Freesurfer

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30084 discussions

changing the index of labels
by Jacobs H (NP) 04 Nov '15

04 Nov '15

Hi, Is there a way to change the index of the segmentation of the hippocampal subfields, so that when I combine left and right, FreeSurfer treats them as different regions? Thanks! Best Heidi > >>I just checked again in freeview and indeed they have the same index >>(e.g. >>CA1 has value 206 for left and also for right). >> >>On 10/27/15, 5:01 PM, "Douglas Greve" <greve(a)nmr.mgh.harvard.edu> wrote: >> >>>The color is not important. The question is whether they have a >>>different index. Can you confirm that lh and rh have the same index? >>> >>>On 10/27/15 11:53 AM, Jacobs H (NP) wrote: >>>> Hi Doug, >>>> >>>> Yes, for the aseg they are. But not for the hippocampal subfields: >>>>left >>>> and right have the same color coding. >>>> I am creating one segmentation, including left and right hippocampal >>>> subfields and aparc, for partial volume correction. >>>> Any idea how I can make the labels for the hippocampal subfields >>>>different >>>> (freesurfer version 6)? >>>> >>>> Thanks >>>> Heidi >>>> >>>> On 10/27/15, 4:32 PM, "Douglas Greve" <greve(a)nmr.mgh.harvard.edu> >>>>wrote: >>>> >>>>> The indices should be different. Eg, 17 is left hippo, 53 is right >>>>> hippo. If you click on them in freeview and different labels appear, >>>>> then FS knows they are different >>>>> >>>>> On 10/24/15 9:29 PM, Jacobs H (NP) wrote: >>>>>> Hi. >>>>>> >>>>>> Just one another related question: now that I was able to combine >>>>>>left >>>>>> and >>>>>> right hippocampal subfields with the aparc-aseg correctly, I noticed >>>>>> that >>>>>> the left and right hippocampal subfields have the same color labels >>>>>>and >>>>>> codes. What would be the best way to make sure that FreeSurfer >>>>>> understand >>>>>> that the left and right subfields (e.g. Left and right CA1) are >>>>>> different >>>>>> areas? >>>>>> >>>>>> Thanks! >>>>>> Heidi >>>>>> >>>>>> On 10/21/15, 11:01 PM, "Jacobs H (NP)" >>>>>> <h.jacobs(a)maastrichtuniversity.nl> >>>>>> wrote: >>>>>> >>>>>>> Thanks! Works wonderful! >>>>>>> Heidi >>>>>>> >>>>>>> On 10/21/15, 10:50 PM, "Douglas N Greve" >>>>>>><greve(a)nmr.mgh.harvard.edu> >>>>>>> wrote: >>>>>>> >>>>>>>> If you want to remove them, you can use mri_binarize with the >>>>>>>> --replace >>>>>>>> option, replacing them with whatever you want. >>>>>>>> >>>>>>>> On 10/21/2015 04:38 PM, Jacobs H (NP) wrote: >>>>>>>>> Hi, >>>>>>>>> >>>>>>>>> I am trying to generate a segmentation file containing the >>>>>>>>>aseg+aparc >>>>>>>>> but replacing the hippocampus with the hippocampal subfields. >>>>>>>>> With mergeseg I was able to merge the segmentations, but >>>>>>>>> unfortunately >>>>>>>>> parts of the ³old² hippocampus (labeled as 17 and 53) are still >>>>>>>>>in >>>>>>>>> there (as the area covered by the subfields is not 100% equal to >>>>>>>>>the >>>>>>>>> hippocampus of the aseg). >>>>>>>>> How can I remove the remains of the old hippocampal labels? >>>>>>>>> >>>>>>>>> Many thanks! >>>>>>>>> Best >>>>>>>>> Heidi >>>>>>>>> >>>>>>>>> >>>>>>>>> _______________________________________________ >>>>>>>>> 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: https://gate.nmr.mgh.harvard.edu/filedrop2 >>>>>>>> www.nmr.mgh.harvard.edu/facility/filedrop/index.html >>>>>>>> Outgoing: >>>>>>>> ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ >>>>>>>> >>>>>>>> _______________________________________________ >>>>>>>> Freesurfer mailing list >>>>>>>> Freesurfer(a)nmr.mgh.harvard.edu >>>>>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>>>>>>> >>>>>>>> >>>>>>>> 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 >>>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>>>>> >>>>>> >>>>> _______________________________________________ >>>>> Freesurfer mailing list >>>>> Freesurfer(a)nmr.mgh.harvard.edu >>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>>> >>>> _______________________________________________ >>>> Freesurfer mailing list >>>> Freesurfer(a)nmr.mgh.harvard.edu >>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>>> >>>> >>> >>>_______________________________________________ >>>Freesurfer mailing list >>>Freesurfer(a)nmr.mgh.harvard.edu >>>https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >

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Re: [Freesurfer] LongitudinalTwoStageModel QDEC Help
by Martin Reuter 04 Nov '15

04 Nov '15

Not sure what is going on. can you find (from the log) the command it runs just before that (something with mris_label_calc) and run it in a terminal (with the SUBJECT_DIR set etc). It could be that it get's confused by the .nii extension, but could also be something else. Martin On 11/04/2015 10:09 AM, Heidi Foo wrote: > Hi Martin, > > I understand what you mean now. Thanks for your advice! > > But I have another error message now: /ERROR 64 : mris_label_calc > intersect did not work? /Is there something I am doing wrong? > > Regards, > Heidi > > > On Wed, Nov 4, 2015 at 10:39 PM, Martin Reuter > <mreuter(a)nmr.mgh.harvard.edu <mailto:mreuter@nmr.mgh.harvard.edu>> wrote: > > Heidi, > > first: you probably need to keep the .nii in the table for now > (depending on how your cross sectional directories are really > named?). If they have the .nii extension, you need to do the same > in the qdec table. > > If down the road the extension creates problems, it will be very > complicated to solve this as the naming is propagated to many > places (in the cross runs, base and long). Cleaning that up > retrospectively is possible but lot's of work and if you miss a > place things will fail. So it might be easier to re-run from > scratch (depending on the size of the data and the edits)? Let's > first wait and see what happens. > > Best, Martin > > > On 11/04/2015 09:34 AM, Heidi Foo wrote: >> Hi Martin, >> >> Thanks so much for your reply, I really appreciate it. >> >> I will change my qdec file for fsid accordingly from >> FS_PD002_1.nii.long.FSBASE_002 to FS_PD002_1. If the file name >> and file extension are causing the problem, do you have any >> suggestions for me overcome this? Would changing the file name help? >> >> Thanks again. >> >> Regards, >> Heidi >> >> On Wed, Nov 4, 2015 at 9:51 PM, Martin Reuter >> <mreuter(a)nmr.mgh.harvard.edu >> <mailto:mreuter@nmr.mgh.harvard.edu>> wrote: >> >> Dear Heidi, >> >> maybe there is a problem with your long.qdec.table.dat file? >> It is used to create the <fsid>.long.<fs_baseid> file names >> and obviously that filename is wrong (containing two .long. >> in it). Make sure that the first column is only the cross >> sectional id and the second one is the base id, so in your case: >> fsid fsid-base >> FS_PD002_1.nii FSBASE_002 >> >> Also it is not a good idea to have the ".nii" as part of the >> subject id, as that is a file extension. Next time, when >> running the cross sectionals, make sure you call the subject >> "FS_PD002_1" without extension. Could be that this leads to >> other problems (or it could just work, we'll see). >> >> Best, Martin >> >> >> >> >> >> On 11/04/2015 08:38 AM, Heidi Foo wrote: >>> Dear FreeSurfer experts, >>> >>> I was running the first stage of analysis of preparing of >>> data - qcache - and I encountered some problems. >>> >>> When using this command, /long_mris_slopes --qdec >>> ./qdec/long.qdec.table.dat --meas thickness --hemi lh >>> --do-avg --do-rate --do-pc1 --do-spc --do-stack --do-label >>> --time years --qcache fsaverage --sd $SUBJECTS_DIR/, an >>> error message saying:" >>> FS_PD002_1.nii.long.FSBASE_002.long.FSBASE_002/label/lh.cortex.label >>> does not exist!" appears. >>> >>> I tried several other ways such as using long_stats_slopes, >>> but I keep receiving error messages similar to the one above. >>> >>> Please advice? >>> >>> Thank you so much for your kind help! >>> >>> Regards, >>> Heidi Foo >> >> -- >> Martin Reuter, PhD >> Assistant Professor of Radiology, Harvard Medical School >> Assistant Professor of Neurology, Harvard Medical School >> A.A.Martinos Center for Biomedical Imaging >> Massachusetts General Hospital >> Research Affiliate, CSAIL, MIT >> Phone:+1-617-724-5652 <tel:%2B1-617-724-5652> >> Web :http://reuter.mit.edu >> >> 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. >> >> > > -- > Martin Reuter, PhD > Assistant Professor of Radiology, Harvard Medical School > Assistant Professor of Neurology, Harvard Medical School > A.A.Martinos Center for Biomedical Imaging > Massachusetts General Hospital > Research Affiliate, CSAIL, MIT > Phone:+1-617-724-5652 <tel:%2B1-617-724-5652> > Web :http://reuter.mit.edu > > -- Martin Reuter, PhD Assistant Professor of Radiology, Harvard Medical School Assistant Professor of Neurology, Harvard Medical School A.A.Martinos Center for Biomedical Imaging Massachusetts General Hospital Research Affiliate, CSAIL, MIT Phone: +1-617-724-5652 Web : http://reuter.mit.edu

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error MRS voxel as seed in FS-FAST
by stdp82＠virgilio.it 04 Nov '15

04 Nov '15

Hi list, this error is still occurring: mri_convert $SUBJECTS_DIR/subj/mri/MRS_MASK.nii.gz $SUBJECTS_DIR//subj/mri/MRS_MASK.mgz fcseed-config -segid 1 -seg $SUBJECTS_DIR//subj/mri/MRS_MASK.mgz -fsd rest -mean -cfg MRS_MASK.config fcseed-sess -s -cfg MRS_MASK.config During fcseed-sess -s subj -cfg MRS_MASK.config Voxel Volume is 64.5752 mm^3 Generating list of segmentation ids Found 1 segmentations Computing statistics for each segmentation 0 1 0 0.000 MRIalloc(0, 1, 1): bad parm Reporting on 0 segmentations Computing spatial average of each frame Writing to /Applications/freesurfer/subjects/fMRI/sub/rest/001/tmp. fcseed-sess.97908/avgwf.mgh Segmentation fault I have read your previous message and you can check the MRS voxel features. MRS voxel mask is in subj directory where I have run recon all -all. data_type FLOAT32 dim1 256 dim2 256 dim3 256 dim4 1 datatype 16 pixdim1 1.000000 pixdim2 1.000000 pixdim3 1.000000 pixdim4 0.010747 cal_max 0.0000 cal_min 0.0000 file_type NIFTI-1+ The features are same of other subject that runs fine. data_type FLOAT32 dim1 256 dim2 256 dim3 256 dim4 1 datatype 16 pixdim1 1.000000 pixdim2 1.000000 pixdim3 1.000000 pixdim4 0.010747 cal_max 0.0000 cal_min 0.0000 file_type NIFTI-1+ Thank you very much. Stefano >----Messaggio originale---- >Da: stdp82(a)virgilio.it >Data: 16-ott-2015 23.15 >A: <freesurfer(a)nmr.mgh.harvard.edu> >Ogg: [Freesurfer] R: Re: R: import FS-FAST results in FSL > >I'd like to open with FSLview the sig.nii.gz which is produced by >selxavg3-sess. >If I use mri_surf2vol, which is the template to added in --template? >It should be in Tailairach space? Where can I find the template that I >should added? >Thanks, > >Stefano > >subj/rest/fc.seed.surf.lh/L_seed/sig.nii.gz >data_type FLOAT32 >dim1 27307 >dim2 1 >dim3 6 >dim4 1 >datatype 16 >pixdim1 1.000000 >pixdim2 1.000000 >pixdim3 1.000000 >pixdim4 1100.000000 >cal_max 49.1815 >cal_min -12.3855 >file_type NIFTI-1+ > > > > > > > >Thanks, > >Stefano > > >>----Messaggio originale---- >>Da: greve(a)nmr.mgh.harvard.edu >>Data: 29-set-2015 22.09 >>A: <freesurfer(a)nmr.mgh.harvard.edu> >>Ogg: Re: [Freesurfer] R: import FS-FAST results in FSL >> >>Do you mean surface-based analysis? You'd have to put them back into >the >>volume using mri_surf2vol, write them out as nifti and then run >fslview >>on them >> >>On 09/29/2015 11:17 AM, stdp82(a)virgilio.it wrote: >>> >>> Hi list, >>> >>> I would like to import FS-FAST results (conjunction maps) in >FSL, >>> opening them by fslview. >>> Could you provide me any suggestion? >>> >>> Thank you very much >>> Best regards, >>> >>> >>> Stefano >>> >>> >>> >>> >>> _______________________________________________ >>> 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: https://gate.nmr.mgh.harvard.edu/filedrop2 >>www.nmr.mgh.harvard.edu/facility/filedrop/index.html >>Outgoing: ftp://surfer.nmr.mgh.harvard. >edu/transfer/outgoing/flat/greve/ >> >>_______________________________________________ >>Freesurfer mailing list >>Freesurfer(a)nmr.mgh.harvard.edu >>https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> >>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 >https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >

2 1

zcat issue, lGI processing
by Andrews, Derek 04 Nov '15

04 Nov '15

Hello Freesurfer Support Team, I have encountered an issue running recon-all -lgi that I believe is due to a zcat issue on mac OSx where a .Z is added to the end of the file name the resulting error looks like this... >> reading filled volume... zcat: can't stat: /Users/dandrews/data/test/12011/surf/tmp-mris_compute_lgi-lh.pial/lh.pial.filled.mgz (/Users/dandrews/data/test/12011/surf/tmp-mris_compute_lgi-lh.pial/lh.pial.filled.mgz.Z): No such file or directory Upon reading through some message boards it appears replacing zcat with gzcat can solve this issue, however I am unsure where this troublesome zcat command is (it does not appear in the mriscomputelgi script). Any suggestions or work throughs would be appreciated. Best, Derek ________________________________ Derek Sayre Andrews, MSc PhD Candidate The Sackler Institute for Translational Neurodevelopment Department of Forensic and Neurodevelopmental Sciences Institute of Psychiatry, Psychology & Neuroscience, King's College London Telephone: +44 (0)20 7848 5701 Email: Derek.Andrews(a)kcl.ac.uk

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Re: [Freesurfer] LongitudinalTwoStageModel QDEC Help
by Martin Reuter 04 Nov '15

04 Nov '15

Heidi, first: you probably need to keep the .nii in the table for now (depending on how your cross sectional directories are really named?). If they have the .nii extension, you need to do the same in the qdec table. If down the road the extension creates problems, it will be very complicated to solve this as the naming is propagated to many places (in the cross runs, base and long). Cleaning that up retrospectively is possible but lot's of work and if you miss a place things will fail. So it might be easier to re-run from scratch (depending on the size of the data and the edits)? Let's first wait and see what happens. Best, Martin On 11/04/2015 09:34 AM, Heidi Foo wrote: > Hi Martin, > > Thanks so much for your reply, I really appreciate it. > > I will change my qdec file for fsid accordingly from > FS_PD002_1.nii.long.FSBASE_002 to FS_PD002_1. If the file name and > file extension are causing the problem, do you have any suggestions > for me overcome this? Would changing the file name help? > > Thanks again. > > Regards, > Heidi > > On Wed, Nov 4, 2015 at 9:51 PM, Martin Reuter > <mreuter(a)nmr.mgh.harvard.edu <mailto:mreuter@nmr.mgh.harvard.edu>> wrote: > > Dear Heidi, > > maybe there is a problem with your long.qdec.table.dat file? It is > used to create the <fsid>.long.<fs_baseid> file names and > obviously that filename is wrong (containing two .long. in it). > Make sure that the first column is only the cross sectional id and > the second one is the base id, so in your case: > fsid fsid-base > FS_PD002_1.nii FSBASE_002 > > Also it is not a good idea to have the ".nii" as part of the > subject id, as that is a file extension. Next time, when running > the cross sectionals, make sure you call the subject "FS_PD002_1" > without extension. Could be that this leads to other problems (or > it could just work, we'll see). > > Best, Martin > > > > > > On 11/04/2015 08:38 AM, Heidi Foo wrote: >> Dear FreeSurfer experts, >> >> I was running the first stage of analysis of preparing of data - >> qcache - and I encountered some problems. >> >> When using this command, /long_mris_slopes --qdec >> ./qdec/long.qdec.table.dat --meas thickness --hemi lh --do-avg >> --do-rate --do-pc1 --do-spc --do-stack --do-label --time years >> --qcache fsaverage --sd $SUBJECTS_DIR/, an error message saying:" >> FS_PD002_1.nii.long.FSBASE_002.long.FSBASE_002/label/lh.cortex.label >> does not exist!" appears. >> >> I tried several other ways such as using long_stats_slopes, but I >> keep receiving error messages similar to the one above. >> >> Please advice? >> >> Thank you so much for your kind help! >> >> Regards, >> Heidi Foo > > -- > Martin Reuter, PhD > Assistant Professor of Radiology, Harvard Medical School > Assistant Professor of Neurology, Harvard Medical School > A.A.Martinos Center for Biomedical Imaging > Massachusetts General Hospital > Research Affiliate, CSAIL, MIT > Phone:+1-617-724-5652 <tel:%2B1-617-724-5652> > Web :http://reuter.mit.edu > > 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. > > -- Martin Reuter, PhD Assistant Professor of Radiology, Harvard Medical School Assistant Professor of Neurology, Harvard Medical School A.A.Martinos Center for Biomedical Imaging Massachusetts General Hospital Research Affiliate, CSAIL, MIT Phone: +1-617-724-5652 Web : http://reuter.mit.edu

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Re: [Freesurfer] LongitudinalTwoStageModel QDEC Help
by Martin Reuter 04 Nov '15

04 Nov '15

Dear Heidi, maybe there is a problem with your long.qdec.table.dat file? It is used to create the <fsid>.long.<fs_baseid> file names and obviously that filename is wrong (containing two .long. in it). Make sure that the first column is only the cross sectional id and the second one is the base id, so in your case: fsid fsid-base FS_PD002_1.nii FSBASE_002 Also it is not a good idea to have the ".nii" as part of the subject id, as that is a file extension. Next time, when running the cross sectionals, make sure you call the subject "FS_PD002_1" without extension. Could be that this leads to other problems (or it could just work, we'll see). Best, Martin On 11/04/2015 08:38 AM, Heidi Foo wrote: > Dear FreeSurfer experts, > > I was running the first stage of analysis of preparing of data - > qcache - and I encountered some problems. > > When using this command, /long_mris_slopes --qdec > ./qdec/long.qdec.table.dat --meas thickness --hemi lh --do-avg > --do-rate --do-pc1 --do-spc --do-stack --do-label --time years > --qcache fsaverage --sd $SUBJECTS_DIR/, an error message saying:" > FS_PD002_1.nii.long.FSBASE_002.long.FSBASE_002/label/lh.cortex.label > does not exist!" appears. > > I tried several other ways such as using long_stats_slopes, but I keep > receiving error messages similar to the one above. > > Please advice? > > Thank you so much for your kind help! > > Regards, > Heidi Foo -- Martin Reuter, PhD Assistant Professor of Radiology, Harvard Medical School Assistant Professor of Neurology, Harvard Medical School A.A.Martinos Center for Biomedical Imaging Massachusetts General Hospital Research Affiliate, CSAIL, MIT Phone: +1-617-724-5652 Web : http://reuter.mit.edu

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Re: [Freesurfer] unit in 'search area' in the glmfit log
by Jeni Chen 03 Nov '15

03 Nov '15

Thank you Doug. I was actually referring to the following values (example of my log output below): $Id: mri_glmfit.c,v 1.196.2.8 2012/11/01 18:51:41 greve Exp $ cwd /Volumes/pathname cmdline mri_glmfit --y /Volumes/pathname/lh.Group_abcd.thickness.10.mgh --C ./pathname/tmp.mri_glmfit-sim-34418/Group-diff_abcd.mtx --C ./pathname/tmp.mri_glmfit-sim-34418/Group-avg_abcd.mtx --mask ./pathname/mask.mgh --sim mc-z 5000 1.3 ./pathname/csd/mc-z.abs.1.3.j001 --sim-sign abs --fwhm 13.034857 --fsgd ./pathname/y.fsgd dods --label /Volumes/pathname/lh_abcd_mask.label --surf fsaverage lh white sysname Darwin hostname computer.local machine x86_64 user jeni FixVertexAreaFlag = 1 UseMaskWithSmoothing 1 fwhm 13.034857 niters 125.000000 OneSampleGroupMean 0 y /Volumes/pathname/lh.Group_abcd.thickness.10.mgh logyflag 0 usedti 0 FSGD ./pathname/y.fsgd labelmask /Volumes/pathname/lh_abcd_mask.label maskinv 0 glmdir (null) IllCondOK 0 ReScaleX 1 DoFFx 0 Loading y from /Volumes/pathname/lh.Group_abcd.thickness.10.mgh INFO: gd2mtx_method is dods Normalized matrix condition is 14.1782 Matrix condition is 289425 Found 9260 points in label. Found 7440 voxels in mask Reshaping mriglm->mask... search space = 3795.353314 DOF = 37 thresh = 1.3, threshadj = 0.99897 I do see that it gives information on the number of voxels in the mask (which is 7440 in the above example). What I was referring to is the next number "search space = 3795.35..." Is that the search area? Also in your reply, I see the need to specify the mask.mgh. How do I specify it if my mask is a label file and not in mgh format? Thanks again. Jeni > On Fri, 30 Oct 2015 08:21 PM Douglas Greve wrote: > That number is in voxels or vertices. If you want surface area, then use > mri_segstats something like >> mri_segstats --i $SUBJECTS_DIR/fsaverage/surf/lh.white.avg.area.mgh >> --seg glmdir/mask.mgh --id 1 --accumulate --sum sum.dat >> >> doug >> >> On 10/29/15 5:10 PM, Jeni Chen wrote: >> > Hello, >> > >> > When running the Clusterwise Correction for Multiple Comparisons, I used a >> > label as a mask to restrict search area. I want to find out the size of that >> > label, so I guess I can pull that information out from the "mri_glmfit.log", >> > specifically under 'searchspace'? Also I only see a numerical value there, I >> > assume it is in mm2? >> > >> > Thanks. >> > >> > Jeni

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Re: [Freesurfer] A mixed effect model approach in within subject dataset {Disarmed}
by pablo najt 03 Nov '15

03 Nov '15

Dear FS experts.I have query about a relating to a previous email (below). I am aiming to run a LME analysis on cross-sectional data from different families and have variable 'family' (number of families) as my NI vector. My design has three groups and therefore I am not able to use qdec. I am running the matlab commands below and finding some difficulty would really appreciate if you could help out.ThanksPablo Start analysis as follows: 1-Read your label eg.: lhcortex = fs_read_label('freesurfer/subjects/fsaverage/label/lh.cortex.label'); 2-Read the data file eg.: [lhY, lhmri] = fs_read_Y('lh.thickness.mgh'); %---------------------I input the concatenated .mgh image from preproc and mris_surf2surf-----------------------------------------------------------------------% 3-Fit a vertex-wise lme model with random effects.: lhstats = lme_mass_fit_vw(X, [1 2], lhY, ni, lhcortex); Here I am getting the following problems:%-------------------- If I use number of families as my ni get the following------------------------------------------------------------------------------------------------%lhstats = lme_mass_fit_vw(X, [1 2], lhY, 82, lhcortex);Error using lme_mass_fit (line 108)The total number of measurements, indicated by sum(ni), mustbe the same as the number of rows of the designmatrix X Error in lme_mass_fit_vw (line 73)[stats1,st1] = lme_mass_fit(X,[],Xrows,Zcols,Y,ni,prs,e); My matrix is organised in "family", "group", Sex" and "age" columns". 4-Perform vertex-wise inference eg.: CM.C = [your contrast matrix]; F_lhstats = lme_mass_F(lhstats, CM); 5-Save results eg.: fs_write_fstats(F_lhstats, lhmri,' sig.mgh', 'sig'); Date: Thu, 10 Sep 2015 13:44:36 +0000 From: jbernal0019(a)yahoo.es To: freesurfer(a)nmr.mgh.harvard.edu Subject: Re: [Freesurfer] A mixed effect model approach in within subject dataset Hi Pablo I think you can use LME to analyze your data by ordering the rows of your design matrix appropriately. You can consider all subjects belonging to the same family as if they were a single subject in a longitudinal analysis. You can put in your design matrix all subjects belonging to family1 first, then all subjects belonging to family 2 and so on. Then the 'ni' required by lme_mass_fit_vw is a vector with the number of subjects in each family as its entries (ordered according to your design matrix). So the length of the 'ni' vector is equal to the number of different families in your data. Now you can go further and additionally order the rows of your design matrix within each family by age. This will allow you to test the effect of age within family. When choosing the random effects for your statistical model remember that a random effect can only be the intercept term or any covariate that varies within family. For example you can compare a model with a single random effect for the intercept term against the same model but considering both the intercept term and age as random effects. Hope that helps Cheers -Jorge De: pablo najt <pablonajt(a)hotmail.com> Para: "freesurfer(a)nmr.mgh.harvard.edu" <freesurfer(a)nmr.mgh.harvard.edu> Enviado: Jueves 10 de septiembre de 2015 8:07 Asunto: [Freesurfer] A mixed effect model approach in within subject dataset Dear Freesurfer users,I wanted to enquire if anyone had successfully been able to implement Bernal's Linear Mixed Effects (LME) Models in cross-section dataset *not longitudinal* (please see previous thread below). I am willing to perform a LME (3 groups (HC, PT and Unaffected_relatives) and 3 covariates (sex, age, and family) with "family" variable been a within-subject factor. LME will allow to control for the non-independence of data contributed by patients and relatives from the same families.Thanks in advance!Pablo From: michaelnotter(a)hotmail.com To: freesurfer(a)nmr.mgh.harvard.edu Date: Wed, 19 Feb 2014 13:10:09 +0100 Subject: [Freesurfer] Analysis of structural data acquired from multiple sites by using a mixed effect model approach Hi everybody, I want to compare the surface data of 3 groups (GroupA, GroupB and Controlls) but have the problem that they were acquired from 4 different scanner sites. As I can see it, there are three ways how I could tackle this problem: 1. I could use mri_glmfit and create a qdec table / fsgd-file with 12 classes: Class GroupA_site1; Class GroupA_site2,... And then use the contrasts [0.25 0.25 0.25 0.25 0 0 0 0 -0.25 -0.25 -0.25 -0.25] to compare GroupA to the Controlls. My Problem with this approach is, that the sites don't contribute the same amount of subjects to the analysis. I'm not sure if this could be handled by simply using a weighted contrast. Meaning, if Site1 and Site2 had twice as many subjects than Site3 and Site4, I could modify the contrast to [0.33 0.33 0.17 0.17 0 0 0 0 -0.33 -0.33 -0.17 -0.17]. 2. I could create dummy variables to account for the variability between sites. In this case, I only need to specify 3 classes (Class GroupA; Class GroupB; Class Controlls) in my fsgd-file. And I use a design matrix that has 4 dummy variables at the end, which specify to which site a subject belongs. This approach might work, but I'm not confident that it is the right one. 3. I could use a mixed effect model approach and specify site as a random effect. If I understand it correctly, the mixed effect model approach would be the best one, as it accounts for the variability within sites. Is that correct or are there other issues/better approaches? I tried to implement a mixed effect model by using Bernal's Linear Mixed Effects (LME) Models (http://surfer.nmr.mgh.harvard.edu/fswiki/LinearMixedEffectsModels) but run into some problems. I'm not sure if LME can only be applied on longitudinal data or if my implementation is wrong. I have a design matrix X that specifies the characteristics of each subject per row as follows: Intercept GroupA GroupB Controll Age IQ Site1 Site2 Site3 Site4 1 1 0 0 11.1 99 0 0 1 0 1 0 1 0 11.1 101 0 0 1 0 1 1 0 0 11.4 95 1 0 0 0 1 0 0 1 12.4 100 1 0 0 0 ... As I have no repeated measures, 'ni' is just a vector with length X containing '1's. If I do now the vertex-wise linear mixed-effects estimation, I get the following output: >> stats = lme_mass_fit_vw(X,[7 8 9 10],Y,ni,lhcortex); Starting matlabpool using the 'local' profile ... connected to 8 workers. Starting model fitting at each location ... Location 24994: Index exceeds matrix dimensions. Location 24994: Algorithm did not converge. Initial and final likelihoods: -10000000000, -10000000000. Location 62484: Index exceeds matrix dimensions. Location 62484: Algorithm did not converge. Initial and final likelihoods: -10000000000, -10000000000. ... I've checked the matrix dimensions of X, Y, ni and lhcortex and compared them to the LME mass_univariate example stored in ADNI_Long_50sMCI_vs_50cMCI.mat but couldn't find any divergence. Has anybody encountered similar problems? Is my approach of specifying 'ni' as a vector of'1's even legitimate? Thanks, Michael _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer 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 https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer 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 https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer 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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1.5T vs 3.0T longitudinal study...
by Gonzalo Rojas Costa 03 Nov '15

03 Nov '15

Hi: I have two timepoints of the same patient: the first is in 1.5T and the second in 3.0T... Is it possible to do the longitudinal study (subcortical volumes) using the Workflow Summary described in https://surfer.nmr.mgh.harvard.edu/fswiki/LongitudinalProcessing ?... Sincerely, Gonzalo Rojas Costa -- Gonzalo Rojas Costa Laboratory for Advanced Medical Image Processing Department of Radiology Clínica las Condes Lo Fontecilla 441, Las Condes, Santiago, Chile. Tel: 56-2-2105170 Cel: 56-9-97771785 www.clc.cl ------------------------------------ Gonzalo Rojas Costa Laboratory for Advanced Medical Image Processing Department of Radiology Clinica las Condes Lo Fontecilla 441, Las Condes, Santiago, Chile Tel: 56-2-2105170 Cel: 56-9-97771785 www.clc.cl

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Re: [Freesurfer] Monte Carlo in mri_glmfit-sim
by Douglas N Greve 03 Nov '15

03 Nov '15

The correct command line is --cache 4 neg --cache-label AC On 11/03/2015 03:36 PM, smcl(a)u.washington.edu wrote: > Hi Doug, > > > > So if I pass cope7ACroi_rh.osgm.rfx and get rid of the --grf (cannot > find any documentation about what to put instead of --grf), as in > > mri_glmfit-sim --glmdir > /Volumes/Data_Local/ACTWF01_ILD/PrecByLvR_ILD_xsubject/cope7ACroi_rh.osgm.rfx > --cache-label AC 4 neg --cwpvalthresh 0.05 --2spaces > > I get back "ERROR: Flag 4 is unrecognized." > > If I try just --cache instead of --cache-label AC, I get back "ERROR: > cannot find > /Volumes/Data_Local/ACTWF01_ILD/PrecByLvR_ILD_xsubject/cope7ACroi_rh.osgm.rfx/rh.cope7.mgh" > > Any thoughts? > > Many thanks, > Susan > > On Tue, 3 Nov 2015, Douglas N Greve wrote: > >> The fwhm.dat file was in the right place. You passed the wrong folder to >> mri_glmfit-sim. You should pass it >> >> cope7ACroi_rh.osgm.rfx >> >> doug >> >> >> On 11/03/2015 02:40 PM, smcl(a)u.washington.edu wrote: >>> It's: >>> >>> mri_glmfit --y >>> /Volumes/Data_Local/ACTWF01_ILD/PrecByLvR_ILD_xsubject/lh.cope$cope.mgh >>> --osgm --glmdir >>> /Volumes/Data_Local/ACTWF01_ILD/PrecByLvR_ILD_xsubject/cope$cope\ACroi_lh.osgm.rfx >>> --surf fsaverage lh --label >>> /Applications/freesurfer/subjects/fsaverage/label/lh.AC.label >>> >>> fwhm.dat is actually in [MyData]/cope7ACroi_rh.osgm.rfx rather than >>> [MyData]/cope7ACroi_rh.osgm.rfx/osgm. I think that actually also >>> happened for some other files needed and I moved them. Is the >>> problem something in my mri_glmfit command? >>> >>> Susan >>> >>> On Tue, 3 Nov 2015, Douglas N Greve wrote: >>> >>>> it cannot find this file >>>> >>>> /Volumes/Data_Local/ACTWF01_ILD/PrecByLvR_ILD_xsubject/cope7ACroi_rh.osgm.rfx/osgm/fwhm.dat >>>> >>>> >>>> which should have been created by mri_glmfit. What is your mri_glmfit >>>> command line? >>>> >>>> Also, don't use --grf, that is for volumes only >>>> >>>> >>>> On 11/03/2015 02:27 PM, smcl(a)u.washington.edu wrote: >>>>> Hi DOug, >>>>> >>>>> doug.log is attached >>>>> >>>>> the bash equivalent for |& is 2>&1 | >>>>> >>>>> thanks, >>>>> Susan >>>>> >>>>> On Tue, 3 Nov 2015, Douglas N Greve wrote: >>>>> >>>>>> I meant &. The & works for tcsh (or csh). Are you using bash? I'm >>>>>> not >>>>>> sure what the bash equivalent is. Maybe |2 instead of |& >>>>>> perhaps some bash experts can weigh in >>>>>> >>>>>> On 11/03/2015 01:41 PM, smcl(a)u.washington.edu wrote: >>>>>>> Hi Doug, >>>>>>> >>>>>>> Do you mean: >>>>>>> >>>>>>> mri_glmfit-sim --debug --glmdir >>>>>>> /Volumes/Data_Local/ACTWF01_ILD/PrecByLvR_ILD_xsubject/cope7ACroi_rh.osgm.rfx/osgm >>>>>>> >>>>>>> --cache-label AC --grf 4 neg --cwpvalthresh 0.05 --2spaces |7 tee >>>>>>> doug.log? >>>>>>> >>>>>>> When I tried running the same code with |& tee doug.log at the end, >>>>>>> I kept getting: >>>>>>> >>>>>>> syntax error near unexpected token `&' >>>>>>> >>>>>>> Thanks, >>>>>>> Susan >>>>>>> >>>>>>> On Tue, 3 Nov 2015, Douglas N Greve wrote: >>>>>>> >>>>>>>> Can you run >>>>>>>> >>>>>>>> mri_glmfit-sim --debug --glmdir [my data >>>>>>>> dir]/cope7ACroi_rh.osgm.rfx/osgm --cache-label AC --grf 4 neg >>>>>>>> --cwpvalthresh 0.05 --2space |& tee doug.log >>>>>>>> >>>>>>>> and send me doug.log? >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>> On 11/02/2015 05:08 PM, smcl(a)u.washington.edu wrote: >>>>>>>>> Hi experts, >>>>>>>>> >>>>>>>>> I am having trouble performing a Monte Carlo correction using >>>>>>>>> mri_glmfit-sim. >>>>>>>>> >>>>>>>>> My data were sampled to fsaverage and smoothed at fwhm 5, using >>>>>>>>> mris_preproc. I then ran mri_glmfit on the data. >>>>>>>>> >>>>>>>>> I want to do my analysis/correction only in auditory cortex (AC) >>>>>>>>> so I did my own simulation in AC of each hemisphere using >>>>>>>>> mri_mcsim (as per >>>>>>>>> http://freesurfer.net/fswiki/BuildYourOwnMonteCarlo) >>>>>>>>> >>>>>>>>> So far, so good. >>>>>>>>> >>>>>>>>> But when I try to run: >>>>>>>>> >>>>>>>>> mri_glmfit-sim --glmdir [my data dir]/cope7ACroi_rh.osgm.rfx/osgm >>>>>>>>> --cache-label AC --grf 4 neg --cwpvalthresh 0.05 --2space >>>>>>>>> >>>>>>>>> I get "fwhm: Undefined variable." I tried adding --fwhm-override >>>>>>>>> 5, but it didn't help. >>>>>>>>> >>>>>>>>> Any thoughts? Also, can you clarify which comparison neg vs pos >>>>>>>>> will give me? >>>>>>>>> >>>>>>>>> Thank you, >>>>>>>>> >>>>>>>>> Susan McLaughlin, PhD >>>>>>>>> Research Scientist >>>>>>>>> Laboratory for Auditory Brain Sciences & Neuroengineering >>>>>>>>> Institute for Learning & Brain Sciences (I-LABS) >>>>>>>>> Portage Bay Bldg. Room 204 >>>>>>>>> University of Washington, Box 357988 >>>>>>>>> Seattle, WA 98195-7988 >>>>>>>>> >>>>>>>>> Ph: (206) 616-0102 Fx: (206) 221-6472 >>>>>>>>> Cell: 206-850-8638 >>>>>>>>> E-mail: smcl(a)uw.edu >>>>>>>>> >>>>>>>>> >>>>>>>>> _______________________________________________ >>>>>>>>> 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: https://gate.nmr.mgh.harvard.edu/filedrop2 >>>>>>>> www.nmr.mgh.harvard.edu/facility/filedrop/index.html >>>>>>>> Outgoing: >>>>>>>> ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ >>>>>>>> >>>>>>>> _______________________________________________ >>>>>>>> Freesurfer mailing list >>>>>>>> Freesurfer(a)nmr.mgh.harvard.edu >>>>>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>>>>>>> >>>>>>>> >>>>>>>> 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 >>>>>>> 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: https://gate.nmr.mgh.harvard.edu/filedrop2 >>>>>> www.nmr.mgh.harvard.edu/facility/filedrop/index.html >>>>>> Outgoing: >>>>>> ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ >>>>>> >>>>>> _______________________________________________ >>>>>> Freesurfer mailing list >>>>>> Freesurfer(a)nmr.mgh.harvard.edu >>>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>>>>> >>>>> >>>>> _______________________________________________ >>>>> 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: https://gate.nmr.mgh.harvard.edu/filedrop2 >>>> www.nmr.mgh.harvard.edu/facility/filedrop/index.html >>>> Outgoing: >>>> ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ >>>> >>>> _______________________________________________ >>>> Freesurfer mailing list >>>> Freesurfer(a)nmr.mgh.harvard.edu >>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>>> >>> _______________________________________________ >>> 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: https://gate.nmr.mgh.harvard.edu/filedrop2 >> www.nmr.mgh.harvard.edu/facility/filedrop/index.html >> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ >> >> _______________________________________________ >> 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: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/

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