Freesurfer November 2015

freesurfer@nmr.mgh.harvard.edu

138 participants
239 discussions

TRACULA bedpostx error
by denizzgursel 13 Nov '15

13 Nov '15

Hello, I am running TRACULA on one subject, I ran trac-all -prep without problem. However, when I run trac-all -bedp, it is not successfully completed. Although it says, all slices processed, it gives the error: bedpostx_mgh: line 345: kill: (18735) - No such process I am missing many outputs such as mean_s0samples, mean_dsamples, dyads_dispersion that are necessary for reconstruction of the pathways. Does anybody have an idea how to solve this? Thanks. Best, -- Deniz

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R: Re: R: Re: R: Re: R: Re: error MRS voxel as seed in FS-FAST
by stdp82＠virgilio.it 13 Nov '15

13 Nov '15

Thanks. But the MRS_mask should be in Tal, MNI or native? Now I'm using a masks that overlaps orig.nii.gz. Second, if I would like to create a sphere and use it as seed, there is a specific command line? Stefano >----Messaggio originale---- >Da: greve(a)nmr.mgh.harvard.edu >Data: 9-nov-2015 23.24 >A: <freesurfer(a)nmr.mgh.harvard.edu> >Ogg: Re: [Freesurfer] R: Re: R: Re: R: Re: error MRS voxel as seed in FS-FAST > >So that mask has 22926 non-zero voxels? The only other thing I can think >of is that the registration is off. Have you checked that? > >On 11/06/2015 07:16 AM, stdp82(a)virgilio.it wrote: >> I hope that this information are fine >> >> fslinfo $SUBJECTS_DIR/Control22/MRS_MASK.nii.gz >> data_type FLOAT32 >> dim1 256 >> dim2 256 >> dim3 256 >> dim4 1 >> datatype 16 >> pixdim1 1.000000 >> pixdim2 1.000000 >> pixdim3 1.000000 >> pixdim4 0.000000 >> cal_max 0.0000 >> cal_min 0.0000 >> file_type NIFTI-1+ >> >> >> fslstats $SUBJECTS_DIR/Control22/MRS_MASK.nii.gz -V >> 22926 22926.000000 >> >> Thanks, >> >> >> Stefano >> >> >>> ----Messaggio originale---- >>> Da: greve(a)nmr.mgh.harvard.edu >>> Data: 5-nov-2015 23.43 >>> A: <freesurfer(a)nmr.mgh.harvard.edu> >>> Ogg: Re: [Freesurfer] R: Re: R: Re: error MRS voxel as seed in FS- >> FAST >>> How many non-zero voxels are in MRS_MASK.mgz? Is MRS_MASK.mgz 256^3, >> 1mm3 ? >>> On 11/05/2015 04:47 PM, stdp82(a)virgilio.it wrote: >>>> Please see the file attached. >>>> Thanks >>>> >>>> Stefanofile >>>> >>>> ----Messaggio originale---- >>>> Da: greve(a)nmr.mgh.harvard.edu >>>> Data: 5-nov-2015 15.43 >>>> A: <freesurfer(a)nmr.mgh.harvard.edu> >>>> Ogg: Re: [Freesurfer] R: Re: error MRS voxel as seed in FS- FAST >>>> >>>> sorry, should have been >>>> >>>> fcseed-sess -debug -s Control22_FS -cfg MRS_MASK.config |& tee >> doug.log >>>> >>>> >>>> On 11/4/15 6:05 PM, stdp82(a)virgilio.it wrote: >>>>> Hi Dough, >>>>> in summary: >>>>> I have the MRS_MASK.mgz within $SUBJECTS_DIR/Control22/mri >>>>> thus, I have copy this file in fMRI directory >> (fMRI/Control22_FS) the >>>>> MRS_MASK.mgz >>>>> and run: >>>>> fcseed-config -segid 1 -seg Control22_FS/MRS_MASK.mgz -fsd >> rest -mean - >>>>> cfg MRS_MASK.config >>>>> fcseed-sess -s Control22_FS -cfg MRS_MASK.config >>>>> >>>>> ...Writing to >>>>> >> /Applications/freesurfer/subjects/fMRI/Control22_FS/rest/001/tmp. >> fcseed- >>>>> sess.12305/avgwf.mgh >>>>> Segmentation fault >>>>> >>>>> Therefore, according with your suggestion, I have now run: >>>>> fcseed-sess -debug -s -cfg MRS_MASK.config | & tee doug.log >>>>> ERROR: cound not find session -cfg >>>>> >>>>> The doug.log is attached. >>>>> >>>>> Thanks, >>>>> >>>>> >>>>> Stefano >>>>> >>>>> >>>>> >>>>> >>>>>> ----Messaggio originale---- >>>>>> Da:greve@nmr.mgh.harvard.edu >>>>>> Data: 4-nov-2015 16.58 >>>>>> A:<freesurfer(a)nmr.mgh.harvard.edu> >>>>>> Ogg: Re: [Freesurfer] error MRS voxel as seed in FS-FAST >>>>>> >>>>>> First, when running fcseed-config, don't give it the full >> path, just >>>>> the >>>>>> path relative to subject/mri (in this case only MRS_MASK. mgz) >>>>>> >>>>>> However, I don't think that is the problem. Please run >>>>>> >>>>>> fcseed-sess -debug -s -cfg MRS_MASK.config |& tee doug.log >>>>>> >>>>>> and send me doug.log >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> On 11/04/2015 04:14 AM,stdp82(a)virgilio.it wrote: >>>>>>> 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@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@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 >>>>>>> _______________________________________________ >>>>>>> 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 >>>> >>>> >>>> >>>> >>>> _______________________________________________ >>>> 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 >

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recon_checker missing output files
by Lauren Bystrom 12 Nov '15

12 Nov '15

Dear Experts, I am trying to run recon_checker on a set of subjects with brain tumors. Since FreeSurfer cannot deal with this, I am using recon_checker -s SUBJID -ignore lh. to try and ignore the processes on the hemisphere with the tumor, but it keeps checking for those files anyway. Also, it gives me an html file that is supposed to display my snapshot but the images aren't appearing where the code says they should be. Could this be caused by the absence of specific files that were missing in the recon_all, on both hemispheres, and if so is there a way to get my snapshot images without these files? Lauren Bystrom

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'mri_normalize' & 'mri_nu_correct', how do they work?
by Guido Orlando Pascariello 12 Nov '15

12 Nov '15

Hi FS Experts I'm bioengineering student and I'm working on my final project to get my degree. it's about process neuroimaging (IRM) in order to cuantific some parameter which could be helpful for medicine (clinical neurology). I'm using FreeSurfer to process my data. It works realy good. But it will be so much helpful to me if you can answer me a few question about it! *FIRST ONE*: I've been using 'mri_normalize' and I read the paper which describe it. But: 1. In step 4: Discard outliers from the array: You suppose variation in intensity due to magnetic field inhomogeneities is smooth across space. But, field inhomogeneities are corrected in 'NuCorrect' module using N3. 2. I understood the 1D normalization process. However the 3D normalization process works estimating a bias field like that which is corrected by 'NuCorrect' module. Could you tell me why did you that? and what are diferences with 'NuCorrect' module? *SECOND ONE*: It's abuou 'mri_nu_correct': I've read the description but I'm not sure about it. Does it use the N3 algorithm to work? In the description is written that "changing the number of iterations should be done carefully, because this can exacerbate artifacts". Could you tell me what are these artifact? and why is the default number of iteration four? I'll be grateful if you can help Being all for now, I await a reply Guido PASCARIELLO Facultad de Ingeniería - Universidad Nacional de Entre Ríos Argentina

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Downsampling the surface
by Ray Razlighi 12 Nov '15

12 Nov '15

Dear All, I can't find the mris_decimate command any more in the new freesurfer distribution. I assume there is substitute. Would someone direct me to the substitute. Also, I remember using mris_decimate changed the vertices coordinates. I was wondering if there is any way to downsample the surface in a way that the new vertices on the downsampled surface always fall on one of the original ones. I know this is not possible with exact downsample ratio; However I do not need exact downsampling ratio. -- Sincerely, Ray

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group mean greater than X
by Dace Apshvalka 12 Nov '15

12 Nov '15

Sorry, I was not very clear. I meant, how do I test whether the group mean is greater than 5, for example. The default is 0, but can I change it somehow? Dace --

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Computing Statistics with Custom ROI Masks
by Shady El Damaty 12 Nov '15

12 Nov '15

Hi FS-ers, I'm a bit stuck trying to compute cortical and subcortical statistics using the Buckner 2011 Cerebellum mask. I tried using mri_segstats to generate the .stats file for the provided image: mri_segstats --seg > Buckner2011_7Networks_MNI152_FreeSurferConformed1mm_LooseMask.nii.gz --sum > test.summary --ctab-gca Buckner2011_7Networks_ColorLUT.txt --nonempty > $Id: mri_segstats.c,v 1.75.2.9 2013/02/16 00:09:33 greve Exp $ > cwd > cmdline mri_segstats --seg > Buckner2011_7Networks_MNI152_FreeSurferConformed1mm_LooseMask.nii.gz --sum > test.summary --ctab-gca Buckner2011_7Networks_ColorLUT.txt --nonempty > sysname Darwin > hostname Apricot.local > machine x86_64 > user shady > UseRobust 0 > Loading > Buckner2011_7Networks_MNI152_FreeSurferConformed1mm_LooseMask.nii.gz > Segmentation fault: 11 Clearly I am doing something wrong. Can someone throw a pointer my way about how I can go about computing statistics on my subjects (or any arbitrary volume) using this mask? In the end I would like to be able to generate a .stats file for every subject in my SUBJECTS_DIR using any custom mask.. how can I make this possible? Your help would be very greatly appreciated!

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Re: [Freesurfer] Freesurfer@nmr.mgh.harvard.edu
by Douglas N Greve 12 Nov '15

12 Nov '15

/ really? So if you run ls -l /Users/nnidementia/Documents/PDFS/FSVASE_002/surf/lh.thickness.fwhm10.fsaverage.mgz/ what do you get? On 11/11/2015 07:59 PM, Heidi Foo wrote: > Hi Dr Greve, > > Yes it does, for all base templates, there > are lh(rh).long.thickness-avg(pc1, rate, and > spc).fwhm0(5,10,20,25).fsaverage.mgh files. > > I did the following steps in preprocessing: > > 1. recon-all -all -s <tpNid> -i path_to_tpN_dc m > 2. recon-all -base <templateid> -tp <tp1id> -tp <tp2id> ... -all > 3. recon-all -long <tpNid> <templateid> -all > 4. long_mris_slopes --qdec > /Users/nnidementia/Documents/PDFS/long.qdec.table.txt --meas thickness > --hemi lh --do-avg --do-rate --do-pc1 --do-spc --do-stack --do-label > --time years --qcache fsaverage --sd /Users/nnidementia/Documents/PDFS > 5. long_mris_slopes --qdec > /Users/nnidementia/Documents/PDFS/QDEC/long.qdec.table.txt --meas > thickness --hemi lh --sd /Users/nnidementia/Documents/PDFS --do-pc1 > --do-label --generic-time --fwhm 10 --qcache fsaverage --stack-pc1 > /Users/nnidementia/Documents/PDFS/QDEC/lh.cross.qdec.table.txt.thickness-pc1.stack.mgh > --isec-labels > /Users/nnidementia/Documents/PDFS/QDEC/lh.cross.qdec.table.txt.fsaverage.cortex.label > > Thanks. > > Regards, > Heidi Foo > > > > > On Wed, Nov 11, 2015 at 11:57 PM, Douglas Greve > <greve(a)nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> wrote: > > does that file exist? Did you run recon-all -qcache ? > > > On 11/11/15 7:54 AM, Heidi Foo wrote: >> Apologies, the error message should be /Error in >> analyze: couldn't open >> /Users/nnidementia/Documents/PDFS/FSVASE_002/surf/lh.thickness.fwhm10.fsaverage.mgz >> or .mgh file./ >> >> On Wed, Nov 11, 2015 at 8:48 PM, Heidi Foo <heidifoo92(a)gmail.com >> <mailto:heidifoo92@gmail.com>> wrote: >> >> Hi Dr Greve, >> >> Thank you for your advice, it is deeply appreciated. I >> removed the blank lines of wmh.levels and included a carriage >> return at the end of the long.qdec.table.txt. >> >> However, there is still /error in analyze: Couldn't open >> /Users/nnidementia/Documents/PDFS/FS_PD002_1.nii/surf/lh.thickness.fwhm10.fsaverage.mgz >> or .mgh file./ >> / >> / >> I checked my qdec.table.txt (both cross and long) but I did >> not see any fsaverage included in the list of subjects. Am I >> missing something? >> >> Thank you. >> >> Regards, >> Heidi Foo >> / >> / >> >> On Wed, Nov 11, 2015 at 12:28 AM, Douglas N Greve >> <greve(a)nmr.mgh.harvard.edu >> <mailto:greve@nmr.mgh.harvard.edu>> wrote: >> >> Also, try removing the blank line at the end of >> wmh.levels, and make sure you have a carriage return at >> the end of long.qdec.table.txt. This may fix the 2nd error >> >> On 11/09/2015 10:38 PM, Heidi Foo wrote: >> >> Dear Dr Greve, >> >> Thanks for your reply. I have already linked >> fsaverage to my SUBJECTS_DIR but the error still >> persists. >> >> Attached is my qdec (long and cross) files. >> >> Thanks. >> >> Regards, >> Heidi Foo >> >> >> >> On Tue, Nov 10, 2015 at 6:36 AM, 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: >> >> >> >> On 11/06/2015 09:35 PM, Heidi Foo wrote: >> >> Dear FreeSurfer experts, >> >> I am trying to compare between stable WMH >> group and rapid >> progressed WMH group in regards to the >> cortical thickness as >> well as volume changes in the gray matter. >> The nuisance >> variable in my case is age. I ran my analysis >> using QDEC but >> encountered a few problems: >> >> 1. There is error in analyze: couldn't open file >> >> It looks like it cannot find fsaverage. Link it >> to your >> SUBJECTS_DIR if you have not already. >> >> 2. If this error doesn't appear, another one >> does. >> QdecGlmDesign::Create: zero factors! >> (Attached the screenshot of the errors for >> your perusal) >> >> please send the qdec file >> >> >> I am hoping that you could give me a solution >> to my problems. >> >> Thank you so much. >> >> Regards, >> Heidi >> >> >> -- 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: https://gate.nmr.mgh.harvard.edu/filedrop2 >> 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> >> Outgoing: >> ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ >> >> >> >> 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: https://gate.nmr.mgh.harvard.edu/filedrop2 >> www.nmr.mgh.harvard.edu/facility/filedrop/index.html >> <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> >> Outgoing: >> ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ >> >> >> > > -- 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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Re: [Freesurfer] How to compute area of subcortical structures
by anirudh nihalani 12 Nov '15

12 Nov '15

Hi Bruce, Thank you very much for your quick reply. Sorry I hadn't been able to reply faster as I was trying to figure out the below mentioned issue from two days. I have computed surface area of left-hippocampus using the commands mri_tessellate and mris_info. However I found that in freeview by selecting Tools->show label stats, I am able to display area of any label (PFA a screenshot) but these area stats do not match with the areas obtained using mri_tessellate and mris_info. I have two queries regarding this: 1) Surface areas of labels displayed in freeview doesn't match with subcortical structures' areas obtained by running mri_tesselate and mris_info. For example the attached screenshot shows that area of left-hippocampus is 71 mm^2 where as mri_tessellate followed by mris_info found the area for left-hippocampus to be 3586 (PFA the output of mris_tessellate and mris_info). Why is there a mismatch? 2) Based on your reply I thought area stats are not calculated for subcortical structures during "recon-all". If that is the case, how is freeview displaying area stats for subcortical areas? Also which file does freeview use to display these stats? Is it stats/[l/r]h.aparc.stats? I ask because even cortical structures' areas displayed by freeview are not matching with what is stored in these files. Please let me know. Thank you. Regards, Anirudh

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dilating labels within a parcellation
by David Grayson 11 Nov '15

11 Nov '15

Hi all, Is there a tool to surface-dilate all the labels contained within an annotation file simultaneously, while preserving the non-overlapping nature of the labels? I saw there is a development version of mri_label2label that works for individual label files separately, but that gets me into the problem of overlap and arbitrary starting points. Thanks very much, David

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