Freesurfer July 2014

freesurfer@nmr.mgh.harvard.edu

163 participants
257 discussions

QDEC Cluster Analysis
by Mohammed Goryawala 01 Aug '14

01 Aug '14

Hello All, I have some questions related to the qdec analysis I have run. 1. On running the qdec I see that FWHM is an input which changes cluster definition significantly. How would I choose the right FWHM for the analysis and can it be related to any imaging parameters? 2. Secondly, on completion of the qdec analysis I want to export the clusters created by the qdec analysis into a volumetric file (which I can later convert to .nii). Please also suggest a way that would let me only export clusters above a particular size threshold. Thank you very much in advance. Mohammed Goryawala Department of Radiology University of Miami, Miller School of Medicine

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GLM error in QDEC
by McLaughlin, Katie 01 Aug '14

01 Aug '14

Hi Doug et al, I'm trying to run an analysis in QDEC and continue to get an error that says that the QDEC GLM design creates 0 factors. I'm attaching my data table here as well as the output of QDEC. I've tried deleting all variables in my data file other than one and testing just that comparison, but no luck. Any thoughts are much appreciated. Thanks, Kate SUBJECTS_DIR is '/net/rc-fs-nfs/ifs/data/Shares/DMC-Sheridan2/projects/SAS/FreeSurfer/FS_5.3' Input table: /neuro/labs/sheridanlab/projects/SAS/FreeSurfer/FS_5.3/qdec/qdec.table.maltreatment.dat Subj#, SubjID, Data... 1 1009 c 2 1014 c 3 1032 c 4 1034 c 5 1041 m 6 1043 m 7 1047 c 8 1058 m 9 1077 c 10 1094 m 11 1096 c 12 1097 c 13 1099 c 14 1100 m 15 1114 m 16 1119 m 17 1123 m 18 1125 c 19 1126 c 20 1128 c 21 1134 c 22 1137 m 23 1139 m 24 1142 m 25 1143 m 26 1153 m 27 1154 m 28 1157 c 29 1158 m 30 1163 m 31 1165 m 32 1166 m 33 1167 m 34 1171 c 35 1173 c 36 1175 c 37 1176 c 38 1177 m 39 1178 m 40 1179 c 41 1180 c 42 1181 c 1 maltreatment discrete 2 1 c 2 m Continuous Factors: Mean: StdDev: ------------------- ----- ------- Number of subjects: 42 Number of factors: 1 (1 discrete, 0 continuous) Number of classes: 2 Number of regressors: 2 ============================================================ ERROR: QdecGlmDesign::Create: zero factors!

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YANQ follow-up
by Krieger, Donald N. 01 Aug '14

01 Aug '14

Thanks again for the pointer, Bruce. You wrote: ... mri_convert -rl rawavg.mgz <input vol> <output vol> which does produce an output volume from which I now need to extract RAS voxel coordinates. A pointer to a keyboard command would be most welcome. Of interest is the difference between the color mappings for the input and output volumes in freeview. When using the lookup table in freeview they are quite different whereas in grayscale they are almost identical. I wonder if this is contributing to my difficulty in finding a tool to extract the voxel coordinates. Thanks again. Regards, Don Don Krieger, Ph.D. Department of Neurological Surgery University of Pittsburgh (412)648-9654 Office (412)521-4431 Cell/Text

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tkmedit error
by wang kangcheng 01 Aug '14

01 Aug '14

Dear experts when I use the tkedit, it report the error (in the following). How could I solve it? tkmedit started: Thu Jul 31 10:41:56 2014 /Applications/freesurfer/tktools/tkmedit.bin patient_con_sub126 brainmask.tight.mgz -aux T1.mgz $Id: tkmedit.c,v 1.343 2011/03/01 01:41:22 nicks Exp $ $Name: stable5 $ Set user home dir to /Users/haha/Desktop/brainmask/control Set subject home dir to /Users/haha/Desktop/brainmask/control/patient_con_sub126 Using interface file /Applications/freesurfer/tktools/tkmedit.tcl Segfault Setting global interpreter xDebug stack (length: 2) 01: main() 01: Setting global interpreter 00: 00: Wang Kangcheng

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ERROR: dimension mismatch between input volume and seg
by Jon Wieser 31 Jul '14

31 Jul '14

hi freesurfer experts I am compiling the FA segment stats for several subject I used mri_vol2vol --mov fa.nii --reg register.dat --fstarg ../mri/orig.mgz --interp nearest --o fa.anat.mgh then I used: mri_segstats --seg mri/wmparc.mgz --ctab $FREESURFER_HOME/FreeSurferColorLUT.txt --i dti/fa.anat.mgh --sum dti/fa.stats for some of my subjects, Iam getting the following error: mri_segstats --seg mri/wmparc.mgz --ctab $FREESURFER_HOME/FreeSurferColorLUT.txt --i dti/fa.anat.mgh --sum dti/fa.stat $Id: mri_segstats.c,v 1.75.2.9 2013/02/16 00:09:33 greve Exp $ cwd cmdline mri_segstats --seg mri/wmparc.mgz --ctab /Applications/freesurfer/FreeSurferColorLUT.txt --i dti/fa.anat.mgh --sum dti/fa.stat sysname Darwin hostname psy-blackbird.ad.uwm.edu machine x86_64 user wieser UseRobust 0 Loading mri/wmparc.mgz Loading dti/fa.anat.mgh ERROR: dimension mismatch between input volume and seg input 256 256 192 seg 256 256 256 can you tell me how to fix this? thanks Jon -- Jon Wieser Research Specialist UW-Milwaukee Psychology Department, Pearse Hall Rm 366 2441 East Hartford Ave Milwaukee, WI 53211 Phone: 414-229-7145 Fax: 414-229-5219

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Global mean FA
by Alshikho, Mohamad J. 31 Jul '14

31 Jul '14

Hi Fs Experts, In order to calculate the global white matter fractional anisotropy FA I used (wm.mgz ) the output of recon-all as a mask in the following command line mri_segstats --seg $SUBJECTS_DIR/015601/mri/wmparc.mgz --ctab $FREESURFER_HOME/FreeSurferColorLUT.txt --mask wm.mgz --i fa.anat.mgh --sum fa.stats Kindly, Is this correct? Thanks Mohamad

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Surface "resampling" for Qdec using -qcache
by "Christoph Abé" 31 Jul '14

31 Jul '14

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Re: [Freesurfer] tkmedit doesn't show lines distinguishing grey and white matter
by Talia Raney 31 Jul '14

31 Jul '14

Hi, What seems to be happening is that I insert this command: tkmedit subject_id brainmask.mgz rh.white -aux T1.mgz -aux-surface lh.white -segmentation aseg.mgz $FREESURFER_HOME/FreeSurferColorLUT.txt it should show me the subcortical segmentation overlayed with the pial, white, and orig surface lines shown. It no longer shows me this after I made some control points in the coronal view. [image: Inline image 1] This is what should show [image: Inline image 2] Why is this? Talia On Mon, Jul 28, 2014 at 10:40 AM, Talia Raney <talia.raney(a)gmail.com> wrote: > Hi, > I'm having issues with tkmedit. I'm doing visual inspection and I checked > tkregister to be sure that the white matter is outlined in the functional > image. However, when I open tkmedit for surface and cortical segmentation, > it doesn't show up the red and green lines that distinguish the boundaries > of the grey and white matter. It had previously and I put a few control > points but now it doesn't show up at all. > Why might this be and how can it be fixed? > Thanks! > Talia > > >

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mpr2mni305 failed
by Francesco Deleo 31 Jul '14

31 Jul '14

I all! I have the same problem in about 15% of MRI scans, all made with the same scanning protocol (T1 MPRAGE in a SIEMENS Avanto 1,5 T) during the recon-all -all process. I can't recognize any difference between those scans which work correctly and those not. I have never found the same error on 3T MRI scans. I've already tried to add these flags to the recon-all -all command: -use-mritotal -talairach -use-mritotal -notalairach but I've always received an error message Thank you very much ERROR: mpr2mni305 failed, see transforms/talairach_avi.log Darwin pro-di-villani.besta.local 13.3.0 Darwin Kernel Version 13.3.0: Tue Jun 3 21:27:35 PDT 2014; root:xnu-2422.110.17~1/RELEASE_X86_64 x86_64 Thanks for your attention Francesco Deleo Milan, Italy --------------------------------------------------------------------- FREESURFER_HOME: /Applications/freesurfer Build stamp: freesurfer-Darwin-lion-stable-pub-v5.3.0 Kernel info: Darwin 13.3.0 x86_64 --------------------------------------------------------------------- LAST LINES IN TALAIRACH_AVI.LOG parameters 9.0270 134.9373 110.8627 -84.3566 -7.5458 -11.3475 eta,q 0.95791 3.72402 0.0485 0.0470 0.0477 0.0513 0.0470 0.0452 0.0475 0.0471 0.0478 0.0513 0.0457 0.0435 0.0472 0.0472 0.0476 0.0428 0.0434 0.0415 0.0471 0.0471 0.0476 0.0435 0.0430 0.0415 0.0470 0.0478 0.0457 0.0525 0.0415 0.0430 0.0473 0.0511 0.0430 0.0548 0.0442 0.0453 0.0486 0.0426 0.0406 0.0672 0.0431 0.0503 niter,ni,del,rscale 7 3 12.0000 1.2000 imgrege: no voxels in register ERROR: 'imgreg_4dfp /Applications/freesurfer/average/711-2C_as_mni_average_305 /Applications/freesurfer/average/711-2B_as_mni_average_305_mask talsrcimg_g11 none talsrcimg_to_711-2C_as_mni_average_305_t4 1283' failed! status=254 ERROR: mpr2mni305 execution aborted

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Re: [Freesurfer] NIH Staff Scientist Position available, Bethesda, MD, USA
by Xiaomin Yue 31 Jul '14

31 Jul '14

The title has been FedEx for overnight. Please let me know after getting it. Xiaomin ________________________________ From: Thomas, Adam (NIH/NIMH) [E]<mailto:adamt@nih.gov> Sent: ‎7/‎30/‎2014 6:36 AM To: freesurfer(a)nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>; FSL - FMRIB's Software Library<mailto:FSL@JISCMAIL.AC.UK>; spm(a)jiscmail.ac.uk<mailto:spm@JISCMAIL.AC.UK>; announce(a)fmrib.ox.ac.uk<mailto:announce@fmrib.ox.ac.uk> Subject: [Freesurfer] NIH Staff Scientist Position available, Bethesda, MD, USA Posted on behalf of Dr. Judy Rapoport: Department of Health and Human Services (DHHS) National Institutes of Health (NIH) National Institute of Mental Health (NIMH) Division of Intramural Research Programs (DIRP) Section on Childhood Neuropsychiatric Disorders (SCND) Child Psychiatry Branch (CPB) Staff Scientist position available The Child Psychiatry Branch, in Bethesda, Maryland, is recruiting applicants for a Staff Scientist position. As a Staff Scientist, the primary duties will include conducting statistical analyses on clinical, neurobiological and treatment studies carried out in the Branch. This includes but is not limited to tasks such as maintaining the appropriate data sets, clearly conveying statistical results and methods both orally and in writing, reviewing and writing statistical content for manuscripts prior to submission, and working closely with and providing statistical support for all Branch members. The Staff Scientist position entails 25% time allotted to pursuing individual research interests. The Child Psychiatry Branch is a highly productive and collaborative group with a rich, multimodal dataset that seeks to understand neuro-developmental disorders, with a focus on childhood-onset schizophrenia. There is a strong scientific and statistical computing core facility in existence, which can benefit this work. For more information about the Child Psychiatry Branch, please utilize the following link: http://www.nimh.nih.gov/labs-at-nimh/research-areas/clinics-and-labs/chp/in dex.shtml Interested candidates should have a Ph.D., M.D. or equivalent doctoral degree and five years post-doctoral experience. Applicants should have a strong background in statistics as well as interests and experience in neuroimaging and behavioral research. The recruit should be adept at writing his/her own code to clean, organize, analyze, and visualize data. In addition some highly desirable skills include: experience analyzing structural MRI, functional MRI and/or MEG data; knowledge of cognitive neuroscience or clinical psychology; a solid foundation in multivariate statistics and longitudinal data analysis; proficiency in statistical programs such as R and MATLAB and visualization methods. SALARY RANGE: Salary is commensurate with experience and accomplishments. BENEFITS: The federal government offers a comprehensive benefits package including vacation, sick leave, holidays, life insurance, health benefits, and participation in the Federal Employees Retirement System. For more information go to new employee benefits at the NIH (http://hr.od.nih.gov/Benefits/permanentemployee.htm) and other employee benefits information (http://tiny.cc/saVcr) Interested applicants should send their CV and cover letter to: Dr. Judith Rapoport, NIMH, 10 Center Drive, Bldg. 10, Rm. 3N202 (MSC-1600), Bethesda, MD 20892 USA, or by email: rapoporj(a)mail.nih.gov SUBMISSION DEADLINE: September 1, 2014 NIH and DHHS are Equal Opportunity Employers. _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer 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.

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Freesurfer July 2014