Freesurfer

freesurfer@nmr.mgh.harvard.edu

19 participants
30088 discussions

problem with generating cesvar.nii
by SHAHIN NASR 19 Oct '11

19 Oct '11

Hi, I have generated two different functional connectivity maps for two different ROI-based seeds. These maps are based on group-average of the same subjects (generated by using separate isxconcat-sess commands ), and now I want to see the difference map. To do so, I used mris_calc as below. > mris_calc -o diff_map/rh.ces.nii map1/rh.ces.nii sub map2/rh.ces.nii Also, to generate the rh.cesvar.nii file I used this command: > mris_calc -o diff_map1/rh.cesvar.nii map1/rh.cesvar.nii sub map2/rh.cesvar.nii But then when I used the glmfit with WLS option as below: > mri_glmfit --y rh.ces.nii --osgm --glmdir rh.ffx.osgm.wls --nii --mask ../rh.mask.nii --yffxvar rh.cesvar.nii --ffxdofdat ../ffxdof.dat --surf fsaverage rh --wls rh.cesvar.nii I faced an error saying: "Error: MRInormWeights: values less than or eq to 0" which I assumed is related to an error in rh.cesvar.nii file (am I right?). Would you tell me how can I fix this problem? P.S.: please note that sequence of subjects and all MRI parameters are exactly the same between the two maps. -- Shahin Nasr PhD in Cognitive Neuroscience Martinos Imaging Center, MGH Harvard Medical School

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Re: [Freesurfer] reg-feat2anat failure
by Douglas N Greve 19 Oct '11

19 Oct '11

This file is created when you run reg-feat2anat and should be the one that gets changed with --manxfm func2anat. You can handle this differently if you 1. Manually edit the anat2exf.register.dat so that it is relatively close (no need to be perfect) cd feat/reg/freesurfer tkregister2 --mov ../../example_func.nii.gz --reg anat2exf.register.dat --surfs 2. Run bbregister: cp anat2exf.register.dat backup.anat2exf.register.dat # Make a backup bbregister --mov ../../example_func.nii.gz --init-reg anat2exf.register.dat --reg anat2exf.register.dat --bold this second step will fine-tune your hand-edited version. Then go back and run aparc2feat, etc. doug Michelle Umali wrote: > Hi Doug, > The file that changed was exf2std.register.dat. How do I specify > that I wanted that anat2exf.register.dat is supposed to be edited? At > what point in the processing stream does this occur? > > Did editing exf2std.register.dat do anything? > > Thanks. > Michelle > > > > On Tue, Oct 18, 2011 at 2:17 PM, Douglas N Greve > <greve(a)nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> wrote: > > The registration that should be used for all of these is > anat2exf.register.dat found in feat/reg/freesurfer. Can you verify > that that was the one that you manually changed? Look at the time > stamp as compared to the other files in that folder. > doug > > Michelle Umali wrote: > > Hi Doug, > I am using reg-feat2anat on the feat directory of each run. > reg-feat2anat --feat feadir.feat --subject XX > Then I checked and adjusted the registration with: > reg-feat2anat --feat featdir.feat --manual > Next I checked and adjusted the registration to the standard with: > reg-feat2anat --feat featdir.feat --manxfm func2std > > To generate cortical binary masks I used: > aparc2feat --feat featdir.feat --annot BA > fslmaths featdir.feat/reg/freesurfer/lh.BA.nii.gz -thr 10 > -uthr 10 featdir.feat/reg/freesurfer/V1_l.nii.gz > > To generate subcortical binary masks I did: > aseg2feat --feat featdir.feat --aseg aparc+aseg > fslmaths featdir.feat/reg/freesurfer/aparc+aseg.nii.gz > -thr 54 -uthr 54 featdir.feat/reg/freesurfer/amygdala_r.nii.gz > > When I looked at the masks in FSLview and checked the masks > against the other atlases, everything was off even after > painstakingly editing the registrations. > Is there something I am doing wrong? > > Thanks. > Michelle > > On Mon, Oct 17, 2011 at 1:36 PM, 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>>> wrote: > > How are you generating the masks? > doug > > Michelle Umali wrote: > > Hi Freesurfers, > I've run reg-feat2anat on several subjects in order to > generate binary masks to use in an FSL ppi. > For 3 subjects, this completely failed. > > When I looked at the fsl's own registration of fsl feat 2 > standard (via tkregister2), the registration is fine, but > after running reg-feat2anat, the registration of the > feat to > the freesurfer anatomical and the feat to standard are > completely off. > > I manually fixed and saved the registration edits via > reg-feat2anat --manual, but when I generated the masks > again, > they were totally wrong still. > When looking at freesurfer's feat to standard > registration, it > looks like all the brains weren't tall enough in the > saggital > view. Am I supposed to stretch the feat brain to fit? > > How can I fix this so that the masks are accurate? > > Thanks. > Michelle > > ------------------------------------------------------------------------ > > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@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 > <mailto:greve@nmr.mgh.harvard.edu> > <mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu>> > Phone Number: 617-724-2358 <tel:617-724-2358> > <tel:617-724-2358 <tel:617-724-2358>> Fax: 617-726-7422 > <tel:617-726-7422> > <tel:617-726-7422 <tel:617-726-7422>> > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > <http://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> > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > > > > > 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. > > > ------------------------------------------------------------------------ > > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu > <mailto:Freesurfer@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 <mailto:greve@nmr.mgh.harvard.edu> > Phone Number: 617-724-2358 <tel:617-724-2358> Fax: 617-726-7422 > <tel:617-726-7422> > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > <http://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

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Re: [Freesurfer] QDec questions
by Douglas N Greve 18 Oct '11

18 Oct '11

Yes, see the answer to your first question below. doug krista kelly wrote: > Am I able to do vertex-by-vertex analyses using freesurfer if I have > more than 2 discrete variables? If so, how? > > Is it also ok to use the unsmoothed data when doing surface area label > analyses? > > Thanks! > > On Tue, Oct 18, 2011 at 3:14 PM, Douglas N Greve > <greve(a)nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> wrote: > > Sorry, I meant to say that you cannot use QDEC with more than 2 > discrete variables (you have 3). You do not need to extract data > from the smoothed thickness files, but the results you get from > your ROI analysis may then differ a bit from that you get from the > QDEC analysis. > doug > > krista kelly wrote: > > Thanks Doug! Just a few more things: > > I only have two groups, so my contrast was wrong. Should it > only be 1 -1, even if I have other variables I want to control > for? Or should I have a contrast file for each discrete variable? > > How would I extract the smoothed data using mri_anatomical_stats? > > I realize the importance of smoothing data while doing a > vertex-by-vertex analysis in QDec, but if I'm doing an ROI > analysis by extracting the average thickness in a certain > label (i.e. v1), is it necessary to do the stats on the > smoothed data from each participant? > > Thanks! > > > On Tue, Oct 18, 2011 at 2:23 PM, 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>>> wrote: > > > > krista kelly wrote: > > Hi, just wondering if anyone has any advice on the > following > questions: > > I'm using QDEC to analyze cortical thickness differences > between groups and I have a few questions: > > 1) There are a few variables that I need to control > for. First > variable is scanner - I used two different scanners of > different field strengths (1.5T GE and 3T Siemens) so I > wanted > to control for scanner. I also wanted to control for > age and > gender. Here's my ideal design setup: > > discrete variables - groups, scanner, gender > nuisance variable - age > > contrast would be 1 -1 0 0 0 0 > I realize that scanner, gender, and group are all discrete > variables, and that age would be a continuous one. > However, in > the design tab, I am not able to select all 3 discrete > variables (groups, scanner, and gender). Should I designate > scanner or gender as a nuisance variable instead? Would it > matter which one I use as the nuisance variable? > Possible setup: > > discrete vars - groups, scanner > nuisance vars - age, gender > > contrast - 1 -1 0 0 (Correct?) > > Unfortunately, you cannot use QDEC if you have three groups. > You'll have to create an FSGD file and contrasts by hand, > then run > mri_glmfit. Do a search for FSGD on our wiki and go to the > examples page. I think there is an example there for what > you want > to do. > > > 2) If I use DODS, should I demean the ages if age is a > nuisance variable? > > You should actually test whether there is an interaction > between > age and your group contrast of interest (using the DODS > model). If > there is not interaction, then switch to a DOSS where demeaning > does not matter. > > > 3) If I use a smoothing kernel during the analysis, then > create an ROI and map that ROI to each individual subject, > will the resulting .stats file in each subjects stats > folder > reflect the smoothed data or does mapping onto each ROI > just > extract the raw unsmoothed data from each vertex? > > It depends on how you do the extraction. If you are using > mris_anatomical_stats on each individual's unsmoothed data, > then > it will reflect the unsmoothed. > > doug > > > Thanks! > Krista > > ------------------------------------------------------------------------ > > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@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 > <mailto:greve@nmr.mgh.harvard.edu> > <mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu>> > Phone Number: 617-724-2358 <tel:617-724-2358> > <tel:617-724-2358 <tel:617-724-2358>> Fax: 617-726-7422 > <tel:617-726-7422> > <tel:617-726-7422 <tel:617-726-7422>> > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > <http://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> > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > > > > > 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. > > > > -- > 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 <tel:617-724-2358> Fax: 617-726-7422 > <tel:617-726-7422> > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > <http://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

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Re: [Freesurfer] Surface area measure
by Douglas N Greve 18 Oct '11

18 Oct '11

I don't know if that has ever been explored. doug krista kelly wrote: > Great! Do you know if it is better to use one surface area (i.e. WM or > pial) over the other when investigating differences between groups? > > On Tue, Oct 18, 2011 at 2:24 PM, Douglas N Greve > <greve(a)nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> wrote: > > The white surface. > doug > > krista kelly wrote: > > When I extract surface area data using the following > commands, which measure of surface area am I getting, the pial > surface, the WM surface, or the total of both combined? > > aparcstats2table --subjects 1 2 3 4 --parc aparc.a2009 --hemi > rh --meas area --tablefile aparc_stats_rh.txt > > Thanks! > Krista > || > ------------------------------------------------------------------------ > > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu > <mailto:Freesurfer@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 <mailto:greve@nmr.mgh.harvard.edu> > Phone Number: 617-724-2358 <tel:617-724-2358> Fax: 617-726-7422 > <tel:617-726-7422> > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > <http://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> > > > > 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. > > -- 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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Re: [Freesurfer] QDec questions
by Douglas N Greve 18 Oct '11

18 Oct '11

Sorry, I meant to say that you cannot use QDEC with more than 2 discrete variables (you have 3). You do not need to extract data from the smoothed thickness files, but the results you get from your ROI analysis may then differ a bit from that you get from the QDEC analysis. doug krista kelly wrote: > Thanks Doug! Just a few more things: > > I only have two groups, so my contrast was wrong. Should it only be 1 > -1, even if I have other variables I want to control for? Or should I > have a contrast file for each discrete variable? > > How would I extract the smoothed data using mri_anatomical_stats? > > I realize the importance of smoothing data while doing a > vertex-by-vertex analysis in QDec, but if I'm doing an ROI analysis by > extracting the average thickness in a certain label (i.e. v1), is it > necessary to do the stats on the smoothed data from each participant? > > Thanks! > > > On Tue, Oct 18, 2011 at 2:23 PM, Douglas N Greve > <greve(a)nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> wrote: > > > > krista kelly wrote: > > Hi, just wondering if anyone has any advice on the following > questions: > > I'm using QDEC to analyze cortical thickness differences > between groups and I have a few questions: > > 1) There are a few variables that I need to control for. First > variable is scanner - I used two different scanners of > different field strengths (1.5T GE and 3T Siemens) so I wanted > to control for scanner. I also wanted to control for age and > gender. Here's my ideal design setup: > > discrete variables - groups, scanner, gender > nuisance variable - age > > contrast would be 1 -1 0 0 0 0 > I realize that scanner, gender, and group are all discrete > variables, and that age would be a continuous one. However, in > the design tab, I am not able to select all 3 discrete > variables (groups, scanner, and gender). Should I designate > scanner or gender as a nuisance variable instead? Would it > matter which one I use as the nuisance variable? Possible setup: > > discrete vars - groups, scanner > nuisance vars - age, gender > > contrast - 1 -1 0 0 (Correct?) > > Unfortunately, you cannot use QDEC if you have three groups. > You'll have to create an FSGD file and contrasts by hand, then run > mri_glmfit. Do a search for FSGD on our wiki and go to the > examples page. I think there is an example there for what you want > to do. > > > 2) If I use DODS, should I demean the ages if age is a > nuisance variable? > > You should actually test whether there is an interaction between > age and your group contrast of interest (using the DODS model). If > there is not interaction, then switch to a DOSS where demeaning > does not matter. > > > 3) If I use a smoothing kernel during the analysis, then > create an ROI and map that ROI to each individual subject, > will the resulting .stats file in each subjects stats folder > reflect the smoothed data or does mapping onto each ROI just > extract the raw unsmoothed data from each vertex? > > It depends on how you do the extraction. If you are using > mris_anatomical_stats on each individual's unsmoothed data, then > it will reflect the unsmoothed. > > doug > > > Thanks! > Krista > ------------------------------------------------------------------------ > > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu > <mailto:Freesurfer@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 <mailto:greve@nmr.mgh.harvard.edu> > Phone Number: 617-724-2358 <tel:617-724-2358> Fax: 617-726-7422 > <tel:617-726-7422> > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > <http://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> > > > > 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. > > -- 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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eTIV in qdec
by dolphinede＠aol.com 18 Oct '11

18 Oct '11

Dear FreeSurfer experts, my idea was to put the eTIV as a variable in qdec. I have put this in my qdec.table.dat and when I run qdec and choose eTIV as variable I get the following error and qdec closes some seconds later automatically: Creating output directory /Users/dolphinede/Desktop/Probanden/qdec/Untitled Loading y from /Users/dolphinede/Desktop/Probanden/qdec/Untitled/y.mgh INFO: gd2mtx_method is dods Saving design matrix to /Users/dolphinede/Desktop/Probanden/qdec/Untitled/Xg.dat Normalized matrix condition is 389.695 Matrix condition is 1e+08 Found 148151 points in label. Pruning voxels by thr: 0.000000 Found 148142 voxels in mask Saving mask to /Users/dolphinede/Desktop/Probanden/qdec/Untitled/mask.mgh Reshaping mriglm->mask... search space = 73700.662359 DOF = 77 Starting fit and test Fit completed in 0.0607667 minutes Computing spatial AR1 on surface Residual: ar1mn=0.995148, ar1std=0.005328, gstd=5.802773, fwhm=13.664487 Writing results lh-Avg-Intercept-thickness maxvox sig=35.9893 F=546.618 at index 1515 0 0 seed=1319335878 lh-Avg-thickness-eTIV-Cor maxvox sig=6.48644 F=31.2833 at index 51144 0 0 seed=1319335878 mri_glmfit done ninputs = 2 Checking inputs nframestot = 2 Allocing output Done allocing nframes = 2 Writing to /Users/dolphinede/Desktop/Probanden/qdec/Untitled/contrasts.sig.mgh reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt) reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt) gdfReadHeader: reading /Users/dolphinede/Desktop/Probanden/qdec/Untitled/y.fsgd INFO: ignoring tag Creator INFO: ignoring tag SUBJECTS_DIR INFO: ignoring tag SynthSeed INFO: NOT demeaning continuous variables Continuous Variable Means (all subjects) 0 eTIV 1.45233e+06 147517 Class Means of each Continuous Variable 1 Main 1452332.4051 MatrixMultiply: m1 is null! No such file or directory I have no idea what is wrong. Best regards Daniel Klein

2 1

Surface area measure
by krista kelly 18 Oct '11

18 Oct '11

When I extract surface area data using the following commands, which measure of surface area am I getting, the pial surface, the WM surface, or the total of both combined? aparcstats2table --subjects 1 2 3 4 --parc aparc.a2009 --hemi rh --meas area --tablefile aparc_stats_rh.txt Thanks! Krista

2 1

QDec questions
by krista kelly 18 Oct '11

18 Oct '11

Hi, just wondering if anyone has any advice on the following questions: I'm using QDEC to analyze cortical thickness differences between groups and I have a few questions: 1) There are a few variables that I need to control for. First variable is scanner - I used two different scanners of different field strengths (1.5T GE and 3T Siemens) so I wanted to control for scanner. I also wanted to control for age and gender. Here's my ideal design setup: discrete variables - groups, scanner, gender nuisance variable - age contrast would be 1 -1 0 0 0 0 I realize that scanner, gender, and group are all discrete variables, and that age would be a continuous one. However, in the design tab, I am not able to select all 3 discrete variables (groups, scanner, and gender). Should I designate scanner or gender as a nuisance variable instead? Would it matter which one I use as the nuisance variable? Possible setup: discrete vars - groups, scanner nuisance vars - age, gender contrast - 1 -1 0 0 (Correct?) 2) If I use DODS, should I demean the ages if age is a nuisance variable? 3) If I use a smoothing kernel during the analysis, then create an ROI and map that ROI to each individual subject, will the resulting .stats file in each subjects stats folder reflect the smoothed data or does mapping onto each ROI just extract the raw unsmoothed data from each vertex? Thanks! Krista

2 1

reg-feat2anat failure
by Michelle Umali 18 Oct '11

18 Oct '11

Hi Freesurfers, I've run reg-feat2anat on several subjects in order to generate binary masks to use in an FSL ppi. For 3 subjects, this completely failed. When I looked at the fsl's own registration of fsl feat 2 standard (via tkregister2), the registration is fine, but after running reg-feat2anat, the registration of the feat to the freesurfer anatomical and the feat to standard are completely off. I manually fixed and saved the registration edits via reg-feat2anat --manual, but when I generated the masks again, they were totally wrong still. When looking at freesurfer's feat to standard registration, it looks like all the brains weren't tall enough in the saggital view. Am I supposed to stretch the feat brain to fit? How can I fix this so that the masks are accurate? Thanks. Michelle

2 3

mri_ca_register error
by Oya, Hiroyuki (UI Health Care) 18 Oct '11

18 Oct '11

Hello , I am running recon-all with -cm switch and getting following error. Is there any workaround? Without -cm switch , recon-all completes all the processing just fine. Thank you. Hiroyuki mri_ca_register -invert-and-save transforms/talairach.m3z mri passed volume size is different from the one used to create M3D data Loading, Inverting, Saving, Exiting ... Reading transforms/talairach.m3z zcat transforms/talairach.m3z Inverting GCAM ERROR: mri_ca_register with non-zero status 0 ________________________________ Notice: This UI Health Care e-mail (including attachments) is covered by the Electronic Communications Privacy Act, 18 U.S.C. 2510-2521, is confidential and may be legally privileged. If you are not the intended recipient, you are hereby notified that any retention, dissemination, distribution, or copying of this communication is strictly prohibited. Please reply to the sender that you have received the message in error, then delete it. Thank you. ________________________________

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