Freesurfer

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30099 discussions

tkmedit is not working
by Saurabh Thakur 04 Feb '14

04 Feb '14

Hi Everyone, Terminal output is: ///------------------------------------------------------------------------------------------------------////// saurabh@saurabh-Dell-System-XPS-L502X:/usr/local/freesurfer$* tkmedit* /usr/local/freesurfer/tktools*/tkmedit.bin: Command not found.* saurabh@saurabh-Dell-System-XPS-L502X:/usr/local/freesurfer$ *tksurfer* /usr/local/freesurfer/tktools*/tksurfer.bin: Command not found*. saurabh@saurabh-Dell-System-XPS-L502X:/usr/local/freesurfer$ *recon-all* WARNING: tcsh v6.17.06 has an exit code bug! Please update tcsh! USAGE: recon-all Required Arguments: -subjid <subjid> -<process directive> Fully-Automated Directive: -all : performs all stages of cortical reconstruction -autorecon-all : same as -all Manual-Intervention Workflow Directives: -autorecon1 : process stages 1-5 (see below) -autorecon2 : process stages 6-23 after autorecon2, check white surfaces: a. if wm edit was required, then run -autorecon2-wm b. if control points added, then run -autorecon2-cp c. proceed to run -autorecon3 -autorecon2-cp : process stages 12-23 (uses -f w/ mri_normalize, -keep w/ mri_seg) -autorecon2-wm : process stages 15-23 -autorecon2-inflate1 : 6-18 -autorecon2-perhemi : tess, sm1, inf1, q, fix, sm2, inf2, finalsurf, ribbon -autorecon3 : process stages 24-34 if edits made to correct pial, then run -autorecon-pial -hemi ?h : just do lh or rh (default is to do both) . . . . ///--------------------------------------------------------------------------------------------------// can any one help me in this problem.....? Why* tkmedit *is not working. I am seriously looking for solution asap. Thanks in advance. *Saurabh *

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Re: [Freesurfer] Installation error
by Saurabh Thakur 04 Feb '14

04 Feb '14

Hi, I am using laptop with 8Gb RAM, i7 Core processor, and enough HDD.... still i m getting same erro ( */usr/local/freesurfer/tktools/tkmedit.bin: Command not found*. ) because i m working on laptop...? or "recon-all --help " is working but *tkmedit is not working* Hope to get response asap. Thanks in advance. Saurabh Thakur, On Tue, Feb 4, 2014 at 2:09 PM, Markus Gschwind <markus.gschwind(a)gmail.com>wrote: > Hi Saurabh, > > I recently installed FS un ubuntu 12.04, and it was not difficult. > > I would recommend that you again download the file from here > http://surfer.nmr.mgh.harvard.edu/fswiki/Download (I took the Centos4 > file) > > to make sure that it is complete. > > Than you "untar" the file at any given place (most people recomment > /usr/local/ but you need to do it in "sudo" mode). > > Then make sure that you put the license file at the right place ( > http://surfer.nmr.mgh.harvard.edu/fswiki/LinuxInstall) > > and adapt the configuration file ( > http://surfer.nmr.mgh.harvard.edu/fswiki/SetupConfiguration) > > I used bash and it worked well. > > Take care that you have writing permission on the folders you want to use > ($SUBJECT_DIR). > For that reason I copied the folder "bert" to my home folder in order to > be able to run the installation test as recommended here: > http://surfer.nmr.mgh.harvard.edu/fswiki/TestingFreeSurfer > > Hope that helps! > Cheers, > Markus > > 2014-02-04 Saurabh Thakur <srbhthkr(a)gmail.com>: > >> Hello everyone, >> >> Can u anyone help me in simplest and best way to install freesurfer on >> >> *i m not able to run command : * >> >> >> >> *1. tkmedit 2. tksurfer.System specification: * >> >> Dell laptop >> Ubuntu 12.04 LTS >> RAM 8Gb >> Graphics cards: Nvidia cards 1 Gb >> >> Thanks in advance. >> >> Saurabh Thakur, >> >> >> >> >> _______________________________________________ >> 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. >> >> >

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Join my network on LinkedIn
by Ting Xu via LinkedIn 04 Feb '14

04 Feb '14

LinkedIn ------------ Ting Xu requested to add you as a connection on LinkedIn: ------------------------------------------ Je vous invite à faire partie de mon réseau professionnel en ligne sur le site LinkedIn. Accept invitation from Ting Xu http://www.linkedin.com/e/-qq80um-hr8w2fp3-5t/qaAr-Z_86TRZ5lXG-dA9kZQ49qSe5… View profile of Ting Xu http://www.linkedin.com/e/-qq80um-hr8w2fp3-5t/rso/321047558/rnBM/name/66471… ------------------------------------------ You are receiving Invitation emails. This email was intended for Freesurfer List. Learn why this is included: http://www.linkedin.com/e/-qq80um-hr8w2fp3-5t/plh/http%3A%2F%2Fhelp%2Elinke… (c) 2012, LinkedIn Corporation. 2029 Stierlin Ct, Mountain View, CA 94043, USA.

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Installation error
by Saurabh Thakur 04 Feb '14

04 Feb '14

Hello everyone, Can u anyone help me in simplest and best way to install freesurfer on *i m not able to run command : * *1. tkmedit 2. tksurfer.System specification: * Dell laptop Ubuntu 12.04 LTS RAM 8Gb Graphics cards: Nvidia cards 1 Gb Thanks in advance. Saurabh Thakur,

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CentOS 5.8
by jh kim 03 Feb '14

03 Feb '14

Dear FreeSurferers Just a quick question. Is CentOS 5.8 fully compatible with FS 5.3? Thank you. Kim

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Re: [Freesurfer] Freesurfer, Matlab and Maverick
by Dusan Hirjak 03 Feb '14

03 Feb '14

Dear Freesurferexperts, I still have the Problem because I can not run the the mris-command to estimate the gyrification-index, because Freesurfer is not recognizing Matlab: "ERROR: Matlab is required to run mris_compute_lgi"Im not sure why this is happening? Does someone have an idea??? Im starting Freesurfer as follows: FREESURFER_HOME=/Users/dhirjak/freesurfer source $FREESURFER_HOME/SetUpFreeSurfer.sh (than I get the following output) Dusan-Hirjaks-MacBook-Pro:~ dhirjak$ source $FREESURFER_HOME/SetUpFreeSurfer.sh-------- freesurfer-Darwin-snowleopard-i686-stable-pub-v5.3.0 --------Setting up environment for FreeSurfer/FS-FAST (and FSL)FREESURFER_HOME /Users/dhirjak/freesurferFSFAST_HOME /Users/dhirjak/freesurfer/fsfastFSF_OUTPUT_FORMAT nii.gzSUBJECTS_DIR /Users/dhirjak/MRI/Freesurfer_2MNI_DIR /Users/dhirjak/freesurfer/mniFSL_DIR /Users/dhirjak/fsl export SUBJECTS_DIR=/Users/dhirjak/MRI/Freesurfer In have the following lines in my matlab startup-file: fshome = getenv('FREESURFER_HOME'); fsmatlab = sprintf('%s/matlab',fshome); if (exist(fsmatlab) == 7) path(path,fsmatlab); end clear fshome fsmatlab; fsfasthome = getenv('FSFAST_HOME'); fsfasttoolbox = sprintf('%s/toolbox',fsfasthome); if (exist(fsfasttoolbox) == 7) path(path,fsfasttoolbox); end clear fsfasthome fsfasttoolbox; Thanks!!! Dusan Hirjak

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mri_convert error during make_average_subject
by Jonathan Holt 03 Feb '14

03 Feb '14

Hello FS experts, I’m trying to make an average subject and I had an unfortunate error during the mri_convert stage, specifically an mghWrite error. I failed to save the output so I cannot recall the exact details, are there any specific things I should be looking out for to prevent this? best, Jon

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Re: [Freesurfer] Create a surf from a special volume?
by Douglas N Greve 03 Feb '14

03 Feb '14

Please remember to post to the list. Thanks! You cannot do that with mri_vol2surf. You'll have to create a binarization of the white matter, then use mrs_tessellate doug On 02/03/2014 05:24 PM, Markus Gschwind wrote: > Thank you Doug! > > But actually I want to produce a *surface*, not an overlay. > > What is the right command for that? It should be a file type surf.w I > guess. > > Thanks > Markus > > > 2014-02-03 Douglas N Greve <greve(a)nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu>>: > > > mri_vol2surf will produce an overlay, not a surface. If you want an > overlay, use .nii or .mgh instead of .w or .gii (no need for > --out_type) > doug > > > On 02/03/2014 04:33 PM, Markus Gschwind wrote: > > Hi Bruce, > > > > Thank you! The creation of register.data worked perfectly. > > > > Now in order to create the mesh file (I suppose .w) of the altered > > brain with cut out temporal lobe (brain_T1fin), would this > command be OK? > > > > mri_vol2surf --src FREESURFER/mri/brain_T1fin.nii.gz --srcreg > > FREESURFER/mri/register2.dat --hemi lh --projfrac 0.5 --out > > FREESURFER/mri/brain_T1fin_surf.w --out_type nifti > > > > ...however I get > > ERROR: could not determine type of FREESURFER/mri/brain_T1fin_surf.w > > > > And when using output_type 'paint' or 'gii' (without the ' ' ) it is > > calculating something, but freeview crashes when I try to look at > > it... Actually I have no clue what the output_type should be... > > > > Thanks so much! > > Markus > > > > > > 2014-02-03 Bruce Fischl <fischl(a)nmr.mgh.harvard.edu > <mailto:fischl@nmr.mgh.harvard.edu> > > <mailto:fischl@nmr.mgh.harvard.edu > <mailto:fischl@nmr.mgh.harvard.edu>>>: > > > > Hi Markus > > > > the --s option should be a subject name, not a path to a volume > > > > cheers > > Bruce > > > > On Mon, 3 Feb 2014, Markus Gschwind wrote: > > > > Hi again, > > It is certainly a beginners question, and probably the code > > examples given > > below are not right... > > > > Is there anyone that could advice me how to do this? > > > > Thanks so much! > > Markus > > > > > > 2014-02-01 Markus Gschwind <markus.gschwind(a)gmail.com > <mailto:markus.gschwind@gmail.com> > > <mailto:markus.gschwind@gmail.com > <mailto:markus.gschwind@gmail.com>>>: > > Dear all, > > I want to create a surface of a partially altered brain T1 > > (temporal > > lobe cut away by hand). > > > > I figured out that this would be done with mri_vol2surf. > > > > This command asks for a register.dat file. > > > > I think that I can get it using this command: > > > > SUBJECT_DIR=/Users/FREESURFER > > > > bbregister --s /mri/brain_T1.mgz --mov > > /Users/FREESURFER/mri/brain_T1_ins.mgz --reg > > /FREESURFER/mri/register.dat --t1 --init-spm > > > > I well starts calculation, but suddenly stops and complains > > that there > > is no brainmask > > /Users/FREESURFER/mri/brain_T1.mgz/mri/brainmask.mgz > > > > which makes somehow no sense as the brainmask is in > > /Users/FREESURFER/mri/brainmask.mgz of course. > > > > But I don't find a option to specify the brainmask in > bbregister. > > > > What am I doing wrong? > > > > Thanks for any help! > > Markus > > > > > > > > > > > > > > > > > > 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 > <mailto:Freesurfer@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 <mailto:greve@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> > FileDrop: 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/ > > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu <mailto:Freesurfer@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: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/

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Create a surf from a special volume?
by Markus Gschwind 03 Feb '14

03 Feb '14

Dear all, I want to create a surface of a partially altered brain T1 (temporal lobe cut away by hand). I figured out that this would be done with mri_vol2surf. This command asks for a register.dat file. I think that I can get it using this command: SUBJECT_DIR=/Users/FREESURFER bbregister --s /mri/brain_T1.mgz --mov /Users/FREESURFER/mri/brain_T1_ins.mgz --reg /FREESURFER/mri/register.dat --t1 --init-spm I well starts calculation, but suddenly stops and complains that there is no brainmask /Users/FREESURFER/mri/brain_T1.mgz/mri/brainmask.mgz which makes somehow no sense as the brainmask is in /Users/FREESURFER/mri/brainmask.mgz of course. But I don't find a option to specify the brainmask in bbregister. What am I doing wrong? Thanks for any help! Markus

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Difference between aseg.stats and mri_segstats
by Jonathan Holt 03 Feb '14

03 Feb '14

Hi All, I'm interested in the cerebellar volume on a particular subject and I was wondering why I am seeing a slight difference between the volume listed in aseg.stats and the volume produced by mri_segstats with aseg.mgz as the input. It's a very slight difference, 44452mm^3 vs 45137.7mm^3 (mri_segstats and aseg.stats, respectively) but I am wondering what the reason is and which is more accurate. best, jon

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