Freesurfer

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30084 discussions

Cortical thickness values on a vertex base level
by Aicha Dijkshoorn 18 Nov '19

18 Nov '19

External Email - Use Caution Dear developers, For a case-control study we are comparing the cortical thickness and cortical surface area on a vertex-base level, for which we found significant differences throughout the brain. Is it possible that, in addition to the significance values (p < .05 after FDR correction) on a vertex-base level, we can include the exact thickness or surface area value (or difference) of the significant clusters on a vertex base-level between the groups. In order words, to provide some measures to highlight the size of the significant cluster or the differences in cortical thickness / cortical surface area to provide clinically useful context. For instance, a command comparable to 'voxel size' in TBSS. As this is my first time using Freesurfer any help that you could offer on this matter would be highly appreciated. Best wishes, Brigitte Dijkshoorn

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Questions for PetSurfer
by Soo-Jong Kim 18 Nov '19

18 Nov '19

External Email - Use Caution Dear FreeSurfer experts, I am a student in neuroimaging using FreeSurfer. I have some questions and I don't know where to send questions. That's why I found this mail and writing. I've studied PetSurfer for partial volume correction of PET. I saw the tutorial in website. Originally, I want to use RBV method for pvcorrected PET for SUVR analysis. After generating gtmseg and coregistration to make lta file, I followed this code and changed some. *mri_gtmpvc --i PET.nii --reg subj1.reg.lta --psf 5 --seg gtmseg.mgz * *--default-seg-merge --auto-mask PSF .01 --no-rescale --no-reduce-fov --rbv --o output_pvc* After this, rbv.nii.gz file was generated. and SUVR analysis was performed as reference region (cerebellar cortex). But Compared to original un-pvc PET, Cortex SUVR was reduced... In ideal pv-corrected PET, cortex SUVR was higher than un-pvc PET. Is is okay if I use the output file as rbv.nii.gz ? in Thomas et al, 2011, He used aparc+aseg.mgz file from FreeSurfer. and he merged some regions. Frontal, Temporal, Occipital and so on. (Only gray matter to correct PET using RBV method) In that case, What are the regions to make rbv.nii.gz method in PetSurfer? Can I use the rbv.nii.gz as partial volume corrected PET from RBV method? If not, Please tell me what is the correct command of mri_gtmpvc. I need only partial volume corrected PET using RBV method. Sincerely, Soo-Jong Kim

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Multiple comparisons
by Juan Rivas 18 Nov '19

18 Nov '19

External Email - Use Caution I would like to know how the correction is made for multiple comparisons in the statistical analysis? We are using QDEC, with False Discovery Rate or Montecarlo Null-Z. Is there a better way to do that? Best, JC.

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Question about design matrix for surface group analysis
by 邓刊 18 Nov '19

18 Nov '19

External Email - Use Caution Dear freesurfer users, I have a question about the design matrix.We want to analyse the relationship between the cortical thickness and the neuropsychological test. We have two groups:TLE and extralTLE,one discrete variable:gender,and two continuous variable: neuropsychological test and age. we make the FSGD files like this:Title OSGM Class MaleTLE Class MaleextraTLE Class FemaleTLE Class FemaleexatrTLE Variables Age Neuropsychology Input subject1 MaleTLE 30 5 Input subject2 MaleextraTLE 40 6 Input subject3 FemaleTLE 50 8 Input subject4 FemaleLextraTLE 60 7 Is it right? And we want to analyze the relationship between the cortical thickness and the neuropsychology regressing out the effects of gender and age, how to make the design matrix? Look forward to your reply. Sincerely, Kan Deng

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Spatial smoothing for cortical folding measures
by huyang 18 Nov '19

18 Nov '19

External Email - Use Caution Dear FS experts, Is it necessary to do spatial smoothing for cortical folding measures (curv/sulc/smoothwm.FI.crv/pial_lgi, etc.)? These cortical folding measures are inherently smooth based on the computation methods used. If spatial smoothing is still needed, what's the recommended smoothing kernel size? Thanks! Yang Hu

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Processor speed/cores vs cache size
by Pradyumna Bharadwaj 18 Nov '19

18 Nov '19

External Email - Use Caution Hello, For running recon-all or tracula on a local workstation, is it recommended to go for a higher processor speed/number of cores, or a larger cache size for the processor (Intel Xeon W series). Or is it likely to be a more complex interplay between the number of recon-all processes running at any given time? Thanks, Pradyumna

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Fwd: recon-all error: ltMNIreadEx: could not open file transforms/talairach.xfm
by Dalton Bermudez 18 Nov '19

18 Nov '19

External Email - Use Caution ---------- Forwarded message --------- From: Dalton Bermudez <daltonhbermudez(a)gmail.com> Date: Wed, Nov 13, 2019 at 1:54 PM Subject: recon-all error: ltMNIreadEx: could not open file transforms/talairach.xfm To: <freesurfer(a)nmr.mgh.harvard.edu> Dear FreeSurfer Developers, I am attempting to obtain a average cortical surface for two structural MRI nii dataset. However, when I run the command, I obtain the following errors. error: No such file or directory error: ltMNIreadEx: could not open file transforms/talairach.xfm error: mghRead(/home/dbermudez/Documents/subjects/00_0086/mri/orig.mgz, -1): could not open file ERROR readMNI: cannot read src MRIorig.mgz FreeSurfer version: freesurfer-linux-centos6_x86_64-dev Platform: Linux Ubuntu 18.05 recon-all.log: see attachment

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HBT hippocampal segmentation
by Daniel Callow 18 Nov '19

18 Nov '19

External Email - Use Caution Hello, I was just asked by a reviewer how the head body and tail of the Freesurfer subfield segmentation is determined. I know that there is no differentiation of the tail, however, there are differentiations between the head and body of the different subfields. Are there specific anatomical boundary rules that drive the algorithm to differentiate between head and body in the HBT segmentation output. Thank you for any guidance you can provide! Best, *Daniel Callow* *Graduate Student, Neuroscience and Cognitive Science* Exercise for Brain Health Lab University of Maryland, College Park *ddcc2442(a)gmail.com <ddcc2442(a)gmail.com>* 443-254-6298

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Fwd: Regarding Issue in reading binary files inside DICOM Directory
by sudhakar Mishra 18 Nov '19

18 Nov '19

External Email - Use Caution Hi, I am facing problem in reading dicom files arranged in a way described in attached image. I want to convert from this format to .nii format. Please help me with this. Thanks very much for considering my request Sudhakar Mishra Research Scholar

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Request regarding Lobular pooling
by Samson Nivins 17 Nov '19

17 Nov '19

External Email - Use Caution Hi, I am interested in summing up the lobes or make individual lobes like frontal, parietal etc. I tried using lobes strict, however, I am unable to get the data in the label format. Rather I get as annot form. Can you please help me Looking forward to hear from you " mri_annotation2label --subject 1008 --hemi rh --lobesStrict --outdir ./location" Best regards, Sam Samson Nivins | PhD Student A The University of Auckland, Liggins Institute Building 505, Level 2, 85 Park Road, Auckland Ph +(64) 21 256 5964 E samson.nivins(a)gmail.com<mailto:samson.nivins@gmail.com> [cid:image001.png@01D4C1F6.9273DF90]

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