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30132 discussions

dt_recon registration
by Antonella Kis 14 Nov '11

14 Nov '11

Dear Bruce, I was reading the dt_recon tutorial and also the tutorial for the DTI Basics and I am very confused regarding how I should use my dt_recon in order to register my subjects on the CVS space and do a group study for FA and mean diffusivity. 1) I will be very grateful if you can confirm if my coding is write. First can you please let me know if by default dt_recon is re-sample FA to talairch space? In this case because I want to register on CVS should I add the --no-tal flag? I am asking this question because after I ran the following command I see in my output directory called P07_dti a file called fa_tal.nii as well as fa_tal.nii.reg. 2) Do I need this files if I want to do a group study for my FA and mean diffusivity, similar to TBSS in FSL? 3) Can I use the talairch registration or should I use the CVS? 4) Should I add the flag --no-tal? This is what I was running: setenv FREESURFER_HOME /usr/local/freesurfer setenv SUBJECTS_DIR $FREESURFER_HOME/subjects/DTI_FS/dtrecon dt_recon --i P07_dti.nii.gz -- b P07.bvals P07.bvects --s P07 --o P07_dti where P07_dti.nii.gz is my DTI volume P07.bvals P07.bvects are the bvals and bvects for my subject P07 is my structural recons data for my P07 subject 5) From the dt_recon --help I understand that dt_recon is doing the registration of lowb to same-subject anatomical using FSLs flirt (creates mask.nii and register.dat). mri_vol2vol --mov /usr/local/freesurfer/subjects/DTI_FS/dtrecon/P07_dti/lowb.nii \ --targ $SUBJECTS_DIR/P07/mri/wmparc.mgz \ --inv --interp nearest --o $SUBJECTS_DIR/P07/mri/wmparc2diff.mgz \ --reg /usr/local/freesurfer/subjects/DTI_FS/dtrecon/P07_dti/register.dat --no-save-reg 6) Should I run mri_vol2vol to re-sample the structural volume in the diffusion space and register in the CVS space: mri_vol2vol --targ $FREESURFER_HOME/subjects/cvs_avg35/mri/norm.mgz \ --m3z $SUBJECTS_DIR/$subj/cvs/combined_tocvs_avg35_elreg_afteraseg-norm.m3z \ --noDefM3zPath --reg $TUTORIAL_DIR/$subj/dtrecon/register.dat \ --mov /usr/local/freesurfer/subjects/DTI_FS/dtrecon/dti_15_p7/fa-masked.mgz \ --o /usr/local/freesurfer/subjects/DTI_FS/dtrecon/dti_15_p7/fa-masked.ANAT+CVS-to-avg35.mgz \ --interp trilin --no-save-reg 7) I found online that the default CVS template is cvs_avg35 which is supplied with my FreeSurfer distribution. Can you please tell me in which directory is located or how I can obtain the cvs_avg35? Thank you very much for your time, your valuable explanations and help. Antonella

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CVS template for registration
by Antonella Kis 14 Nov '11

14 Nov '11

Dear all: Based on the DTI Basic Tutorial I understood that MRI data can be resampled & registered in CVS space (by running mri_cvs_register), but alternatively can be normalized in any other (for example, MNI or Talairach). Can you please let me know how this can be done in MNI152 space? Should I run mri_mni152_register? Is CVS a good template for younger subjects (children age 6-13)? Many thanks, Antonella

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DTI Group Analysis Study
by Antonella Kis 14 Nov '11

14 Nov '11

Hi, I am trying to do a DTI Group Analysis study using a MNI152 standard space for registration. 1). I wonder in case I want to use MNI 152 and not CVS space using TRACULA if I have to follow all the steps starting Setting Up a Configuration File to run Tracula and then to continue with the following three steps in the TRACULA processing stream (which is called by the command trac-all): * Pre-processing * FSL's bedpostX * Reconstructing white-matter (WM) pathways 2). Can I check the registration for individual subjects to see if it worked well or not on the MNI 152 template? 3) How can I see if there are clusters that survives to multiple comparison in group 1 (controls) versus group 2 (patients) without and covariant (not gender, not age). Can I get a txt file as output for this clusters? Thank you. Antonella

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error with mri_glmfit and question about registering rh to lh
by kelsi 14 Nov '11

14 Nov '11

Hi all, I receive the error: ERROR: MRISread: cannot read surface data from file ./long/surf/lh.thickness.fsaverage.S1-S3.mgh! when I run mri_glmfit with the command: mri_glmfit --glmdir long/g1v0 --surf long lh thickness.fsaverage.S1-S3.mgh --fsgd long/S1-S3.fsgd --osgm I am working on mri_glmfit for a one sample ttest of the thickness of multiple patients, all qcached to fsaverage. I ran the reconstruction and then ran -qcache for each subject. I then used mri_calc to find the difference in thicknesses of Session 1 and 3 for each patient (in fsaverage) and concatenated with mri_concat for the glm. But when I run the glm, it gives me the above error. How would I fix this? Also, I am wondering if there is a way to register the right hemisphere to the left hemisphere, since we are working with stroke patients and would like to compare all the contralesional hemispheres. Thank you! Kelsi

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reconstruction stop
by LAOUCHEDI MAKHLOUF 14 Nov '11

14 Nov '11

hi i am new in freesurfer (even if i used it many times doing reonstructions using the script reconn-all in the past and on another machine), i launched a reconstruction of one patient using the reconn-all script and i gave before this the path to the SUBJECTS_dir. and one or two minutes later it stopped and prompted "recon-all finished without error at Mon Nov 14 13:44:11 CET 2011 done" and all the directories in the SUBJECTS_DIR were created with the mgz file created. thank you

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mri_glmfit error
by kelsi 13 Nov '11

13 Nov '11

Hi Freesurfers, I am having problems with mri_glmfit. I am doing a one sample ttest with thickness values. However, when i enter "-surf Subject1 lh thickness.fsaverage.mgh", I receive an error message saying that the surface could not be opened. The path is correct and I entered "setenv SUBJECTS_DIR ./" in my directory before running the glm. How would I fix this error? Thank you! Kelsi Hirai

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Amazon EC2 Version of FreeSurfer 5.1 Available
by Pedro Paulo de Magalhães Oliveira Junior 11 Nov '11

11 Nov '11

Some weeks ago I was asked about a public image (AMI) to run in the Amazon EC2 infrastructure If you want to use FreeSurfer in the EC2 infrastructure you can use this public AMI: *060244368407/FREESURFER51* Just for your information this AMI can run a recon-all in 23 hours in an Amazon AWS Small Instance. So with the current Amazon cost per Small Instance/Hour you'll have a recon-all for USD 2.04 Amazon request a credit card in order to create an account in http://aws.amazon.com Hope it helps, Pedro Paulo Jr. --------------------------------------------------------------------- Pedro Paulo de Magalhães Oliveira Junior Netfilter & SpeedComm Telecom -- www.netfilter.com.br -- For mobile: http://itunes.apple.com/br/artist/netfilter/id365306441

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using expert-options on initial run
by Michael Harms 11 Nov '11

11 Nov '11

Hi guys, There is an issue with recon-all abending if you use the -expert option on the very first call to recon-all, because recon-all attempts to copy to $subjid/scripts/expert-options before the scripts directory has been created. As an attempted workaround I manually created an empty $subjid/scripts directory so that the directory already existed. However, in conjunction with the -i flag this then triggers the error of "existing subject" and the -force option no longer exists to force the process to proceed. cheers, -MH -- Michael Harms, Ph.D. -------------------------------------------------------------------- Conte Center for the Neuroscience of Mental Disorders Washington University School of Medicine Department of Psychiatry, Box 8134 Renard Hospital, Room 6604 Tel: 314-747-6173 660 South Euclid Ave. Fax: 314-747-2182 St. Louis, MO 63110 Email: mharms(a)wustl.edu --------------------------------------------------------------------

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mri_glmfit search space = 0
by kevin bickart 11 Nov '11

11 Nov '11

Hi all, I am conducting a contrast of z (r) maps from 3 seed-based resting-state networks (e.g., 1 > 2 and 3). To eliminate the influence of anticorrelations on the contrast results, I thresholded the z (r) maps at 0 before running mri_glmfit, thereby eliminating voxels with negative z (r) values. The command completed successfully but the resulting sig maps did not contain voxels with any values. I have attached the fsgd and contrast files and pasted the command and output below. Can anyone identify the problem here? Thanks, Kevin *Potentially problematic portion of output:* Pruning voxels by thr: 0.000000 Found 0 voxels in mask Saving mask to LR_Amy_lOFC2_glm2/mask.mgh search space = 0.000000 *Entire command and output: * [kreature:kbickart_fcmap_ASN_Anchor_AmyPks_buckner_YC] (nmr-stable5.1-env) mri_glmfit --y LR_Amy_lOFCpk2 _vs_vmPFCpk2_and_cACCpk2_pos_4D.nii.gz --allowsubjrep --fsgd /autofs/homes/006/kbickart/AmySubNet_glm/pa ired3.fsgd doss --C /autofs/homes/006/kbickart/AmySubNet_glm/paired.mat --glmdir LR_Amy_lOFC2_glm2 gdfReadHeader: reading /autofs/homes/006/kbickart/AmySubNet_glm/paired3.fsgd INFO: DeMeanFlag keyword not found, DeMeaning will NOT be done. Continuous Variable Means (all subjects) 0 roi1_vs_roi2_vs_roi3 0 0.707107 Class Means of each Continuous Variable 1 Class_081028_BC77WB 0.0000 2 Class_081028_XE45TK 0.0000 3 Class_081028_YY28TK 0.0000 .... $Id: mri_glmfit.c,v 1.196.2.6 2011/05/05 20:54:25 greve Exp $ cwd /autofs/cluster/animal/rs-fmri/YC/GROUP_STATS/kbickart/FCMAP/kbickart_fcmap_ASN_Anchor_AmyPks_buckne r_YC cmdline mri_glmfit --y LR_Amy_lOFCpk2_vs_vmPFCpk2_and_cACCpk2_pos_4D.nii.gz --allowsubjrep --fsgd /autof s/homes/006/kbickart/AmySubNet_glm/paired3.fsgd doss --C /autofs/homes/006/kbickart/AmySubNet_glm/paired .mat --glmdir LR_Amy_lOFC2_glm2 sysname Linux hostname kreature machine x86_64 user kbickart FixVertexAreaFlag = 1 UseMaskWithSmoothing 1 OneSampleGroupMean 0 y /autofs/cluster/animal/rs-fmri/YC/GROUP_STATS/kbickart/FCMAP/kbickart_fcmap_ASN_Anchor_AmyPks_buckn er_YC/LR_Amy_lOFCpk2_vs_vmPFCpk2_and_cACCpk2_pos_4D.nii.gz logyflag 0 usedti 0 FSGD /autofs/homes/006/kbickart/AmySubNet_glm/paired3.fsgd glmdir LR_Amy_lOFC2_glm2 IllCondOK 0 ReScaleX 1 DoFFx 0 Creating output directory LR_Amy_lOFC2_glm2 Loading y from /autofs/cluster/animal/rs-fmri/YC/GROUP_STATS/kbickart/FCMAP/kbickart_fcmap_ASN_Anchor_Am yPks_buckner_YC/LR_Amy_lOFCpk2_vs_vmPFCpk2_and_cACCpk2_pos_4D.nii.gz llINFO: gd2mtx_method is doss Saving design matrix to LR_Amy_lOFC2_glm2/Xg.dat Normalized matrix condition is 1 Matrix condition is 44.5 Pruning voxels by thr: 0.000000 Found 0 voxels in mask Saving mask to LR_Amy_lOFC2_glm2/mask.mgh search space = 0.000000 DOF = 177 Starting fit and test Fit completed in 0.0148667 minutes Computing spatial AR1 in volume. fMRIspatialAR1(): hit 0 voxels WARNING: no voxels in AR1 computation Residual: ar1mn = (nan,nan,nan) fwhm = (nan,nan,nan) nan Writing results paired maxvox sig=0 F=0 at index 0 0 0 seed=1321328111 mri_glmfit done -- Kevin Bickart MD-PhD Student Department of Anatomy and Neurobiology Boston University School of Medicine live UP to it

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Job posting for Purdue BME (fwd)
by Bruce Fischl 11 Nov '11

11 Nov '11

FYI ---------- Forwarded message ---------- Date: Fri, 11 Nov 2011 11:58:19 -0500 From: Thomas Talavage <tmt(a)purdue.edu> Subject: Job posting for Purdue BME Hi all --- Purdue has posted a job announcement for our BME department, including (substantial) potential to hire someone into medical imaging (with an emphasis on MRI). If any of you have current or recent graduates/post-docs who might be interested in a faculty position, please encourage them to submit their materials. We will probably start looking at applications sometime in December, with interviews in the Spring. The job posting (and information about submission) may be found at: https://engineering.purdue.edu/BME/AboutUs/FacultyPositions >From the MRI perspective, with the formation of a new College of Health and Human Sciences, there is now a growing interest in expanding our present clinical/research partnership to include an on-campus, research-only facility, with the potential for us to be pushing for this to be a non-clinical strength system. I am hopeful that if we can find an outstanding MRI-centric candidate, that we can help push this agenda as a part of the search/hiring process. Tom Talavage

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