Re: [Freesurfer] dmri_train malloc error
Hi Kevin - This is unfortunately a problem with the macos freesurfer distribution, which is still built on leopard instead of snow leopard b/c of compatibility issues with some libraries unrelated to tracula. It's possible to compile tracula on snow leopard (in fact that's what I use) but you'd have to download the source code. Since several people have written about this by now, I'm considering something that'd be less of a pain for users, which is to create a tarball with only the tracula executables compiled on snow leopard and make it available. a.y On Fri, 22 Jul 2011, Dabbs (Kevin) wrote: Freesurfer users, I have ran into a malloc error running trac-all. Looks like the same error that Stijn posted to the list on 17 Jun 2011. I did not see a solution posted. It occurs in dmr_train using trac-all -prep –c dmrirc.txt. Also tried using trac-all –prior –c dmrirc.txt with the same results. Reset the tcsh limits for datasize, …. * Loading segmentation from /Applications/freesurfer5_1/trctrain/trc029/dlabel/mni/aparc+aseg.nii.gz Loading cortex mask from /Applications/freesurfer5_1/trctrain/trc029/dlabel/mni/cortex+2mm.nii.gz dmri_train(54615) malloc: *** mmap(size=159744) failed (error code=12) *** error: can't allocate region *** set a breakpoint in malloc_error_break to debug MRIalloc(218, 182, 182): could not allocate 158704 bytes for 26th slice Cannot allocate memory ** My system Model Name: Mac Pro Model Identifier: MacPro3,1 Processor Name: Quad-Core Intel Xeon Processor Speed: 2.8 GHz Number Of Processors: 2 Total Number Of Cores: 8 L2 Cache (per processor): 12 MB Memory: 18 GB System Version: Mac OS X 10.5.8 Thanks for any advice or suggestions! Kevin Dabbs SMPH/Neurology UW-Madison ___ Freesurfer mailing list Freesurfer@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.
[Freesurfer] dcm conversion
Dear Bruce, I am a little confused and I will be very grateful if you can make it a little more clear: So I start converting the dicom files from 3DAx_T1 (having the first file called 1.3.46.670589.11.17385.5.0.8952.2011042600464496394) series by running: mri_convert 2011042600464496394.dcm 3DAx_T1.nii.gz (I suppose I need to write only the last numbers). Then I am doing the same thing for all the dicom files in this series? After I finish the 3DAx_T1 I am moving further and do the same for all my series? Which series I shoul duse to run the recon-all for cortical thickness's studies? Sorry for this silly question but for all my other subjects I had only one file .nii.gz and I have no clue from where is coming. Thank you very much. Antonella From: Bruce Fischl To: Antonella Kis Cc: "freesurfer@nmr.mgh.harvard.edu" Sent: Thursday, July 21, 2011 11:08 AM Subject: Re: dcm conversion to nii Hi Antonella, for each acquisition you give mri_convert *one* dicom file in that series and it will figure out the rest. You will then have one volume file per series. Something like: mri_convert Good morning Bruce, > > Thank you for your answer and yes, I am posting my question to the list. > > For all my other subjects I had the MRI data converted by somebody else into > one file .nii.gz for each subject. My question is how I can > convert the MRI data (.dcm) for a new subject in a .nii.gz file? I have > multiple file from MRI: 3DAx_T1, 3DSag_T1, Ax_Flair, Ax_PD, Ax_T2, > BOLD, DTI_15, DTI_32 each of them containing lots of .dcm files. Do I need to > convert all of them? If I give mri_convert one slice in each > dicom series and convert each one to it's own volume how I can further use > this data? Do I get an .nii.gz for each dicom file? > > I attached a type of file .nii.gz from another subject so you can see what > type of files I need to get by conversion. > > Thank you very much. > Antonella > > > From: Bruce Fischl > To: Antonella Kis > Sent: Wednesday, July 20, 2011 4:12 PM > Subject: Re: dcm conversion to nii > > Hi Antonella > > can you post this type of question to the list so others can answer? I don't > think you want them in one file as they probably have > different resolution etc... Give mri_convert one slice in each dicom series > and convert each one to it's own volume. > > cheers > Bruce > On Wed, 20 Jul 2011, Antonella Kis wrote: > > > Dear Bruce, > > > > I have the MRI data (.dcm) for my subject p27 within the following files: > > > > 3DAx_T1, 3DSag_T1, Ax_Flair, Ax_PD, Ax_T2, BOLD, DTI_15, DTI_32. > > > > I would like to convert this data into one file.nii.gz. It will be correct > > if I will run: > > > > mri_convert p27 NPI027.nii.gz? > > > > Will FS know to convert based on this statement all my dcm files into one > > nii.gz file? If not how should I do it? > > > > > > Many thanks. > > Antonella > > > > > > > > > > > > > > > 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@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.
Re: [Freesurfer] dcm conversion
Hi Antonella, no, you pick *one* file in each series (it doesn't matter which one, mri_convert will figure out the rest), and do something like: mri_convert 1.3.46.670589.11.17385.5.0.8952.2011042600464496394.dcm 3DAx_T1.nii.gz the only one(s) FreeSurfer will use are the 3D T1-weighted scans such as mp-rages. Those you will give to recon-all as inputs. cheers Bruce On Fri, 22 Jul 2011, Antonella Kis wrote: Dear Bruce, I am a little confused and I will be very grateful if you can make it a little more clear: So I start converting the dicom files from 3DAx_T1 (having the first file called 1.3.46.670589.11.17385.5.0.8952.2011042600464496394) series by running: mri_convert 2011042600464496394.dcm 3DAx_T1.nii.gz (I suppose I need to write only the last numbers). Then I am doing the same thing for all the dicom files in this series? After I finish the 3DAx_T1 I am moving further and do the same for all my series? Which series I shoul duse to run the recon-all for cortical thickness's studies? Sorry for this silly question but for all my other subjects I had only one file .nii.gz and I have no clue from where is coming. Thank you very much. Antonella ___ From: Bruce Fischl To: Antonella Kis Cc: "freesurfer@nmr.mgh.harvard.edu" Sent: Thursday, July 21, 2011 11:08 AM Subject: Re: dcm conversion to nii Hi Antonella, for each acquisition you give mri_convert *one* dicom file in that series and it will figure out the rest. You will then have one volume file per series. Something like: mri_convert Good morning Bruce, > > Thank you for your answer and yes, I am posting my question to the list. > > For all my other subjects I had the MRI data converted by somebody else into one file .nii.gz for each subject. My question is how I can > convert the MRI data (.dcm) for a new subject in a .nii.gz file? I have multiple file from MRI: 3DAx_T1, 3DSag_T1, Ax_Flair, Ax_PD, Ax_T2, > BOLD, DTI_15, DTI_32 each of them containing lots of .dcm files. Do I need to convert all of them? If I give mri_convert one slice in each > dicom series and convert each one to it's own volume how I can further use this data? Do I get an .nii.gz for each dicom file? > > I attached a type of file .nii.gz from another subject so you can see what type of files I need to get by conversion. > > Thank you very much. > Antonella > > > From: Bruce Fischl > To: Antonella Kis > Sent: Wednesday, July 20, 2011 4:12 PM > Subject: Re: dcm conversion to nii > > Hi Antonella > > can you post this type of question to the list so others can answer? I don't think you want them in one file as they probably have > different resolution etc... Give mri_convert one slice in each dicom series and convert each one to it's own volume. > > cheers > Bruce > On Wed, 20 Jul 2011, Antonella Kis wrote: > > > Dear Bruce, > > > > I have the MRI data (.dcm) for my subject p27 within the following files: > > > > 3DAx_T1, 3DSag_T1, Ax_Flair, Ax_PD, Ax_T2, BOLD, DTI_15, DTI_32. > > > > I would like to convert this data into one file.nii.gz. It will be correct if I will run: > > > > mri_convert p27 NPI027.nii.gz? > > > > Will FS know to convert based on this statement all my dcm files into one nii.gz file? If not how should I do it? > > > > > > Many thanks. > > Antonella > > > > > > > > > > > > > > > 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@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.
[Freesurfer] Error in qdec longitudinal 5.1
Dear list, I got an error after following the newer version of the longitudinal stream 5.1. long_mris_slopes worked without problems for my data which was longtudinally processed in 4.5. I also split the qdec.table to the cross for being able to be loaded in qdec GUI. Somehow I got the error that the Templatesubxx/surf/xh.thickness.fwhm.xx.fsaverage.mgh. I went back to check inside the Templatesubxx/surf has only the xh.long.thickness-xxx.fwhmx.fsaverage.mgh Is there something I am missing? Thanks a lot for the help ___ Freesurfer mailing list Freesurfer@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.
[Freesurfer] PySurfer - A package for visualizing surfaces
Dear Freesurfers, We are pleased to announce the 0.1 release of PySurfer, a Python-based package for the visualization of surface data from Freesurfer. Please see our website at http://pysurfer.github.com/ for information on how to install the package and a gallery of examples. We hope you'll find it useful in your research! Best, Michael Waskom Alexandre Gramfort Scott Burns ___ Freesurfer mailing list Freesurfer@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.
Re: [Freesurfer] PySurfer - A package for visualizing surfaces
Hi Michael, Out of curiosity, does this also support the GIFTI format? If so, one could use it to view surface data from a wide variety of software packages. Thanks, Matt. -Original Message- From: freesurfer-boun...@nmr.mgh.harvard.edu [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Michael Waskom Sent: Friday, July 22, 2011 1:07 PM To: Freesurfer@nmr.mgh.harvard.edu Cc: Alexandre Gramfort; Scott Burns Subject: [Freesurfer] PySurfer - A package for visualizing surfaces Dear Freesurfers, We are pleased to announce the 0.1 release of PySurfer, a Python-based package for the visualization of surface data from Freesurfer. Please see our website at http://pysurfer.github.com/ for information on how to install the package and a gallery of examples. We hope you'll find it useful in your research! Best, Michael Waskom Alexandre Gramfort Scott Burns ___ Freesurfer mailing list Freesurfer@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. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] Converting from volume label RAS to Talairach
I'm at my wits' end with what seems like it should be an easy question. I have a lot of volume labels that have been saved for a lot of brains. I want the Talairach coordinates corresponding to those points. It seems like mri_label2label should be able to do this, by putting in 'talairach' as the target subject, but this returns an error that the subject 'talairach' isn't found: mri_label2label --srcsubject m00045 --srclabel label/all.label --trgsubject talairach --trglabel all_talairach.label --regmethod volume It seems like I should be able to do it manually by loading the talairach.xfm generated by recon-all and multiplying that matrix by the RAS points in the labels; this yields results that are pretty close to those given in tkmedit, but not that close. Usually within a few, sometimes off by more. Probably my inability to do this reflects some misunderstanding or lack of information, but I've been poring over documentation, forum, and wiki for hours now and feel like I've hit a wall. Any suggestions? Thanks so much, Jed ___ Freesurfer mailing list Freesurfer@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.
Re: [Freesurfer] PySurfer - A package for visualizing surfaces
Hi Matt, In theory it could, as we use Nibabel for i/o and they support Gifti. However, I have no data in Gifti format at the moment to work with, so at the moment I would say we are Freesurfer specific. Best, Michael On Fri, Jul 22, 2011 at 2:09 PM, Matt Glasser wrote: > Hi Michael, > > Out of curiosity, does this also support the GIFTI format? If so, one could > use it to view surface data from a wide variety of software packages. > > Thanks, > > Matt. > > -Original Message- > From: freesurfer-boun...@nmr.mgh.harvard.edu > [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Michael Waskom > Sent: Friday, July 22, 2011 1:07 PM > To: Freesurfer@nmr.mgh.harvard.edu > Cc: Alexandre Gramfort; Scott Burns > Subject: [Freesurfer] PySurfer - A package for visualizing surfaces > > Dear Freesurfers, > > We are pleased to announce the 0.1 release of PySurfer, a Python-based > package for the visualization of surface data from Freesurfer. Please > see our website at http://pysurfer.github.com/ for information on how > to install the package and a gallery of examples. We hope you'll find > it useful in your research! > > Best, > Michael Waskom > Alexandre Gramfort > Scott Burns > ___ > Freesurfer mailing list > Freesurfer@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. > > ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] PySurfer - A package for visualizing surfaces
hi mike, In theory it could, as we use Nibabel for i/o and they support Gifti. > However, I have no data in Gifti format at the moment to work with, so > at the moment I would say we are Freesurfer specific. > freesurfer does support giftis. mris_convert --combinesurfs fsaverage/surf/lh.inflated fsaverage/surf/rh.inflated test.gii mris_convert fsaverage/surf/lh.inflated ./lh.test2.gii would be awesome to be able to have gifti support and direct nifti overlay with a bbreg.dat registration or identity instead of having to create an overlay file. cheers, satra > > Best, > Michael > > On Fri, Jul 22, 2011 at 2:09 PM, Matt Glasser wrote: > > Hi Michael, > > > > Out of curiosity, does this also support the GIFTI format? If so, one > could > > use it to view surface data from a wide variety of software packages. > > > > Thanks, > > > > Matt. > > > > -Original Message- > > From: freesurfer-boun...@nmr.mgh.harvard.edu > > [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Michael > Waskom > > Sent: Friday, July 22, 2011 1:07 PM > > To: Freesurfer@nmr.mgh.harvard.edu > > Cc: Alexandre Gramfort; Scott Burns > > Subject: [Freesurfer] PySurfer - A package for visualizing surfaces > > > > Dear Freesurfers, > > > > We are pleased to announce the 0.1 release of PySurfer, a Python-based > > package for the visualization of surface data from Freesurfer. Please > > see our website at http://pysurfer.github.com/ for information on how > > to install the package and a gallery of examples. We hope you'll find > > it useful in your research! > > > > Best, > > Michael Waskom > > Alexandre Gramfort > > Scott Burns > > ___ > > Freesurfer mailing list > > Freesurfer@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. > > > > > > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > ___ Freesurfer mailing list Freesurfer@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.
[Freesurfer] Pre-processing issues
Dear Bruce, I have two more questions for today, please: 1). Just to be sure that I understood correct: for my cortical thickness studies and also for a group studies analysis I will use only the data from the 3DAx_T1series which was converted to a .nii.gz file. Is this right? 2). If I want to shortness the pre-processing time while running the recon-all for my subjects, can I run recon-all for three subjects by opening three terminals in the same time? Running more subjects in the same time will induce more errors for a manual correction or the results will be the same with the one while running each subject individual/only one terminal at the time. Thank you and have a great weekend. Antonella___ Freesurfer mailing list Freesurfer@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.
Re: [Freesurfer] Pre-processing issues
Hi Antonella do you know what the type of acquisition is? That name isn't enough to know for sure, but it might be. And yes, you can run more than 1 recon at a time assuming you have enough ram on your machine. It won't go faster of course unless you have multiple cpus cheers Bruce On Fri, 22 Jul 2011, Antonella Kis wrote: Dear Bruce, I have two more questions for today, please: 1). Just to be sure that I understood correct: for my cortical thickness studies and also for a group studies analysis I will use only the data from the 3DAx_T1series which was converted to a .nii.gz file. Is this right? 2). If I want to shortness the pre-processing time while running the recon-all for my subjects, can I run recon-all for three subjects by opening three terminals in the same time? Running more subjects in the same time will induce more errors for a manual correction or the results will be the same with the one while running each subject individual/only one terminal at the time. Thank you and have a great weekend. Antonella ___ Freesurfer mailing list Freesurfer@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.
Re: [Freesurfer] PySurfer - A package for visualizing surfaces
Hey, On Fri, Jul 22, 2011 at 02:06:41PM -0400, Michael Waskom wrote: > We are pleased to announce the 0.1 release of PySurfer, a Python-based > package for the visualization of surface data from Freesurfer. Please > see our website at http://pysurfer.github.com/ for information on how > to install the package and a gallery of examples. We hope you'll find > it useful in your research! Thanks for going free software! Packaging for NeuroDebian is work-in-progress Michael -- Michael Hanke http://mih.voxindeserto.de ___ Freesurfer mailing list Freesurfer@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.
Re: [Freesurfer] Aseg and Cerebellum
I have been working with Michael Murray on the problems we are having stripping/segmenting the cerebellum. We have tried various things, including a range of watershed parameters (1-10), gcut, as well as running these adjustments in succession (as you suggested below) with various combinations and parameter settings, but we have yet to be successful. It either does not cut much if any excess at all, or it cuts too much and takes out sections of both the cortex and the cerebellum. Are there any others ways that we may be able to address this problem, other than by adjusting watershed parameters or doing manual edits on every subject? Thanks very much. Heather Lugar -Original Message- From: freesurfer-boun...@nmr.mgh.harvard.edu [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Allison Stevens Sent: Wednesday, July 20, 2011 6:38 PM To: Bruce Fischl Cc: Murray, Michael; freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Aseg and Cerebellum If it is, you can try running the skullstrip step a second time. On Jul 20, 2011, at 7:14 PM, Bruce Fischl wrote: > Hi Michael, > > if cerebellar gray matter is not something you are terribly interested in > quantifying then you are fine. > > cheers > Bruce > > On Wed, 20 Jul 2011, Murray, Michael wrote: > >> Hi all, >> >> We've using version 5.1 to conduct a longitudinal study involving over 150 >> subjects with up to three time points apiece, and we're having >> some issues with regards to aseg in the areas around the cerebellum. >> Attached is an image of the problem - some dura or something else is >> being classified as cerebellum. It's particularly troubling because this >> issue is present in most of our images, but to varying degrees. >> We've tried adjusting the watershed parameters (using multistrip) as well as >> using gcut, but neither method was effective in removing the >> offending voxels. >> >> It seems like our only other option is to manually edit the brainmask.mgz, >> but with so many subjects and time points, we're wondering if >> there is another automated fix that we haven't tried. Otherwise, is this >> something that we'll have to manually fix, or can it be left >> alone? >> >> Thank you, >> >> Michael Murray >> > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@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. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Converting from volume label RAS to Talairach
You're so close! Use fsaverage as the target subject. The output coordinates will be in MNI305 space. doug Jed Singer wrote: > I'm at my wits' end with what seems like it should be an easy question. I > have a lot of volume labels that have been saved for a lot of brains. I want > the Talairach coordinates corresponding to those points. It seems like > mri_label2label should be able to do this, by putting in 'talairach' as the > target subject, but this returns an error that the subject 'talairach' isn't > found: > > mri_label2label --srcsubject m00045 --srclabel label/all.label --trgsubject > talairach --trglabel all_talairach.label --regmethod volume > > It seems like I should be able to do it manually by loading the talairach.xfm > generated by recon-all and multiplying that matrix by the RAS points in the > labels; this yields results that are pretty close to those given in tkmedit, > but not that close. Usually within a few, sometimes off by more. > > Probably my inability to do this reflects some misunderstanding or lack of > information, but I've been poring over documentation, forum, and wiki for > hours now and feel like I've hit a wall. Any suggestions? > > Thanks so much, > Jed > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@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 ___ Freesurfer mailing list Freesurfer@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.
[Freesurfer] Fwd: questions about high resolution atlas on the Freesurfer
Dear FS experts, Freesurfer could provide for every participant a standardized partition of the cortex into 66 regional areas. My aim is to use freesurfer to subdivide these regional areas into a set of small and compact regions, resulting in high resolution atlas covering the entire cortex (taken from Hagmann et al. (2008) in PLoS Biol). We tried to used the mris_divide_parcellation fsaverage rh aparc.annot 100 rh_annot_100 (However, this creates a parcellation of long strips per region, that is not a good partition for what we want.) Then, we used the "mris_make_face_parcellation lh.orig $FREESURFER_HOME/lib/bem/ic3.tri ./lh.ic3.annot". The results look nice, but I have the following questions: (1)Can i used the "mris_make_face_parcellation" based on the "aparc.annot"? (2)How can i conver the .annot file into .hdr/.img mask files? I read the introduction about "mri_label2vol", but i was still confused. If i want to convert aparc.annot files in fsaverage, what the input files are for "--temp" and "--seg"? (3)I read the "lh.ic3.annot" in Matlab (read_annotation.m). For "colortable.struct_names", the name is "ic3.tri_vertex_0"(to "ic3.tri_vertex_641"), how to know which brain regions it belong to? how to know each vertex's MNI coordinate? (4)"mris_make_face_parcellation lh.orig $FREESURFER_HOME/lib/bem/ic3.tri ./lh.ic3.annot" . I only see 7 options in: $FREESURFER_HOME/lib/bem/ic[1-7].tri (as per the program usage). Can I specify custom ic*.tri files (and also, how would those be generated)? -- Good Luck Life Sciences Research Center Xidian University Xi'an China http://life.xidian.edu.cn liuji...@life.xidian.edu.cn liujixin2...@gmail.com ___ Freesurfer mailing list Freesurfer@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.
Re: [Freesurfer] Fwd: questions about high resolution atlas on the Freesurfer
Hi Jixin, mris_make_face_parcellation uses an icosahedral sampling, so you cannot use it with an arbitrary annotation, and the parcels in it will not correspond to the brain regions in any of the annots but rather will cut across boundaries. You could certainly use matlab for example to compile a list of all the different annotation names from the aparc.annot that are in each of the lh.ic3.annot annotations. For 4), I guess you could generate your own .tri files that are not supertesselated icosahedra as long as they are valid tesselations of the sphere, but we don't have any. If you want to convert to nifti/analyze, you probably want to first sample them into the volume (mri_label2vol). cheers Bruce On Fri, 22 Jul 2011, Jixin Liu wrote: Dear FS experts, Freesurfer could provide for every participant a standardized partition of the cortex into 66 regional areas. My aim is to use freesurfer to subdivide these regional areas into a set of small and compact regions, resulting in high resolution atlas covering the entire cortex (taken from Hagmann et al. (2008) in PLoS Biol). We tried to used the mris_divide_parcellation fsaverage rh aparc.annot 100 rh_annot_100 (However, this creates a parcellation of long strips per region, that is not a good partition for what we want.) Then, we used the "mris_make_face_parcellation lh.orig $FREESURFER_HOME/lib/bem/ic3.tri ./lh.ic3.annot". The results look nice, but I have the following questions: (1)Can i used the "mris_make_face_parcellation" based on the "aparc.annot"? (2)How can i conver the .annot file into .hdr/.img mask files? I read the introduction about "mri_label2vol", but i was still confused. If i want to convert aparc.annot files in fsaverage, what the input files are for "--temp" and "--seg"? (3)I read the "lh.ic3.annot" in Matlab (read_annotation.m). For "colortable.struct_names", the name is "ic3.tri_vertex_0"(to "ic3.tri_vertex_641"), how to know which brain regions it belong to? how to know each vertex's MNI coordinate? (4)"mris_make_face_parcellation lh.orig $FREESURFER_HOME/lib/bem/ic3.tri ./lh.ic3.annot" . I only see 7 options in: $FREESURFER_HOME/lib/bem/ic[1-7].tri (as per the program usage). Can I specify custom ic*.tri files (and also, how would those be generated)? -- Good Luck Life Sciences Research Center Xidian University Xi'an China http://life.xidian.edu.cn liuji...@life.xidian.edu.cn liujixin2...@gmail.com ___ Freesurfer mailing list Freesurfer@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.
[Freesurfer] dmri_train malloc error
Freesurfer users, I have ran into a malloc error running trac-all. Looks like the same error that Stijn posted to the list on 17 Jun 2011. I did not see a solution posted. It occurs in dmr_train using trac-all -prep –c dmrirc.txt. Also tried using trac-all –prior –c dmrirc.txt with the same results. Reset the tcsh limits for datasize, …. * Loading segmentation from /Applications/freesurfer5_1/trctrain/trc029/dlabel/mni/aparc+aseg.nii.gz Loading cortex mask from /Applications/freesurfer5_1/trctrain/trc029/dlabel/mni/cortex+2mm.nii.gz dmri_train(54615) malloc: *** mmap(size=159744) failed (error code=12) *** error: can't allocate region *** set a breakpoint in malloc_error_break to debug MRIalloc(218, 182, 182): could not allocate 158704 bytes for 26th slice Cannot allocate memory ** My system Model Name: Mac Pro Model Identifier: MacPro3,1 Processor Name: Quad-Core Intel Xeon Processor Speed: 2.8 GHz Number Of Processors: 2 Total Number Of Cores: 8 L2 Cache (per processor): 12 MB Memory: 18 GB System Version: Mac OS X 10.5.8 Thanks for any advice or suggestions! Kevin Dabbs SMPH/Neurology UW-Madison ___ Freesurfer mailing list Freesurfer@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.
