Freesurfer

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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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Re: [Freesurfer] missing anterior temporal lobe
by Xiaomin Yue 29 Jul '14

29 Jul '14

Hi, I had successfully reconstructed a primate brain using fs5.3. But one part of left anterior temporal lobe was not correct, even with the accurate wm.mgz. See attached image for what I mean. Are there parameters to be used to correct this problem? Thanks,Xiaomin

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newbie questions - mri_convert+
by Krieger, Donald N. 29 Jul '14

29 Jul '14

I have an MPRAGE dicom file sequences on which I wish to run recon-all . Here is the command I am using: mri_convert DICOM_DIRECTORY SubjectName/mri/orig/001.mgz It returns immediately with the error message: corRead(): can't open file DICOM_DIRECTORY/COR-.info Your suggestions would be welcome. Here are 2 other simple questions: (1) Where do I find the list of which labels correspond to which structures? (2) Are there labels for the white matter volumes or only for the gray matter volumes? If they exist, where are they? Regards, Don

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Determining problems for subjects using recon-all.log
by Vy Dinh 28 Jul '14

28 Jul '14

Dear Freesurfer develops, I'm having issues running recon-all -all on 2 of our subjects using the raw t1.nii file. According to their recon-all log, both subjects' recon-all -all command errs when encountering the mris_sphere step. I'm not sure how to address this problem, considering we have no known issues with these subject's data for our other data processing (VBM, etc). Any help will be much appreciated. Please not that I've attached recon-all.logs for both subjects. Thank you. Best, -- Vy Dinh MD Candidate, Class of 2017 University of Wisconsin School of Medicine and Public Health

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preserve manual edits?
by Jason Tourville 28 Jul '14

28 Jul '14

Hi there, We have performed manual volume edits on a number of scans. Recently, we ran those scans through recon-all with a new Tal volume target. The seg and surfaces are improved using the new target but most of the manual edits performed on the earlier version would improve the surfaces. Is there an established means for porting the manually edited voxel values to the volumes of the new re-con? Thanks, Jason -- Jason A. Tourville, Ph.D. Research Assistant Professor Department of Speech, Language, and Hearing Sciences Boston University 677 Beacon St. Boston, MA 02215 Phone: (617)353-9484 Fax: (617)353-7755

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Cerebellum white matter mask {Disarmed}
by Alshikho, Mohamad J. 28 Jul '14

28 Jul '14

Hi Fs expers, What is the best way in Freesurfer to create a mask for the cerebellum white matter from the output of T1 segmentation? Thanks mohamad

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