Freesurfer

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30132 discussions

Re: [Freesurfer] specifying multiple contrasts
by Douglas N Greve 12 Jun '12

12 Jun '12

The FSGD file is incorrect. It has multiple subjects listed, and the string after the subject name is not the name of a class (Tract1_FA is not the same as Tract1). I would suggest working through the example on the wiki tutorial and/or looking at the slides on group analysis. doug On 06/12/2012 06:05 PM, Shantanu Ghosh wrote: > Hi Doug > > I set up my .fsgd file as follows (4 tracts of interest, 59 subjects > belonging to 2 different groups, CON and PAT): > > GroupDescriptorFile 1 > Title tract_fa > MeasurementName thickness > Class Tract1 > Class Tract2 > Class Tract3 > Class Tract4 > Input Subject1 Tract1_FA > Input Subject1 Tract2_FA > Input Subject1 Tract3_FA > Input Subject1 Tract4_FA > Input Subject2 Tract1_FA > Input Subject2 Tract2_FA > Input Subject3 Tract3_FA > Input Subject3 Tract4_FA > . > . > Input Subject59 Tract4_FA > > and set up the .mtx file for mri_glmfit as: > > C = [zeros(3) eye(4)] > > Is that correct? How do I define the contrast variables = -1 and 0 for the > test? > > I am a little confused. > > Thanks and regards, > shantanu > > On Tue, June 12, 2012 4:57 pm, Douglas N Greve wrote: >> Did you look at the FSGD examples on our wiki? Do a search for FSGD >> doug >> >> On 06/12/2012 04:46 PM, Shantanu Ghosh wrote: >>> Hello Freesurfer experts, >>> >>> How can I specify multiple contrasts for my thickness study with two >>> groups AA and BB, having different number of subjects in each group? My >>> variables are tract-wise FA values, age and IQ. >>> >>> Thanks in advance, >>> Shantanu >>> >>> >>> >> -- >> 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 >> >> >> > -- 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

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matrix error
by mdkruepke＠uwalumni.com 12 Jun '12

12 Jun '12

Hello- I am trying to analyze the cortical thickness between two groups of subjects Cl1 and CL2. When i run the GLM i receive the error: matrix is ill-conditioned or badly scaled, condno = 1e+08 I am under the impression the error could be due to the non-uniformity in the range/scale of the regressors. here is my information: contrast is 1 -1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1) mri_glmfit --y lh.PvNPeverything.10.mgh --fsgd PvNPeverything.fsgd dods --C PvNP_everything.mtx --surf UNM_ALLGOOD lh --cortex --glmdir lh.PvNPeverything.glmdir 2) (sample of my fsgd) - there are no columns with all 0's in them GroupDescriptorFile 1 Title Methedone Comparison Class Cl1 Class Cl2 Variables WAISIQ trait_anxiety alcohol_year heroin_year cocaine_year cannabis_year meth_year amphetamines_year meth_amphet_year hallucinogens_year inhalants_year methodne_year opiates_year pills_year opitates_pills_year other_year total_years Input M87160505 Cl1 86 33 10 3 9 11 0 1 1 1 8 0 0 6 6 0 49 Input M87161888 Cl1 109 59 0 0 7 22 0 0 0 0 0 0 0 0 0 0 32 Input M87107477 Cl1 89 34 12 0 9 13 0 9 9 6 10 0 1 9 10 0 57 Input M87199897 Cl1 117 44 0 23 0 10 0 0 0 0 0 9 15 0 15 3 60 Input M87146570 Cl1 94 42 26 0 3 8 0 0 0 0 0 0 0 0 0 6 37 Input M87189755 Cl1 111 59 11 0.5 2 15 0 3 3 1.5 0 0 0 0 0 0 36 Input M87169696 Cl1 86 22 2 0 11 14 0 0 0 0 0 0 0 0 0 0 25 Input M87187366 Cl1 106 51 28 0 27 0 0 20 20 0 0 0 0 0 0 0 75 Input M87178857 Cl2 117 48 0 4 4 8 0 5 5 7 0 4 0 0.08 0.08 0 42.08 Input M87165923 Cl2 103 40 5 2 0 15 0 0 0 0 0 0 0 1 1 0 23 Input M87110556 Cl2 134 60 4 0 1 15 0 0 0 0 0 0 0 0 0 0 20 Input M87183811 Cl2 97 43 15 0 8 3 0 0 0 0 0 0 0 0 0 0 26 3) design matrix 1 0 86 0 33 0 10 0 3 0 9 0 11 0 0 0 1 0 1 0 1 0 8 0 0 0 0 0 6 0 6 0 0 0 49 0 1 0 109 0 59 0 0 0 0 0 7 0 22 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 32 0 1 0 89 0 34 0 12 0 0 0 9 0 13 0 0 0 9 0 9 0 6 0 10 0 0 0 1 0 9 0 10 0 0 0 57 0 1 0 89 0 40 0 15 0 5 0 2 0 30 0 10 0 0 0 10 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 59 0 1 0 77 0 44 0 0 0 0 0 3 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 3 0 1 0 91 0 22 0 6 0 0 0 3 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 8 0 1 0 103 0 29 0 20 0 3 0 11 0 27 0 0 0 11 0 11 0 5 0 0 0 0 0 0 0 1 0 1 0 0 0 78 0 1 0 117 0 44 0 0 0 23 0 0 0 10 0 0 0 0 0 0 0 0 0 0 0 9 0 15 0 0 0 15 0 3 0 60 0 1 0 94 0 42 0 26 0 0 0 3 0 8 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 6 0 37 0 1 0 91 0 38 0 20 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 20 0 1 0 86 0 45 0 3 0 1 0 2 0 7 0 0 0 0 0 0 0 1 0 0 0 0 0 1 0 0 0 1 0 1 0 14 0 1 0 114 0 50 0 5 0 1 0 3 0 10 0 0 0 0.08 0 0.08 0 0 0 0 0 0.33 0 1 0 0 0 1 0 0 0 20.42 0 1 0 109 0 27 0 5 0 5 0 4 0 14 0 0 0 0 0 0 0 5 0 0 0 0 0 1 0 4 0 5 0 0 0 38 0 1 0 97 0 29 0 23 0 1 0 22 0 24 0 0 0 15 0 15 0 12 0 0 0 0 0 14 0 0 0 14 0 0 0 111 0 1 0 106 0 23 0 7 0 0 0 4 0 6 0 0 0 2 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 19 0 1 0 131 0 25 0 0 0 0 0 0 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 0 1 0 74 0 54 0 12 0 0 0 0 0 16 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 6 0 6 0 0 0 32 0 1 0 123 0 41 0 0 0 0.17 0 0 0 4 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 5.17 0 1 0 100 0 27 0 4 0 0 0 2 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0 86 0 37 0 7 0 3 0 1 0 7 0 0 0 5 0 5 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 23 0 1 0 91 0 40 0 12 0 0 0 0 0 12 0 8 0 0 0 8 0 0 0 0 0 0 0 0.5 0 0 0 0.5 0 0 0 32.5 0 1 0 97 0 42 0 1.5 0 0 0 2 0 6 0 4 0 0 0 4 0 0.5 0 0 0 0 0 0 0 0 0 0 0 0 0 14 0 1 0 91 0 37 0 0 0 0 0 0 0 8 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 12 0 1 0 91 0 48 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0.25 0 0 0 0 0 0 0 0 0 0 0 0 0 4.25 0 1 0 94 0 58 0 1 0 0 0 0.67 0 4 0 5 0 0 0 5 0 0 0 3 0 0 0 0 0 0 0 0 0 0 0 13.67 0 1 0 114 0 48 0 17 0 0 0 6 0 17 0 0 0 7 0 7 0 5 0 0 0 0 0 0 0 2 0 2 0 0 0 50 0 1 0 106 0 54 0 15 0 0 0 7 0 15 0 0 0 15 0 15 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 44 0 1 0 74 0 46 0 0 0 0 0 0 0 5 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 5 0 1 0 91 0 43 0 0 0 0 0 0 0 0 0 0 0 0.33 0 0.33 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0.33 0 1 0 80 0 27 0 3 0 30 0 0 0 30 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 60 0 1 0 97 0 33 0 0.5 0 0 0 0.25 0 2 0 2 0 0 0 2 0 0 0 0.17 0 0 0 0 0 0 0 0 0 0 0 4.92 0 1 0 100 0 31 0 6 0 0 0 0 0 5 0 0 0 0 0 0 0 0 0 0 0 0 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6 0 11 0 6 0 0 0 0 0 0 0 0 0 0 0 0 0 90 0 1 0 117 0 35 0 0 0 0 0 0 0 3 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 5 0 1 0 80 0 51 0 7 0 4 0 0 0 8 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 19 0 1 0 103 0 28 0 9 0 0 0 1 0 1 0 0 0 8 0 8 0 8 0 0 0 0 0 0 0 0 0 0 0 0 0 27 0 1 0 103 0 74 0 6 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 6 0 1 0 89 0 57 0 10 0 0 0 0 0 0 0 15 0 0 0 15 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 18 0 1 0 109 0 33 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 109 0 28 0 3 0 0 0 2 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 5 0 1 0 91 0 27 0 20 0 0 0 15 0 0 0 3 0 0 0 3 0 0 0 0 0 0 0 17 0 0 0 17 0 0 0 55 0 1 0 89 0 48 0 9 0 0 0 0.25 0 10 0 20 0 0 0 20 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 39.25 0 1 0 97 0 28 0 10 0 0 0 4 0 10 0 5 0 0 0 5 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 29 0 1 0 100 0 40 0 3 0 0 0 0 0 0.17 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 3.17 0 1 0 89 0 21 0 20 0 8 0 25 0 25 0 10 0 0 0 10 0 0 0 2 0 0 0 0 0 0 0 0 0 0 0 90 0 1 0 103 0 54 0 10 0 0 0 2 0 0 0 0 0 2 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 12 0 1 0 77 0 49 0 0 0 0 0 10 0 12 0 0 0 4 0 4 0 0 0 0 0 0 0 0 0 0 0 0 0 2 0 42 0 1 0 89 0 42 0 0 0 0 0 4 0 10 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 14 0 1 0 117 0 34 0 25 0 0 0 2 0 25 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 52 0 1 0 83 0 56 0 12 0 0 0 0 0 15 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 15 0 1 0 91 0 33 0 0 0 0 0 0 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 0 1 0 106 0 36 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 120 0 50 0 1 0 0 0 0 0 2 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 6 -- Michael D. Kruepke PhD - University of Illinois at Urbana-Champaign BA - Psych - University of Wisconsin-Madison mdkruepke(a)gmail.com (262)-483-7449

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specifying multiple contrasts
by Shantanu Ghosh 12 Jun '12

12 Jun '12

Hello Freesurfer experts, How can I specify multiple contrasts for my thickness study with two groups AA and BB, having different number of subjects in each group? My variables are tract-wise FA values, age and IQ. Thanks in advance, Shantanu -- Shantanu Ghosh, Ph.D. Martinos Center for Biomedical Imaging Harvard-MIT Program in Health Sciences & Technology

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(no subject)
by Shantanu Ghosh 12 Jun '12

12 Jun '12

1 0

Correction for Multiple Comparisons
by mdkruepke＠uwalumni.com 12 Jun '12

12 Jun '12

Hey all- This may be a simple question to answer, but in an analysis looking at say cortical thickness between Group 1 and Group 2 with say 3 continues variables (age, anxiety, IQ) there would be a contrast matrix of 1 -1 0 0 0 . How does free surfer correctly remove the effects of the continues variables? -- Michael D. Kruepke PhD - University of Illinois at Urbana-Champaign BA - Psych - University of Wisconsin-Madison mdkruepke(a)gmail.com (262)-483-7449

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urgent help with cortical areas
by Rashmi Singh 12 Jun '12

12 Jun '12

Hello experts, I have the aparcstat files for corticla thickness. I would want to know is there any information on how may I group these regions more broadly ex frontal , temporal lobe areas. Thanks Rashmi. ________________________________ This document may contain information covered under the Privacy Act, 5 USC 552(a), and/or the Health Insurance Portability and Accountability Act (PL 104-191) and its various implementing regulations and must be protected in accordance with those provisions. Healthcare information is personal and sensitive and must be treated accordingly. If this correspondence contains healthcare information it is being provided to you after appropriate authorization from the patient or under circumstances that don't require patient authorization. You, the recipient, are obligated to maintain it in a safe, secure and confidential manner. Redisclosure without additional patient consent or as permitted by law is prohibited. Unauthorized redisclosure or failure to maintain confidentiality subjects you to application of appropriate sanction. If you have received this correspondence in error, please notify the sender at once and destroy any copies you have made.

3 2

ICV measurement in freesrufer
by Ayaz, Muhammad 12 Jun '12

12 Jun '12

Dear all, How does the freesurfer calculate the ICV? By adding up all the cortical and sub-cortical volumes including WM and GM and CSF? If so does it also include cerebellum and brain stem? Thanks Ayaz The information contained in this message and any attachments is intended only for the use of the individual or entity to which it is addressed, and may contain information that is PRIVILEGED, CONFIDENTIAL, and exempt from disclosure under applicable law. If you are not the intended recipient, you are prohibited from copying, distributing, or using the information. Please contact the sender immediately by return e-mail and delete the original message from your system.

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Re: [Freesurfer] [martinos-tech] isxconcat-sess problem
by Douglas N Greve 12 Jun '12

12 Jun '12

Not sure. In principle no, but it might cause the brain to be non-centered or out of the field of view. I would just run tkregister2 --fstal --s subject and get it more-or-less right (or at least check that it is not out of the field of view). doug On 06/12/2012 09:32 AM, Yue, Xiaomin wrote: > Hi Doug, > > Sorry for the slow response. The isxconcat went through without > errors. I apology for confusion my question caused. My original > question should this. After reconstructing a monkey brain with a lot > of manual intervention, I generated a talairach.xfm manually from an > identity matrix. my question was whether this 'arbitrary' > talairach.xfm would cause any fundamental problem in > the functional data analysis. > > Thanks, > Xiaomin > > ------------------------------------------------------------------------ > *From:* Douglas Greve <greve(a)nmr.mgh.harvard.edu> > *To:* "Yue, Xiaomin" <yuexm1(a)yahoo.com> > *Sent:* Friday, June 8, 2012 10:29 PM > *Subject:* Re: [martinos-tech] isxconcat-sess problem > > so, there was not an error in that output. I'm confused. Can you try > running isxconcat again? > > On 6/8/12 7:03 PM, Yue, Xiaomin wrote: >> It can write to the location. I just gave a wrong directory. >> Attached is the output. >> >> Xiaomin >> >> ------------------------------------------------------------------------ >> *From:* Douglas Greve <greve(a)nmr.mgh.harvard.edu> >> <mailto:greve@nmr.mgh.harvard.edu> >> *To:* "Yue, Xiaomin" <yuexm1(a)yahoo.com> <mailto:yuexm1@yahoo.com> >> *Sent:* Friday, June 8, 2012 6:51 PM >> *Subject:* Re: [martinos-tech] isxconcat-sess problem >> >> ok, that's a different error. Why can't it write to that location? >> >> On 6/8/12 6:28 PM, Yue, Xiaomin wrote: >>> Here is the terminal output: >>> >>> dromos/misc/data41/yuex/monkeyfMRI/mky_curvature/subjs% (stable450) >>> >mri_vol2vol --mov >>> /misc/data41/yuex/monkeyfMRI/mky_curvature/subjs/butters022712/bold/mkycurvature/mask.nii >>> --reg >>> /misc/data41/yuex/monkeyfMRI/mky_curvature/subjs/butters022712/bold/register.dat >>> --o >>> butteravg022712_031212/mkycurvature/tmp-isxconcat0.21717-sess/butters022712-mkycurvat >>> re-mask-tal.mgh --no-save-reg --interp nearest --tal --talres 2 >>> movvol >>> /misc/data41/yuex/monkeyfMRI/mky_curvature/subjs/butters022712/bold/mkycurvature/mask.nii >>> outvol >>> butteravg022712_031212/mkycurvature/tmp-isxconcat0.21717-sess/butters022712-mkycurvature-mask-tal.mgh >>> regfile >>> /misc/data41/yuex/monkeyfMRI/mky_curvature/subjs/butters022712/bold/register.dat >>> invert 0 >>> tal 1 >>> talres 2 >>> regheader 0 >>> noresample 0 >>> interp nearest (0) >>> precision float (3) >>> Gdiag_no -1 >>> Compute R for talairach space >>> >>> Final tkRAS-to-tkRAS Matrix is: >>> 0.499 -0.027 0.001 -3.313; >>> 0.018 0.335 0.371 2.944; >>> -0.021 -0.370 0.336 16.638; >>> 0.000 0.000 0.000 1.000; >>> >>> >>> Vox2Vox Matrix is: >>> 0.666 0.001 0.036 7.194; >>> -0.027 0.448 0.493 -32.996; >>> -0.024 -0.494 0.447 14.848; >>> 0.000 0.000 0.000 1.000; >>> >>> Resampling >>> mghWrite(butteravg022712_031212/mkycurvature/tmp-isxconcat0.21717-sess/butters022712-mkycurvature-mask-tal.mgh, >>> -1): could not open file >>> INFO: writing registration matrix to >>> butteravg022712_031212/mkycurvature/tmp-isxconcat0.21717-sess/butters022712-mkycurvature-mask-tal.mgh.reg >>> >>> mri_vol2vol done >>> >>> >>> Xiaomin >>> ------------------------------------------------------------------------ >>> *From:* Douglas N Greve <greve(a)nmr.mgh.harvard.edu> >>> <mailto:greve@nmr.mgh.harvard.edu> >>> *To:* "Yue, Xiaomin" <yuexm1(a)yahoo.com> <mailto:yuexm1@yahoo.com> >>> *Sent:* Friday, June 8, 2012 6:15 PM >>> *Subject:* Re: [martinos-tech] isxconcat-sess problem >>> >>> I can't replicate. Can you run this command and send me the terminal >>> output? >>> >>> mri_vol2vol --mov >>> /misc/data41/yuex/monkeyfMRI/mky_curvature/subjs/butters022712/bold/mkycurvature//mask.nii >>> --reg >>> /misc/data41/yuex/monkeyfMRI/mky_curvature/subjs/butters022712/bold/register.dat >>> --o >>> butteravg022712_031212/mkycurvature/tmp-isxconcat0.21717-sess/butters022712-mkycurvature--mask-tal.mgh >>> --no-save-reg --interp nearest --tal --talres 2 >>> >>> On 06/08/2012 06:05 PM, Yue, Xiaomin wrote: >>> > The anatomical data is here: >>> /cluster/tootell/xiaomin/3/NIH_projects/butters >>> > The functional data is here: >>> /cluster/tootell/xiaomin//3/NIH_projectos/mky_curvature/butters022712 >>> > >>> > Thanks, >>> > Xiaomin >>> > >>> > >>> ------------------------------------------------------------------------ >>> > *From:* Douglas N Greve <greve(a)nmr.mgh.harvard.edu >>> <mailto:greve@nmr.mgh.harvard.edu>> >>> > *To:* "Yue, Xiaomin" <yuexm1(a)yahoo.com <mailto:yuexm1@yahoo.com>> >>> > *Sent:* Friday, June 8, 2012 5:59 PM >>> > *Subject:* Re: [martinos-tech] isxconcat-sess problem >>> > >>> > Can you tar up the anatomical analysis? Not the functional >>> analysis, just the anatomical. You can put it on the mgh network or >>> upload it to our file drop. >>> > doug >>> > >>> > On 06/08/2012 05:49 PM, Yue, Xiaomin wrote: >>> > > attached. If more convenient, I can upload the whole analysis >>> directory to space under my MGH account. >>> > > >>> > > Xiaomin >>> > > >>> > > >>> ------------------------------------------------------------------------ >>> > > *From:* Douglas N Greve <greve(a)nmr.mgh.harvard.edu >>> <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu >>> <mailto:greve@nmr.mgh.harvard.edu>>> >>> > > *To:* "Yue, Xiaomin" <yuexm1(a)yahoo.com <mailto:yuexm1@yahoo.com> >>> <mailto:yuexm1@yahoo.com <mailto:yuexm1@yahoo.com>>> >>> > > *Sent:* Friday, June 8, 2012 5:44 PM >>> > > *Subject:* Re: [martinos-tech] isxconcat-sess problem >>> > > >>> > > Can you send me the result of >>> > > mri_info >>> /misc/data41/yuex/monkeyfMRI/mky_curvature/subjs/butters022712/bold/mkycurvature//mask.nii >>> >>> > > >>> > > On 06/08/2012 05:37 PM, Yue, Xiaomin wrote: >>> > > > attached are the files. >>> > > > >>> > > > Thanks, >>> > > > Xiaomin >>> > > > >>> > > > >>> ------------------------------------------------------------------------ >>> > > > *From:* Douglas N Greve <greve(a)nmr.mgh.harvard.edu >>> <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu >>> <mailto:greve@nmr.mgh.harvard.edu>> >>> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> >>> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>>>> >>> > > > *To:* martinos-tech(a)yahoogroups.com >>> <mailto:martinos-tech@yahoogroups.com> >>> <mailto:martinos-tech@yahoogroups.com >>> <mailto:martinos-tech@yahoogroups.com>> >>> <mailto:martinos-tech@yahoogroups.com >>> <mailto:martinos-tech@yahoogroups.com> >>> <mailto:martinos-tech@yahoogroups.com >>> <mailto:martinos-tech@yahoogroups.com>>> >>> > > > *Cc:* "Yue, Xiaomin" <yuexm1(a)yahoo.com >>> <mailto:yuexm1@yahoo.com> <mailto:yuexm1@yahoo.com >>> <mailto:yuexm1@yahoo.com>> <mailto:yuexm1@yahoo.com >>> <mailto:yuexm1@yahoo.com> <mailto:yuexm1@yahoo.com >>> <mailto:yuexm1@yahoo.com>>>> >>> > > > *Sent:* Friday, June 8, 2012 5:32 PM >>> > > > *Subject:* Re: [martinos-tech] isxconcat-sess problem >>> > > > >>> > > > Can you send the talairach.xfm and the >>> /misc/data41/yuex/monkeyfMRI/mky_curvature/subjs/butters022712/bold/register.dat >>> ? >>> > > > >>> > > > On 06/08/2012 05:18 PM, Yue, Xiaomin wrote: >>> > > > > I am sorry for the long delay to your response. What I did >>> try was to use a identity matrix for the talairach.xfm. >>> > > > > >>> > > > > Transform_Type = Linearl >>> > > > > Linear_Transform = >>> > > > > 1.0 0.0 0.0 0.0 >>> > > > > 0.0 1.0 0.0 0.0 >>> > > > > 0.0 0.0 1.0 0.0 >>> > > > > >>> > > > > Is it right? >>> > > > > >>> > > > > Thanks >>> > > > > Xiaomin >>> > > > > >>> > > > > >>> ------------------------------------------------------------------------ >>> > > > > *From:* Douglas Greve <greve(a)nmr.mgh.harvard.edu >>> <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu >>> <mailto:greve@nmr.mgh.harvard.edu>> >>> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> >>> <mailto:greve@nmr.mgh.harvard.edu >>> <mailto:greve@nmr.mgh.harvard.edu>>> >>> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> >>> <mailto:greve@nmr.mgh.harvard.edu >>> <mailto:greve@nmr.mgh.harvard.edu>> >>> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> >>> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>>>>> >>> > > > > *To:* martinos-tech(a)yahoogroups.com >>> <mailto:martinos-tech@yahoogroups.com> >>> <mailto:martinos-tech@yahoogroups.com >>> <mailto:martinos-tech@yahoogroups.com>> >>> <mailto:martinos-tech@yahoogroups.com >>> <mailto:martinos-tech@yahoogroups.com> >>> <mailto:martinos-tech@yahoogroups.com >>> <mailto:martinos-tech@yahoogroups.com>>> >>> <mailto:martinos-tech@yahoogroups.com >>> <mailto:martinos-tech@yahoogroups.com> >>> <mailto:martinos-tech@yahoogroups.com >>> <mailto:martinos-tech@yahoogroups.com>> >>> <mailto:martinos-tech@yahoogroups.com >>> <mailto:martinos-tech@yahoogroups.com> >>> <mailto:martinos-tech@yahoogroups.com >>> <mailto:martinos-tech@yahoogroups.com>>>> >>> > > > > *Cc:* "Yue, Xiaomin" <yuexm1(a)yahoo.com >>> <mailto:yuexm1@yahoo.com> <mailto:yuexm1@yahoo.com >>> <mailto:yuexm1@yahoo.com>> <mailto:yuexm1@yahoo.com >>> <mailto:yuexm1@yahoo.com> <mailto:yuexm1@yahoo.com >>> <mailto:yuexm1@yahoo.com>>> <mailto:yuexm1@yahoo.com >>> <mailto:yuexm1@yahoo.com> <mailto:yuexm1@yahoo.com >>> <mailto:yuexm1@yahoo.com>> <mailto:yuexm1@yahoo.com >>> <mailto:yuexm1@yahoo.com> <mailto:yuexm1@yahoo.com >>> <mailto:yuexm1@yahoo.com>>>>> >>> > > > > *Sent:* Friday, March 16, 2012 1:53 PM >>> > > > > *Subject:* Re: [martinos-tech] isxconcat-sess problem >>> > > > > >>> > > > > >>> > > > > >>> > > > > Check the talairach.xfm for those subjects. Even if it is >>> monkey, it needs to be something that will bring the brains into >>> alignment. >>> > > > > doug >>> > > > > >>> > > > > On 3/16/12 12:43 PM, Yue, Xiaomin wrote: >>> > > > >> Hi All, >>> > > > >> >>> > > > >> I am runing a isxconcat-sess on two session of an animal >>> scans. I got the following error. I checked mask.nii and >>> register.dat, both are there and looks like right. Any ideas? >>> > > > >> >>> > > > >> Thanks >>> > > > >> Xiaomin >>> > > > >> >>> > > > >> >>> ########################################################################################################################################## >>> > > > >> isxconcat-sess log file >>> > > > >> $Id: isxconcat-sess,v 1.25.2.7 2009/04/17 21:12:18 greve Exp $ >>> > > > >> Fri Mar 16 12:38:00 EDT 2012 >>> > > > >> Linux dromos 2.6.18-274.18.1.el5 #1 SMP Thu Feb 9 12:45:44 >>> EST 2012 x86_64 x86_64 x86_64 GNU/Linux >>> > > > >> /misc/data41/yuex/monkeyfMRI/mky_curvature/subjs >>> > > > >> /opt/freesurfer-450/fsfast/bin/isxconcat-sess >>> > > > >> -sf subjgrp -d . -a mkycurvature -all-contrasts -o >>> butteravg022712_031212 >>> > > > >> uid=34912(yuex) gid=11(braincop) groups=11(braincop) >>> > > > >> cd /misc/data41/yuex/monkeyfMRI/mky_curvature/subjs >>> > > > >> isxconcat0-sess -reg register.dat -a mkycurvature -m mask >>> -o butteravg022712_031212/mkycurvature/tal.masks.nii -interp nearest >>> -fsd bold -talres 2 -sf subjgrp -d . >>> > > > >> ------------------------------------ >>> > > > >> /misc/data41/yuex/monkeyfMRI/mky_curvature/subjs >>> > > > >> mri_vol2vol --mov >>> /misc/data41/yuex/monkeyfMRI/mky_curvature/subjs/butters022712/bold/mkycurvature//mask.nii >>> --reg >>> /misc/data41/yuex/monkeyfMRI/mky_curvature/subjs/butters022712/bold/register.dat >>> --o >>> butteravg022712_031212/mkycurvature/tmp-isxconcat0.21717-sess/butters022712-mkycurvature--mask-tal.mgh >>> --no-save-reg --interp nearest --tal --talres 2 >>> > > > >> MatrixMultiply: m2 is null! >>> > > > >> >>> > > > >> movvol >>> /misc/data41/yuex/monkeyfMRI/mky_curvature/subjs/butters022712/bold/mkycurvature//mask.nii >>> > > > >> outvol >>> butteravg022712_031212/mkycurvature/tmp-isxconcat0.21717-sess/butters022712-mkycurvature--mask-tal.mgh >>> > > > >> regfile >>> /misc/data41/yuex/monkeyfMRI/mky_curvature/subjs/butters022712/bold/register.dat >>> > > > >> invert 0 >>> > > > >> tal 1 >>> > > > >> talres 2 >>> > > > >> regheader 0 >>> > > > >> noresample 0 >>> > > > >> interp nearest (0) >>> > > > >> precision float (3) >>> > > > >> Gdiag_no -1 >>> > > > >> Compute R for talairach space >>> > > > >> No such file or directory >>> > > > >> >>> > > > > >>> > > > > >>> > > > > 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. >>> > > > > >>> > > > > >>> > > > > >>> > > > > __._,_.___ >>> > > > > Reply to sender <mailto:yuexm1@yahoo.com >>> <mailto:yuexm1@yahoo.com> <mailto:yuexm1@yahoo.com >>> <mailto:yuexm1@yahoo.com>> <mailto:yuexm1@yahoo.com >>> <mailto:yuexm1@yahoo.com> <mailto:yuexm1@yahoo.com >>> <mailto:yuexm1@yahoo.com>>> <mailto:yuexm1@yahoo.com >>> <mailto:yuexm1@yahoo.com> <mailto:yuexm1@yahoo.com >>> <mailto:yuexm1@yahoo.com>> <mailto:yuexm1@yahoo.com >>> <mailto:yuexm1@yahoo.com> <mailto:yuexm1@yahoo.com >>> <mailto:yuexm1@yahoo.com>>>>?subject=Re%3A%20%5Bmartinos-tech%5D%20isxconcat-sess%20problem> >>> | Reply to group <mailto:martinos-tech@yahoogroups.com >>> <mailto:martinos-tech@yahoogroups.com> >>> <mailto:martinos-tech@yahoogroups.com >>> <mailto:martinos-tech@yahoogroups.com>> >>> <mailto:martinos-tech@yahoogroups.com >>> <mailto:martinos-tech@yahoogroups.com> >>> <mailto:martinos-tech@yahoogroups.com >>> <mailto:martinos-tech@yahoogroups.com>>> >>> <mailto:martinos-tech@yahoogroups.com >>> <mailto:martinos-tech@yahoogroups.com> >>> <mailto:martinos-tech@yahoogroups.com >>> <mailto:martinos-tech@yahoogroups.com>> >>> <mailto:martinos-tech@yahoogroups.com >>> <mailto:martinos-tech@yahoogroups.com> >>> <mailto:martinos-tech@yahoogroups.com >>> <mailto:martinos-tech@yahoogroups.com>>>>?subject=Re%3A%20%5Bmartinos-tech%5D%20isxconcat-sess%20problem> >>> | Reply via web post >>> <http://groups.yahoo.com/group/martinos-tech/post;_ylc=X3oDMTJwNzlwbHY3BF9TA… >>> <http://groups.yahoo.com/group/martinos-tech/post;_ylc=X3oDMTJwNzlwbHY3BF9TA…> >>> <http://groups.yahoo.com/group/martinos-tech/post;_ylc=X3oDMTJwNzlwbHY3BF9TA… >>> <http://groups.yahoo.com/group/martinos-tech/post;_ylc=X3oDMTJwNzlwbHY3BF9TA…>>> >>> | Start a New Topic >>> <http://groups.yahoo.com/group/martinos-tech/post;_ylc=X3oDMTJlZTNpM2NqBF9TA…> >>> >>> > > > > Messages in this topic >>> <http://groups.yahoo.com/group/martinos-tech/message/5645;_ylc=X3oDMTM0Ym4ya…> >>> (5) >>> > > > > Recent Activity: >>> > > > > >>> > > > > Visit Your Group >>> <http://groups.yahoo.com/group/martinos-tech;_ylc=X3oDMTJlcWJsMTJxBF9TAzk3Mz…> >>> >>> > > > > Yahoo! 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Greve, Ph.D. >>> > > > MGH-NMR Center >>> > > > greve(a)nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> >>> <mailto:greve@nmr.mgh.harvard.edu >>> <mailto:greve@nmr.mgh.harvard.edu>> >>> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> >>> <mailto:greve@nmr.mgh.harvard.edu >>> <mailto:greve@nmr.mgh.harvard.edu>>> >>> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> >>> <mailto:greve@nmr.mgh.harvard.edu >>> <mailto:greve@nmr.mgh.harvard.edu>> >>> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> >>> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@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 >>> <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> >>> > > > >>> > > > >>> > > > >>> > > >>> > > -- Douglas N. Greve, Ph.D. >>> > > MGH-NMR Center >>> > > greve(a)nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> >>> <mailto:greve@nmr.mgh.harvard.edu >>> <mailto:greve@nmr.mgh.harvard.edu>> >>> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> >>> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@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 >>> <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> >>> > > >>> > > >>> > > >>> > >>> > -- Douglas N. Greve, Ph.D. >>> > MGH-NMR Center >>> > greve(a)nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> >>> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@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 >>> <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> >>> > >>> > >>> > >>> >>> -- Douglas N. Greve, Ph.D. >>> MGH-NMR Center >>> greve(a)nmr.mgh.harvard.edu <mailto:greve@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 >>> <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> >>> >>> >>> >> >> > > -- 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

1 0

spmT.img maps into fsaverage
by Yolanda Vives 12 Jun '12

12 Jun '12

Dear Freesurfer experts, How could I overlay spmT.img maps from a VBM study on fsaverage? I would like to convert the significant clusters into labels. Thank you in advance, Yolanda

2 1

MNI to RAS surface coordinates
by Yolanda Vives 12 Jun '12

12 Jun '12

Dear Freesurfer experts, I have performed a VBM analysis with SPM, using some VOIs. Now I would like to compare the volumetric results obtained with SPM with those of cortical thickness obtained with Freesurfer in the same VOIs (approximately). For this purpose, I would like to transform the MNI coordinates of my SPM VOIs into RAS surface coordinates of fsaverage, to draw a label of more or less the same size of the SPM VOI and to propage it to all the subjects in order to obtain an average cortical thickness of this label (VOI) for each subject. 1) Would this procedure be correct? 2) How could I transform my MNI coordinates into RAS surface coordinates? Thank you in advance, Yolanda

2 4

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