Freesurfer July 2012

freesurfer@nmr.mgh.harvard.edu

128 participants
194 discussions

Re: [Freesurfer] mri_vol2surf and Spherical Surfaces
by Luis R. Piloto 03 Jul '12

03 Jul '12

Hi Doug, Thanks for getting back to me. I'm right around the vicinity of my desired results, but had just three more questions. 1) When running the mri_vol2surf command and specifying --reg, is there any way I can pass in a registration file generated by FSL's flirt command (i.e. flirt -in functional.nii -ref structurual.nii.gz ... -omat functional.mat, where functional.mat is the registration file from my functional to my structural) Currently, I'm using a register.dat file generated by bbregister, but I'd rather use the flirt outputted regustration file because it's being used in other parts of my pipeline. Is there perhaps a way to convert from the flirt output to a register.dat file? I thought using bbregister with init-fsl might let me specify a flirt registration file, but this was not the case. 2) To the best of my understanding, when used on functional data and outputting to .w files (and subsequently viewing the .w file in ascii form), the mri_vol2surf command generates a surface file where each vertex has attached to it a weight corresponding to the functional activity. However, how does this work when I use a 4D functional file as input? I'd expect the same sort of output, but instead each vertex would have a series of weights (instead of just a single weight) corresponding to the functional activity at each timepoint. Even when I output to a .mgh file while using a 4D volume with mri_vol2surf and overlay the resulting .mgh file in tksurfer, it still seems like there is only one "weight" for each vertex. Am I missing something? 3) Is there a way to overlay the resulting .mgh (or .w or .asc) from mri_vol2surf in freeview? Thanks again for all of your help. Regards, Luis ---------------------------------------------------------------------- Message: 1 Date: Tue, 26 Jun 2012 12:54:20 -0400 From: Douglas N Greve <greve(a)nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] mri_vol2surf and Spherical Surfaces To: freesurfer(a)nmr.mgh.harvard.edu Message-ID: <4FE9E93C.3090206(a)nmr.mgh.harvard.edu> Content-Type: text/plain; charset=ISO-8859-1; format=flowed Hi Luis, yes there is a more efficient way. Specify the native res functional as the --mov argument and specify the registration that you used to create the hires_functional as the --reg argument (instead of --regheader). While you can use a .w file, I would recommend instead a .mgh file (we're trying to phase out the .w); If you use mgh format, not need to spec a --out_type. That command will convert to the native subject surface. If you want to go to fsaverage you can either run mri_surf2surf after that or spec --trgsubject fsaverage doug On 06/25/2012 03:43 PM, Luis R. Piloto wrote: > Hello Fellow Freesurfers, > > I need some verification that my method for mapping functional data onto a spherical surface is sound. > > What I'm currently doing is running recon-all on my high-resolution, structural volume (.nii.gz format). After that, I take a single timepoint of my functional data (that has been both registered and upsampled to the high-res structural space), and run it through mri_vol2surf with the following command: > mri_vol2surf --mov highres_functional_slice00.niii.gz --hemi lh --regheader my_subject_name --out_type paint -o ./my_output_surface.w > > What I'm most worried about is whether this method of registration (i.e. specifying --regheader) is sufficient to go from the upsampled/registered functional to the surface? Also is there some more efficient way of doing this? I feel like there might be a smarter way to go from the functional to the structural without having to explicitly register and upsample before using mri_vol2surf. > > After this step, I simply pass my_output_surface.w to a program that reads the corresponding vertex and functional activity at that location and look up the vertex coordinates in my lh.sphere file. Any feedback would be really appreciated as I'm still really new to this software suite and was given a highly specific task to take care of. Thanks in advance! > > Regards, > Luis Piloto > > > _______________________________________________ > 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

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Re: [Freesurfer] qdec_glmfit problem
by Douglas N Greve 03 Jul '12

03 Jul '12

Hi Nicolai, your first column and second column are redundant. You cannot have both. doug ps. Please remember to send these things to the freesurfer list instead of directly to me. thanks! On 07/03/2012 02:55 PM, Nicolai Grüner-Hegge wrote: > Hi Doug, > > I have been trying to run qdec but have been having an error message > pop up. The error message that popped up is provided below: > > > > Design matrix ------------------ > 1.000 18.000 2.485; > 1.000 18.000 2.526; > 1.000 18.000 2.531; > 1.000 18.000 2.492; > 1.000 18.000 2.456; > 1.000 18.000 2.444; > 1.000 18.000 2.538; > 1.000 18.000 2.529; > -------------------------------- > ERROR: matrix is ill-conditioned or badly scaled, condno = 1e+08 > Possible problem with experimental design: > Check for duplicate entries and/or lack of range of > continuous variables within a class. > If you seek help with this problem, make sure to send: > 1. Your command line: > mri_glmfit --y > /Users/christine/Desktop/TEST_NGH/Reproducibility_FS/RECON/qdec/Untitled/y.mgh > --fsgd > /Users/christine/Desktop/TEST_NGH/Reproducibility_FS/RECON/qdec/Untitled/qdec.fsgd > dods --glmdir > /Users/christine/Desktop/TEST_NGH/Reproducibility_FS/RECON/qdec/Untitled > --surf fsaverage lh --C > /Users/christine/Desktop/TEST_NGH/Reproducibility_FS/RECON/qdec/Untitled/contrasts/lh-Avg-Intercept-thickness.mat > --C > /Users/christine/Desktop/TEST_NGH/Reproducibility_FS/RECON/qdec/Untitled/contrasts/lh-Avg-thickness-Age-Cor.mat > > 2. The FSGD file (if using one) > 3. And the design matrix above > Error in Analyze: command failed: mri_glmfit --y > /Users/christine/Desktop/TEST_NGH/Reproducibility_FS/RECON/qdec/Untitled/y.mgh > --fsgd > /Users/christine/Desktop/TEST_NGH/Reproducibility_FS/RECON/qdec/Untitled/qdec.fsgd > dods --glmdir > /Users/christine/Desktop/TEST_NGH/Reproducibility_FS/RECON/qdec/Untitled > --surf fsaverage lh --C > /Users/christine/Desktop/TEST_NGH/Reproducibility_FS/RECON/qdec/Untitled/contrasts/lh-Avg-Intercept-thickness.mat > --C > /Users/christine/Desktop/TEST_NGH/Reproducibility_FS/RECON/qdec/Untitled/contrasts/lh-Avg-thickness-Age-Cor.mat > > > > I do not know what an FSGD file is so I guess I am not using one. My > measurement was thickness with a smoothing of 10 and the left > hemisphere. I have tried it for other parts of the brain and the same > message is displayed. Thank you for your time! > > Best Regards, > Nicolai -- 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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nearest vertex from talairach coordinates
by Matthew Panichello 03 Jul '12

03 Jul '12

Hi, I would like to jump to various points on the fsaverage inflated brain in tksurfer based on talairach coordinates reported in a paper. It seems like the easiest way to do this would be to convert the coordinates the closest vertex index, then punch this into the tksurfer gui. A thread on the mailing list from a couple years back listed a couple of commands that could compute this conversion: select_talairach_point and print_nearest_vertex_to_talairach_point. But both of these seem defunct. Is there another way to accomplish this? Thanks, Matt

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different fs versions
by L. Koenders 03 Jul '12

03 Jul '12

Dear Freesurfer people, We attended the Freesurfer course in Amsterdam last week, thank you so much for the information! During the course it was mentioned that it is a very bad idea to mix Freesurfer versions during the analysis. However, we did all the preprocessing on an external server, using version 5.0.0 ('freesurfer-Linux-centos4_x86_64-stable-pub-v5.0.0') and we are currently doing all of our group-analysis on a different server, which has version 5.1.0 on it (' freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0'). Because both servers are used by a lot of people, it will become difficult to do an update on either one of these versions. Will this become a problem, or is there a way to avoid problems while still using these different versions? Thanks in advance for your help! Kind regards, Marise Machielsen, MD. Laura Koenders, MSc. Laura Koenders PhD-student AMC, Academic Psychiatric Centre Department Early Psychosis Room: PA3-138 Meibergdreef 5 1105 AZ Amsterdam +31 (0) 20 8913 609 +31 (0) 614 285 301 www.group-project.nl www.amcpsychiatrie-psychose.nl De informatie opgenomen in dit bericht kan vertrouwelijk zijn en is uitsluitend bestemd voor de geadresseerde. Indien u dit bericht onterecht ontvangt, wordt u verzocht de inhoud niet te gebruiken en de afzender direct te informeren door het bericht te retourneren. Het Academisch Medisch Centrum is een publiekrechtelijke rechtspersoon in de zin van de W.H.W. (Wet Hoger Onderwijs en Wetenschappelijk Onderzoek) en staat geregistreerd bij de Kamer van Koophandel voor Amsterdam onder nr. 34362777. De Algemene Inkoop Voorwaarden van het AMC zijn van toepassing op en maken integraal onderdeel uit van alle rechtsbetrekkingen, daaronder mede verstaan alle inkoop opdrachten en overeenkomsten, tussen AMC en derden. Deze voorwaarden zijn te raadplegen op www.amc.nl en worden op verzoek toegezonden. ________________________________ This message may contain confidential information and is intended exclusively for the addressee. If you receive this message unintentionally, please do not use the contents but notify the sender immediately by return e-mail. Academic Medical Center is a legal person by public law and is registered at the Chamber of Commerce for Amsterdam under no. 34362777. The AMC General Purchase Terms constitute an integral part of all legal relations, including but not limited to all purchase orders and contracts, between the AMC and third parties. These terms can be downloaded at the website www.amc.nl and will be sent to you at your request.

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sagittal sinus
by Kolody, Brianna 03 Jul '12

03 Jul '12

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Qdec Questions
by mdkruepke＠uwalumni.com 03 Jul '12

03 Jul '12

Freesurfers- When running analysis in qdec is it possible to use each individual subjects brain volume (white matter + gray matter) as a covariate? If so, what would be the easiest way to go about getting this information. Best- Michael -- Michael D. Kruepke PhD - University of Illinois at Urbana-Champaign BA - Psych - University of Wisconsin-Madison mdkruepke(a)gmail.com (262)-483-7449

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qdec factor.levels problem
by Anne Uhlmann 03 Jul '12

03 Jul '12

Hello FreeSurfers, I have a similar problem as described in an old thread (http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg12357.html) - qdec doesn't read my factor.levels properly. I have checked the files with gedit and can't see any control characters, which might have caused the problem. Any other ideas? I have also attached the diagnosis.levels file Thank you! Anne Using /home/virtualuser/freesurfer/lib/tcl/fsgdfPlot.tcl Loading data table /media/MyPassport_/poster/qdec/insula.qdec.table.dat... Number of columns: 3 fsid column: 1 Number of factors: 2 Number of subjects: 18 Reading discrete factor levels from config file /media/MyPassport_/poster/qdec/diagnosis.levels Psychosis Control done. ERROR: Subject MAS082 has an invalid level 'Psychosis' in the diagnosis column INFO: If 'diagnosis' is a discrete factor, then create a file named 'diagnosis.levels' containing the valid factor names one per line. Cape Universities Brain & Behaviour Initiative Department of Psychiatry & Mental Health University of Cape Town Tel: 021 406 6843 ### UNIVERSITY OF CAPE TOWN This e-mail is subject to the UCT ICT policies and e-mail disclaimer published on our website at http://www.uct.ac.za/about/policies/emaildisclaimer/ or obtainable from +27 21 650 9111. This e-mail is intended only for the person(s) to whom it is addressed. If the e-mail has reached you in error, please notify the author. If you are not the intended recipient of the e-mail you may not use, disclose, copy, redirect or print the content. If this e-mail is not related to the business of UCT it is sent by the sender in the sender's individual capacity. ###

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-nobigventricles
by Richard Binney 02 Jul '12

02 Jul '12

Out of curiosity, I would like to know what the flag -nobigventricles in the ca_reg and ca_label commands does exactly. Please help. Richard

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regeneration of aseg.mgz following edits
by Richard Binney 02 Jul '12

02 Jul '12

Hi Freesurfers, I've been trying to understand the implications of various types of edits in an attempt to solidify some standardized procedures regarding editing strategies, particularly in severely lesioned (and thus highly vulnerable to RECON failure) brains. In doing so I've been comparing volumes surfaces and segmentions pre- and post- edits/re-running RECON. I've noticed that changes in surface reconstruction is, as expected, followed by changes in the aparc.2009s+aseg.mgz segmentation (exapnded/contracted in accordnace with surface) but I don't see similar alterations in the aseg.mgz segmentation.In fact the aseg.mgz is identical pre- and post-edits despite large changes in the WM.mgz and pial/WM surfaces. Could you explain why this might be? Thanks Richard

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Sagittal sinus
by Kolody, Brianna 02 Jul '12

02 Jul '12

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Freesurfer July 2012