Freesurfer

freesurfer@nmr.mgh.harvard.edu

18 participants
30067 discussions

Convert mgz figure
by shi yao wang 05 Jul '17

05 Jul '17

Dear FS expert, Is that possible to extract .jpg or .tiff files by using command line? Or convert .mgz file to other format file? If ok , then I can write a program to do this action automatically. Thanks Lawrence

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To get postings
by vittal korann 05 Jul '17

05 Jul '17

vittalkorann(a)gmail.com *Best* *Vittal*

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Effect of continuous time-varying covariate across time in LME models
by Matthieu Vanhoutte 05 Jul '17

05 Jul '17

Dear Freesurfer’s experts, I would like to test if neuropsychological score across time (continuous time-varying covariate) has an effect on metabolism maps. However, I don’t manage to understand how to define design matrix and contrast associated to assess it with LME models. I picked up from one former mailing list discussion including Jorge: we recommended to order the columns of the design matrix in the following way: Column 1: the intercept term (which is a column of ones) Colum 2: the time covariate if it varies across subjects (eg. time from baseline) Column 3-q: any time-varying covariates (eg. training: 0 before training, 1 after training) Column q+1-r: the group covariates of interest (eg. a binary variable indicating whether or not the subject is a patient), for n groups you will have n-1 binary covariates Column r+1-s: interactions between group covariates with the time-varying covariates (only the interesting interactions) Column s+1-p: any other nuisance time-invariant covariates (eg. age-at-baseline, gender, etc...) 1) If I apply these advices, I would define in Column 3 my neuropsychological scores as my time-varying covariate but should I have to normalize these scores ? 2) If I want to correlate my metabolic maps (inputs) with my neuropsychological time-varying covariate should I have to define a column of interaction between neuropsychological time-varying covariate and (group or time) ? 3) How should I define contrast matrix to assess this effect ? Thank you for your advices !! Best regards, Matthieu

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sulcus in the orbitofrontal wm
by Manuel Delgado 05 Jul '17

05 Jul '17

Dear list: We are editing wm and facing a problem we do not know how to solve. In the orbitofrontal wm there is a sulcus that has been fully included into the wm boundary. However there is not wm mask to be erased. I have uploaded the file 40_001 and I would be grateful if could take a look. This problem is located on coordinates Talairach (wm) 110.66, 158.70, 165.37 In addition, there is an hyperintensity in the extreme of the orbitofrontal wm we would like you to take a look and work out the best solution (I gess control points would fix it?) This is on coordinates 111.29, 161.59, 178.55. Thanks in advance -- *Manuel Delgado Alvarado, MD* *Predoctoral Researcher* *Neuroimaging Unit, IDIVAL* *Avda. Cardenal Herrera Oria s/n* *39011 Santander, Spain*

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lopsided hemisphere
by Michael Davies 04 Jul '17

04 Jul '17

Hello, I have encountered a lopsided hemisphere when analysing the data. What procedure do i need to employ to fix the problem? Any advice would be greatly appreciated! Kind regards, Michael

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Anterior and posterior insula in fsaverage space
by Juergen Haenggi 04 Jul '17

04 Jul '17

Dear FS experts I am wondering whether there exist labels of the insula other than that provided by aparac and aparc.a2009s. I am searching for labels of the anterior and posterior insula in the fsaverage space. I have drawn such regions (see attachment), but these are rather subjective. Any suggestions are welcome. Thanks in advance Regards Jürgen Hänggi ----------------------------------------------------------------------------------------------------- University of Zurich Dr. Jürgen Hänggi, Ph.D. Department of Psychology Division Neuropsychology Binzmuehlestrasse 14, PO Box 25 8050 Zurich, Switzerland 0041 44 635 73 97 (phone office) 0041 76 445 86 84 (phone mobile) 0041 44 635 74 09 (fax office) BIN 4.D.04 (office room number) j.haenggi(a)psychologie.uzh.ch (email) http://www.psychologie.uzh.ch/neuropsy/ (website) http://www.juergenhaenggi.ch (private website) This email (and any attachment/s) contains confidential and/or privileged information. If you are not the intended recipient (or have received this email in error) please notify the sender immediately and destroy this email. Any unauthorised copying, disclosure or distribution of the material in this email is strictly forbidden. -----------------------------------------------------------------------------------------------------

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Re: [Freesurfer] Surface edits: Cortex that extends into the putamen + Missing gray matter
by Vincent Koppelmans 03 Jul '17

03 Jul '17

Hi Bruce, Thank you for your reply. The aseg seems to be okay: https://www.dropbox.com/s/j1ac0ftxw8iiv34/Putamen.png?dl=0 <https://www.dropbox.com/s/j1ac0ftxw8iiv34/Putamen.png?dl=0> Do you have any other suggestions? Here is an extra image of the cortical ribbon. Maybe this helps: https://www.dropbox.com/s/ycav96v91e4ncbg/Cortex.png?dl=0 <https://www.dropbox.com/s/ycav96v91e4ncbg/Cortex.png?dl=0> Thanks! - Vincent On Mon, 03 Jul 2017, Bruce Fischl wrote: Hi Vincent the putamen error probably means that the aseg is wrong, and if so, you can correct the aseg and rerun autorecon2-wm and autorecon3 I believe. For the medial ttemporal lobe issue is that really cortex? I can't really tell from the single coronal slice. I'll cc Jean Augustinack to see if she has an opinion. cheers Bruce On Fri, 30 Jun 2017, Vincent Koppelmans wrote: Hi all, I was wondering how to fix the following issues: 1) The cortical ribbon extends into the gray matter of the putamen (see the top row of the attached image). 2) Cortical gray matter is missing in the medial temporal lobes (see the bottom row of the attached image). I can’t find solutions for these particular issues under https://surfer.nmr.mgh.harvard.edu/fswiki/Edits <https://surfer.nmr.mgh.harvard.edu/fswiki/Edits> <https://surfer.nmr.mgh.harvard.edu/fswiki/Edits <https://surfer.nmr.mgh.harvard.edu/fswiki/Edits>> How should I approach this? Suggestions are very much welcome. Thank you! - Vincent

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Surface edits: Cortex that extends into the putamen + Missing gray matter
by Vincent Koppelmans 03 Jul '17

03 Jul '17

Hi all, I was wondering how to fix the following issues: 1) The cortical ribbon extends into the gray matter of the putamen (see the top row of the attached image). 2) Cortical gray matter is missing in the medial temporal lobes (see the bottom row of the attached image). I can’t find solutions for these particular issues under https://surfer.nmr.mgh.harvard.edu/fswiki/Edits <https://surfer.nmr.mgh.harvard.edu/fswiki/Edits> How should I approach this? Suggestions are very much welcome. Thank you! - Vincent

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Strange Discrepancy Between Activation Location on Surface vs. Volume
by Taylor, Johnmark 03 Jul '17

03 Jul '17

Hello, I am running into an odd issue. In particular, I have run a GLM analysis in *volume* space, and I am visualizing the results both on the surface using tksurfer, and on the volume using tkmedit. In both cases, I am using the register.dof6.dat file to do the registration. Oddly, when I visualize the results on the *surface*, the activation patch falls on the medial surface of the hemisphere, in the *precuneus*, whereas when I visualize the results on the *volume*, the patch is in the *intraparietal sulcus* (which is where we expect to see this particular activation). I have made a label out of the activation in both cases and viewed it in the other space just to make sure that it is in fact the same activation, and it is. Any idea what might be going on? It seems to me that it can't be an issue with the BOLD volume --> structural volume registration, since the activations look normal on tkmedit. It seems to me, then, that it must have to do with the relationship between the anatomical volume and the anatomical surface--could this be where the problem lies? Maybe an imperfect surface reconstruction? Thank you very much, JohnMark

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bad file conversion
by Michael Davies 03 Jul '17

03 Jul '17

Hello, i was wondering if you could possibly help me with a subjects file that has loaded badly. It not only loaded up-side down but looks as though there are additional deficits that need correcting. Any tips or advice would be greatly appreciated! Kind regard, Michael

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