Freesurfer

freesurfer@nmr.mgh.harvard.edu

18 participants
30087 discussions

Brain Volume
by Justin Eisenberg 27 Jan '11

27 Jan '11

Hi all, What is the best way to calculate total brain volume? It seems that there are multiple ways to do it--mris_volume and mris_wm_volume, add up the structures in the aseg.stats and ?h.aparc.stats files, or using the BrainSegVol or BrainSegVolNotVent from aseg.stats. What do you recommend? Thanks! Justin -- Justin Eisenberg Washington University in St. Louis Arts & Sciences | 2013 JEisenberg(a)wustl.edu JEisenberg323(a)gmail.com 262.914.4648

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mri_glmfit error
by Rafa x 27 Jan '11

27 Jan '11

Dear Freesurfers, In Freesurfer v5.0 when I try to run the command: mri_glmfit --surf CNTRL_MCI_RAFA_average lh --C contrast.mat --fsgd fsgd.txt dods --mask lh.fsgd_subj/mask.mgh --y CNTRL_MCI_RAFA_stats/lh.fsgd_subj.mgh --sim perm 625 2.301 csd1 --sim-sign pos --seed 6555731749 I always get the following error: ERROR: you must supply --fwhm with --sim, even if it is 0 Is there a bug in the mri_glmfit function? Thank you all in advance, Rafael.

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mkblockpar
by Kathryn Devaney 27 Jan '11

27 Jan '11

Hi all, I may be the only one still using mkblockpar, but I'm wondering if there's an update for the new version of freesurfer? Currently it still outputs 2-column par files. Thanks! Katie

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New v5.0.0 release
by Nick Schmansky 26 Jan '11

26 Jan '11

Announcement! There is a new release of FreeSurfer, v5.0.0! Features and fixes are described in the ReleaseNotes page: http://surfer.nmr.mgh.harvard.edu/fswiki/ReleaseNotes It is available for download at: http://surfer.nmr.mgh.harvard.edu/fswiki/DownloadAndInstall Please pose questions about the release to the freesurfer mailing list. The FreeSurfer Team

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CUDA installation and configuration...
by Gonzalo Rojas Costa 26 Jan '11

26 Jan '11

Hi: I am currently configuring Freesurfer 5 in a new workstation that we received... That workstation has Ubuntu 10.10, and a NVIDIA Quadro FX 1800 graphics card... Could you please send me the steps necessary to install and configure CUDA support ?... Sincerely, -- Gonzalo Rojas Costa Laboratory for Advanced Medical Image Processing Department of Radiology Clínica Las Condes Lo Fontecilla 441, Las Condes, Santiago, Chile. Tel: 56-2-2105170 Cel: 56-9-97771785 www.clc.cl

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mnc2nii input file problem
by Alexander Zaitsev 25 Jan '11

25 Jan '11

Hello: When I am trying to convert mnc file into nifti, the mnc2nii converter gives me an error $FREESURFER_HOME/mni/bin/mnc2nii fileName.mnc fileName.nii "Can't find input file fileName.mnc" Prepending a whole path to the file name does not help - same error message I am using FreeSurver 5.0.0 (MAC/Darwin/i686) build Any suggestions? Thank you, Alex Zaitsev

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discrepant outputs from recon-all/mri_ca_normalize
by Tossi Ikuta 25 Jan '11

25 Jan '11

Hi everyone, I'm wondering whether there are multiple versions of recon-all v 1.313.2.6 (2010/08/04 15:50:56), and/or mri_ca_normalize stable5. I have been testing recon-all and compared our output against the sample processed-data in FS/TUtorial. I found that the output obtained was different from the sample, despite the fact that I ran recon-all with the same options as the sample outputs, on the same input files. recon-all -s bert -i /analysis/Tests/FSTest_Tossi/Samples2/buckner_data/tutorial_subjs/bert/mri/orig/001.mgz -i /analysis/Tests/FSTest_Tossi/Samples2/buckner_data/tutorial_subjs/bert/mri/orig/002.mgz -i /analysis/Tests/FSTest_Tossi/Samples2/buckner_data/tutorial_subjs/bert/mri/orig/003.mgz -all -debug -clean -norandomness -allowcoredump -time -subjid BertByTossi20110119A I performed a line-by-line comparison of the recon-all log between the sample and one from my run and found that our log differs from the sample (buckner_data/tutorial_subjs/bert/scripts/recon-all.log) at line 1034, where mri_ca_normalize runs the first path of smoothing (with sigma=0.200). Whereas the sample has 38 recursions, my run had 18 recursions for this section. The outputs hereafter differed from each other. I used the same version as the sample was processed, recon-all: v 1.313.2.6 (2010/08/04 15:50:56), and mri_ca_normalize: stable5. Not to mention, the input files are identical. Also, I ran the exact same line of the command more than three times, and obtained the exact same result. Therefore, I believe this is not due to any randomization introduced (if any) in normalization/smoothing. I used an x86_64 processor, the same as the sample. Thus, I do not believe this is due to any floating point resolution difference between architectures, either. The only possible reason I can think of that might account for the discrepancy is that there are multiple versions or compiles "stable5" mri_ca_normalize. I obtained the sample input and result from; ftp://surfer.nmr.mgh.harvard.edu/pub/data/bert.recon.tgz Our download md5sum matches the one posted. Here's a list of input files; $ls -l /analysis/Tests/FSTest_Tossi/Samples2/buckner_data/tutorial_subjs/bert/mri/orig/ total 17776 -rw-rw-r-- 1 tossi mrilab 5996899 2010-08-09 13:01 001.mgz -rw-rw-r-- 1 tossi mrilab 6077242 2010-08-09 13:01 002.mgz -rw-rw-r-- 1 tossi mrilab 6083164 2010-08-09 13:01 003.mgz Thank you very much in advance. Tossi /********************************************* Tossi Ikuta, Ph.D. Research Scientist The Feinstein Institute for Medical Research The Zucker Hillside Hospital (718) 470-4486 <tikuta(a)nshs.edu> *********************************************/

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Bbregister for fsl tractography
by Lena Palaniyappan 25 Jan '11

25 Jan '11

Dear Doug & others The FSL page on fa to freesurfer registration ( http://www.fmrib.ox.ac.uk/fsl/fdt/fdt_surface.html) contain info that uses tkregister2. To determine freesurfer_to_fa space registration file, do we need to go through the freesurfer_to_struc and then struc_to_fa rooutine given in fsl pages.? I wonder if the registration can be done using the bbregister currently. If that is the case how to get the fsl-type registration file? tkregister2 had an option for this but it is not working with bbregister Cheers Lena _______________________________________________________ Lena Palaniyappan Clinical Lecturer & Honorary StR | Division of Psychiatry ( University of Nottingham) South Block 'A' floor| Queens Medical Centre | Nottingham | NG7 2UH This message and any attachment are intended solely for the addressee and may contain confidential information. If you have received this message in error, please send it back to me, and immediately delete it. Please do not use, copy or disclose the information contained in this message or in any attachment. Any views or opinions expressed by the author of this email do not necessarily reflect the views of the University of Nottingham. This message has been checked for viruses but the contents of an attachment may still contain software viruses which could damage your computer system: you are advised to perform your own checks. Email communications with the University of Nottingham may be monitored as permitted by UK legislation.

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CUDA installation and configuration...
by Gonzalo Rojas Costa 25 Jan '11

25 Jan '11

Hi: I am currently configuring Freesurfer 5 in a new workstation that we received... That workstation has Ubuntu 10.10, and a NVIDIA Quadro FX 1800 graphics card... Could you please send me the detailed steps necessary to install and configure CUDA support ?... Sincerely, -- Gonzalo Rojas Costa Laboratory for Advanced Medical Image Processing Department of Radiology Clínica Las Condes Lo Fontecilla 441, Las Condes, Santiago, Chile. Tel: 56-2-2105170 Cel: 56-9-97771785 www.clc.cl

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Which surface to mesh_vertex_nearest
by Gabriele Arnulfo 25 Jan '11

25 Jan '11

Hi again, looking in previous emails in the list i found that the best way to find the nearest vertex number to a certain point is by using the matlab script mesh_vertex_nearest. So far I've used it with input parameters: the vertices read through read_surf(rh_pial) and a matrix of Cartesian Coordinates. In this context I'd like to know which surface is the right choice, if there should be a choice. I've inserted either the pial and inflated surface having different result (vertex index) for the same point (RAS xyz). Cheers, g. -- In a world without wall, how needs WINDOWS??

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