Freesurfer July 2012

freesurfer@nmr.mgh.harvard.edu

128 participants
194 discussions

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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Freesurfer July 2012