Freesurfer July 2014

freesurfer@nmr.mgh.harvard.edu

163 participants
257 discussions

NIH Staff Scientist Position available, Bethesda, MD, USA
by Thomas, Adam (NIH/NIMH) [E] 30 Jul '14

30 Jul '14

Posted on behalf of the CPB: 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 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 neurodevelopmental 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 must have five years post-doctoral experience. Applicants should have a strong background in statistics and programming/computer science, 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. Unix and python programming skills are also preferable. In addition some highly desirable skills include: experience analyzing structural MRI, functional MRI and/or MEG data; a solid foundation in multivariate statistics (e.g., cluster analysis, principal components analysis, independent components analysis), and a background in longitudinal data analysis (e.g., mixed model regression/hierarchical linear modeling); 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<mailto:rapoporj@mail.nih.gov> SUBMISSION DEADLINE: June 1, 2014 NIH and DHHS are Equal Opportunity Employers.

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Mask custom ROI with automated parcellation (aparc)
by Bastian Cheng 30 Jul '14

30 Jul '14

Dear Freesurfers, Is there a way to mask a custom ROI (or label) with a volume / label from automated parcellations? I have an overlay with fMRI activations and am only interested in the precentral cortex (as segmented in rh.aparc). I could do masking either on the label level (fMRI activation label * rh.precentral.label) OR on a volume level (fMRI ROI volume * rh.precentral volume) ultimately, I would only be interested in surface thickness of my fMRI hotspots limited to the precentral cortex. So the most elegant way would be if there were a function in mri_segstats that allows outputs of thickness values to be "sorted" by the automated parcellation. But any help leading there is appreciated! Best, Bastian

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Freesurfer] QDEC error and analysis termination during 'concatenating volumes'
by Isotalus, Hanna 29 Jul '14

29 Jul '14

Dear FreeSurfer experts, Bruce/Doug, I am running my analysis on a server. I have a total of 128 GB RAM, when I run my analysis and when it stops I'm consuming ~44, having about 83 free. I can run 1224 subjects but no more than that. As soon as I have 1225 subjects the analysis won't run (but it does run for all the remaining subjects if I run them separately). I tried to run the analysis on different servers, some that had 72GB and some that had 128GB and the pattern stayed the same; none of the 12 servers could run 1225 subjects but all could run 1224 subjects. This may mean it's not a memory problem (?) but it doesn't seem to be a problem with subject files either as all of them work, just not all at the same time. All the servers I have access to have a 24-core processor, if that's important. Any further suggestions on what might be going on? Best wishes, Hanna ------------------------------ Date: Fri, 25 Jul 2014 09:50:51 -0400 (EDT) From: Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] QDEC error and analysis termination during 'concatenating volumes' To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> Message-ID: <alpine.LRH.2.03.1407250949560.20368(a)nmr.mgh.harvard.edu> Content-Type: text/plain; charset="utf-8" Hi Hanna seems like you are running out of memory. How much RAM do you have on your machine? Are there other things running on it that you can kill, or is there a larger RAM machine you can use? Doug will be back next week and perhaps will comment also. If you don't hear from him you should repost. cheers Bruce On Fri, 25 Jul 2014, Isotalus, Hanna wrote: > > Dear FreeSurfer gurus, > > > I am using QDEC to run my analyses on a large data set. The analysis works > fine with up to 1224 subjects but as soon as I add subject 1225 I get an > error and the analysis stops. The error displays during 'concatenating > volumes' and it just displays file names. When I try to run the analysis on > the remaining subjects (around 360 of them) the analysis runs fine ? so I am > inclined to think there's nothing wrong with the data files. I've tried > rotating the order of subjects and it just doesn't seem to allow me to run > the analysis on all of them. Do you have any suggestions? > > > > Here's a link to a screenshot of the error I get: > > https://www.dropbox.com/s/08pqnmgep6crmr5/error%20message.gif > > I can't actually see all of the error message, here's it from the beginning > of what I can see and it continues like that ? displaying all file names I > think. > > > Thank you and best wishes, >Hanna

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The difference between wm.mgz and wm.seg.mgz
by Alshikho, Mohamad J. 29 Jul '14

29 Jul '14

Dear Fs Experts, What is the difference between (wm.mgz and wm.seg.mgz)_ in the output of recon-all? i.e is wm.mgz means the whole white matter (right_left hemispheres and brain stem except the cerebellum) Thanks Mohamad

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qdec error
by Jon Alan Wieser 29 Jul '14

29 Jul '14

HI freesurfer experts, I am running a qdec analysis, my first factor has 3 levels, my other 2 factors have 2 levels, I select my first and second factors and hit "Analyze" I get the error ? : Error in Analyze: command failed ERROR: QdecGlmDesign::GenerateContrasts: factor 1 must have 2 levels how can I analyze with a factor that has three levels? thanks JOn

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error when using -hemi flag for recon -all command
by C. Paula de los Angeles 29 Jul '14

29 Jul '14

Hi Freesurfer team, I am running into an issue when I am specify the -hemi flag for the recon -all command (in this case recon -all -hemi rh). The command seems to work for the most part, except it errored at the end and seemed to be looking for a file for the other hemisphere. How do I get this command to work without exiting with errors? Is there an alternative set of commands that you recommend or something that I can add to ignore this step but still get the output that I need? Thanks in advance for your help. See log output below (and let me know if you need more information from me to help me): #@# Cortical Parc 3 rh Tue Jul 29 05:55:38 CDT 2014 /tmp/ 14663415.qsched02.quest.it.northwestern.edu/GBM/20140728_132405/DN6741NMFF/… mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.mgz -seed 1234 DN6741NMFF rh ../surf/rh.sphere.reg /projects/p20394/software/freesurfer-v5.3.0/average/rh.DKTatlas40.gcs ../label/rh.aparc.DKTatlas40.annot setting seed for random number generator to 1234 using ../mri/aseg.mgz aseg volume to correct midline $Id: mris_ca_label.c,v 1.35 2011/03/02 00:04:27 nicks Exp $ $Id: mrisurf.c,v 1.693.2.7 2013/05/12 22:28:01 nicks Exp $ reading atlas from /projects/p20394/software/freesurfer-v5.3.0/average/rh.DKTatlas40.gcs... reading color table from GCSA file.... average std = 0.9 using min determinant for regularization = 0.008 0 singular and 237 ill-conditioned covariance matrices regularized input 0: MEAN CURVATURE, flags 0, avgs 5, name mean_curvature labeling surface... 1840 labels changed using aseg relabeling using gibbs priors... 000: 2985 changed, 153010 examined... 001: 741 changed, 12861 examined... 002: 207 changed, 4026 examined... 003: 98 changed, 1267 examined... 004: 48 changed, 574 examined... 005: 17 changed, 275 examined... 006: 10 changed, 87 examined... 007: 8 changed, 58 examined... 008: 5 changed, 53 examined... 009: 3 changed, 29 examined... 010: 3 changed, 20 examined... 011: 4 changed, 17 examined... 012: 2 changed, 17 examined... 013: 0 changed, 13 examined... 200 labels changed using aseg 000: 131 total segments, 98 labels (1131 vertices) changed 001: 34 total segments, 1 labels (1 vertices) changed 002: 33 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 48 changed) rationalizing unknown annotations with cortex label relabeling unknown label... relabeling corpuscallosum label... 803 vertices marked for relabeling... 803 labels changed in reclassification. writing output to ../label/rh.aparc.DKTatlas40.annot... classification took 1 minutes and 6 seconds. #----------------------------------------- #@# Parcellation Stats 3 rh Tue Jul 29 05:56:44 CDT 2014 /tmp/ 14663415.qsched02.quest.it.northwestern.edu/GBM/20140728_132405/DN6741NMFF/… mris_anatomical_stats -mgz -cortex ../label/rh.cortex.label -f ../stats/rh.aparc.DKTatlas40.stats -b -a ../label/rh.aparc.DKTatlas40.annot -c ../label/aparc.annot.DKTatlas40.ctab DN6741NMFF rh white computing statistics for each annotation in ../label/rh.aparc.DKTatlas40.annot. reading volume /tmp/ 14663415.qsched02.quest.it.northwestern.edu/GBM/20140728_132405/DN6741NMFF/…. .. reading input surface /tmp/ 14663415.qsched02.quest.it.northwestern.edu/GBM/20140728_132405/DN6741NMFF/…. .. reading input pial surface /tmp/ 14663415.qsched02.quest.it.northwestern.edu/GBM/20140728_132405/DN6741NMFF/…. .. reading input white surface /tmp/ 14663415.qsched02.quest.it.northwestern.edu/GBM/20140728_132405/DN6741NMFF/…. .. INFO: assuming MGZ format for volumes. INFO: using ../label/rh.cortex.label as mask to calc cortex NumVert, SurfArea and MeanThickness. reading colortable from annotation file... colortable with 36 entries read (originally /Applications/freesurfer/average/colortable_desikan_killiany.txt) Saving annotation colortable ../label/aparc.annot.DKTatlas40.ctab table columns are: number of vertices total surface area (mm^2) total gray matter volume (mm^3) average cortical thickness +- standard deviation (mm) integrated rectified mean curvature integrated rectified Gaussian curvature folding index intrinsic curvature index structure name 1734 1086 2805 2.403 0.674 0.235 0.238 118 16.1 caudalanteriorcingulate 3720 2180 4531 2.150 0.629 0.245 0.364 522 54.9 caudalmiddlefrontal 2021 1319 2928 2.047 0.780 0.290 0.395 159 41.7 cuneus 1035 578 1950 2.643 0.868 0.283 0.593 113 25.1 entorhinal 3294 2144 5529 2.550 0.826 0.261 0.323 355 33.0 fusiform 8115 4699 12385 2.474 0.681 0.218 0.385 1067 111.9 inferiorparietal 5792 3558 11712 2.670 0.824 0.258 0.651 1276 80.5 inferiortemporal 1182 694 1693 2.338 0.774 0.235 0.286 111 10.8 isthmuscingulate 8508 5665 10029 1.913 0.707 0.287 0.317 913 98.2 lateraloccipital 4737 2826 8278 2.610 0.800 0.243 0.312 580 69.6 lateralorbitofrontal 4163 2801 5096 1.844 0.654 0.323 0.712 1466 80.9 lingual 2241 1422 4125 2.433 0.741 0.280 1.242 844 33.4 medialorbitofrontal 6452 3907 13716 2.889 0.770 0.231 0.251 568 60.1 middletemporal 1215 702 1834 2.439 0.696 0.215 0.276 84 13.3 parahippocampal 2949 1703 2784 1.862 0.622 0.303 0.470 972 53.7 paracentral 2339 1409 3508 2.338 0.507 0.222 0.404 180 32.0 parsopercularis 1339 758 2560 2.812 0.683 0.252 0.325 143 15.7 parsorbitalis 2072 1187 3544 2.675 0.574 0.213 0.238 230 26.1 parstriangularis 1751 1204 1751 1.571 0.476 0.330 0.389 329 27.5 pericalcarine 6976 4154 8485 1.915 0.698 0.215 0.212 560 65.5 postcentral 2082 1283 2695 2.149 0.562 0.258 0.288 171 22.4 posteriorcingulate 8338 5164 9837 1.901 0.590 0.249 0.295 848 109.7 precentral 5984 3699 7924 2.173 0.596 0.272 0.408 950 79.8 precuneus 956 553 1572 2.876 0.582 0.216 0.274 61 11.1 rostralanteriorcingulate 8324 4521 10959 2.272 0.615 0.230 0.340 1301 122.1 rostralmiddlefrontal 19072 11009 25827 2.268 0.664 0.265 0.528 4152 282.6 superiorfrontal 9478 5499 12173 2.169 0.589 0.230 0.323 1069 108.6 superiorparietal 8064 4853 14648 2.618 0.807 0.249 0.505 1153 118.9 superiortemporal 5940 3499 8741 2.426 0.605 0.210 0.346 1138 81.6 supramarginal 723 669 1016 1.703 0.586 0.357 0.317 102 8.4 transversetemporal 2944 1804 5524 3.067 0.820 0.251 0.310 203 33.4 insula #-------------------------------------------- #@# Cortical ribbon mask Tue Jul 29 05:57:22 CDT 2014 /tmp/ 14663415.qsched02.quest.it.northwestern.edu/GBM/20140728_132405/DN6741NMFF/… mris_volmask --label_left_white 2 --label_left_ribbon 3 --label_right_white 41 --label_right_ribbon 42 --save_ribbon DN6741NMFF *SUBJECTS_DIR is /tmp/14663415.qsched02.quest.it.northwestern.edu/GBM/20140728_132405/DN6741NMFF/FreeSurfer <http://14663415.qsched02.quest.it.northwestern.edu/GBM/20140728_132405/DN67…> MRISread(/tmp/14663415.qsched02.quest.it.northwestern.edu/GBM/20140728_1324… <http://14663415.qsched02.quest.it.northwestern.edu/GBM/20140728_132405/DN67…>): could not open file loading input data...No such file or directory Exception caught while processing input files std::exceptionLinux qnode0621 2.6.32-358.7.1.el6.x86_64 #1 SMP Tue Apr 9 18:08:17 EDT 2013 x86_64 x86_64 x86_64 GNU/Linux recon-all -s DN6741NMFF exited with ERRORS at Tue Jul 29 05:57:22 CDT 2014For more details, see the log file /tmp/14663415.qsched02.quest.it.northwestern.edu/GBM/20140728_132405/DN6741NMFF/FreeSurfer/DN6741NMFF/scripts/recon-all.log <http://14663415.qsched02.quest.it.northwestern.edu/GBM/20140728_132405/DN67…> To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting>* -- C. Paula de los Angeles, MD/PhD student Medical Scientist Training Program Northwestern University Feinberg School of Medicine

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QDEC error and analysis termination during 'concatenating volumes' and different results from Monte Carlo Simulation from QDEC & Command line
by Isotalus, Hanna 29 Jul '14

29 Jul '14

Dear Doug, Thanks for the quick response. I will try running the analyses on the command line. I've put the whole error message here if that is of any use and sheds any light to the problem? https://www.dropbox.com/s/1h1wzwidt3k1scu/ErrorMessage.txt Also, when I try to plot the stats tables using QDEC I get the following error: X Error of failed request: BadAlloc (insufficient resources for operation) I've a screenshot of this error here:https://www.dropbox.com/s/1jf9vd4bms0zv99/x%20error.pdf I get this when I try to plot stats tables for those subjects on whom the analysis works on QDEC. Could this be related to my initial problem? I haven't tried generating these stats tables on the command line yet. I also have an additional question. When I run the analysis on QDEC (for those subjects it works for) I get one cluster after correcting for multiple comparisons but when I correct for multiple comparisons using the same settings (?) on the command line I get three clusters. The settings I chose on QDEC were Monte Carlo Null Z at 1.3 (0.05) and with the abs setting. The first of these three clusters matches the one I get on QDEC. I used the following command: mri_glmfit-sim --glmdir directory --cache 1.3 abs --sim-sign abs Why am I getting different results? Thank you so much for your time and help. Best wishes, Hanna ------------------------------ Date: Mon, 28 Jul 2014 12:22:16 -0400 From: Douglas N Greve <greve(a)nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] QDEC error and analysis termination during 'concatenating volumes' To: freesurfer(a)nmr.mgh.harvard.edu Message-ID: <53D678B8.7060904(a)nmr.mgh.harvard.edu> Content-Type: text/plain; charset=UTF-8; format=flowed I can't make anything out of the error msg gif. Somewhere in there, there should be a mris_preproc command line. Can you try cutting and pasting that into a shell? Trying to do this in the context of qdec will be difficult doug On 07/25/2014 05:09 AM, Isotalus, Hanna wrote: > > Dear FreeSurfer gurus, > > > I am using QDEC to run my analyses on a large data set. The analysis > works fine with up to 1224 subjects but as soon as I add subject 1225 > I get an error and the analysis stops. The error displays during > 'concatenating volumes' and it just displays file names. When I try to > run the analysis on the remaining subjects (around 360 of them) the > analysis runs fine ? so I am inclined to think there's nothing wrong > with the data files. I've tried rotating the order of subjects and it > just doesn't seem to allow me to run the analysis on all of them. Do > you have any suggestions? > > > > Here's a link to a screenshot of the error I get: > > https://www.dropbox.com/s/08pqnmgep6crmr5/error%20message.gif > > I can't actually see all of the error message, here's it from the > beginning of what I can see and it continues like that ? displaying > all file names I think. > > > Thank you and best wishes, > > ? > > > > > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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apply transform matrix to coordinates
by Manuel Mercier 29 Jul '14

29 Jul '14

Dear Freesurfers I want to apply the transform matrix talairach.xfm, to a set of discrete points. (in order to get mni coordinate and use template brain). These are electrodes, with coordinates in the brain.mgz space. Here is what I did following the advices from the Coordinates systems page : get Norig and Torig using mri_info, then apply the transform: VOX_coor_tr = (tr_mat*Norig*inv(Torig)*VOX_coor)'; with tr_mat = [talairach.xfm;0 0 0 1]; and VOX_coor = [(n electrodes by 3 coordinates))' ; ones(1,length(VOX_coor))]; Looking at the result, it looks like something is wrong. Electrodes are few centimeters too lateral and anterior/frontal. I have been struggling with this problem for sometime and I am hoping that someone could help. Thanks, Manuel

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tkmedit doesn't show lines distinguishing grey and white matter
by Talia Raney 29 Jul '14

29 Jul '14

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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localGI - results interpretation
by elisa veronese 29 Jul '14

29 Jul '14

Dear FS users, can anybody help me in understanding the results of the localGI pipeline? After calling the recon-all -s *subj *-localGI recon-all -s *subj* -qcache -measure pial_lgi mri_segstats --annot *subj *lh aparc --i $SUBJECTS_DIR/*subj*/surf/lh.pial_lgi --sum lh.aparc.pial_lgi.stats what I obtain is a text file with 10 columns, i.e. # TableCol 1 ColHeader Index # TableCol 2 ColHeader SegId # TableCol 3 ColHeader NVertices # TableCol 4 ColHeader Area_mm2 # TableCol 5 ColHeader StructName # TableCol 6 ColHeader Mean # TableCol 7 ColHeader StdDev # TableCol 8 ColHeader Min # TableCol 9 ColHeader Max # TableCol 10 ColHeader Range and 34 rows (i.e. 34 ROIs). What I cannot understand is the meaning of the last five columns (*intensity mean, stdev, min, max, range*). Is this "intensity" measure linked to the gyrification index? If yes, how? And, if no, how can I obtain the actual gyrification index? Thank you. Best, Elisa -- Elisa Veronese - PhD *Research Unit on Brain Imaging and Neuropsychology (RUBIN)* *Inter-University Center for Behavioral Neurosciences (ICBN)University of Udine and University of Verona, ItalyICBN Website: http://icbn.uniud.it/tiki-index.php <http://icbn.uniud.it/tiki-index.php>*

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Freesurfer July 2014