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Re: [Freesurfer] GLM problems
by Allie Rosen 19 Apr '11

19 Apr '11

Namely, I was following the directions from the following: https://surfer.nmr.mgh.harvard.edu/fswiki/Fsgdf2G1V On Tue, Apr 19, 2011 at 12:33 PM, Allie Rosen <rosen.allie(a)gmail.com> wrote: > Hi Doug, > > It worked with +1 -1 0. But I also have an agediff.mat file (0 0 +1 -1) > that I'd like to look at. Therefore I'd be looking at age differences and > also sex differences. Can I do this using DODS? I'm not sure if I'd be able > to do that with 3 regressors. > > So honestly I'm not even sure whether I should use DOSS or DODS. My groups > are male and female and I'm not sure if there are differences between them. > I thought that the first 2 regressors were male and female, and the 3rd and > 4th were age. Am I correct? > > Thanks, > Allie > > > > > On Tue, Apr 19, 2011 at 12:26 PM, Douglas N Greve < > greve(a)nmr.mgh.harvard.edu> wrote: > >> Hi Alli,e you are running it with DOSS which will create 4 regressors >> (MaleOffset, FemaleOff, AgeSlope). Your contrast has 4 columns. So change to >> DODS or change the number of column in your contrast. If you go with DODS, >> make sure to test for an interaction (ie, a contrast of 0 0 +1 -1). If you >> have substantial interaction, then testing the offsets is tricky. If you >> don't have an interaction, then change to DOSS and use (+1 -1 0). >> >> doug >> >> Allie Rosen wrote: >> >>> Update: ran on a different computer in the lab and progressed a little, >>> but got the following error: "dimension mismatch between X and contrast >>> sexdiff.mat X has 3 cols, C has 4 cols" >>> >>> I am not positive what X is, but here is my FSGD file (abbreviated): >>> >>> GroupDescriptorFile 1 >>> Class Male >>> Class Female >>> Variables Age >>> >>> Input C1 Female 27 >>> Input C2 Female 53 >>> Input C3 Male 22 >>> Input C4 Female 62 >>> Input C5 Male 27 >>> >>> And here is my contrast file: >>> >>> 1 -1 0 0 >>> >>> Any ideas? >>> >>> Thank you, >>> Allie >>> >>> >>> >>> >>> On Tue, Apr 19, 2011 at 11:51 AM, Allie Rosen <rosen.allie(a)gmail.com<mailto: >>> rosen.allie(a)gmail.com>> wrote: >>> >>> Hi All, >>> >>> I am running mri_glmfit and get the following error: >>> >>> mri_glmfit --y lh.insula.thickness.6.mgz --fsgd fsgd2.txt doss >>> --glmdir lh.insula.thickness.6.glmdir --surf fsaverage lh --C >>> sexdiff.mat >>> gdfReadHeader: reading fsgd2.txt >>> INFO: DeMeanFlag keyword not found, DeMeaning will NOT be done. >>> Continuous Variable Means (all subjects) >>> 0 Age 37.9483 >>> Class Means of each Continuous Variable >>> 1 Male 34.5417 >>> 2 Female 40.3529 >>> INFO: gd2mtx_method is doss >>> Reading source surface >>> /media/AMMONIS/fsSubjects/AR_normals/fsaverage/surf/lh.white >>> Number of vertices 163842 >>> Number of faces 327680 >>> Total area 65416.648438 >>> AvgVtxArea 0.399267 >>> AvgVtxDist 0.721953 >>> StdVtxDist 0.195470 >>> >>> $Id: mri_glmfit.c,v 1.187.2.1 2010/07/26 15:54:39 greve Exp $ >>> cwd /media/AMMONIS/fsSubjects/AR_normals >>> cmdline mri_glmfit --y lh.insula.thickness.6.mgz --fsgd fsgd2.txt >>> doss --glmdir lh.insula.thickness.6.glmdir --surf fsaverage lh --C >>> sexdiff.mat >>> sysname Linux >>> hostname Caduceus >>> machine x86_64 >>> user arosen >>> FixVertexAreaFlag = 1 >>> UseMaskWithSmoothing 1 >>> OneSampleGroupMean 0 >>> y /media/AMMONIS/fsSubjects/AR_normals/lh.insula.thickness.6.mgz >>> logyflag 0 >>> usedti 0 >>> FSGD fsgd2.txt >>> labelmask >>> /media/AMMONIS/fsSubjects/AR_normals/fsaverage/label/lh.cortex.label >>> maskinv 0 >>> glmdir lh.insula.thickness.6.glmdir >>> IllCondOK 0 >>> DoFFx 0 >>> Creating output directory lh.insula.thickness.6.glmdir >>> Segmentation fault >>> >>> >>> The directory IS created, but contains only "mri_glmfit.log". Here >>> are the contents: >>> >>> >>> $Id: mri_glmfit.c,v 1.187.2.1 2010/07/26 15:54:39 greve Exp $ >>> cwd /media/AMMONIS/fsSubjects/AR_normals >>> cmdline mri_glmfit --y lh.insula.thickness.6.mgz --fsgd fsgd2.txt >>> doss --glmdir lh.insula.thickness.6.glmdir --surf fsaverage lh --C >>> sexdiff.mat >>> sysname Linux >>> hostname Caduceus >>> machine x86_64 >>> user arosen >>> FixVertexAreaFlag = 1 >>> UseMaskWithSmoothing 1 >>> OneSampleGroupMean 0 >>> y /media/AMMONIS/fsSubjects/AR_normals/lh.insula.thickness.6.mgz >>> logyflag 0 >>> usedti 0 >>> FSGD fsgd2.txt >>> labelmask >>> /media/AMMONIS/fsSubjects/AR_normals/fsaverage/label/lh.cortex.label >>> maskinv 0 >>> glmdir lh.insula.thickness.6.glmdir >>> IllCondOK 0 >>> DoFFx 0 >>> >>> If this all sounds familiar, I realize that I've submitted this >>> problem back in January and haven't managed to work it out. Any >>> help would be appreciated! >>> >>> Thank you, >>> Allie Rosen, MSc Candidate >>> Graduate Student, Department of Neurosurgery >>> Toronto Western Hospital 14-327 >>> 399 Bathurst St. >>> University of Toronto >>> >>> >>> ------------------------------------------------------------------------ >>> >>> _______________________________________________ >>> 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 >> >> >> >> 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. >> >> >

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GLM problems
by Allie Rosen 19 Apr '11

19 Apr '11

Hi All, I am running mri_glmfit and get the following error: mri_glmfit --y lh.insula.thickness.6.mgz --fsgd fsgd2.txt doss --glmdir lh.insula.thickness.6.glmdir --surf fsaverage lh --C sexdiff.mat gdfReadHeader: reading fsgd2.txt INFO: DeMeanFlag keyword not found, DeMeaning will NOT be done. Continuous Variable Means (all subjects) 0 Age 37.9483 Class Means of each Continuous Variable 1 Male 34.5417 2 Female 40.3529 INFO: gd2mtx_method is doss Reading source surface /media/AMMONIS/fsSubjects/AR_normals/fsaverage/surf/lh.white Number of vertices 163842 Number of faces 327680 Total area 65416.648438 AvgVtxArea 0.399267 AvgVtxDist 0.721953 StdVtxDist 0.195470 $Id: mri_glmfit.c,v 1.187.2.1 2010/07/26 15:54:39 greve Exp $ cwd /media/AMMONIS/fsSubjects/AR_normals cmdline mri_glmfit --y lh.insula.thickness.6.mgz --fsgd fsgd2.txt doss --glmdir lh.insula.thickness.6.glmdir --surf fsaverage lh --C sexdiff.mat sysname Linux hostname Caduceus machine x86_64 user arosen FixVertexAreaFlag = 1 UseMaskWithSmoothing 1 OneSampleGroupMean 0 y /media/AMMONIS/fsSubjects/AR_normals/lh.insula.thickness.6.mgz logyflag 0 usedti 0 FSGD fsgd2.txt labelmask /media/AMMONIS/fsSubjects/AR_normals/fsaverage/label/lh.cortex.label maskinv 0 glmdir lh.insula.thickness.6.glmdir IllCondOK 0 DoFFx 0 Creating output directory lh.insula.thickness.6.glmdir Segmentation fault The directory IS created, but contains only "mri_glmfit.log". Here are the contents: $Id: mri_glmfit.c,v 1.187.2.1 2010/07/26 15:54:39 greve Exp $ cwd /media/AMMONIS/fsSubjects/AR_normals cmdline mri_glmfit --y lh.insula.thickness.6.mgz --fsgd fsgd2.txt doss --glmdir lh.insula.thickness.6.glmdir --surf fsaverage lh --C sexdiff.mat sysname Linux hostname Caduceus machine x86_64 user arosen FixVertexAreaFlag = 1 UseMaskWithSmoothing 1 OneSampleGroupMean 0 y /media/AMMONIS/fsSubjects/AR_normals/lh.insula.thickness.6.mgz logyflag 0 usedti 0 FSGD fsgd2.txt labelmask /media/AMMONIS/fsSubjects/AR_normals/fsaverage/label/lh.cortex.label maskinv 0 glmdir lh.insula.thickness.6.glmdir IllCondOK 0 DoFFx 0 If this all sounds familiar, I realize that I've submitted this problem back in January and haven't managed to work it out. Any help would be appreciated! Thank you, Allie Rosen, MSc Candidate Graduate Student, Department of Neurosurgery Toronto Western Hospital 14-327 399 Bathurst St. University of Toronto

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Re: [Freesurfer] Pial surface error
by Allie Rosen 19 Apr '11

19 Apr '11

Hi Sita, Thanks for all the responses! I've actually had the same problem for multiple subjects. I'm using version 5.0.0. I'll try fixing the cerebellum as well. I've attached pictures of where I am adding wm voxels. They aren't really in the same places as in the online tutorials. Could you take a quick look to see if they're in the right place? Thanks, Allie On Mon, Apr 18, 2011 at 12:31 PM, Sita Kakunoori <sita(a)nmr.mgh.harvard.edu>wrote: > > Hi Allie, > > pial surface which looks like this can only be corrected by correcting the > wm.mgz. Also I would suggest to try and fix the cerebellum and see if it > corrects the surfaces as well. Since part of the cerebellum is stripped off, > it's probably affecting the segmentation as well but I could be wrong. what > version of freesurfer are you using. > > > Sita. > > > > On Mon, 18 Apr 2011, Allie Rosen wrote: > > Hi Sita, >> >> Can I still add voxels to wm.mgz even though the points would be outside >> even the pial boundary? >> >> Thanks >> Allie >> >> >> >> On Mon, Apr 18, 2011 at 12:18 PM, Sita Kakunoori >> <sita(a)nmr.mgh.harvard.edu>wrote: >> >> >>> Hi Allie, >>> >>> This probably needs white matter edits but it's hard to tell from one >>> slice. Please refer to our white matter edits wiki and toplogical defects >>> wiki and see if it helps in fixing the errors in your datasets. Also it >>> looks like part of the Cerebellum is stripped off. You might want to >>> correct >>> that as well. >>> >>> https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/WhiteMatterEdits >>> >>> https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/TopologicalDefect >>> >>> >>> Sita. >>> >>> >>> >>> >>> On Mon, 18 Apr 2011, Allie Rosen wrote: >>> >>> Hi, >>> >>>> >>>> Once processed, several of my subjects have had errors around the >>>> occipital >>>> lobe. Attached is an example. I've already tried editing brainmask.mgz >>>> and >>>> running recon-all, but as you can see, this didn't change the pial or wm >>>> borders. What can I do to fix this? >>>> >>>> Thank you, >>>> Allie Rosen, MSc Candidate >>>> Graduate Student, Department of Neurosurgery >>>> Toronto Western Hospital 14-327 >>>> 399 Bathurst St. >>>> University of Toronto >>>> >>>> >>>> >>> 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. >>> >>> >>> >>

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roi from icbm152 to fsaverage inflated surface
by Boris Bernhardt 19 Apr '11

19 Apr '11

Dear Freesurfers, Using FreeSurfer 4.5.0, I am trying to map a binary *.nii roi-mask (defined in ${LABEL}) that has been outlined on the icbm-152 template in mni space to the inflated surface model of fsaverage. The approach below gives me a solution that looks very trustworthy, however, I'd like to verify with the experts whether it is 100% accurate. These are the commands I am using: # to map the label to the fsaverage target mri_label2vol --seg ${LABEL} --temp fsaverage/mri/orig.mgz --reg ${FREESURFER_HOME}/average/mni152.register.dat --invertmtrx -fillthresh 0.5 --o ${LABEL%.nii}_fsa.nii # to intersect it with the wm surface, and then map it to the sphere (note that identity.dat has been generate prior to running the command). mri_vol2surf --src ${LABEL%.nii}_fsa.nii --reg identity.dat --hemi lh --surf white --interp nearest --surfreg sphere.reg --icoorder 7 --out ${LABEL%.nii}_fsasurf_lh.mgh # to convert the mgh to ascii mris_convert -c ${LABEL%.nii}_fsasurf_lh.mgh fsaverage/surf/lh.white {LABEL%.nii}_fsasurf_lh.asc Many thanks, Boris

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Retinotopy-polar angle
by Michelle Umali 19 Apr '11

19 Apr '11

Dear Freesurfers, I'm having issues trying to display the polar angle data using the color wheel. Unfortunately, I can't resizing the Configure Overlay Display window. No matter what I try, I can't actually see the Apply button. Any suggestions? Also, is there a quickie guide on defining the boundaries of visual areas? Thanks. Michelle

2 2

Fedora 14
by roger.jou＠yale.edu 18 Apr '11

18 Apr '11

Hi all, Quick question: will the latest Linux 32-bit install work with Fedora 14? Please let me know if there are known issues. Thanks, Roger

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Grey Matter Not Included In Pial Surface
by andrewmains12＠berkeley.edu 18 Apr '11

18 Apr '11

Hi all, I have several subjects whose cortical grey matter continues to not be included in the pial surface even after adding numerous control points to the white matter as suggested in https://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/2007-July/005649.html . Some of the control points I added were outside of the pial surface boundary--does this cause them to be ignored? I have white matter areas with multiple control points that are still not included in either the pial or white matter boundaries. I can supply images if it would be helpful. Thanks for any help! Andrew

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question regarding clusterwise correction for multiple comparisons
by Ilana Hairston 18 Apr '11

18 Apr '11

Hi there, After running mri_glmfit with several different contrasts, all stored in the same folder (e.g., gender controlling for age: 1 -1 0 0; interaction of gender with age: 0 0 1 -1, etc.), i am interested in correcting for only one of the effects (e.g., gender). However, the mri_glmfit-sim doesn't seem to specify which contrast. I guess i'm not clear as to what information is used for the montecarlo thanks ilana -- ******************************* peligro! flaca pero mala! ******************************

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Re: [Freesurfer] Question about "bbregister"
by Douglas N Greve 18 Apr '11

18 Apr '11

Hi Xiaojian, you can use mri_vol2surf or mri_vol2vol. doug ps. Please send these types of questions to the freesurfer list and not to me directly. Thanks! XJ Kang wrote: > Hi Dr Greve, > > Thank you for your prompt reply. > > By "registration matrix", do you mean the matrix in "register.dat"? > Could you please remind me how to apply it in all the frames? I am > using spm to process all the data. Maybe there are some freesurfer > functions to apply the matrix for all the frames. Or any help page in > FreeSurferWiki? > > Again, thank you for your time. > > Xiaojian > > > > On 4/18/2011 11:23 AM, Douglas N Greve wrote: >> Hi Xiaojian, what is usually done is to run motion correction on your >> fMRI time series picking the middle time point as a reference. Then >> registration matrix for the middle time point will be appropriate for >> all the frames in the time series. >> >> 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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Re: [Freesurfer] Question about "bbregister"
by Douglas N Greve 18 Apr '11

18 Apr '11

Hi Xiaojian, what is usually done is to run motion correction on your fMRI time series picking the middle time point as a reference. Then registration matrix for the middle time point will be appropriate for all the frames in the time series. doug XJ Kang wrote: > Dear Dr. Greve, > > I am trying to apply "bbregister" to our EPI data after I read your > 2009 Neuroimage paper "Accurate and robust brain image alignment using > boundary-based registration". > > One thing I found that bbregister will not save the coregistered > information to the original --mov frame. Instread, it incorporated the > info into "register.dat" or in the resampled "--o " image. Then I > have to register all the EPI frames one by one and resampled them into > the orig.mgz (256^3) space to compare them. > > Is there any way or option that I can save the bbregistered frame (in > low resolution EPI) in its own space? Then I can realign all other > EPIs to this coregistered frame in the EPI resolution space. > > Thank you for your time. > > Sincerely, > Xiaojian Kang > > -- 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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