Freesurfer

freesurfer@nmr.mgh.harvard.edu

15 participants
30097 discussions

optimal T1 protocol
by Jason Tourville 20 May '16

20 May '16

Hello freesurfer experts, Do you have a recommended "optimal" T1 protocol on Bay 1 for cortical reconstruction? For the past couple years, we've been using the 'tf1_mgh_multiecho_1mm_iso" protocol which has PAT = 2 and a TA = 6:02. 􀀈􀀎 I'm wondering if a faster option at the same resolution is now available that is recon-approved? For instance, a multi-band option? Thanks for any feedback, Jason

2 1

Cluster Color
by Timothy Hendrickson 20 May '16

20 May '16

Free Surfer Support, I have been using the command line version for group analysis since my data set has too many factors for QDEC. There are a few things that I enjoy about QDEC that I wish I could incorporate into the command line. 1) In QDEC the cluster color is not set arbitrarily, but rather based on significance. Is there any way to have the cluster color be set based on significance at command line? Is there a way to restrict the available colors that the clusters can be set as? Occasionally, cluster colors are a very similar color to the inflated underlay making it difficult to determine the outline of said cluster. 2) In QDEC one is able to visualize a scatter plot for a particular cluster. Is there any way to do this via the command line option? Thank you, -Tim Hendrickson -- Timothy Hendrickson Department of Psychiatry University of Minnesota Mobile: 507-259-3434 (texts okay)

1 1

segfault using brainstem module from dev version
by Vincent Beliveau 20 May '16

20 May '16

Hi list (and Eugenio), I've ran the brainstem module from the dev version on some data processed with FS v5.3. The module created some great segmentations of brainstem but when taking a closer look at the log file, there is 2 seg faults which occur when calls to mri_robust_register are made, with the following output (full log attached, see line 319 and 371): /data1/vbeliveau/software/freesurfer-Linux-centos4_x86_64-dev-110516/bin//mri_robust_register: line 3: 36835 Segmentation fault mri_robust_register.bin "$@" /data1/vbeliveau/software/freesurfer-Linux-centos4_x86_64-dev-110516/bin//mri_robust_register --mov imageDump.mgz --dst /indirect/data1/vbeliveau/atlas/proc/MR/recon_final/f5249_GD/tmp/BS_T1based//BS-DE-binaryMask_autoCropped.mgz -lta trash.lta --mapmovhdr imageDump_coregistered.mgz --sat 50: Segmentation fault mv: cannot stat ?imageDump_coregistered.mgz?: No such file or directory I'm curious about how is this affecting the overall process, as otherwise everything appears to be working smoothly. Best, Vincent. -- Vincent Beliveau, MSc Neurobiology Research Unit Juliane Maries Vej 28, 3rd floor Rigshospitalet, building 6931 DK-2100 Copenhagen, Denmark phone: +45 3545 6718 e-mail: vincent.beliveau(a)nru.dk

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Question about group analysis
by Josh Gray 20 May '16

20 May '16

Hello, I've got a very basic question related to group analysis. If I want run a correlation of voxels in the cortex with a variable *controlling *for another continous variable, how do I do this. I know how to run them both in a GLM simultaneously by coding the matrix 0 1 1, however, how do I look at the first variable after controlling for the other? Here is an example of my current fsgd input (I want to control for income): GroupDescriptorFile 1 Title MyTitle Class Class1 plus blue CLASS Class2 circle green SomeTag Variables impulsivity income Input subjid1 Main 10 100 Input subjid2 Main 20 200 etc. -- Graduate Student Psychology Dept. - Clinical Program Experimental & Clinical Psychopharmacology Laboratory University of Georgia

1 0

R: MASK.label from fsaverage to volume in subject space
by stdp82＠virgilio.it 20 May '16

20 May '16

Specifically, I have a .label from tksurfer and I would like to report this label on subj orig.nii.gz ----Messaggio originale---- Da: stdp82(a)virgilio.it Data: 20-mag-2016 10.36 A: <freesurfer(a)nmr.mgh.harvard.edu> Ogg: [Freesurfer] MASK.label from fsaverage to volume in subject space Hi list, to trasform a MASK.label (created by tk surfer) from surface to volume is correct to use: 1. mri_surf2surf to register the mask from fsaverage to subj space2. mri_surf2vol to report the label (subj space) to volume (subj space) Thanks. Stefano

2 1

MASK.label from fsaverage to volume in subject space
by stdp82＠virgilio.it 20 May '16

20 May '16

Hi list, to trasform a MASK.label (created by tk surfer) from surface to volume is correct to use: 1. mri_surf2surf to register the mask from fsaverage to subj space2. mri_surf2vol to report the label (subj space) to volume (subj space) Thanks. Stefano

1 0

create a table from measures under multiple subjects
by Liu Y 20 May '16

20 May '16

Hi Freesurfers, I calculated the thicknesses of a cluster for some subjects, and each of the measure was saved under each subject' s folder. How to create a table containing all the measures? What is the command? Thanks, Yawu

2 2

Error with mris_anatomical_stats
by Mahtab Farahbakhsh 19 May '16

19 May '16

Dear FreeSurfer, I have a problem when I use mris_anatomical_stats. It gives me an error saying that it couldn't read the input volume which is the wm.mgz file. would you please help me how I should fix this problem? Best Regards, Mahtab.

3 6

Estimation of FWHM on surface.
by Jan Willem Koten 19 May '16

19 May '16

1 0

Help with error in mkcontrast-sess command
by José Paredes Pacheco 19 May '16

19 May '16

Hi Freesurfers I am doing FSFAST with my own data and have a problem. After I run mkanalysis-sess command succesfully, I try to run mkcontrast-sess command but I get an error during the process. The text in my terminal window is the following: root@usuario2:/home/usuario2... mkcontrast-sess -analysis event.sm5.lh -contrast NW-mayor-Rest -c 1 -a 2 INFO: Found 2 Non-Null Conditions INFO: Found 1 Delays Condition Weights: -1.00000000000000000000 1.00000000000000000000 mkcontrast2 -config event.sm5.lh/NW-mayor-Rest.config -anadir event.sm5.lh -wcond -1.00000000000000000000 1.00000000000000000000 -sumconds -o event.sm5.lh/NW-mayor-Rest.mat -wdelay 1 -no-octave $Id: mkcontrast2,v 1.2 2015/12/10 22:51:30 zkaufman Exp $ cmtxfile event.sm5.lh/NW-mayor-Rest.mat nconds 2, wcond -1.00000000000000000000 1.00000000000000000000 ndelays 1, wdelay 1 ndelays 1, wpsa sumconds 1 sumdelays 0 nircorr 0 TER 0.050000 rdelta rtau cmtxfile event.sm5.lh/NW-mayor-Rest.mat monly 0 NCond 2 WCond -1.00000000000000000000 1.00000000000000000000 NDelay 1 WDelay 1 TER 0.050000 sumconds 1 sumdelays 0 nircorr 0 TPreStim 0 RmPreStim 0 rdelta 0 0 rtau 0 0 ndelays 1 CNorm 1 setwdelay 0 setwcond 0 Matlab file is /tmp/mkcontrast2.10601.m MATLAB is selecting SOFTWARE OPENGL rendering. < M A T L A B (R) > Copyright 1984-2015 The MathWorks, Inc. R2015b (8.6.0.267246) 64-bit (glnxa64) August 20, 2015 To get started, type one of these: helpwin, helpdesk, or demo. For product information, visit www.mathworks.com. Academic License >> Undefined function or variable 'mkcontrast2m'. >> jue may 19 16:28:24 CEST 2016 root@usuario2:/home/usuario2... It doesn't find the function or variable 'mkcontrast2m' and I don't know what I have to do. Can somebody help me? Thanks you in advance. All the best, José

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