Freesurfer

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30089 discussions

qdec factor.levels problem
by Anne Uhlmann 03 Jul '12

03 Jul '12

Hello FreeSurfers, I have a similar problem as described in an old thread (http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg12357.html) - qdec doesn't read my factor.levels properly. I have checked the files with gedit and can't see any control characters, which might have caused the problem. Any other ideas? I have also attached the diagnosis.levels file Thank you! Anne Using /home/virtualuser/freesurfer/lib/tcl/fsgdfPlot.tcl Loading data table /media/MyPassport_/poster/qdec/insula.qdec.table.dat... Number of columns: 3 fsid column: 1 Number of factors: 2 Number of subjects: 18 Reading discrete factor levels from config file /media/MyPassport_/poster/qdec/diagnosis.levels Psychosis Control done. ERROR: Subject MAS082 has an invalid level 'Psychosis' in the diagnosis column INFO: If 'diagnosis' is a discrete factor, then create a file named 'diagnosis.levels' containing the valid factor names one per line. Cape Universities Brain & Behaviour Initiative Department of Psychiatry & Mental Health University of Cape Town Tel: 021 406 6843 ### UNIVERSITY OF CAPE TOWN This e-mail is subject to the UCT ICT policies and e-mail disclaimer published on our website at http://www.uct.ac.za/about/policies/emaildisclaimer/ or obtainable from +27 21 650 9111. This e-mail is intended only for the person(s) to whom it is addressed. If the e-mail has reached you in error, please notify the author. If you are not the intended recipient of the e-mail you may not use, disclose, copy, redirect or print the content. If this e-mail is not related to the business of UCT it is sent by the sender in the sender's individual capacity. ###

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-nobigventricles
by Richard Binney 02 Jul '12

02 Jul '12

Out of curiosity, I would like to know what the flag -nobigventricles in the ca_reg and ca_label commands does exactly. Please help. Richard

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regeneration of aseg.mgz following edits
by Richard Binney 02 Jul '12

02 Jul '12

Hi Freesurfers, I've been trying to understand the implications of various types of edits in an attempt to solidify some standardized procedures regarding editing strategies, particularly in severely lesioned (and thus highly vulnerable to RECON failure) brains. In doing so I've been comparing volumes surfaces and segmentions pre- and post- edits/re-running RECON. I've noticed that changes in surface reconstruction is, as expected, followed by changes in the aparc.2009s+aseg.mgz segmentation (exapnded/contracted in accordnace with surface) but I don't see similar alterations in the aseg.mgz segmentation.In fact the aseg.mgz is identical pre- and post-edits despite large changes in the WM.mgz and pial/WM surfaces. Could you explain why this might be? Thanks Richard

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Sagittal sinus
by Kolody, Brianna 02 Jul '12

02 Jul '12

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Re: [Freesurfer] error longitudinal processing
by j janssen 02 Jul '12

02 Jul '12

Hi Martin, changing the dir-names and qdec table to: fsid fsid-base ISI_years Group Gender Age ICV 11298_1 11298_template 0 patient F 16 1441 11298_2 11298_template 1.83 patient F 17.92 1396 solved my problem. -joost On Sun, Jul 1, 2012 at 4:33 PM, j janssen <joost.janssen76(a)gmail.com> wrote: > Hi Martin, > > thanks. > > i changed 11298 to 11298_1 and got the same error. are you suggesting that > some recon-all error may have happened because of the file names? no error > messages were reported in any of the log files, all (cross-sectional and > longitudinal) finished without error. does the error point to two > intra-subject surfaces which should have the same # of vertices but do not > have so? if so, which surfaces? > > thanks, > -joost > > > > > On Fri, Jun 29, 2012 at 8:50 PM, Martin Reuter < > mreuter(a)nmr.mgh.harvard.edu> wrote: > >> Hi Joost, >> >> the tp id cannot be the same as the base id: >> >> fsid fsid-base ISI_years Group Gender Age ICV >> 11298 11298 0 patient F 16 1441 >> 11298_2 11298 1.83 patient F 17.92 1396 >> >> I am amazed that you were able to process it this way? >> >> So either call the first time point >> 11298_1 >> or call the base 11298_base in both cases. >> >> Also make sure your longitudinal processing is correct (I mean the >> recon-all, not the post processing that you are trying here). >> >> Best, Martin >> >> On Fri, 2012-06-29 at 13:35 +0200, j janssen wrote: >> > Hi (Martin), >> > >> > - version 5.1 (Ubuntu 64b) >> > - command: long_mris_slopes --qdec ./qdec/long.qdec.table.n114.dat >> > --meas thickness --hemi lh --do-avg --do-rate --do-pc1 --do-spc >> > --do-stack --do-label --time ISI_years --qcache fsaverage >> > - attached: first 3 lines of qdec table containing the info for >> > subject 11298 >> > - attached: on screen error output. >> > - i have 2 timepoints/subject. >> > >> > things go awry in the "SUBJECT 11298 Running Within-Subject GLM" step >> > (see attachment): >> > >> > Reshaping mriglm->mask... >> > ERROR: mri_reshape: number of elements cannot change >> > >> > what am i doing wrong? >> > >> > -joost >> > >> > _______________________________________________ >> > 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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request for move through slices
by Michael Scheel 02 Jul '12

02 Jul '12

Dear FS experts, I am trying out freeview and am extremely fond of it. I have one feature request. In tkmedit in navigate mode it was possible moving through slices just using the mouse (middle mouse button pressed). Is it possible to implement the same in freeview - it appears that in freeview there are two zoom mouse actions scroll wheel and pressing-middle-mouse-button while moving up and down. Having this feature would ease checking and correcting data a lot. Thanks, Michael

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Re: [Freesurfer] Talairach transform/coordinates not present in mgz files and/or not shown in tkmedit
by Andrew R. Dykstra 01 Jul '12

01 Jul '12

Thanks Bruce. I'll give that a try. But it seems strange to me that after processing different subjects with autorecon1 that the transform info would be missing from the header of some subjects but not others. Can you think of any reason why this might happen? Cheers, Andy On Sun, Jul 1, 2012 at 4:16 PM, Bruce Fischl <fischl(a)nmr.mgh.harvard.edu>wrote: > Hi Andrew > > try running: > > mri_add_xform_to_header -c \ > $SUBJECTS_DIR/$subject/mri/transforms/talairach.xfm \ > $SUBJECTS_DIR/$subject/mri/orig.mgz \ > $SUBJECTS_DIR/$subject/mri/orig.mgz > > or whatever volume (instead of orig.mgz) you were viewing in tkmedit. This > gets done automatically during the recon-all process, but possibly you > skipped that step. > > cheers > Bruce > > > On > Sun, 1 Jul 2012, Andrew R. Dykstra wrote: > > > Dear Freesurfers, > > I am experiencing a strange issue when processing some, but not all, > > subjects with the recommended recon stream. After autorecon1, which > > includes Talairach registration step, I cannot see Talairach coordinates > in > > the tkmedit interface ('none' appears in the text box where the > coordinates > > usually are - attached screenshot). This is despite the registration > step > > supposedly succeeding (I can view and adjust the reg with tkregister2). > I > > think this may be causing further problems when trying to compute the > > forward solution in MNE (I get messages there about not being able to > read > > the coordinate transformation). Has anyone experienced an issue like > this? > > > > Cheers, > > Andy > > > > -- > > Andrew R. Dykstra, PhD Auditory Cognition Lab > > Neurologie und Poliklinik > > Universitätsklinikum Heidelberg > > Im Neuenheimer Feld 400 > > 69120 Heidelberg > > > > "How small the cosmos. How paltry and puny compared to human > consciousness > > . . . to a single individual recollection." - Vladimir Nabokov > > > > > > > > > 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. > -- Andrew R. Dykstra, PhD Auditory Cognition Lab Neurologie und Poliklinik Universitätsklinikum Heidelberg Im Neuenheimer Feld 400 69120 Heidelberg "How small the cosmos. How paltry and puny compared to human consciousness . . . to a single individual recollection." - Vladimir Nabokov

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Talairach transform/coordinates not present in mgz files and/or not shown in tkmedit
by Andrew R. Dykstra 01 Jul '12

01 Jul '12

Dear Freesurfers, I am experiencing a strange issue when processing some, but not all, subjects with the recommended recon stream. After autorecon1, which includes Talairach registration step, I cannot see Talairach coordinates in the tkmedit interface ('none' appears in the text box where the coordinates usually are - attached screenshot). This is despite the registration step supposedly succeeding (I can view and adjust the reg with tkregister2). I think this may be causing further problems when trying to compute the forward solution in MNE (I get messages there about not being able to read the coordinate transformation). Has anyone experienced an issue like this? Cheers, Andy -- Andrew R. Dykstra, PhD Auditory Cognition Lab Neurologie und Poliklinik Universitätsklinikum Heidelberg Im Neuenheimer Feld 400 69120 Heidelberg "How small the cosmos. How paltry and puny compared to human consciousness . . . to a single individual recollection." - Vladimir Nabokov

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can I run recon-all in parallel
by Dian "Oscar" Jiao 30 Jun '12

30 Jun '12

Hi, I am new to freesurfer. It seems recon-all is the most time-consuming command. I tried to run it on a HPC cluster with MPI and got the error "ERROR: it appears that recon-all is already running and re-run" and the job stopped right away. Is the code even parallelized? I had no problem running the same job on a single processor. ~Oscar

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Qdec Error (more/better info)
by Kairys, Anson 29 Jun '12

29 Jun '12

Hi everyone, I got the error I just mentioned. Terminal window says "no contrasts specified". I am trying to use "timepoint" (1-4) as a discrete factor to look at thickness across time. I guess I will have to resort to longitudinal processing? Thanks for the help -Anson ********************************************************** Electronic Mail is not secure, may not be read every day, and should not be used for urgent or sensitive issues

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