Freesurfer February 2011

freesurfer@nmr.mgh.harvard.edu

103 participants
152 discussions

Re: [Freesurfer] Contrasts for GLM DODS with both discrete as continues covariates
by Douglas N Greve 15 Feb '11

15 Feb '11

Yes, that all looks correct. The only other thing you may want to do is to demean (ie, remove the mean from) your continuous variables. When you test for a difference in thickness (as opposed to slope), you are implicitly testing at your variables=0. Eg, if age is one of your variables, then you are testing at age=0 (birth). If there is not an interaction between age and group, then this is not a problem. If there is an interaction, then the difference will depend on what age you compute the difference. So, it's a good idea to test for an interaction between group and your continuous variables. The contrasts would basically look the same (ie, four 0.25s, four -0.25s, and 24 zeros), they will just be rearranged differently. doug Habets P (SP) wrote: > Hi Doug, > > Just a final check that my fsgd and contrasts are properly defined. > This is now my fsgd file > > GroupDescriptorFile 1 > Title fsgd_pat_con.txt > MeasurementName CorticalThickness > > Class controls_male_mdeft > Class controls_female_mdeft > Class controls_male_adni > Class controls_female_adni > Class patients_male_mdeft > Class patients_female_mdeft > Class patients_male_adni > Class patients_female_adni > > Variables Age Education Handedness > > Input C001 controls_female_mdeft 25 6 100 > Input C002 controls_female_mdeft 27 6 100 > Input C003 controls_male_mdeft 46 5 -89.47368622 > Input C004 controls_female_mdeft 43 4 100 > Input C005 controls_male_mdeft 25 8 100 > Input C006 controls_male_mdeft 19 7 100 > Input P001 patients_male_mdeft 32 7 -100 > Input P002 patients_female_mdeft 46 3 -23.07691956 > Input P003 patients_male_mdeft 26 6 100 > Input P004 patients_female_mdeft 19 6 60 > Input P005 patients_male_mdeft 23 5 100 > Input P006 patients_male_mdeft 21 3 100 > > My hypothesis is than patients differ from controls with regard to cortical thickness, regressing out the effects for gender scantype age educational level and handedness. > So my contrast is: > 0.25 0.25 0.25 0.25 -0.25 -0.25 -0.25 -0.25 and 24 zero's (together 32 regressors) > > Is this properly defined? > Thx! > Bw Petra > > -----Original Message----- > From: freesurfer-bounces(a)nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] On Behalf Of Douglas N Greve > Sent: Friday, February 11, 2011 5:10 PM > To: Habets P (SP) > Cc: freesurfer(a)nmr.mgh.harvard.edu; Gronenschild Ed (NP) > Subject: Re: [Freesurfer] Contrasts for GLM DODS with both discrete as continues covariates > > Hi Petra, you have mixed up a class with the level of a factor (an easy > thing to do). From your FSGD, it looks like you would need 8 classes, > each class would be a combination of a level from each factor. So one > class would be control-male-adni, etc. Once you have a proper FSGD file, > FreeSurfer will create the proper design matrix. After you looked at the > FSGD examples on the wiki? Do a search for FSGD, and they will pop up. > > doug > > Habets P (SP) wrote: > >> I want to run a GLM DODS in Freesurfer to test whether patients differ >> from controls with regard to cortical thickness, meanwhile I want to >> control for several variables, both discrete as continues. >> >> This is my manually made fsgd file >> >> GroupDescriptorFile 1 >> >> Title fsgd pat con.txt >> >> MeasurementName Cortical Thickness >> >> Class controls >> >> Class patients >> >> Class female >> >> Class male >> >> Class mdeft >> >> Class adni >> >> Variables Age Education Handedness >> >> input C002 controls female mdeft 27 6 100 >> >> input C003 controls male mdeft 46 5 -89.47368622 >> >> input C004 controls female mdeft 43 4 100 >> >> input P001 patients male mdeft 32 7 -100 >> >> input P003 patients male mdeft 26 6 100 >> >> input P004 patients female mdeft 19 6 60 >> >> The problem I have is how to specify contrasts, on the Freesurfer >> website I found that : >> >> For DODS, the number of regressors is Nc*(Nv+1) >> >> In my case that would be 6* (3+1) = 24 >> >> Would the contrast than be: >> >> 1 -1 and 22 zero's >> >> Does Freesurfer automatically create the correct design matrix using >> the fsgd file? Because it is not clear to me how I should create the >> design matrix with some discrete variables as confounders. >> >> Bw Petra Habets >> >> * * >> >> ------------------------------------------------------------------------ >> >> _______________________________________________ >> 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

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Fw: Question about FreeSurfer Tutorial
by Tali Shrem 15 Feb '11

15 Feb '11

Hi, I was trying to use the FreeSurfer tutorials for the first time, and had a problem whenever I tried to use the command tksurfer. After I defined FREESURFER_HOME, TUTORIAL_DATA and SUBJECTS_DIR I tried to visualise a surface. The result was that a window opened where the surface should have appeared but nothing appeared in it (however, the menu underneath did open properly). Here is the terminal output: assafs $ tksurfer 004 lh inflated -annot aparc.annot subject is 004 hemi is lh surface is inflated surfer: current subjects dir: /usr/local/freesurfer/AudSpaceAdaptation/PitchSpace/buckner_data/tutorial_subjs/group_analysis_tutorial surfer: not in "scripts" dir ==> using cwd for session root surfer: session root data dir ($session) set to: surfer: /mnt/newdataarch2/Leon_Lab/Experiments/AudSpaceAdaptation/PitchSpace/buckner_data/tutorial_subjs/group_analysis_tutorial Reading image info (/usr/local/freesurfer/AudSpaceAdaptation/PitchSpace/buckner_data/tutorial_subjs/group_analysis_tutorial/004) Reading /usr/local/freesurfer/AudSpaceAdaptation/PitchSpace/buckner_data/tutorial_subjs/group_analysis_tutorial/004/mri/orig.mgz surfer: Reading header info from /usr/local/freesurfer/AudSpaceAdaptation/PitchSpace/buckner_data/tutorial_subjs/group_analysis_tutorial/004/mri/orig.mgz surfer: vertices=152763, faces=305522 reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt) Found embedded color table in annotation. 9938 vertices did not have an annotation! surfer: single buffered window surfer: tkoInitWindow(004) Window type not found! surfer: failed, trying double buffered window surfer: using interface /usr/local/freesurfer/lib/tcl/tksurfer.tcl Reading /usr/local/freesurfer/lib/tcl/tkm_common.tcl Reading /usr/local/freesurfer/lib/tcl/tkm_wrappers.tcl Reading /usr/local/freesurfer/lib/tcl/fsgdfPlot.tcl Reading /usr/local/freesurfer/lib/tcl/tkUtils.tcl Successfully parsed tksurfer.tcl reading white matter vertex locations... % I am using Linux version Fedora, Release 12 (Constantine). The FreeSurfer version I am using is stable v.5.0.0. Thanks, Tali Shrem

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Re: [Freesurfer] Probabilistic V1 labels to volume
by Douglas N Greve 14 Feb '11

14 Feb '11

When you say the original T1, do you mean the data directly from the dicom files? FS analysis is generally done in our "conformed" space (1mm isotropic, 256^3). One of those volumes is called "T1" and one is called "orig" -- this understandably confuses a lot of newbies (and oldbies). doug Jennifer Evans wrote: > > The original T1 to start with would be good. I did try: > > bbregister --s $SUBJ --mov T1.mgz --reg register.dat --t1 --init-header > > but I can't figure out whether I've got a problem viewing it or with > the commands. > > Thanks, > Jen > > On 02/14/2011 05:49 PM, Douglas N Greve wrote: >> What volume do you want to project them to? >> doug >> >> Jennifer Evans wrote: >>> Hi there, >>> >>> I'm not really familar with freesurfer and am missing the step on what >>> to register to create the register.dat file required to use >>> mri_label2vol to convert the probabilistic V1 label file outputs from a >>> single subject to a volume. I thought the labels are already on the >>> surface/volume and registered... but using an identity matrix isn't >>> right. Which volumes/command create/s the right register.dat file? I >>> rooted around in the wiki but couldn't figure out the right >>> relationships. >>> >>> Thanks, >>> Jen >>> >>> _______________________________________________ >>> 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

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Probabilistic V1 labels to volume
by Jennifer Evans 14 Feb '11

14 Feb '11

Hi there, I'm not really familar with freesurfer and am missing the step on what to register to create the register.dat file required to use mri_label2vol to convert the probabilistic V1 label file outputs from a single subject to a volume. I thought the labels are already on the surface/volume and registered... but using an identity matrix isn't right. Which volumes/command create/s the right register.dat file? I rooted around in the wiki but couldn't figure out the right relationships. Thanks, Jen

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(no subject)
by Angela Cosentino 14 Feb '11

14 Feb '11

Salve! Sto utilizzando freesurfer per un lavoro di tesi e ho incontrato problemi per la fase di preprocessing. Allora ho ricevuto dei file in fomrato ".nii" e li ho converiti con il comando: "recon-all -i "file_name.nii" -s "nuovo_nome". Ora dovrei processarli, tramite il comando "recon-all -i file_name.dcm -s subject_name -all. Potreste dirmi cosa evo mettere di preciso al posto del campo "file_name.dcm"; mi dà sempre errore. Sto utilizzando la versione 5 di FreeSurfer, su Linux. Grazie!

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Blocked Design
by Mandy Nagy 14 Feb '11

14 Feb '11

Hello, We are attempting to run an analysis using selxavg3-sess but keep getting an error. We are using: freesurfer v5 Our subjects directory: /cluster/manoach/milton/subjects Command that was run: selxavg3-sess -analysis mandylh2 -fwhm -s PAMST06 Output that was given: Creating Design Matrix ... creation time = 0.006 sec DoMCFit = 1 ntptot = 250, nX = 5, DOF = 245 Saving X matrix to /autofs/cluster/manoach/milton/subjects/PAMST06/bold/mandylh2/Xtmp.mat ??? Error using ==> svd Input to SVD must not contain NaN or Inf. Error in ==> cond at 40 s = svd(A); Error in ==> fast_selxavg3 at 256 XCond = cond(XtX); >> ------------------------------------------ ERROR: fast_selxavg3() failed\n Do you know what might cause this? Thanks! --Mandy

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FreeSurfer coordinates
by Douglas N Greve 14 Feb '11

14 Feb '11

I have created some use cases on how to transform coordinates in one space to those in another space (eg, a point on the surface to MNI305 space or to the col, row, slice of a functional volume). Let me know if you have any questions or have other use cases you'd like me to add. http://surfer.nmr.mgh.harvard.edu/fswiki/CoordinateSystems doug -- 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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Segmentation into native space
by Yolanda Vives 14 Feb '11

14 Feb '11

Dear freesurfer's, I have run a conventional recon-all process and I am interested in isolating the caudate from my subjects. I have applied the following commands: *./mri_label2vol --seg $SUBJECTS_DIR/$subj/mri/aseg.mgz --temp $SUBJECTS_DIR/$subj/mri/rawavg.mgz --o $SUBJECTS_DIR/$subj/mri/aseg-in-rawavg.mgz --regheader $SUBJECTS_DIR/$subj/mri/aseg.mgz * *./mri_extract_label $SUBJECTS_DIR/$subj/mri/aseg-in-rawavg.mgz 11 $PROJDIR/$subj.nii.gz * I had seen in the wiki that these commands should be used when we need the images in native space. ¿Does it mean that my caudates are "denormalized" or on the contrary, that the images have only been resliced to the original size? If it is the second case, how could I obtain the caudates from the original image? Thank you for your help, Yolanda

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Opening positions
by Xinian Zuo 11 Feb '11

11 Feb '11

Opening positions (postdoc, research assistant, or professorship) for collaborative projects from the Center for Human Brain Research, Hangzhou Normal University (Professor WENG Xuchu, wengxc(a)psych.ac.cn) Key Laboratory of Cognitive Neuroscience and Learning, Beijing Normal University (Professor ZANG Yufeng, zangyf(a)gmail.com) and Institute of Psychology, Chinese Academy of Science (Professor ZUO Xi-Nian, zuoxinian(a)gmail.com) Any applicant with relevant neuroimaging background is welcome, including neuroscience, medicine, psychology, biology, physics, mathematics, computer and information science, and so on. Salary and compensation are almost the best in China. Please send your CV to any of the three e-mail addresses listed above if you are interested in these jobs. -- Xi-Nian Zuo, Ph.D of Applied Mathematics (http://lfcd.psych.ac.cn)

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position ad for image analysis
by Bruce Fischl 11 Feb '11

11 Feb '11

A full-time position as image analysis specialist is available at the Section of Biomedical Image Analysis (SBIA), of the Department of Radiology, University of Pennsylvania. The successful candidate must have a Bachelor's or Master's degree in Electrical or Biomedical Engineering, or Computer Science, or related field. Experience with medical images is a plus. The work will involve applying, testing and extending image processing algorithms and protocols on medical images. SBIA has been a dynamically growing medical image analysis group (www.rad.upenn.edu/sbia) including 40 researchers and many collaborators from diverse fields. Please e-mail or mail CV's to christos(a)rad.upenn.edu Christos Davatzikos, Ph.D. Professor of Radiology, and Electrical and Systems Engineering, Director, Section of Biomedical Image Analysis Joint Affiliations: Bioengineering and Applied Math graduate groups University of Pennsylvania 3600 Market street, Suite 380 Tel.: 215-349-8587 Email: christos(a)rad.upenn.edu http://www.rad.upenn.edu/sbia Christos Davatzikos 3600 Market street, Suite 380 Philadelphia, PA 19104 The information contained in this e-mail message is intended only for the personal and confidential use of the recipient(s) named above. If the reader of this message is not the intended recipient or an agent responsible for delivering it to the intended recipient, you are hereby notified that you have received this document in error and that any review, dissemination, distribution, or copying of this message is strictly prohibited. If you have received this communication in error, please notify us immediately by e-mail, and delete the original message.

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Freesurfer February 2011