Freesurfer

freesurfer@nmr.mgh.harvard.edu

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30089 discussions

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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

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

2 1

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.

2 1

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 . 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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

repost - large-scale reconstruction errors
by Nicole Senecal 12 Jun '12

12 Jun '12

Hi, In reconstructing some normal adult MPRAGEs, I've had a couple of different fairly large errors that I haven't been able to fix: (1) In a handful of subjects, more than half of the brain is lost, I think during the skullstripping step (ie, isn't present on the white matter or brainmask volumes later). This seems to be primarily on scans from a 3T Siemens with a 32channel head coil. I have tried adding control points, but this doesn't help. (2) In another handful of subjects, a large portion of the cerebellum is designated as cortex, and is labeled on the aseg maps. Any suggestions on how to fix these two types of problems? thanks, Nicole -- Nicole Senecal Neuroscience Graduate Group Kable Lab 3720 Walnut St., Room C37 Philadelphia, PA 19104 Lab phone: 215-746-4371

2 2

How to avoid overlaps between volume labels?
by Yuko Yotsumoto 12 Jun '12

12 Jun '12

Hello, With FreeSurfer v4.5, I have three functionally localized surface labels (A.label, B.label, C.label), and converted this label to volume by using mri_label2vol with --proj. I now have three volume labels, A.mgz, B.mgz, and C.mgz. Because these three labels are adjacent to each other, [A.mgz and B.mgz] and [B.mgz and C.mgz] share many voxels, and [A.mgz and C.mgz] also share a small number of voxels, while there is no overlap in the surface labels. I'd like to make these volume labels independent by somehow creating boundary into the volume so that each volume labels never share any voxels. What would be the best way to do so? Is there anything I can do using a command line? Best, Yuko Yotsumoto

4 4

qdec issue
by Kushal Kapse 11 Jun '12

11 Jun '12

hi, i am trying to do group analysis in qdec...my fixed factor = gender; continuous factors= age, lhthickness and rhthickness for some reason i am coming across two following issues over and over: 1- the qdec shows fixed factors are gender, lh thickness and rhthickness while covariate as age I did mention gender.levels file as female and male as per described in tutorial, but still it keeps showing me lh/rh thickness as fixed factor 2- out of 900 some subjects, it only picks 78 subjects and displays following: ERROR: Subject 126921_005547 seems to have a mismatched number of continuous factors (expected 3, found 1) ERROR: Subject 126921_005547 seems to have a mismatched number of discrete factors (expected 1, found 3) i checked my qdec.table.dat and it looks fine.....i used this command 'mac2unix' as i imported my data from csv to emacs..... may i please know where am i heading wrong? thanks kk

2 2

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