Freesurfer February 2014

freesurfer@nmr.mgh.harvard.edu

128 participants
236 discussions

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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Re: [Freesurfer] Hippocampal subfields script.
by Alan Francis 03 Feb '14

03 Feb '14

Thanks Eugenio. On Mon, Feb 3, 2014 at 2:57 PM, Juan Eugenio Iglesias < iglesias(a)nmr.mgh.harvard.edu> wrote: > Hi Alan, > there's indeed such a script: > kvlQuantifyHippocampalSubfieldSegmentations.sh > Check out the documentation at: > http://surfer.nmr.mgh.harvard.edu/fswiki/HippocampalSubfieldSegmentation > Cheers, > /E > > On Mon, 2014-02-03 at 14:52 -0500, Alan Francis wrote: > > Hi Eugenio: > > > > > > I have HSF data on 60 Asperger brains. Is there a script that will > > allow me to extract the volumes into a single location? > > > > > > thanks so much, > > > > > > Alan Francis > > Martinos Center > > > > > 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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Hippocampal subfields script.
by Alan Francis 03 Feb '14

03 Feb '14

Hi Eugenio: I have HSF data on 60 Asperger brains. Is there a script that will allow me to extract the volumes into a single location? thanks so much, Alan Francis Martinos Center

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Cortical parcellation: what are the black spots?
by Qingyang Li 03 Feb '14

03 Feb '14

Dear Freesurfer experts, I was looking at the results of my data when I found that there were some black spots in my parcellation results (Please see the attached screenshot, the black spots were indicated by arrows). I did not see any hole or other errors in the surfaces generated for this subject. I hope you can help me with why the black spots were there? is it a big deal or something that I can ignore? If they need to be fixed, what should I do? Thanks! I am sorry if this question has been posted here. I really tried to find the answer by myself but I did not find anything. Thanks, Yang ------ Qingyang Li Balance and focus.

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Freesurfer February 2014