Freesurfer

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30132 discussions

coregistration - FA to Freesurfer
by Joana Braga Pereira 14 Oct '11

14 Oct '11

Dear FreeSurfers, I'm trying to coregister FA images pre-processed with FSL to Freesurfer, however i'm having a few problems and was wondering if someone could help me out. These are the steps that i carried out: mri_convert subj_01/mri/brain.mgz brain.nii.gz fslswapdim brain.nii.gz x z -y brain_swap.nii.gz flirt -ref brain_swap.nii.gz -in nodif_brain.nii.gz -out XXX.nii.gz -omat XXX.mat -cost corratio -dof 6 -interp trilinear flirt -in myFA.nii.gz -ref XXX.nii.gz -out myFA_coregistered.nii.gz -applyxfm -init XXX.mat Unfortunately myFA_coregistered.nii.gz was not as good as i expected since I want to extract the mean FA values of a subcortical ROI from freesurfer and to do that you need quite good coregistration. Does anyone know a better way to do this? Many thanks, Joana

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Re: [Freesurfer] mri_concat
by Douglas Greve 13 Oct '11

13 Oct '11

Hi Cooper, try using the --f option to mri_concat. This takes a text file in which you can list all the files you want. doug On 10/13/11 5:40 PM, Cooper Roddey wrote: > I think my problem is not with mri_concat after all, but with matlab's > 'unix' function. In any case, reading a list of input files saved in a > single file would be a nice option... > > CR > > On Thu, Oct 13, 2011 at 2:28 PM, Cooper Roddey<cooper.roddey(a)gmail.com> wrote: >> Hi Doug, >> >> I have run into a command line length problem when using mri_concat to >> compile about 1000 .mgh files together. The command line is about 133k >> characters long, and the max length on my Linux box appears to be >> 128k. I have a temporary work-around involving symbolic links but I'm >> looking for a more robust solution. Is it possible for mri_concat to >> read a text file containing the full paths of my 1000 .mgh files, >> instead of including all the files explicitly in the command line? >> Have others run into this problem? >> >> Cheers, >> Cooper >> >

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inhomogeneity causes poor segementation
by Ping-Hong Yeh 13 Oct '11

13 Oct '11

Hello, We have a quite a few 3T data got poor result due to the field inhomogeneity, especially in the occipital region (see attached). We've tried several ways of correcting inhomogeneity beforehand, but still not getting good results. Any suggestions in fixing these without manually editing the pial and wm? Thank you, Ping

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Re: [Freesurfer] question about contrast file during group analysis with command line
by Douglas N Greve 13 Oct '11

13 Oct '11

ZhiLiangLong wrote: > > Hi doug > Thanks for your suggestions. I have another two questions: > 1: I can't clearly understand that why i should firstly run DODS to > find interaction between my group variables and age,then run DOSS to > obtain difference between groups specified in my contrast files if > there are no interactions as you suggested.If the interactions > exist,does it mean that DOSS is not suitable for this situation and > only DODS can be used ? If there is an interaction, then DOSS is not suitable because there is no simple difference between the groups. > 2: If i want to obtain the main effect of factor(difference between > the three groups),how can i setup my contrast file? Do a search on our Wiki for FSGD. There's a page of examples there, including an example of your current design. doug > Hope you can give me some suggestions > > At 2011-10-12 00:21:34,"Douglas N Greve" <greve(a)nmr.mgh.harvard.edu> wrote: > >Yes, that looks correct. Since you have a covariate as a nuisance > >variable, you should first run your analysis with a DODS model > >(different-offset, different-slope) and look for an interaction between > >your group variables and age (the contrasts are similar, swap the first > >6 numbers with the last 6 zeros). If you do not find an interaction, > >then re-run the analysis with DOSS and use a contrast that has 7 > >numbers: the first 6 as you have given, the last number = 0. > > > >doug > > > >ZhiLiangLong wrote: > >> Hi all : > >> I'm performing general linear model (GLM) analysis in the surface,the > >> attachments above are FSGD file and contrast files(the last three > >> attachments).i wonder if my contrast files are correct. > >> the attachment named diff-C-H-thickness.txt is about difference > >> between C and H and the last two are about difference between C and p > >> and difference between P and H,Here,C H and P represent three groups > >> Any suggestions appreciated > >> > >> > >> ------------------------------------------------------------------------ > >> > >> _______________________________________________ > >> 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 > > > > > -- 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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rtview: trouble finding files
by Michelle Umali 13 Oct '11

13 Oct '11

Dear Freesurfers, I know this is a very simple question. I'm just having trouble specifying the correct directories for rtview based on the example. When I run rtview, it can't find the image files that really do exist in the directory. For the following example in the help section: I did what I thought were the proper replacements Example: cd sess/bold/rtopy.lh rtview --s subject --lh --eccen \ --real eccen/real.nii --imag eccen/imag.nii --fsig eccen/fsig.nii What I did: cd $SUBJECTS_DIR/retinotopy/sj07/bold/rtopy.self.lh rtview --s sj07 --lh --eccen \ --real eccen/real.nii --imag eccen/imag.nii --fsig eccen/fsig.nii Then I tried getting rid of the --s and --lh flags because I was already in that directory, but that didn't help either. If I'm already in the in the correct folder why do I still have to specify --s and --lh? Thanks. Michelle

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Group Average of Retinotopy Results
by Michelle Umali 12 Oct '11

12 Oct '11

Hi Doug, I'm a little confused as to how to assign functional data to the fsaverage space. 1) Do you mean just change each subject's subjectname file to fsaverage and then do the same thing as before for each person? 2) Also, when I specify the analysis do I change -rtopy.self.lh to rtopy.fsaverage.lh, i.e. will isconcat later be sensitive to analysis name? e.g. mkanalysis-sess -a rtopy.self.lh -surface self lh -TR 2 -retinotopy 48 -paradigm rtopy.par -nskip 4 -fwhm 0 -fsd bold -force then the same for selxavg3-sess and fieldsign-sess and then isxconcat-sess would be: isxconcat-sess -sf sessid -analysis rtopy.fsaverage.lh -o group_lh Thanks. Michelle

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QDEC labels vs annotations
by krista kelly 12 Oct '11

12 Oct '11

I'm using the labels saved in QDEC to extract cortical thickness values for certain regions. For example, I've used the lh.v1.label to map onto the fsaverage brain and then to map this onto each individual subject. When I load the lh.PALS_B12_Brodmann.annot or the lh.PALS_B12_Visuotopic.annot onto the fasaverage brain, the areas that are named v1 do not quite match up with the actual lh.v1.label. The more inferior part of the lh.v1.label is considered v2 in the the annotation space. Should I be worried about this? Or can I still use the lh.v1.label to extract information for v1 (even though the annotation file would consider it v2). Thanks!

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Group Average of Retinotopy Results
by Michelle Umali 12 Oct '11

12 Oct '11

Dear Freesurfers, I've generated individual polar, eccentricity, and fieldsign maps for each of my subjects. I would like to generate group average maps of these that I can visualize on the fsaverage brain. When I ran: isxconcat-sess -sf sessid -analysis rtopy.self.lh -o group_lh I got: ERROR: analysis space is self surface, not supported How do I do a group average for the 3 different maps? Thanks. Michelle For each person I ran recon-all and flattened occipital patches. Then: mkanalysis-sess -a rtopy.self.lh -surface self lh -TR 2 -retinotopy 48 -paradigm rtopy.par -nskip 4 -fwhm 0 -fsd bold -force mkanalysis-sess -a rtopy.self.rh -surface self rh -TR 2 -retinotopy 48 -paradigm rtopy.par -nskip 4 -fwhm 0 -fsd bold -force preproc-sess -surface self lhrh -fwhm 5 -per-run -s sjXX -fsd bold -force selxavg3-sess -a rtopy.self.lh -s sjXX -force selxavg3-sess -a rtopy.self.rh -s sjXX -force fieldsign-sess -a rtopy.self.lh -occip -fwhm 20 -s sjXX fieldsign-sess -a rtopy.self.rh -occip -fwhm 20 -s sjXX

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Brain stem volume
by Lugar, Heather 12 Oct '11

12 Oct '11

I was wondering if Freesurfer has a standard way of cutting off the measurement of brain stem volume across subjects, or does the volume of the brain stem depend on the individual's skull strip? In the two examples below, you can see that the brain stem of the second individual extends beyond that of the first (visually and according to its aseg label). Theoretically, could the reported volumes of these two individuals' brain stems be different just because their skull strip was different? Thank you, Heather [cid:image001.png@01CC88D6.715115A0] [cid:image002.png@01CC88D6.715115A0]

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Re: [Freesurfer] WM hypointensities and corpus callosum mislabeling
by Warren Winter 12 Oct '11

12 Oct '11

Let me try this again. Here's one that mislabeled parts of the CC as left cerebral white matter at the center slice: Another one mislabels nearly the entire CC at the center slice: Here you can see the light purple blotches above the caudate (light blue); those are labeled as white matter hypointensities: And again here: The overall quality is not great, but we're trying to make the best of what we have. Any advice on correcting these common problems in our dataset (apart from manually doctoring them) would be greatly appreciated! Warren On Oct 11, 2011, at 6:44 PM, Warren Winter wrote: > Here's one that mislabeled parts of the CC as left cerebral white matter at the center slice: > > <Screen shot 2011-10-11 at 6.31.19 PM.png> > Another one mislabels nearly the entire CC at the center slice: > > <Screen shot 2011-10-11 at 6.21.35 PM.png> > > You can see the light purple blotches above the caudate (light blue); those are labeled as white matter hypointensities. > > <Screen shot 2011-10-11 at 6.31.05 PM.png> > > And again here: > > <Screen shot 2011-10-11 at 6.20.18 PM.png> > > The overall quality is not great, but we're trying to make the best of what we have. Any advice on correcting these common problems in our dataset (apart from manually doctoring them) would be greatly appreciated! > > Warren > > On Oct 10, 2011, at 7:59 PM, Bruce Fischl wrote: > >> Hi Warren >> >> can you send us some images to show us what you mean? Or upload an >> example dataset for us to look at? >> >> cheers >> Bruce >> On Mon, 10 Oct 2011, Warren Winter wrote: >> >>> Hello, >>> In a number of our subjects I've been finding white matter hypointensities around the anterior edge of the caudate, as well as mislabelings of the corpus callosum as cerebral >>> white matter (at and/or around slice 128, sagittal). Has anyone else encountered these problems, and are there fixes that don't involve manually doctoring the mislabelings >>> (such as setting a particular flag for recon)? >>> >>> I am quite new to FS so please forgive any rudimentary misunderstandings. >>> >>> Thank you! >>> >>> Warren >>> >>> -- >>> Warren Winter >>> Lab Coordinator >>> Children's Hospital Boston >>> Division of Developmental Medicine >>> 1 Autumn Street, AU 650 >>> Boston, MA 02215 >>> 857-218-5224 >>> >>> >>> >> >> >> 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. > > -- Warren Winter Research Coordinator Children's Hospital Boston Sheridan Laboratory of Cognitive Neuroscience Division of Developmental Medicine 1 Autumn Street, AU 650 Boston, MA 02215 857-218-5224

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