[Freesurfer] Fwd: calloc error

2013-08-19 Thread Arno Klein
i have tried running the centos 4 & 6 versions of freesurfer on ubuntu 12.04, and with either i am getting a memory error when i simply run mri_info on an mgz file (this does not happen on my osx machine for the same file , and the license file is fine): """ znzTAGskip: tag=1667787808, failed to c

[Freesurfer] Fwd: calloc error

2013-08-20 Thread Arno Klein
please ignore the previous post -- the calloc errors i was getting were restricted to only certain files that somehow got corrupted. cheers, @rno ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo

[Freesurfer] memory allocation error with mris_register for one subject

2012-06-18 Thread Arno Klein
hello! i am able to run mris_register on all of the OASIS brain images that i have tested except for one: OAS1_0061_MR1: mris_register -curv OASIS-0061_MR1/surf/rh.sphere templates/freesurfer/rh.OASIS_template.tif OASIS-0061_MR1/surf/rh.sphere_to_OASIS_template.reg using smoothwm curvature for

Re: [Freesurfer] memory allocation error with mris_register for one subject

2012-06-18 Thread Arno Klein
? And run mris_info or > mris_euler_number on it? I'm wondering if it is corrupted. > Bruce > > On Mon, 18 Jun 2012, Arno Klein wrote: > > >> hello! >> >> i am able to run mris_register on all of the OASIS brain images that i >> have >> tested except for

[Freesurfer] mris_label2annot mislabeling

2012-06-20 Thread Arno Klein
hello! i have saved a couple of .label files and am trying to convert them to a .annot file with: mris_label2annot --h lh --s MMRR-21-1 --l lh.superiorfrontal.label --l lh.superiorparietal.label --ctab FreeSurferColorLUT.txt --a output the stdout is: ColorTable atlas_colortable.txt AnnotName

Re: [Freesurfer] mris_label2annot mislabeling

2012-06-24 Thread Arno Klein
u want to be. By > default, it uses FreeSurferColorLUT.txt. > doug > > > On 6/23/12 9:54 PM, Arno Klein wrote: > > > dear doug, > > thank you for your response. for the custom color table, what do i > assign for the different anatomical names and colo

Re: [Freesurfer] mris_label2annot mislabeling

2012-06-25 Thread Arno Klein
our color table? It will assign > the first label to the first entry in the color table. > > > On 06/24/2012 11:43 AM, Arno Klein wrote: > >> >> yes, but i am confused as to how mris_label2annot uses the color table. >> according to http:/

[Freesurfer] how to convert .vtk surface meshes with labels to .annot format?

2012-08-30 Thread Arno Klein
what is the best way to convert a .vtk surface mesh (with labels as scalars) to freesurfer .annot format? i am currently converting the vtk file to freesurfer .label files, then using freesurfer to consolidate these into an .annot file, which is slow, roundabout, and generates a lot of files. che

[Freesurfer] Mindboggle-101 manually labeled brain data now available! {Disarmed} {Disarmed}

2012-12-05 Thread Arno Klein
rains, as a normative dataset to establish morphometric variation in a healthy population for comparison against clinical populations, and contribute to the development, training, testing, and evaluation of automated registration and labeling algorithms..." Cheers, @rno arno klein a...@binary

[Freesurfer] Mindboggle official software release and publication!

2017-02-23 Thread Arno Klein
Announcing the official release of Mindboggle (http://mindboggle.info), open source software and data for analyzing the shapes of brain structures from human MRI data (processed through FreeSurfer and optionally through ANTs). The relea

Re: [Freesurfer] Mindboggle official software release and publication!

2017-02-24 Thread Arno Klein
ave already been processed in earlier > versions of freesurfer. > > If there is a patch or script to update the data processed using earlier > versions of freesurfer, that will save a lot of time than running > everything from scratch in FS6. > > Please let us know. > > B

[Freesurfer] Alzheimer's Disease Sage/DREAM Challenge

2014-06-22 Thread Arno Klein
The Alzheimer's Disease Sage/DREAM Challenge #1 (AD#1) launched earlier this month! The goal of the AD#1 is to apply an open science approach to rapidly identify accurate predictive AD biomarkers that can be used by the scientific, industrial and regulatory communities to improve AD diagnosis and

[Freesurfer] Fwd: Alzheimer's Disease Sage/DREAM Challenge

2014-06-22 Thread Arno Klein
The Alzheimer's Disease Sage/DREAM Challenge #1 (AD#1) launched earlier this month! The goal of the AD#1 is to apply an open science approach to rapidly identify accurate predictive AD biomarkers that can be used by the scientific, industrial and regulatory communities to improve AD diagnosis and

[Freesurfer] New deadline for the Alzheimer's Disease Sage/DREAM Challenge!

2014-09-09 Thread Arno Klein
We have extended the Alzheimer's Disease Sage/DREAM Challenge #1 submission period to October 17th -- Time to enter! https://www.synapse.org/#!Synapse:syn2290704 Of particular interest to the members of this mailing list is subchallenge 3, which leverages brain imaging ​ ( FreeSurfer was used in

[Freesurfer] memory allocation error with mris_register

2012-01-20 Thread Arno Klein
i get the following memory allocation error for only one out of 20 oasis subjects that i processed with freesurfer 5.1 on an ubuntu 11.10 machine with 24gb memory: mris_register -curv subjects/OAS1_0061_MR1/surf/lh.sphere templates_freesurfer/lh.KKI_2.tif subjects/OAS1_0061_MR1/surf/lh.sphere_to_K

Re: [Freesurfer] memory allocation error with mris_register

2012-01-20 Thread Arno Klein
und is to convert the > orig.mgz to itself using mri_convert in the dev environment, ie, > > mri_convert orig.mgz orig.mgz > > doug > > Arno Klein wrote: > >> >> i get the following memory allocation error for only one out of 20 oasis >> subjects that

Re: [Freesurfer] memory allocation error with mris_register

2012-01-20 Thread Arno Klein
dear doug, sadly, no dice. cheers, @rno On Fri, Jan 20, 2012 at 4:45 PM, Douglas N Greve wrote: > Try doing it in matlab, so > a = MRIread('orig.mgz'); > MRIwrite(a,'orig.mgz'); > > doug > > Arno Klein wrote: > >> >> dear doug, &g

Re: [Freesurfer] memory allocation error with mris_register

2012-01-20 Thread Arno Klein
dear bruce, you're right -- i am able to view the pial surface, but when i try to view the spherical surface with tksurfer i get the same memory error. is there any way to fix the sphere without affecting anything else? neuromorphometrics has painstakingly manually edited the freesurfer labels g

Re: [Freesurfer] memory allocation error with mris_register

2012-01-21 Thread Arno Klein
thank you -- this worked! cheers, @rno On Fri, Jan 20, 2012 at 6:43 PM, Bruce Fischl wrote: > you can just rerun the mris_sphere command that is in the recon-all.log > (or recon-all.cmd) > > cheers > Bruce > > On Fri, 20 Jan 2012, Arno Klein wrote: > > >> de

[Freesurfer] mri_surf2surf source and target annot formats

2012-05-24 Thread Arno Klein
hello! in mri_surf2surf, does anyone know how to specify the source and target formats if --sval is annot without using --sval-annot, as in "--sfmt" or "--tfmt"? cheers, @rno ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mg