Freesurfer February 2011

freesurfer@nmr.mgh.harvard.edu

103 participants
152 discussions

possible tkregister2 bugs on OSX 10.6
by Jason Webster 05 Feb '11

05 Feb '11

I couldn't get either of the built-in functions to work to check the registration between two volumes which should have been the same. I also noticed that the tkregister2 wiki page<http://surfer.nmr.mgh.harvard.edu/fswiki/tkregister2>contains no info about the command, though it does have a link to the TkRegister2 Guide <http://surfer.nmr.mgh.harvard.edu/fswiki/TkRegister2Guide>, which does not exist. --------------------------------------------------------------------- FREESURFER_HOME: /Applications/freesurfer Build stamp: freesurfer-Darwin-leopard-i686-stable-pub-v5.0.0 Kernel info: Darwin 10.6.0 i386 --------------------------------------------------------------------- swi> tkregister2 --targ SWI1.nii.gz --mov SWI2.nii --identity tkregister_tcl /Applications/freesurfer/lib/tcl/tkregister2.tcl ERROR: no registration file specified swi> tkregister2 --targ SWI1.nii.gz --mov nsLGH_26Aug10_10.nii --check-reg tkregister_tcl /Applications/freesurfer/lib/tcl/tkregister2.tcl target volume SWI1.nii.gz movable volume SWI2.nii reg file /tmp/reg.tmp.1297311621.dat LoadVol 1 ZeroCRAS 0 $Id: tkregister2.c,v 1.117.2.1 2010/08/02 17:42:03 greve Exp $ Diagnostic Level -1 regio_read_register(): No such file or directory Could not open /tmp/reg.tmp.1297311621.dat ERROR: reading /tmp/reg.tmp.1297311621.dat

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freeview and control points
by Mehul Sampat 04 Feb '11

04 Feb '11

Hi Folks, We used to use tkmedit to add control points and recently started using freeview. I have a few basic questions about saving controls points created with freeview. 1. I noticed that in tkmedit edit controls points were saved as "control.dat" in the "subject_dir"/tmp (e.g. bert/tmp). When I use freeview I assume I should also save the control points in the same location ? 2. If so, is there a way to configure freeview so that it saves it to "subject_dir"/tmp ? (currently the default location where freeview saves the control points in the current subject directory.) 3. Also I believe tkmedit saved the control points as "control.dat" but for freeview one has to specify the name manually. Is there a command line argument to set the name of the file as "control.dat" by default ? Thanks Mehul

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right hippocampus bad segmentation...
by Gonzalo Rojas 04 Feb '11

04 Feb '11

Hi: I processed the T1 volume of a patient... I got bad segmentation of the right hippocampus (see attached images)... How can I correct the segmentation ?... Sincerely, Gonzalo Rojas Costa

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problem with spmregister on mac
by Maryam Vaziri Pashkam 04 Feb '11

04 Feb '11

Hi, I am new to freesurfer and I am analyzing fmri data on a Mac OSX 10.5.8 computer using freesurfer 4.5. I have SPM 8 and FSL also installed. I have two versions of matlab (matlab R2009b & R2008a) on my computer. I think spm runs through the R2009b on my computer. I have added the SPM path to the startup.m of both matlabs by adding the following line (they both point to the same startup.m ): path(path,'/Applications/spm8'); I run preprocessing on the data using the following command: preproc-sess -nosmooth -sf retino-sess -df retino.dir then I run automatic registration with the following command: spmregister-sess -sf retino-sess -df retino.dir It runs smoothly and there seems to be no errors. But when I try to check the registration with this command: tkregister-sess -sf retino-sess -df retino.dir -inorm what I see is not a good registration. Isn't spm register supposed to do a good job in automatic registration? The one that I get still needs a lot of manual adjustment. Am I doing something wrong? I have attached the log files for spmregister and tkregister and a screen shot of the image that I get after running tkregister. I would appreciate any help in this matter. Thanks, Maryam

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Variables meaning -White matter hypointensities vs. non-WM-hypointensities?
by San Jung 03 Feb '11

03 Feb '11

Hi. I'm visiting researcher for Behavior neurology. I'm trying to compare pathology and MRI image data in ischemic vascular disease patients. In our group, there are a lot of image researchers and they already made MRI free surfer DATA. My PI advised me to use free surfer data for my study. Using those files, I hope to know the volume of white matter lesion on MRI. In subcortical volume data, there are 2 variables for white matter volumes. One is "Volume (white matter parcellation) of non-WM-hypointensities region in mm3" and the other is "Volume (white matter parcellation) of WM-hypointensities region in mm3". I think hypo-intensity region means the lesion area in T1 sequence. However I am not sure the meaning of non-white matter hypointensities region in subcortical volume data. Can you help me to define two variables? . San Jung MD

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reconstruction question
by Evan Luther 03 Feb '11

03 Feb '11

Hello, My name is Evan Luther and I have been working with Dr. David Ress at the University of Texas at Austin to create a high resolution (.7 mm) volume using FreeSurfer. In the last step of our data pipeline I enter the command: recon-all -segmentation -fill -tessellate -smooth1 -inflate1 -qsphere -fix -smooth2 -inflate2 -finalsurfs -cortribbon -s fsHighRes After running for several hours this reconstruction gets stuck in the mris_fix_topology command. This command does not have much documentation on the FreeSurferWiki although from what I understand it is ensuring that the cortical surface is topologically correct. It picks out about 216 topological errors and gets stuck on the 93rd. I left it running on this error for quite some time (>24 hours) and nothing occurred. Can anyone offer me any insight or help? Thank you very much, Evan Luther

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fsl tutorial data
by Rita Loiotile 03 Feb '11

03 Feb '11

anyone have it saved anywhere?

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Re: [Freesurfer] Regression: Activation as a function of condition
by Adam Nitenson 03 Feb '11

03 Feb '11

Hi Doug and Freesurfers, Now that I have re-processed some of my data in Stable 5, I would like to re-open a previous problem I was trying to tackle: " We are using the Sternberg Item Recognition Paradigm in our study, which involves the memorization and recognition of groups of 1, 3, 5, and 7 letters. Each run has two sets of each condition (load). We want to determine if any regions of the brain activate in a linear pattern with increased task load (# of letters). I have already done regression analyses using genotype, but that was between subjects, while this analysis would be within subjects. Does anyone know how I could structure an analysis that would allow me to look at this? Is this something I have to do at the mkanalysis-sess level?" I had tried doing this in Stable 4 using the method described here https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2010-December/016557… However, I was unable to generate the desired results, so I decided to switch over to Stable 5 as suggested. Thanks, Adam > > > ---------------------------- Original Message ---------------------------- > Subject: Re: [Freesurfer] Regression: Activation as a function of > condition > From: "Douglas N Greve" <greve(a)nmr.mgh.harvard.edu> > Date: Tue, January 11, 2011 11:52 am > To: "Adam Nitenson" <nitenson(a)nmr.mgh.harvard.edu> > -------------------------------------------------------------------------- > > You don't need to re-unpack. you don't run recon-all on the functional, > only the anatomicals. > > Adam Nitenson wrote: >> So this means I will have to start at the unpacksdcmdir command and then >> recon-all to rerun the functionals? >> >> >>> You don't need to re-run the anatomicals, but you will need to rerun >>> the >>> functionals. >>> >>> doug >>> >>> Adam Nitenson wrote: >>> >>>> Hmm...it appears that we might need to make the transition over to >>>> Stable >>>> 5 then. >>>> >>>> Would I have to reprocess all Stable 4 subjects again in Stable 5 >>>> (including the whole recon-all from bourget) process, or is there some >>>> sort of jumping off point from which I can start using the new stable? >>>> >>>> Thanks, >>>> >>>> Adam >>>> >>>> >>>> >>>> >>>>> you can't do it in stable4, but you can in stable 5. >>>>> >>>>> doug >>>>> >>>>> >>>>> Adam Nitenson wrote: >>>>> >>>>> >>>>>> Hello Freesurfers, >>>>>> >>>>>> We are using the Sternberg Item Recognition Paradigm in our >>>>>> study, >>>>>> which involves the memorization and recognition of groups of 1, 3, >>>>>> 5, >>>>>> and 7 letters. Each run has two sets of each condition (load). We >>>>>> want to determine if any regions of the brain activate in a linear >>>>>> pattern with increased task load. I have already done regression >>>>>> analyses using genotype, but that was between subjects, while this >>>>>> analysis would be within subjects. Does anyone know how I could >>>>>> structure an analysis (STABLE 4) that would allow me to look at >>>>>> this? >>>>>> Is this something I have to do at the mkanalysis-sess level? >>>>>> >>>>>> >>>>>> Thanks, >>>>>> >>>>>> Adam Nitenson, B.S. >>>>>> Brain Genomics Lab >>>>>> Massachusetts General Hospital >>>>>> _______________________________________________ >>>>>> 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: www.nmr.mgh.harvard.edu/facility/filedrop/index.html >>>>> >>>>> >>>>> >>>>> >>>>> >>>> Adam Nitenson, B.S. >>>> Brain Genomics Lab >>>> Massachusetts General Hospital >>>> >>>> >>>> >>>> >>> -- >>> 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: www.nmr.mgh.harvard.edu/facility/filedrop/index.html >>> >>> >>> >>> >> >> >> Adam Nitenson, B.S. >> Brain Genomics Lab >> Massachusetts General Hospital >> >> >> > > -- > 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: www.nmr.mgh.harvard.edu/facility/filedrop/index.html > > > > > Adam Nitenson, B.S. > Brain Genomics Lab > Massachusetts General Hospital > > > Adam Nitenson, B.S. Brain Genomics Lab Massachusetts General Hospital

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Surface area interpretation confusion
by Jürgen Hänggi 03 Feb '11

03 Feb '11

Dear FS experts Sorry, for reposting this question, but I'am not sure whether something went wrong. We divided the superior temporal sulcus derived from the aparc.a2009s.annot into parcellations of 300mm2 in size (using mris_divide_parcellation) and computed the mean cortical thickness within each parcellation. But after running mris_anatomical-stats, we noticed that each parcellation has a unique surface area that deviates largely from 300mm2 (ranging between 96mm2 to 480mm2). Does anybody have any ideas? Is this a bug or is this what one should expect? We defined the parcells on the fsaverage template and transformed them back into the native space of each individual. Therefore, we expected some variation in the surface area, but not such large differences. Thanks in advance Regards Jürgen ---------------------------------------------------------------------------- Jürgen Hänggi, Ph.D. Division Neuropsychology Institute of Psychology University of Zurich Binzmuehlestrasse 14, PO Box 25 8050 Zurich, Switzerland 0041 44 635 73 97 (phone office) 0041 76 445 86 84 (phone mobile) 0041 44 635 74 09 (fax office) BIN 4.D.04 (office room number) j.haenggi[at]psychologie.uzh.ch (email) http://www.psychologie.uzh.ch/neuropsy/ (website) http://www.juergenhaenggi.ch (private website) This e-mail (and any attachment/s) contains confidential and/or privileged information. If you are not the intended recipient (or have received this e-mail in error) please notify the sender immediately and destroy this e-mail. Any unauthorised copying, disclosure or distribution of the material in this e-mail is strictly forbidden. ----------------------------------------------------------------------------

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Am I losing T2* info in MEMPRAGE data by differential scaling?
by Carl Anderson 02 Feb '11

02 Feb '11

Dear Freesurfer, I am concerned that I may not be processing the MEMPRAGE images to full take advantage of the T2* info in the multi-echos. I have been separating each echo as 001.mgz, 002.mgz, 003.mgz & 004.mgz when using recon-all. This works well if motion exists in any of the individual echos. However of late, I have noticed a that a reference was made to the problem of losing T2* info by differential scaling in the archive if a particular file format "memprage_echo0.mgz" was not used. Here is the link to the archive note: http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg15303.html It has been hard to identify a difference between our standard MPRAGE images and the MEMPRAGE images (we currently collect both on our Siemens 3T 32 channel system). Am I processing the MEMPRAGE correctly? Thanks! -- <<•>>~<>~<<•>>~<>~<<•>>~<>~<<•>>~<>~<<•>>~<>~<<•>>~<>~<<•>>~<>~<<•>> Carl M. Anderson, Ph.D. (mail stop 204) Assistant Professor of Psychiatry, Harvard Medical School & The Neuroimaging Center, McLean Hospital 115 Mill St. Belmont, MA 02478 Ph: 617-855-2972; Fax: 617-855-2770 e-mail: remfract(a)gmail.com; carl_anderson(a)hms.harvard.edu <<•>>~<>~<<•>>~<>~<<•>>~<>~<<•>>~<>~<<•>>~<>~<<•>>~<>~<<•>>~<>~<<•>>

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Freesurfer February 2011