preproc exited with ERRORS at lun abr 2 13:23:49 COT 2012 > > Another question is related to process my own data. I have to recon-all my structural data and to have the > orig DWI dicoms in order to > use trac-all, right? > > Many thanks, > > Best regards > -- > -- > Carolina Valencia M > > > > > 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. > > > > > -- > -- > Carolina Valencia M > >

1 0

fsgd contrast question
by McGwier, Meghan (NIH/NIMH) [F] 02 Apr '12

02 Apr '12

Dear experts, I've been reading through the tutorial for group analysis, but I am still a little confused about the contrasts and want to make sure that my contrast is set properly for what I'm interested in looking for. I've made my fsgd file, which contains three groups: ADdiagnosisGroup1, ADdiagnosisGroup2, ADdiagnosisGroup3, and one continuous variable: symptom duration. I want to test if thickness differs between groups controlling for symptom duration. I set my contrasts to: [1 0 -1 0 0 0], [1 -1 0 0 0 0], [0 1 -1 0 0 0]. Since there isn't an fsgd example for 3 groups (1 factor, 3 levels), and one covariate, I wasn't sure if this is correct. Thanks in advance, Meghan Meghan McGwier Postbaccalaureate IRTA Fellow Molecular Imaging Branch National Institute of Mental Health Phone: 301-451-2038 Fax: 301-480-3610

2 1

Custom Fill does not fill
by Kiley Seymour 02 Apr '12

02 Apr '12

Dear experts I have just completed all of the steps leading up to overlaying retinotopy activation on an inflated brain. I have been able to Make a Closed Path, but unfortunately when I press the Custom Fill nothing happens. Any ideas why this is the case. I have been using tksurfer-sess -c polar -a rtopy.self.lh -s Subject1 Thanks. Kiley

3 4

TRACULA exited with errors
by Carolina Valencia 02 Apr '12

02 Apr '12

Hi FS users I'm trying to run TRACULA tutorial without sucess. After setting the dmrirc_single_subject and run the first command step trac-all -prep -c $TUTORIAL_DATA/diffusion_tutorial/scripts/dmrirc_single_subject It exited with ERRORS, related to bvecs and bvals which is weird because I downloaded the data via wget and chech the size. #@# Tensor fit lun abr 2 13:23:46 COT 2012 dtifit -k /home/cvalencia/freesurfer/subjects/tracula_tutorial//diffusion_tutorial/Diff001/dmri/dwi.nii.gz -m /home/cvalencia/freesurfer/subjects/tracula_tutorial//diffusion_tutorial/Diff001/dlabel/diff/aparc+aseg_mask.bbr.nii.gz -r /home/cvalencia/freesurfer/subjects/tracula_tutorial//diffusion_tutorial/Diff001/dmri/bvecs -b /home/cvalencia/freesurfer/subjects/tracula_tutorial//diffusion_tutorial/Diff001/dmri/bvals -o /home/cvalencia/freesurfer/subjects/tracula_tutorial//diffusion_tutorial/Diff001/dmri/dtifit Error: bvecs and bvals don't have the same number of entries Linux cvalencia-Precision-WorkStation-T3400 2.6.35-32-generic-pae #67-Ubuntu SMP Mon Mar 5 21:23:19 UTC 2012 i686 GNU/Linux trac-preproc exited with ERRORS at lun abr 2 13:23:49 COT 2012 Another question is related to process my own data. I have to recon-all my structural data and to have the orig DWI dicoms in order to use trac-all, right? Many thanks, Best regards -- -- *Carolina Valencia M*

2 1

Re: [Freesurfer] coreg error
by Douglas N Greve 02 Apr '12

02 Apr '12

There does not appear to be an error at the end. doug On 04/02/2012 12:58 PM, Borzello, Mia wrote: > mri_convert -i ~/subjects/RIH-E1_PostOp_CT/S0000/SE0003/I0000 -o ct.mgz > mri_convert -i /homes/9/miaborz/subjects/RIH-E1_PostOp_CT/S0000/SE0003/I0000 -o ct.mgz > $Id: mri_convert.c,v 1.179.2.2 2011/05/16 20:53:47 greve Exp $ > reading from /homes/9/miaborz/subjects/RIH-E1_PostOp_CT/S0000/SE0003/I0000... > Starting DICOMRead2() > dcmfile = /homes/9/miaborz/subjects/RIH-E1_PostOp_CT/S0000/SE0003/I0000 > dcmdir = /homes/9/miaborz/subjects/RIH-E1_PostOp_CT/S0000/SE0003 > Ref Series No = 6 > Found 138 files, checking for dicoms > Found 136 dicom files in series. > First Sorting > Computing Slice Direction > Vs: 0 0 1.25 > Vs: 0 0 1 > Second Sorting > Counting frames > nframes = 1 > nslices = 136 > ndcmfiles = 136 > PE Dir = UNKNOWN (dicom read) > TransferSyntaxUID: --1.2.840.10008.1.2.1-- > jpegUID: --1.2.840.10008.1.2.4-- > Loading pixel data > TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 > i_ras = (-1, -0, 0) > j_ras = (-0, -1, 0) > k_ras = (-0, -0, 1) > writing to ct.mgz... > ________________________________ > From: freesurfer-bounces(a)nmr.mgh.harvard.edu [freesurfer-bounces(a)nmr.mgh.harvard.edu] on behalf of Douglas Greve [greve(a)nmr.mgh.harvard.edu] > Sent: Monday, April 02, 2012 10:00 AM > To: freesurfer(a)nmr.mgh.harvard.edu > Subject: Re: [Freesurfer] coreg error > > Can you paste the terminal output into the email instead of sending a pic? > > On 4/2/12 9:54 AM, Borzello, Mia wrote: > > Morning guys, > > > I ran the MRI recon Saturday and today was trying to convert the CT dicoms to mgz format using the command "mri_convert -i first ct.dicom -o ct.mgz", but got an error. I'm sure there's a better way to do this, but i attached a screenshot of the error (I don't know how to copy and paste since ctrl + c doesn't work.) > > > > Thanks! > Mia > ________________________________________ > From: freesurfer-bounces(a)nmr.mgh.harvard.edu<mailto:freesurfer-bounces@nmr.mgh.harvard.edu> [freesurfer-bounces(a)nmr.mgh.harvard.edu<mailto:freesurfer-bounces@nmr.mgh.harvard.edu>] on behalf of Borzello, Mia > Sent: Sunday, April 01, 2012 10:59 PM > To: freesurfer(a)nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu> > Subject: [Freesurfer] coreg error > > Hey guys, > > When i run mri_convert to get ct.mgz, everything runs, and i get a ct.mgz > file. but when i use spmregister, it says that spm.reg.dat is > unrecognizable. How can i remedy this? > > Thanks so much! > Mia > > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu<mailto:Freesurfer@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: www.nmr.mgh.harvard.edu/facility/filedrop/index.html

2 6

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