Freesurfer

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30088 discussions

Fwd: using matched pairs in QDEC?
by christian buhl 05 Nov '13

05 Nov '13

Hi - Thank you for a fantastic piece of software :-) - I have en one question: - In the GUI-module QDEC, is it possible to adjust the GLM-model to account for a pair-matched cohort? (diabetes vs non-diabetes - matched pairwise by age, sex and bmi) Kind regards Christian, Denmark Christian Buhl Medical Doctor (MD), PhD-student Institute of Biomedicine, Pharmacology Aarhus University Wilhem Meyers Allé 4, Bldg. 1240 DK-8000 Aarhus C Tel: +45 2986 9829

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Re: [Freesurfer] mri_segment WM/GM limits
by Jonathan Holt 05 Nov '13

05 Nov '13

Also, quick question . . . How exactly do you run a recon from scratch without nifti images? I’d always delete the directory and restart with mri_convert -i … Jon On Nov 5, 2013, at 10:40 AM, Louis Nicholas Vinke <vinke(a)nmr.mgh.harvard.edu> wrote: > Hi Jon, > I see the area you are talking about. I'm rerunning the recon from scratch to start with a clean copy since the case you sent has been rerun multiple times and there are a bunch of control points. The fact that the rh.orig.nofix looks good makes me optimistic that this can be fixed. > > I'll get back to you soon. > -Louis > > On Mon, 4 Nov 2013, Louis Nicholas Vinke wrote: > >> Got it, I'll take a look. >> >> On Mon, 4 Nov 2013, Jonathan Holt wrote: >> >>> OK, >>> >>> been uploaded as JONbrain.tar >>> >>> Please let me know! >>> >>> >>> On Nov 4, 2013, at 1:15 PM, Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> wrote: >>> >>>> Hi Jon >>>> >>>> maybe you should upload your data and we'll take a look >>>> >>>> cheers >>>> Bruce >>>> On Mon, 4 Nov 2013, >>>> Jonathan Holt wrote: >>>> >>>>> Bruce, >>>>> >>>>> If I understand you correctly, you?re saying I should tweak my expert options? Should I further change the limits, how so? You previously advised that I not adjust the -p threshold, is this still the case? >>>>> >>>>> Basically, I?m still confused after your response. >>>>> >>>>> Sorry to bother, >>>>> Jon >>>>> On Nov 4, 2013, at 12:52 PM, Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> wrote: >>>>> >>>>>> Hi Jon >>>>>> >>>>>> this is almost certainly due to a topological defect. Improving the >>>>>> segmentation quality can frequently reduce the # of defects and get rid of >>>>>> big ones, so if you find that the wm segmentation isn't as visually >>>>>> accurate as is usually the case, using expert opts to improve its quality >>>>>> may also get rid of the problem you are seeing >>>>>> >>>>>> cheers >>>>>> Bruce >>>>>> >>>>>> >>>>>> >>>>>> On Mon, 4 Nov 2013, Jonathan Holt wrote: >>>>>> >>>>>>> Hey Louis, >>>>>>> >>>>>>> thanks for your response. It?s actually a bit different, in my case an entire sulcus, including the empty space within it has been segmented and surfaced as white matter. I?m trying to reduce the WM surface such that the empty space is not included. I?ve tried removing segmentation manually and running >>>>>>> >>>>>>> recon-all -autorecon2-noaseg -subjid <SUBJID> >>>>>>> >>>>>>> that doesn?t work, the empty space is simply resegmented and the surface doesn?t change.. I should note that this has worked for me in the past on some brains. >>>>>>> >>>>>>> Since there are no WM voxels to remove I didn?t bother with removing any of them. I ran recon-all -autorecon2 -autorecon3 -expert expert.opts -s <subjID> with mri_segment -wlo/-ghi/-whi all reduced by 10 and that hasn?t worked? >>>>>>> >>>>>>> I?m open for ideas. >>>>>>> >>>>>>> I should also note that this problem is not an issue in rh.orig.nofix >>>>>>> >>>>>>> (sorry about duplicate email, Louis) >>>>>>> >>>>>>> >>>>>>> On Nov 4, 2013, at 11:30 AM, Louis Nicholas Vinke <vinke(a)nmr.mgh.harvard.edu> wrote: >>>>>>> >>>>>>>> Hi Jon, >>>>>>>> The limit numbers correspond to voxel intensities in the brainmask.mgz. I believe you will want a lower number for the -wlo/-wm_low flag to make the wm surf extend further out, assuming that the wm voxels that are not being captured by the surface is hypo-intense (<< 110). >>>>>>>> -Louis >>>>>>>> >>>>>>>> On Thu, 31 Oct 2013, Jonathan Holt wrote: >>>>>>>> >>>>>>>>> HI experts, >>>>>>>>> >>>>>>>>> I?m wondering how these limits work, and whether the limit numbers indicate voxel intensity. If I wanted WM to be segmented more aggressively would I plug in a higher number or a lower number? >>>>>>>>> >>>>>>>>> Jon >>>>>>>>> _______________________________________________ >>>>>>>>> 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 >>>>>>>> >>>>>>>> >>>>>>>> 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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MRISread error
by Anita van Loenhoud 05 Nov '13

05 Nov '13

Hi everyone, I run into an error when I try to do the tutorial on ROI group analysis. I downloaded the tutorial set, but did not put it into FREESURFER_HOME/subjects, because my computer doesn't allow it. I made my own folder and copied everything in there. The error arises when I try to map a label from the fsaverage subject to a target subject: mri_label2label \ > --srcsubject fsaverage \ > --srclabel fsaverage/label/lh.BA45.label \ > --trgsubject 004 \ > --trglabel 004/label/lh.BA45.label \ > --hemi lh \ > --regmethod surface srclabel = fsaverage/label/lh.BA45.label srcsubject = fsaverage trgsubject = 004 trglabel = 004/label/lh.BA45.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR Desktop/anita-vumc/anitapddatabase-freesurfer/buckner_data/tutorial_subjs/group_analysis_tutorial FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 3422 points in source label. Starting surface-based mapping Reading source registration Desktop/anita-vumc/anitapddatabase-freesurfer/buckner_data/tutorial_subjs/group_analysis_tutorial/fsaverage/surf/lh.sphere.reg MRISread(Desktop/anita-vumc/anitapddatabase-freesurfer/buckner_data/tutorial_subjs/group_analysis_tutorial/fsaverage/surf/lh.sphere.reg): could not open file No such file or directory ERROR: could not read Desktop/anita-vumc/anitapddatabase-freesurfer/buckner_data/tutorial_subjs/group_analysis_tutorial/fsaverage/surf/lh.sphere.reg In related posts I read that it might have to do with the creation of symbolic links. I made sure that in my SUBJECTS_DIR, fsaverage is a symbolic link to my FREESURFER_HOME/subjects directory, in which surf/lh.sphere.reg etc are stored. What am I doing wrong? Does it still have to do with the fact that I put the tutorial data in another folder? Hope you can help me, Thanks in advance, Anita

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Literature values of cortical thickness
by Emma Biondetti 05 Nov '13

05 Nov '13

Dear Freesurfers, I need to compare the cortical thickness values, obtained from a data set of 32 healthy subjects, with some reference literature values of cortical thickness. I'd like to check the values of mean and standard deviation for each one of the 32 cortical parcellations automatically generated by Freesurfer. This is to decide if the data set can be used for the following steps of my work or not. On the mailing list, I read an old thread that talks about the existence of a set of literature reference values, obtained by Rauhl Desikan. Would it be possible to access those data? Thank you Emma Biondetti

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fMRI postdoc, Center for Mind/Brain Sciences, University of Trento, Italy
by Angelika Lingnau 05 Nov '13

05 Nov '13

*fMRI postdoc* At the Center for Mind/ Brain Sciences (CIMeC, www.unitn.it/en/cimec) University of Trento, Italy, there will soon be an opening for a postdoc position to work with Angelika Lingnau ( https://sites.google.com/site/angelikalingnau/) in collaboration with Carlo Marzi, University of Verona. The ideal applicant will have completed their PhD (Cognitive Neuroscience, Computer Science, Psychology, Physics, or a related discipline), experience with fMRI design and analysis methods (in particular MVPA), and programming experience with Matlab or C. Additional experience with real-time fMRI and/ or connectivity analyses is very desirable. The CIMeC has been recently ranked as the leading Cognitive Neuroscience research unit in Italy. It offers an international and vibrant research setting with access to state-of-the-art neuroimaging methodologies, including a research-only 4T MRI scanner, MEG, EEG and TMS, as well as behavioral, eye tracking and motion tracking laboratories. English is the official language of the CIMeC, where a large proportion of the faculty, post-docs and students come from a wide range of countries outside of Italy. If you wish to receive further information please contact Angelika Lingnau ( angelika.lingnau(a)gmail.com) or meet her at the SfN Meeting (Poster Board Number BBB19, presentation 273.18).

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LGI path problem
by Linn Mittlestein 05 Nov '13

05 Nov '13

Hi, I am trying to compute lgi measures, and I think my problem lies in the fact that the matlab path is not set correctly; it is calling an older version of matlab however I need it to point to matlab2013b. I have tried numerous things like changing the startup.m file, the .bashrc file and exporting the matlab path, however It keeps calling another version of Matlab. Can someone please tell me how exactly the path is set and where? Best Wishes and thank you, Linn

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mri_surf2vol questions
by Govindarajan, Koushik Athreya 05 Nov '13

05 Nov '13

Hello Freesurfers, I am trying to use mri_surf2vol to convert my thickness files into analyze/nifty format to use with a custom code. Is there a way I can write all output files from mri_surf2vol in axial format? Also, is there a way in FreeSurfer to combine these thickness files from both hemispheres? Thanks in advance Koushik

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glmfit for paired-diff on 2 groups
by Vivian R. Steiger 04 Nov '13

04 Nov '13

Dear FS-Experts, I would like to compare 2 Groups (Responder (N=19) vs. Non-Responder (N=11)) with longitudinal data. Participants from both groups had only 2 scan sessions in each case 10 weeks apart. So far is used the glmfit-variant with --paired-diff option in the first place. (based on http://surfer.nmr.mgh.harvard.edu/fswiki/PairedAnalysis) The paired-fsgd contained then 2 classes (Responder, Non-Responder) which is used in glm-fit for comparison with the contrast (1 -1) for group diffs. This approach confirmed our hypothesized effects but I'm not sure whether I used the right strategy. Could you might help me with this issue? Thank in advance Best, Vivian

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mri_segstats url in 5.3.0 release notes does not exist
by Jonathan Harlap 04 Nov '13

04 Nov '13

The version of mri_segstats that fixes the issue where mri_segstats fails unless -autorecon3 is run returns a file not found at the url ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mri_segstats. Is there a source that the release notes should refer to and which will not disappear, or can it be restored? Cheers, Jonathan

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Fwd: Qdec Questions
by Ashley Shurick 04 Nov '13

04 Nov '13

Great - and this would be true for all models? For example, in the attached graph, I'm looking at a region representing increased cortical thickness for one group compared to the other (orange blob, Q: "Does the average thickness differ between HC and SAD?" nuisance factor: mean thickness). From this plot it appears that SAD > HC, but based on your answer to the previous question I would think this region should represent HC > SAD. Can you please explain this? Thank you! On Wed, Oct 30, 2013 at 7:33 AM, Douglas N Greve <greve(a)nmr.mgh.harvard.edu>wrote: > > In your case you have HC listed first, so red/yellow means HC>SAD, blue > means SAD>HC > doug > > > > > > > On 10/29/2013 11:03 PM, Ashley Shurick wrote: > >> Hi Doug, >> >> Apologies, but I have a rather easy follow-up question that I can't >> figure out: >> >> How do you interpret the effect in each significant region? A previous >> post suggests using ctrl + left mouse click on a blob and examining the >> plot of the data. However, for the model I am looking at ("Does the >> thickness-ERQ correlation differ between HC and SAD?") I still can't >> determine if cortical thinning represents HC<SAD or SAD<HC. I'm attaching a >> representative plot here. >> >> Thank you, >> >> Ashley >> >> >> On Tue, Oct 29, 2013 at 10:25 AM, Ashley Shurick < >> ashley.shurick(a)gmail.com <mailto:ashley.shurick@gmail.**com<ashley.shurick(a)gmail.com>>> >> wrote: >> >> Thank you! >> >> >> On Tue, Oct 29, 2013 at 10:19 AM, Douglas N Greve >> <greve(a)nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.**edu<greve(a)nmr.mgh.harvard.edu>>> >> wrote: >> >> >> On 10/29/2013 01:10 PM, Ashley Shurick wrote: >> > Hi all, >> > >> > I'm running analyses in Qdec and want to verify a few things: >> > >> > 1. When comparing two groups (HC vs patients) I am including >> mean >> > cortical thickness as a covariate, using the following equation: >> > >> > >> > bh.thickness = (lh.thickness*lh.surfarea + >> rh.thickness*rh.surfarea) / >> > (lh.surfarea + rh.surfarea) >> > >> > >> > Is this the best way to calculate global mean thickness? >> Yes >> > >> > >> > 2. I want to regress out any effects of age, therefore I need to >> > demean the ages for my groups as a whole, and not perform this >> > calculation on each group separately, correct? >> Yes, in which case the test of the difference between groups >> will be >> done at an age equal to the mean of the ages. >> > >> > 3. I'm including questionnaires as a covariate of interest - >> do I need >> > to demean these values as well? >> When you do a test on a continuous covariate, that test will be >> unaffected by demeaning of the covariate. Demeaning will >> affect the >> difference between groups if you use a separate covariate for each >> group. If you have a single covariate across groups, demeaning >> will have >> no effect. >> >> doug >> > >> > >> > Thank you in advance for your help! >> > >> > >> > Ashley >> > >> > >> > -- >> > Ashley A. Shurick >> > Ph.D. Candidate >> > Department of Psychology >> > Stanford University >> > >> > >> > ______________________________**_________________ >> > Freesurfer mailing list >> > Freesurfer(a)nmr.mgh.harvard.edu >> <mailto:Freesurfer@nmr.mgh.**harvard.edu<Freesurfer(a)nmr.mgh.harvard.edu> >> > >> >> > https://mail.nmr.mgh.harvard.**edu/mailman/listinfo/** >> freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> >> >> -- >> Douglas N. Greve, Ph.D. >> MGH-NMR Center >> greve(a)nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.**edu<greve(a)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> >> <http://surfer.nmr.mgh.**harvard.edu/fswiki/**BugReporting<http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> >> > >> FileDrop: https://gate.nmr.mgh.harvard.**edu/filedrop2<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<http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> >> > >> >> Outgoing: >> ftp://surfer.nmr.mgh.harvard.**edu/transfer/outgoing/flat/** >> greve/ <ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/> >> >> ______________________________**_________________ >> Freesurfer mailing list >> Freesurfer(a)nmr.mgh.harvard.edu >> <mailto:Freesurfer@nmr.mgh.**harvard.edu<Freesurfer(a)nmr.mgh.harvard.edu> >> > >> >> https://mail.nmr.mgh.harvard.**edu/mailman/listinfo/**freesurfer<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<http://www.partners.org/complianceline>. If the e-mail was >> sent to you in error >> but does not contain patient information, please contact the >> sender and properly >> dispose of the e-mail. >> >> >> >> > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > greve(a)nmr.mgh.harvard.edu > Phone Number: 617-724-2358 > Fax: 617-726-7422 > > Bugs: surfer.nmr.mgh.harvard.edu/**fswiki/BugReporting<http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > FileDrop: https://gate.nmr.mgh.harvard.**edu/filedrop2<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/ <ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/> > >

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