Freesurfer

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30097 discussions

optseq2
by Claire Wilcox 13 Aug '13

13 Aug '13

hello, i'm struggling with how to specify a schedule and then ask optseq2 to identify an optimal timing schedule. specifically i have a conditioned cue and an unconditioned stimulus. the high threat CS always needs to follow with a high pain US and low threat CS with a low pain CS. how can i specify such a schedule in optseq2? i've been trying a number of combinations of below, but am failing miserably with lots of varying warnings and error messages and inability to read files or 'Bus error' what should the --in input schedule file format look like? that might be the missing link .. although that's hard to say for sure. many thanks, claire

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Re: [Freesurfer] QDEC error in asegstats2table
by Douglas N Greve 13 Aug '13

13 Aug '13

Hi Ken, I cannot reproduce this error, and I can't find anything wrong with the file you sent. If you remove this subject, does the process complete? doug On 08/09/2013 10:58 AM, Rando, Kenneth wrote: > Hi Doug, > > Thanks for having a look at these files. The first attached file, from Subject_Dir tb0294, is the file previous to the file with the error, tb0314, attached second. > > Ken > > > Kenneth Rando > Research Assistant 2 > 203-974-7731 > > Yale OCD Research Clinic > Yale University School of Medicine > Connecticut Mental Health Center > 34 Park Street, Room W309 > New Haven, CT 06519 > > > > ________________________________________ > From: freesurfer-bounces(a)nmr.mgh.harvard.edu [freesurfer-bounces(a)nmr.mgh.harvard.edu] on behalf of Douglas N Greve [greve(a)nmr.mgh.harvard.edu] > Sent: Thursday, August 08, 2013 5:23 PM > To: freesurfer(a)nmr.mgh.harvard.edu > Subject: Re: [Freesurfer] QDEC error in asegstats2table > > Ken, can you send the offending file and the file from the 6th subject? > doug > > On 08/08/2013 03:09 PM, Rando, Kenneth wrote: >> Hello Experts, >> >> This QDEC error is one that appears in the archives, but I did not see >> a solution that solves my problem. The error (after some information >> about initialization of the program) is as follows: >> >> >> SUBJECTS_DIR : /home/freesurfer_ocd >> Parsing the .stats files >> ERROR: The stats file /home/freesurfer_ocd/tb0314 /stats/aseg.stats is >> not found or is too small to be a valid statsfile >> Use --skip flag to automatically skip bad stats files >> ERROR: In >> /usr/pubsw/packages/KWWidgets/CVS-vtk560/KWWidgets/vtkKWTkUtilities.cxx, >> line 230 >> vtkKWQdecApp (0x27a1f070): >> Script: >> vtkTemp2 GenerateStatsDataTables >> Returned Error on line 1: >> Uncaught exception: command failed: asegstats2table --common-segs >> --meas volume --tablefile >> /home/freesurfer_ocd/qdec/stats_tables/aseg.volume.stats.dat >> --statsfile=aseg.stats --subjects ta0743 ta0860 tb0168 tb0183 tb0195 >> tb0294 tb0314 tb0341 tb0529 tb0628 tb0728 tb0791 tb0817 tb0850 tb0861 >> tb0892 tb0901 tb1012 tb1043 tb1086 tb1450 tb1464 tb1646 tb1751 tb2002 >> tb2073 tr7582 tr7733 tr7825 tr7901 tr7932 tr7987 tr8167 tr8222 tr8240 >> tr8285 tr8345 tr8511 tr8529 tr8688 tr8740 tr8791 tr8860 tr9043 tr9124 >> tr9222 tr9332 tr9459 tr9515 tr9561 tr9707 tr9746 tr9765 tr9824 >> >> Stack trace: >> Uncaught exception: command failed: asegstats2table --common-segs >> --meas volume --tablefile >> /home/freesurfer_ocd/qdec/stats_tables/aseg.volume.stats.dat >> --statsfile=aseg.stats --subjects ta0743 ta0860 tb0168 tb0183 tb0195 >> tb0294 tb0314 tb0341 tb0529 tb0628 tb0728 tb0791 tb0817 tb0850 tb0861 >> tb0892 tb0901 tb1012 tb1043 tb1086 tb1450 tb1464 tb1646 tb1751 tb2002 >> tb2073 tr7582 tr7733 tr7825 tr7901 tr7932 tr7987 tr8167 tr8222 tr8240 >> tr8285 tr8345 tr8511 tr8529 tr8688 tr8740 tr8791 tr8860 tr9043 tr9124 >> tr9222 tr9332 tr9459 tr9515 tr9561 tr9707 tr9746 tr9765 tr9824 >> >> while executing >> "vtkTemp2 GenerateStatsDataTables" >> >> The error occurs at the seventh subject in the dataset, so it appears >> to be subject-specific. As recommended in previous posts, I have >> verified that the aseg.stats file exists for that subject. I am new to >> Freesurfer, but a comparison of this aseg.stats file to the previous >> subject's file and a few others reveals no obvious differences (e.g., >> missing lines, extreme or corrupt data values). >> >> One response to an earlier post asked the user to run asegstats2table >> -i aseg.stats -t test.dat in the stats directory of the file with the >> error. I followed that advice and it produces a file for this subject. >> There was, however, no follow-up posting, so I don't know what that >> indicates, and how I should follow-up. >> >> Thanks for your help. >> >> Ken >> >> >> >> Kenneth Rando >> Research Assistant 2 >> 203-974-7731 >> >> Yale OCD Research Clinic >> Yale University School of Medicine >> Connecticut Mental Health Center >> 34 Park Street, Room W309 >> New Haven, CT 06519 >> >> >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer(a)nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > greve(a)nmr.mgh.harvard.edu > Phone Number: 617-724-2358 > Fax: 617-726-7422 > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 > www.nmr.mgh.harvard.edu/facility/filedrop/index.html > Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ > > _______________________________________________ > 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. > -- Douglas N. Greve, Ph.D. MGH-NMR Center greve(a)nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/

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mri_glmfit covariates
by Rees, Elin 13 Aug '13

13 Aug '13

Hi, I'm trying to run a cortical thickness group comparison (HD v Controls), controlling for site, gender (1 or 2) and age. Without age as a covariate the results are as expected but once age is added on all significant results disappear. I think this is a problem with the method rather than because all results are dependent on age. My fsgd and contrast files for the glm are below. I would really appreciate your input as to what might be going wrong to effect the results so strongly. Am I doing something wrong? GroupDescriptorFile 1 Title HDvControl Class HD-london-1 Class HD-leiden-1 Class HD-paris-1 Class HD-ulm-1 Class HD-london-2 Class HD-leiden-2 Class HD-paris-2 Class HD-ulm-2 Class C-london-1 Class C-leiden-1 Class C-paris-1 Class C-ulm-1 Class C-london-2 Class C-leiden-2 Class C-paris-2 Class C-ulm-2 Variables Age Input 30009 HD-paris-2 26 Input 30014 C-ulm-2 51 Input 30016 C-london-1 48 Input 30024 C-leiden-1 38 Input 30029 HD-london-2 66 Input 30030 HD-london-1 54 Input 30037 HD-london-2 42 Input 30041 C-london-1 43 Input 30042 HD-london-2 40 Input 30043 HD-london-2 41 Input 30047 HD-london-2 66 Input 30051 C-london-2 45 Input 30054 HD-london-2 55 Input 30056 C-london-2 66 Input 30060 C-london-1 50 Input 30068 C-london-1 51 Input 30071 HD-london-1 43 Input 30072 HD-london-2 44 Input 30074 C-london-2 58 Input 30075 HD-london-2 48 Input 30078 C-london-2 53 Input 30079 HD-london-1 58 Input 30082 C-london-2 62 Input 30089 HD-london-2 54 Input 30093 HD-leiden-1 44 Input 30098 HD-leiden-2 45 Input 30100 HD-leiden-2 42 Input 30102 C-leiden-2 48 Input 30107 HD-leiden-2 61 Input 30112 HD-leiden-2 50 Input 30114 C-leiden-1 48 Input 30115 HD-leiden-2 47 Input 30117 HD-leiden-2 49 Input 30118 C-leiden-1 51 Input 30119 HD-leiden-2 59 Input 30124 C-leiden-1 57 Input 30125 HD-leiden-2 39 Input 30136 C-leiden-2 51 Input 30138 C-leiden-2 56 Input 30139 HD-leiden-2 33 Input 30142 HD-leiden-2 32 Input 30148 HD-leiden-1 48 Input 30154 C-leiden-1 47 Input 30155 HD-leiden-2 46 Input 30160 HD-leiden-2 38 Input 30162 HD-leiden-2 52 Input 30163 C-leiden-2 42 Input 30168 C-ulm-2 58 Input 30177 C-london-2 49 Input 30185 C-ulm-2 34 Input 30189 HD-ulm-1 50 Input 30191 C-ulm-1 44 Input 30193 HD-ulm-1 46 Input 30195 C-ulm-2 50 Input 30198 C-ulm-1 56 Input 30199 HD-ulm-1 53 Input 30208 HD-ulm-1 59 Input 30209 C-ulm-2 44 Input 30210 HD-ulm-1 30 Input 30214 HD-ulm-2 57 Input 30215 HD-ulm-1 34 Input 30220 HD-ulm-2 54 Input 30222 HD-ulm-1 64 Input 30223 C-ulm-1 44 Input 30229 HD-ulm-1 40 Input 30235 HD-ulm-1 48 Input 30240 HD-ulm-1 36 Input 30241 C-paris-2 65 Input 30247 HD-paris-1 24 Input 30248 HD-paris-1 44 Input 30250 HD-paris-2 62 Input 30254 HD-paris-1 37 Input 30256 HD-paris-1 23 Input 30259 HD-paris-1 64 Input 30265 C-paris-2 50 Input 30269 C-paris-2 58 Input 30273 C-paris-2 49 Input 30275 C-paris-1 59 Input 30280 HD-london-2 42 Input 30281 HD-london-2 65 Input 30288 HD-london-2 51 Input 30311 HD-paris-1 40 Input 30312 HD-paris-2 51 Input 30314 HD-paris-2 46 Input 30315 HD-leiden-2 67 Input 30318 C-paris-2 64 Input 30320 C-paris-1 49 Input 30321 HD-paris-1 61 Input 30326 C-paris-2 45 Input 30334 HD-london-1 49 Input 30347 C-paris-1 62 Input 30349 HD-paris-2 48 Input 30352 C-paris-2 66 Input 30357 C-ulm-1 28 Input 30361 HD-paris-2 63 Input 30363 HD-ulm-1 51 Input 30365 C-ulm-2 46 Input 30369 HD-ulm-2 45 Input 30378 C-leiden-1 53 Input 30385 HD-leiden-2 61 Input 30392 HD-ulm-2 51 Contrast: 1 1 1 1 1 1 1 1 -1 -1 -1 -1 -1 -1 -1 -1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 Thanks, Elin

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hippocampal segmentation converting mgz to nii
by lorenzo pasquini 13 Aug '13

13 Aug '13

Dear freesurfer users, I have used freesurfer to segment hippocampal subfields. Then I used freeview to convert the derived .mgz files in .nii files for further analysis. I estimated the hippocampal subfields volumes with the command: kvlQuantifyPosteriorProbabilityImages $ FREESURFER_HOME/ data/ GEMS/ compressionLookupTable.txt posterior_right_* posterior_Right-Hippocampus.mgz I have calculated the number of voxels in the converted .nii files using SPM and realized that they do not fit the estimated volumes through freesurfer Example for CA2-2 estimated voxel number though freesurfer: 6851 voxels found in .nii file: 15812 Did somebody had similar problems? Do you have any suggestion? Are there any incompatibilities between SPM and freesurfer? I did not find any apparent error in my counting script. Thank you very much and regards, Lorenzo Pasquini Can. Ph. D., Medical Life Science and Technology (Technische Universität Muenchen) Neuroimaging Lab, Neuroradiology Klinikum r. d. Isar (Technische Universität) 81675 München Tel.: 0049 (0) 89 4140-7666

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Error when using preproc-sess -per-session in FS-5.3
by Sepide Movaghati 13 Aug '13

13 Aug '13

Hello, I am using freesurfer 5.3 and try to run: preproc-sess -s session1 -surface self lhrh -fsd bold -mni305 -fwhm 5 -per-session it gives me an error: 1/1 session1 1/1 session1 003 lh --------- Mon Aug 12 11:21:09 EDT 2013 ERROR: could not determine file for /export01/data/sepid/subjects/ZY/session1/bold/003/fmcpr however, it works fine when I use -per-run. I have attached complete terminal output. Thanks.

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Electrode Placement
by Nick Collisson 13 Aug '13

13 Aug '13

Hi all, Are point sets and isosurfaces reported in different coordinate systems? Points that are located on the surface of the cortex in Freesurfer appear far away from the brain (rendered from the .vtk file of the saved isosurface) when I export them into MATLAB. Thanks, Nick

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FS and FSL
by Alexopoulos, Dimitrios 13 Aug '13

13 Aug '13

A quick question. Do all versions of FS (even the older 4.4 version) require a full FSL install to run recon-all -all. Would the command run "without error" even if you don't have FSL installed. Jim The materials in this email are private and may contain Protected Health Information. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying, distribution or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return email.

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mris_thickness threshold
by Giusy Chinnici 13 Aug '13

13 Aug '13

Hi all, I'd like to understand the difference in using the default value for maximum threshold (5 mm) instead of a custom value in mris_thickness function. Is the map of cortical thickness the same in both cases and the difference resides in the saturation (all values above 5mm are cut to 5 mm) or do we have a completely different map (all values above 5 mm have their own value but saturated value is displayed from 5 mm and above)? please find in attachment an example of what I'm saying... I aspected to find same values for thickness within the threshold value, why this is not the case? Thanks cheers -- Giusy Chinnici

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Label corresponding to coordinate
by Martin Kavec 13 Aug '13

13 Aug '13

Hi all, Is there a command in Freesurfer, which would return to which label (e.g. superior frontal white matter left) a coordinate x,y,z belongs to? Thanks, Martin Sent from my iPad

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mri_glmfit-sim
by joost janssen 13 Aug '13

13 Aug '13

Hi, Linux jjanssen 3.8.0-25-generic #37-Ubuntu SMP Thu Jun 6 20:47:07 UTC 2013 x86_64 x86_64 x86_64 GNU/Linux command: mri_glmfit-sim --glmdir lh.thickness.20 --cache 2.0 pos error: ERROR: thresh = 1,3, must be 1.3, 2.0, 2.3, 3.0, 3.3, 4.0 i saw 1 prior email about this error message but no solution posted. i'm suing Ubuntu v12.04 thanks, -joost

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