Freesurfer September 2013

freesurfer@nmr.mgh.harvard.edu

124 participants
243 discussions

Fwd: Brainhack 2013 Stipend Program (DEADLINE TO APPLY: 11:59PM EST TONIGHT)
by MCLAREN, Donald 27 Sep '13

27 Sep '13

Dear Colleagues, The Neurobureau is excited to announce a stipend program for Brainhack 2013. The stipend program was created following a generous grant from Siemens Healthcare to assist young investigators in attending Brainhack 2013. Without their support, the stipend program would not exist. The stipend program will provide at least 6 stipends for partial or full registration fees [if 24 attendees apply, you have a 25% chance of getting a stipend]. The exact breakdown of stipends provided will depend on the number of applicants and the cost of attending the conference for those applicants. The application for stipend requires: (1) A poster abstract (2) A 1-2 page Brainhack project proposal (pdf format) (3) NIH Biosketch/CV (pdf format) The Brainhack 2013 Organizing Committee will decide which applications will receive stipends based on their abstract and proposed brainhack projects. The deadline to apply for one of the stipends is 11:59PM EST on September 27th. All decisions will be made by October 3rd and must be accepted within 24 hours of being awarded. To submit the application. Please email the 3 documents above to Donald McLaren (mclaren.donald(a)gmail.com) by 11:59 PM EST tonight. Good luck.

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Brainhack Registration and Payment
by MCLAREN, Donald 27 Sep '13

27 Sep '13

Brainhack.org is currently offline due to technical issues. We hope to have the website back up and running shortly. Here are the details to register (if you have not already) and to complete the payment process (if you pre-registered). The cost for the entire workshop and lodging for 4 nights is 450 Euros. The cost for the conference alone is about 200 Euros. * First step* : Here is the website : http://dr01.azur-colloque.cnrs.fr.<http://dr01.azur-colloque.cnrs.fr> - Choose your language - Choose our “event” : Brain Hack 2013 - Click on “Pre-registration” - Fill the form (as you have already done for the Brainhack.org website). The standard “Tarification” you must check is “Researcher”. *Second step* : - After this “Pre-registration” (*and our validation*), you will receive an email “Confirm a pre-registration”. This message will invite you to payon-line. Please follow the link you will receive. - Several pages need to be validated : - 1st page – “Please enter your information” : to get logged, please enter the information previously used. - 2nd page – “Personal information” : fill the form - 3rd page – “Organization (origin)” : just click on “next step” - 4th page – “Payment” : If your university or other institution will paythe fee for you, please check the second option “Someone else...” and fill the form. - 5th page – “Invoice” : just validate. - 6th page – “Invoice details”. Two options: Credit Card: simple, fast and best payment option. Transfer: Please do not take into account the message in red “only from French public organizations” – you do have the right to use this option, even if you're living in a foreign country. Moreover, once the paymenttransfered, you will receive a confirmation only several days after – do not panic, this is only a delay due to this option. I apologise for the lateness but our website is down. Please, let me know if you have problem or questions. Sincerely yours, Marlène Etienne Please let Donald McLaren know if you have any questions. He can be reached via email: mclaren.donald(a)gmail.com

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Fwd: Question about talairach.m3z file
by Paul Beach 27 Sep '13

27 Sep '13

---------- Forwarded message ---------- From: Paul Beach <pabeach1(a)gmail.com> Date: Fri, Sep 27, 2013 at 2:39 PM Subject: Re: [Freesurfer] Question about talairach.m3z file To: Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> So would you suggest, then, that it would be better to use the mri_vol2vol command to transform subject data (anatomical and functional) to MNI space? On Fri, Sep 27, 2013 at 9:36 AM, Bruce Fischl <fischl(a)nmr.mgh.harvard.edu>wrote: > Hi Paul > > not really. It is a nonlinear transform to our own atlas, which is loosely > in MNI space. Doug can probably give you a more precise answer > > cheers > Bruce > > On Fri, 27 Sep 2013, Paul Beach wrote: > > Hello Freesurfer community, >> I have a question about the file talairach.m3z, which is found in the >> mri/transforms directory of all subjects that have undergone recon-all. I >> am >> utilizing this file in an mri_convert script to resample AFNI processed >> T1volumes (and time-series data) to MNI space. However, I wanted to >> confirm >> which MNI talairach.m3z represents - it's MNI305, correct? >> >> >> Thanks! >> Paul >> -- >> Paul Beach >> DO/PhD candidate - Year VI >> Michigan State University >> - College of Osteopathic Medicine >> - Neuroscience Program - Bozoki Lab: Neurology/Radiology >> >> >> > > 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<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. > -- Paul Beach DO/PhD candidate - Year VI Michigan State University - College of Osteopathic Medicine - Neuroscience Program - Bozoki Lab: Neurology/Radiology -- Paul Beach DO/PhD candidate - Year VI Michigan State University - College of Osteopathic Medicine - Neuroscience Program - Bozoki Lab: Neurology/Radiology

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R: Re: R: Re: R: Re: Import FS data to FSL
by stdp82＠virgilio.it 27 Sep '13

27 Sep '13

Anastasia thank you very much! I have wrote to FSL mail list. They have uploaded a new web page of FDT. Anyway, these are the commands: mris_convert lh.white lh.white.giiecho lh.BA44.label lh.BA45.label > listOfAreas.txt label2surf -s lh.white.gii -o lh.BA44.gii -l listOfAreas.txtStefano ----Messaggio originale---- Da: ayendiki(a)nmr.mgh.harvard.edu Data: 27-set-2013 16.44 A: <stdp82(a)virgilio.it> Cc: <freesurfer(a)nmr.mgh.harvard.edu> Ogg: Re: [Freesurfer] R: Re: R: Re: Import FS data to FSL label2surf is an FSL command, so you can get a more authoritative answer on the FSL list, but I'd try one of the files in the surf/ directory, like lh.white or rh.white. On Fri, 27 Sep 2013, stdp82(a)virgilio.it wrote: > Hi list and Anastasia. > > Thank you very much. mri_annotatiion2label works fine. > > Becouse I should run this command: > > label2surf -s <surface> -o <outputsurface> -l <labels> > > -s,--surf input surface > -o,--out output surface > -l,--labels ascii list of label files > > I should provide also surface file relatively to each .label previously > created with mri_annotatiion2label. > > How can I do? > > Thanks, > > > Stefano > > > ----Messaggio originale---- > Da: ayendiki(a)nmr.mgh.harvard.edu > Data: 26-set-2013 0.57 > A: <stdp82(a)virgilio.it> > Cc: <freesurfer(a)nmr.mgh.harvard.edu> > Ogg: Re: R: Re: [Freesurfer] Import FS data to FSL > > > Try mri_annotation2label. > > On Wed, 25 Sep 2013, stdp82(a)virgilio.it wrote: > > > For FSL guide: > > > > I should transforms a group of labels into a surface > > > > Usage: > > > > label2surf -s <surface> -o <outputsurface> -l <labels> > > > > Compulsory arguments (You MUST set one or more of): > > > > -s,--surf input surface > > > > -o,--out output surface > > > > -l,--labels ascii list of label files > > > > Optional arguments (You may optionally specify one or more of): > > > > -v,--verbose switch on diagnostic messages > > > > -h,--help display this message > > > > > > but I should create a lh/rh.frontal.label and use it for label2surf. > > > > With mdi_binarize I can create .nii.gz but no .label. Is that correct? > > > > How I can do it? > > > > > > Thanks, > > > > > > Stefano > > > > > > > > > > ----Messaggio originale---- > > Da: ayendiki(a)nmr.mgh.harvard.edu > > Data: 25-set-2013 17.49 > > A: <stdp82(a)virgilio.it> > > Cc: <freesurfer(a)nmr.mgh.harvard.edu> > > Ogg: Re: [Freesurfer] Import FS data to FSL > > > > > > 1 - Yes. > > 2 - You can use mri_aparc2aseg to grow the cortical labels into the white > > matter (say, by 2mm). The file that it will produce will be a volume file, > > so then you just run mri_binarize to extract specific labels. Make sure > > you save them in nifti format for FSL. > > > > On Wed, 25 Sep 2013, stdp82(a)virgilio.it wrote: > > > > > Hi list, > > > > > > I have 2 questions, please. > > > > > > 1-The bedpostX that I have run for TRACULA could be used for PROBTRACKX > > > (FSL)? > > > > > > 2-I'd like to export cortical masks from FS to FSL. > > > > > > An option is mri_binarize but this way failed in probtrackx (fsl). > > > FSL list have advised me that I should use label2surf command to convert > > > label to surface files. > > > > > > Where could find the .label (according to FreeSurferColorLUT.txt) to > build > > > mask of frontal, parietal, motor, sensor, temporal and occipital lobes? > > > > > > Do you have other ways that you advise me? > > > > > > > > > Thanks, > > > > > > > > > Stefano > > > > > > > > > > > > > > > > > > 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 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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Red Hat 6 and Freesurfer for CentOS4/CentOS6: different results?
by Garikoitz Lerma-Usabiaga 27 Sep '13

27 Sep '13

Hi, I have two identical Red Hat 6 boxes, to run recon-all-s. I just realized that in one of those I had freesurfer 5.3 for CentOS4 and in the other one I had freesurfer 5.3 for CentOS6. I have one experiment were subjects used boxes indistinctly. According to how the software is built, should I expect different results among them? Many thanks for your help, Gari

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Re: [Freesurfer] Tracula bval and bvec
by Anastasia Yendiki 27 Sep '13

27 Sep '13

Hi Gari - Just looked at your subject. The bottom of the brain is truncated in the DWIs. The slices stop in the middle of the angular bundle, which is why the -prior step failed in that pathway. But I expect there'd be problems with other tracts that reach that inferior, even if they didn't fail completely - corticospinal, uncinate, inferior longitudinal fasciculus. a.y On Thu, 26 Sep 2013, Garikoitz Lerma-Usabiaga wrote: > Hi Anastasia, > I was testing just with one subject and it finished the -prep part with > error. > Please find attached the trac-all.log file. > As this is a test user you will see some other invocations of trac-all. The > last build_stamp starts at row 54.500 aprox. > (just in case: I started new from de DICOMS and the dcm2nii, and I am using > the resulting .nii, .bvec and .bval, just in case I attached the dmrirc > too). > > Thanks again for your help! > Gari > > > On Thu, Sep 26, 2013 at 8:01 AM, Anastasia Yendiki > <ayendiki(a)nmr.mgh.harvard.edu> wrote: > > Hi Gari - Yes, that's your best option right now. Sorry for the > inconvenience. I'll make sure to add the option to have one > gradient file per subject in the next version. > > a.y > > On Thu, 26 Sep 2013, Garikoitz Lerma-Usabiaga wrote: > > Hi! Thanks for the fast answer. If I do: diff > id1.bvec id2.bvec > I can see some clear differences. > > I was told that in FSL I should use the bvecs and > bvals created in dcm2nii > per subject, so I understand I should do the same > now? > Do you think an option would be to script the > creation of a dmrirc file per > each subject and then launch as many trac-alls as > subjects? > > Thanks again, > Gari > > On Thursday, September 26, 2013, Anastasia Yendiki > wrote: > > Hi Gari - Sorry, right now the assumption is > that the gradient > vectors are the same for all subjects. How > different are they? > > a.y > > On Wed, 25 Sep 2013, Garikoitz Lerma-Usabiaga > wrote: > > Hi Anastasia,I am setting up the dmrirc > file to run > Tracula. I am using > Siemens Dicoms, so I did not specify any > setting for > bval and bvec, but when > trac-all -prep starts running it gives > the following > error: mv: cannot stat > > 'paths.../SubjectID/dmri/dwi_orig_flip.mghdti.bvecs': > No such file or > directory > > Ok, so I understand that our problem is > that we > don't have MGH Siemens > Dicom. > > So I used dcm2nii to convert it to .nii > files and > each conversion gives me a > SubjectID.bval and SubjectID.bvec. Every > .bval is > the same file, but every > .bvec file is a different one. > > I can edit "set dcm_list = " to include > all the > newly created .nii files, > but > > My question is: > - How can I specify every .bvec value > for every > subject? In the dmrirc file > everything I see is a "set bvecfile = " > option. > > Thank you very much, > Gari > > > > > 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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R: Re: R: Re: Import FS data to FSL
by stdp82＠virgilio.it 27 Sep '13

27 Sep '13

Hi list and Anastasia. Thank you very much. mri_annotatiion2label works fine. Becouse I should run this command: label2surf -s <surface> -o <outputsurface> -l <labels> -s,--surf input surface -o,--out output surface -l,--labels ascii list of label files I should provide also surface file relatively to each .label previously created with mri_annotatiion2label. How can I do? Thanks, Stefano ----Messaggio originale---- Da: ayendiki(a)nmr.mgh.harvard.edu Data: 26-set-2013 0.57 A: <stdp82(a)virgilio.it> Cc: <freesurfer(a)nmr.mgh.harvard.edu> Ogg: Re: R: Re: [Freesurfer] Import FS data to FSL Try mri_annotation2label. On Wed, 25 Sep 2013, stdp82(a)virgilio.it wrote: > For FSL guide: > > I should transforms a group of labels into a surface > > Usage: > > label2surf -s <surface> -o <outputsurface> -l <labels> > > Compulsory arguments (You MUST set one or more of): > > -s,--surf input surface > > -o,--out output surface > > -l,--labels ascii list of label files > > Optional arguments (You may optionally specify one or more of): > > -v,--verbose switch on diagnostic messages > > -h,--help display this message > > > but I should create a lh/rh.frontal.label and use it for label2surf. > > With mdi_binarize I can create .nii.gz but no .label. Is that correct? > > How I can do it? > > > Thanks, > > > Stefano > > > > > ----Messaggio originale---- > Da: ayendiki(a)nmr.mgh.harvard.edu > Data: 25-set-2013 17.49 > A: <stdp82(a)virgilio.it> > Cc: <freesurfer(a)nmr.mgh.harvard.edu> > Ogg: Re: [Freesurfer] Import FS data to FSL > > > 1 - Yes. > 2 - You can use mri_aparc2aseg to grow the cortical labels into the white > matter (say, by 2mm). The file that it will produce will be a volume file, > so then you just run mri_binarize to extract specific labels. Make sure > you save them in nifti format for FSL. > > On Wed, 25 Sep 2013, stdp82(a)virgilio.it wrote: > > > Hi list, > > > > I have 2 questions, please. > > > > 1-The bedpostX that I have run for TRACULA could be used for PROBTRACKX > > (FSL)? > > > > 2-I'd like to export cortical masks from FS to FSL. > > > > An option is mri_binarize but this way failed in probtrackx (fsl). > > FSL list have advised me that I should use label2surf command to convert > > label to surface files. > > > > Where could find the .label (according to FreeSurferColorLUT.txt) to build > > mask of frontal, parietal, motor, sensor, temporal and occipital lobes? > > > > Do you have other ways that you advise me? > > > > > > Thanks, > > > > > > Stefano > > > > > > > > > > > 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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Conversion question
by pfotiad＠nmr.mgh.harvard.edu 27 Sep '13

27 Sep '13

Hi FS Community, I was wondering whether there is a way to convert a FLOAT type niftii file to an INT type niftii file. Thanks in advance! Best, Panos

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Question about talairach.m3z file
by Paul Beach 27 Sep '13

27 Sep '13

Hello Freesurfer community, I have a question about the file talairach.m3z, which is found in the mri/transforms directory of all subjects that have undergone recon-all. I am utilizing this file in an mri_convert script to resample AFNI processed T1volumes (and time-series data) to MNI space. However, I wanted to confirm *which* MNI talairach.m3z represents - it's MNI305, correct? Thanks! Paul -- Paul Beach DO/PhD candidate - Year VI Michigan State University - College of Osteopathic Medicine - Neuroscience Program - Bozoki Lab: Neurology/Radiology

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mri_volcluster question
by pfotiad＠nmr.mgh.harvard.edu 27 Sep '13

27 Sep '13

Hi FS Community, I am using the mri_volcluster command but for some reason the --sumfile shows up as an unknown flag. Is there another way to get a summary text file? (I am using FS 5.3 stable.) Thank you for your time! Best, Panos

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Freesurfer September 2013