Freesurfer February 2014

freesurfer@nmr.mgh.harvard.edu

128 participants
236 discussions

Fwd: Difficulties with including hypo-intense areas (MS-lesions) as white matter without additionally transforming the lesion into "normal white matter".
by Linn Christin Bonaventure Norbom 03 Feb '14

03 Feb '14

---------- Forwarded message ---------- From: Linn Christin Bonaventure Norbom <linnnorbom(a)gmail.com> Date: Mon, Feb 3, 2014 at 5:44 PM Subject: Re: [Freesurfer] Difficulties with including hypo-intense areas (MS-lesions) as white matter without additionally transforming the lesion into "normal white matter". To: Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> Hi again, Sorry for being unclear. Here is a picture of the lesion. If I understand correctly it is now NOT included as white matter. All I want to do is include it as white matter, so that it will be registered as a hypo-intense area in aseg.stats. So the way to do this is to edit the aseg.mgz and not the wm.mgz? Cheers Linn Norbom On Mon, Feb 3, 2014 at 5:30 PM, Bruce Fischl <fischl(a)nmr.mgh.harvard.edu>wrote: > Hi Linn > I'm not sure I understand, but if you can paste them into the aseg.mgz as > hypointensities I think things should work properly > > cheers > Bruce > > On Mon, 3 Feb 2014, Linn Christin Bonaventure Norbom wrote: > > Hi, >> >> I would like to include unregistered hypo-intense lesions into white >> matter >> (as now they are excluded from cortex, and not registered as anything) >> without transforming the lesion from hypo-intense to normal (110). Is it >> possible to include these areas in white matter and additionally keep the >> statistic volume of these areas as hypo-intense-wm in the aseg.stats? >> >> >> Thank you in advance, >> Regards Linn Norbom >> >> >> > > 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. >

3 2

Difficulties with including hypo-intense areas (MS-lesions) as white matter without additionally transforming the lesion into "normal white matter".
by Linn Christin Bonaventure Norbom 03 Feb '14

03 Feb '14

Hi, I would like to include unregistered hypo-intense lesions into white matter (as now they are excluded from cortex, and not registered as anything) without transforming the lesion from hypo-intense to normal (110). Is it possible to include these areas in white matter and additionally keep the statistic volume of these areas as hypo-intense-wm in the aseg.stats? Thank you in advance, Regards Linn Norbom

2 1

Destrieux Atlas with Kid brains
by Mher Alaverdyan 03 Feb '14

03 Feb '14

Hi all, I just wanted to know if it is acceptable to use the Destrieux atlas in FS for parcellation of brain images of pre-adolescents. If not this atlas, then which would be a recommended atlas to use for this population. Thanks

2 5

calculating spc on lobes annotation in longitudinal structural analysis
by Jeremy Young 03 Feb '14

03 Feb '14

Dear all, I'm trying to get thickness spc stats for the individual lobe labels (specifically the frontal lobe) I created per subject per time point (in subject's longitudinal analysis template space) using: mri_annotation2label --subject $i --hemi ?h --lobesStrict ?h.lobes I've run mris_anatomical_stats to get out the stats and put them in each subject and time point's stats folder: mris_anatomical_stats -a lobes.annot -f $i/stats/lh.lobes.stats $i ?h Now I'm trying to calculate the spc using: long_stats_slopes --qdec long.qdec.table.dat --stats lh.lobes --meas thickness --do-spc --time years --out-spc lh.spc.lobes.txt but I'm getting an error (it works when I use the regular aparc and aseg stats files though). Here's my output: --- Parsing the qdec table: long.qdec.table.dat Working in SUBJECTS_DIR: /home/j/jy/jy72/scratch/AE/FSstruct/ Subject-Template: CISC4962plate INFO: 2 TPs in CISC4962plate , mean age: 0.565 aparcstats2table --common-parcs --hemi lh --parc lobes --subjects CISC4962.long.CISC4962plate CISC4962-2.long.CISC4962plate --meas thickness --tablefile ./tmp-CISC4962plate_lh.lobes_thickness_Hal4Vg/long.lh.lobes.thickness-stack.dat -d space SUBJECTS_DIR : /home/j/jy/jy72/scratch/AE/FSstruct/ Parsing the .stats files Building the table.. Writing the table to ./tmp-CISC4962plate_lh.lobes_thickness_Hal4Vg/long.lh.lobes.thickness-stack.dat Writing ./tmp-CISC4962plate_lh.lobes_thickness_Hal4Vg/X-long.mat ... mri_glmfit --table ./tmp-CISC4962plate_lh.lobes_thickness_Hal4Vg/long.lh.lobes.thickness-stack.dat --X ./tmp-CISC4962plate_lh.lobes_thickness_Hal4Vg/X-long.mat --allow-zero-dof --no-contrasts-ok --glmdir ./tmp-CISC4962plate_lh.lobes_thickness_Hal4Vg/glm $Id: mri_glmfit.c,v 1.196.2.6 2011/05/05 20:54:25 greve Exp $ cwd /mnt/lustre/scratch/jeremy/AE/FSstruct/qdec cmdline mri_glmfit --table ./tmp-CISC4962plate_lh.lobes_thickness_Hal4Vg/long.lh.lobes.thickness-stack.dat --X ./tmp-CISC4962plate_lh.lobes_thickness_Hal4Vg/X-long.mat --allow-zero-dof --no-contrasts-ok --glmdir ./tmp-CISC4962plate_lh.lobes_thickness_Hal4Vg/glm sysname Linux hostname apollo-login machine x86_64 user jy72 FixVertexAreaFlag = 1 UseMaskWithSmoothing 1 OneSampleGroupMean 0 y /mnt/lustre/scratch/jeremy/AE/FSstruct/qdec/tmp-CISC4962plate_lh.lobes_thickness_Hal4Vg/long.lh.lobes.thickness-stack.dat logyflag 0 X ./tmp-CISC4962plate_lh.lobes_thickness_Hal4Vg/X-long.mat usedti 0 glmdir ./tmp-CISC4962plate_lh.lobes_thickness_Hal4Vg/glm IllCondOK 0 ReScaleX 1 DoFFx 0 Creating output directory ./tmp-CISC4962plate_lh.lobes_thickness_Hal4Vg/glm Loading y from /mnt/lustre/scratch/jeremy/AE/FSstruct/qdec/tmp-CISC4962plate_lh.lobes_thickness_Hal4Vg/long.lh.lobes.thickness-stack.dat Found 6 data colums Found 2 data rows Saving design matrix to ./tmp-CISC4962plate_lh.lobes_thickness_Hal4Vg/glm/Xg.dat Normalized matrix condition is 1 Matrix condition is 1.76991 search space = 6.000000 DOF = 0 Starting fit and test Fit completed in 0 minutes Writing results lh.lobes.thickness lh_frontal_thickness lh_cingulate_thickness lh_occipital_thickness lh_temporal_thickness lh_parietal_thickness lh_insula_thickness mri_glmfit done mri_convert --frame 0 ./tmp-CISC4962plate_lh.lobes_thickness_Hal4Vg/glm/beta.mgh ./tmp-CISC4962plate_lh.lobes_thickness_Hal4Vg/beta0.mgh mri_convert --frame 0 ./tmp-CISC4962plate_lh.lobes_thickness_Hal4Vg/glm/beta.mgh ./tmp-CISC4962plate_lh.lobes_thickness_Hal4Vg/beta0.mgh $Id: mri_convert.c,v 1.179.2.2 2011/05/16 20:53:47 greve Exp $ reading from ./tmp-CISC4962plate_lh.lobes_thickness_Hal4Vg/glm/beta.mgh... 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) keeping frame 0 writing to ./tmp-CISC4962plate_lh.lobes_thickness_Hal4Vg/beta0.mgh... mri_convert --frame 1 ./tmp-CISC4962plate_lh.lobes_thickness_Hal4Vg/glm/beta.mgh ./tmp-CISC4962plate_lh.lobes_thickness_Hal4Vg/beta1.mgh mri_convert --frame 1 ./tmp-CISC4962plate_lh.lobes_thickness_Hal4Vg/glm/beta.mgh ./tmp-CISC4962plate_lh.lobes_thickness_Hal4Vg/beta1.mgh $Id: mri_convert.c,v 1.179.2.2 2011/05/16 20:53:47 greve Exp $ reading from ./tmp-CISC4962plate_lh.lobes_thickness_Hal4Vg/glm/beta.mgh... 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) keeping frame 1 writing to ./tmp-CISC4962plate_lh.lobes_thickness_Hal4Vg/beta1.mgh... mris_calc -o ./tmp-CISC4962plate_lh.lobes_thickness_Hal4Vg/long.lh.lobes.thickness-spc.dat.mgh ./tmp-CISC4962plate_lh.lobes_thickness_Hal4Vg/beta1.mgh div ./tmp-CISC4962plate_lh.lobes_thickness_Hal4Vg/beta0.mgh ERROR: mris_calc compute sym. pct. change (spc) problem? --- Am I missing a step somewhere when trying to do this? Please help. Thanks! Jeremy -- Jeremy Young PhD Researcher Behavioural and Clinical Neuroscience School of Psychology University of Sussex Brighton BN1 9QH 01273 872776 J.Young(a)sussex.ac.uk

1 0

tkmedit.bin: Command not found
by Saurabh Thakur 03 Feb '14

03 Feb '14

Hello, I have just installed freesurfer in my linux ubuntu12.04 machine. I am getting error such as : *tkmedit.bin: Command not found* but the recon-all --help is working perfectly. My environment variable is working. Please help me where i m going wrong asap. Saurabh T.

2 2

A question regarding DODS or DOSS
by KimMJ 02 Feb '14

02 Feb '14

Dear Doug and experts My question is about the choice of DODS or DOSS.I want to compare cortical thickness between 2 groups (disease group and control group), while controlling for the effect of age (nuisance covariate).I've already read through the mailing list about the issue of DODS and DOSS designs. If I understand correctly, I have to first use DODS (QDEC) in order to find areas of significant group*age interaction by using the contrast (0 0 1 -1).Given there is no area of interaction that survived multiple comparisons correction, I can go with DOSS (1 -1 0) using mri_glmfit (command line) to test between-group differences in cortical thickness, controlling for the effect of age. Am I right? My another question is that 'MUST' I rerun DOSS model after confirming no group*age interaction in DODS ? Or can I directly use the results of DODS to look for between-group differences controlling for age (1 -1 0 0), since there is no group*age interaction ?Is there much difference in results between the above-mentioned two approaches?I've found a reply by Doug from the mailing list: If there is no interaction, then either DODS or DOSS is appropriate. DOSS will be more powerful and a little more interpretable (http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg33418.html) From this context, what does the 'powerful' mean? Does DOSS yield higher statistical values than DODS? Apology for the beginner's questions.Thank you in advance for your help. MJ

4 5

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 2014