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volumes 2
by carolina.mr 16 Aug '11

16 Aug '11

2 1

Large White Matter Areas Ignored In Surface Detection
by Christopher Luna 16 Aug '11

16 Aug '11

Hello Freesurfers, I'm putting *.IMG files into the program and after correcting talaraich transformations for them, I notice that when the reconstructions have completed, that there are entire lobes of white matter absent from the surfaces detected and from the wm.mgz file. I went through my hand at first to manually fill in the missing white matter for the first case, but after seeing how many were affected, I figured there was some setting I may be missing or some contrast level that may be off. I had tried using control points, but after following the WIKI instructions on regenerating surfaces after placing them, I found no significant difference in white matter detection. How do I ensure all of the white matter in my converted IMGs is identified? Thank you kindly, Christopher Luna MIT Brain and Cognitive Sciences, Class of 2012 Desimone Lab, McGovern Institute for Brain Research MIT Archery Club Alpha Kappa Psi Colony at MIT

3 16

QDEC - generate stats data table error: cannot find /usr/local
by rajeev krishnadas 16 Aug '11

16 Aug '11

Hi all, I am new to this, and wonder if you could help me set this up please. OS: Ubuntu 10.10 ; 64 bit (a complete newbie with linux) I am going through buckner - tutorial for the group analysis with Qdec. I am at the step where I have to import the aseg and aparc data. I clicked on the "generate stats data tables" button - unfortunately an error showed up "again". ---------------------------------------------------------------------------------------------------------------------------------------------------------------- krishnadas-desktop:/usr/local/freesurfer> mkdir -p /usr/local/freesurfer/subjects/qdec/stats_tables/ ---------------------------------------------------------- asegstats2table --common-segs --meas volume --tablefile /usr/local/freesurfer/subjects/qdec/stats_tables/aseg.volume.stats.dat --statsfile=aseg.stats --subjects 140 049 141 084 021 093 080 091 040 017 138 106 108 092 124 129 103 130 039 123 095 067 004 133 097 073 149 045 136 144 032 131 145 111 102 074 114 008 128 099 /usr/local/freesurfer/bin/asegstats2table:5: DeprecationWarning: the sets module is deprecated from sets import Set Building the table.. SUBJECTS_DIR : /usr/local/freesurfer/subjects ERROR: cannot find /usr/local/freesurfer/subjects/140/stats/aseg.stats Use --skip flag if you want to continue in such cases ---------------------------------------------------------------------------------------------------------------------------------------------------------------- The path seems to be right, and the files seems to be there!!! I am doing something wrong, but cannot understand what!!!! Thanks in advance. Cheers Rajeev -- Dr Rajeev Krishnadas MBBS, MD, DipNB, MRCPsych|Clinical Lecturer in Psychological Medicine|Sackler Institute of Psychobiological Research|Southern General Hospital|Glasgow|G51 4TF|T: +44(0)141 232 7699|F: +44(0)141 232 7697|M: +44(0)7525343479 http://etanerceptforpsoriasis.moonfruit.com/#/home/4545962633 | Hasta la victoria siempre |

1 0

Find point on pial surface closest in 3D space to known Talairach coordinates
by David Painter 16 Aug '11

16 Aug '11

Hi Freesurfers, I'm running a brain stimulation (TMS) study and wish to stimulate points on the pial surface that correspond most closely to known Talairach points (from fMRI studies). I'm wondering the best way to find these points using the beautiful Freesurfer cortical reconstructions. I've extracted pial surfaces for 44 brains using recon-all. I'd like to be able to create a label on the point of the pial surface that corresponds most closely to the Talairach point. I've tried creating a label on the inflated surface and dilating it until it becomes visible on the pial surface. But this method highlights adjacent parts of cortex rather than those closest to the Talairach point. I've also tried importing the pial surface into Matlab using mris_display, increasing the transparency of the pial surface, and superimposing the Talaraich points using a scatterplot... (Incidentally, I've been unable to figure out how to transform from Talaraich space to Freesurfer RAS space. I've tried multiplying TT' x tal, where TT = the Talairach transform matrix from talairach.xfm and tal = the Talairach point. But the points are way off where they should be. What am I doing wrong? In the meantime I've solved this problem by working out the Talairach point within Freesurfer)... Using Matlab to display the pial surface and superimposing the scatterplots is producing the best results so far, but it can be very difficult to recognise different parts on the transparent pial surface and this procedure is far from automated. Any ideas? Thanks so much for your time, David Painter, PhD Queensland Brain Institute University of Queensland Australia

1 0

Dmri_trin error in trac-all
by ana ;osp 15 Aug '11

15 Aug '11

Hello freesurfer users. I'm trying to process a trac-all and it works for a while, but i have always the same error when it going to process the error. this is the end of the message Loading cortex mask from /Applications/freesurfer_v5.1//trctrain/trc032/dlabel/mni/cortex+2mm.nii.gz Processing pathway 1 of 18... Matching streamline ends INFO: Have 4088 non-truncated streamlines (min/mean/max length: 60/99/132) INFO: Center of mass of start points: (97+/-3, 96+/-7, 39+/-13) INFO: Center of mass of midpoints: (111+/-3, 109+/-4, 77+/-7) INFO: Center of mass of end points: (113+/-8, 108+/-9, 140+/-6) INFO: Split streamlines into 26 segments Computing path histograms INFO: Total streamline volume is 38001 voxels Computing prior on underlying anatomy (non-truncated streamlines only) dmri_train(23170) malloc: *** mmap(size=16777216) failed (error code=12) *** error: can't allocate region *** set a breakpoint in malloc_error_break to debug terminate called after throwing an instance of 'std::bad_alloc' what(): std::bad_alloc Abort Darwin Kernel Version 10.8.0: Tue Jun 7 16:32:41 PDT 2011; root:xnu-1504.15.3~1/RELEASE_X86_64 x86_64 I read that is due a problem of snow lepard? and one of the propostision is to fix in the source code? does some can help me? I'm running a macbook pro with snow leopard. 6GB and 2x2.4 quad core intel Thanks for help Ana A. UMASS

2 1

Re: [Freesurfer] [freesurfer] FS5.1 talairach issue
by Myriam Siefert 15 Aug '11

15 Aug '11

Hi Nick, Sorry to bother you but I wondered if you had had the time to take a look at my dataset. Thank you very much, Myriam 2011/8/11 Myriam Siefert <myriamsiefert(a)gmail.com> > Hi Nick, > I just would like to make sure that you had received my data, otherwise I > can send it again possibly by another mean if better. > Thanks a lot for your help > Sincerely, > Myriam > > > 2011/8/10 Myriam Siefert <myriamsiefert(a)gmail.com> > >> Hi Bruce and Nick, >> Thank you so much for taking a look! >> Right now I'm uploading the set on the anonymous ftp server ( >> ftp://surfer.nmr.mgh.harvard.edu/transfer/incoming) : >> talairach_issue.zip. It should appear to you in about 1 hour. >> It contains 2 versions of the same subject, the only difference is that >> OK-J-20bis was run with the -use-mritotal flag. >> Please let me know if there's any problem with the upload or if you need >> anything else. >> Sincerely, >> Myriam >> >> >> >> 2011/8/10 Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> >> >>> >>> Hi Myriam >>> Could you send nick a dataset so he can take a look? >>> Thanks >>> Bruce >>> >>> On Aug 10, 2011, at 10:24 AM, Myriam Siefert <myriamsiefert(a)gmail.com> >>> wrote: >>> >>> >>> Hi freesurfers, >>> >>> I'm currently re-processing with FS5.1 some data that i had already >>> processed with FS5.0 and am experiencing some unexpected issues with the >>> linear talairach transform. >>> >>> - While manually checking with Tkregister, I noticed that some off the >>> subjects had quite unsatisfying transforms , while no talairach failure was >>> detected on the log >>> - The transforms looked ok for those subjects in FS 5.0 >>> - I re-run autorecon1 using the -use-mritotal flag >>> - While still no error in the log file, the transforms usually then look >>> acceptable in Tkregister but completely wrong when talairach.xfm is loaded >>> in tkmedit : transformation in the top or bottom left corners, coronal and >>> transversal views interverted, sagittal views rotated by 90 degrees... >>> This happens for a few (not all) of the subjects that I've re-processed >>> with FS5.1 so far. >>> >>> I'm probably doing something wrong but can't figure out what nor what to >>> do about it. >>> Any advice would be highly appreciated. >>> >>> Thanks in advance >>> >>> Myriam Siefert, MD, MS candidate >>> Visiting scholar in SACNlab Northwestern University >>> >>> _______________________________________________ >>> 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. >>> >> >> >

3 5

Hi Ubuntu- error on generate stats
by rajeev krishnadas 15 Aug '11

15 Aug '11

Hi all, I am new to Freesurfer (and to linux) and appreciate if you could please help. Just managed to install FS onto Ubuntu 10.10 64 bit. I am going through buckner - tutorial for the group analysis with Qdec. I am at the step where I have to import the aseg and aparc data. I clicked on the "generate stats data tables" button - unfortunately an error showed up. --------------------------------------------------------------------------------------------------------------------------------------------- mkdir -p /usr/local/freesurfer/subjects/qdec/stats_tables/ mkdir: cannot create directory `/usr/local/freesurfer/subjects/qdec': Permission denied ERROR: In /usr/pubsw/packages/KWWidgets/CVS-vtk520/src/vtkKWTkUtilities.cxx, line 230 vtkKWQdecApp (0x36dd3d0): Script: vtkTemp3 GenerateStatsDataTables Returned Error on line 1: Uncaught exception: command failed: mkdir -p /usr/local/freesurfer/subjects/qdec/stats_tables/ Stack trace: Uncaught exception: command failed: mkdir -p /usr/local/freesurfer/subjects/qdec/stats_tables/ while executing "vtkTemp3 GenerateStatsDataTables" ------------------------------------------------------------------------------------------------------------------------------------------------ I was wondering if you could please guide me about what could be the problem and how to overcome it! I went through the archives and saw a similar message before, but I did not understand how the person overcame this problem. Thanks in advance. Rajeev -- Dr Rajeev Krishnadas MBBS, MD, DipNB, MRCPsych|Clinical Lecturer in Psychological Medicine|Sackler Institute of Psychobiological Research|Southern General Hospital|Glasgow|G51 4TF|T: +44(0)141 232 7699|F: +44(0)141 232 7697|M: +44(0)7525343479 http://etanerceptforpsoriasis.moonfruit.com/#/home/4545962633

2 1

recon-all error with nu_correct
by Ahmed, F, Me <fahmed＠sun.ac.za> 15 Aug '11

15 Aug '11

Hello Freesurfer experts, I am having great difficulty in trying to run the recon-all process on some scans of mine. I have tried running it a number of times, to no avail and the error I have gotten most recently is the nu_correct error. I have attached the log for this recon-all and hope someone may be able to help. Also, I was told that there is a way one can upload a particular scan via FTP, is this correct and if so, how does one go about doing this? Thank you! Fatima

4 5

Re: [Freesurfer] Freesurfer Digest, Vol 90, Issue 54
by carolina.mr 15 Aug '11

15 Aug '11

1 0

Contrast vector for gender difference and cortical/age regresion
by Knut J Bjuland 15 Aug '11

15 Aug '11

Hi I wish to produce a contrast vector for two conditions in the tutorials. I wish to make a hypothesis for age verse cortical thickness and gender verse cortical thickness. The contrast vector for age verse cortical thickness is [1 0] where age is the first x and cortical thickness is y. The situation is less clear for the group difference, but I think the contrast vector is [1 0] as the gender is two categories. I think this seems a bit strange and is different than the contrast produce by qdec which is [1 1]. What is the right contrast vector for group difference and regression between cortical thickness and aging? Can Freesurfer produce contrast vector in any package beside Qdec? Knut J

1 0

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