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Mouse (rodent) Brain atlas
by Gavriel Barkay 27 Sep '13

27 Sep '13

Hi, Is there such atlas available for use with FreeSurfer? Thanks, Gabi -- Gavriel Barkay M.D. M.Sc. Psychiatrist

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Re: [Freesurfer] Tracula bval and bvec
by Anastasia Yendiki 26 Sep '13

26 Sep '13

Hi Gari - It looks from the output like something has gone wrong with the registration, either diffusion to anatomical, or individual to atlas. If you upload for me here all the directories that tracula has created so far (dmri, dmri.bedpostX, dlabel), I'll take a look. http://gate.nmr.mgh.harvard.edu/filedrop2/ Thanks, 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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mri_convert ERROR: could not determine file
by Morgan Hough 26 Sep '13

26 Sep '13

Hi there, I am trying to run reg-feat2anat and having a bit of an odd problem. It runs but doesn't produce a anat2exf.register.dat. If I look at the anat2exf.register.dat.fslregister.log file I see right at the beginning it fail with: /data/results/genDIS mri_convert ERROR: could not determine file for /data/freesurfer_recons/HierGENDIS/WaisgenDIS600/mri/ERROR: /data/results/genDIS/WaisgenDIS600/gendistask_full_search.feat/reg/freesurfer/tmp/refvol.fslregister.nii mri_convert ERROR: could not determine file for /data/freesurfer_recons/HierGENDIS/WaisgenDIS600/mri/ERROR: /data/results/genDIS/WaisgenDIS600/gendistask_full_search.feat/reg/freesurfer/tmp/refvol.fslregister.nii mri_convert: extra arguments ("not" and following) type mri_convert -u for usage This is running on a SGE cluster using Ubuntu 12.04.1, FreeSurfer 5.3 and FSL 5.0.4 which made me think it is is similar to Sal's problem recently. So I added "set fsvol = brainmask" and that seems to have fixed it. Is there a different fix I can make to solve this? Cheers, -Morgan

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No clusters found after Monte Carlo simulation
by ye tian 26 Sep '13

26 Sep '13

Dear Freesurfers, I used the following command line to find significant clusters after glm analysis (before MC clusters attached) mri_glmfit-sim \ --glmdir lh.meditation_age.glmdir \ --sim mc-z 5 4 mc-z.negative \ --sim-sign neg --cwpvalthresh 0.05\ --overwrite I didn't find any, i.e., there are no clusters listed in file mc-z.negative.sig.cluster.summary. Does this mean that I should accept the null hypothesis for the whole cortex? Also, how many iterations of mc do people typically perform? I guess it doesn't make a difference if I do 1000 iterations instead of 5 anyways. Thank you very much! Sincerely, Ye

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Re: [Freesurfer] talaiarch labels to fsaverage
by Douglas N Greve 26 Sep '13

26 Sep '13

I did a quick test using the gray matter volume. I registered that to fsaverage using a 9dof transform fslregister --mov Tissue_Gray_Matter.nii --s fsaverage --reg reg.dof9.Tissue_Gray_Matter.dat --dof 9 The results are not terrible (good by talairach standards), so you could use this. Then just mri_label2vol --seg labelX.nii --reg reg.dof9.Tissue_Gray_Matter.dat --invertmtx --template $SUBJECTS_DIR/fsaverage/mri/orig.mgz --o $SUBJECTS_DIR/fsaverage/mri/labelX.mgz Note that it will be hopeless to try to put these on the surface. doug On 09/26/2013 05:55 PM, Maryam Vaziri Pashkam wrote: > I am not sure. In the online tool it is possible to load the labels on > a volume. > > http://www.talairach.org/applet/ > > There is nothing on their website but I have been in contact with > someone who might know. I just emailed them to ask. > > Actually what I want is labels for brodmann areas 20, 38, 46 and 9. Is > there any way to get those for freesurfer? > > Maryam > > > > > On Thu, Sep 26, 2013 at 5:45 PM, Douglas N Greve > <greve(a)nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> wrote: > > Hi Maryam, it is not easy to do. Do they also supply an anatomical > volume that you can view the labels on? > doug > > > > On 09/26/2013 05:40 PM, Maryam Vaziri Pashkam wrote: > > Hi Doug, > > I have a bunch of label files donlowded from talairach Daemon > website that I would like to upload to freesurfer and I am > having trouble with it: http://www.talairach.org/nii/gzip/ > > I could read the files to matlab using MRI_read and they are > volume masks of zeros and ones with the size: 172x141x110 > Now I would like to import these into freesurfer and visualize > them on the fsaverage suface or volume. The volume size in the > mri folder of fsaverage is 256*256*256 and even though there > is a transform function I am not sure how to match two volumes > with very different sizes. > Is this even possible? > > Thanks, > Maryam > > > -- > 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/ > > > > 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. > > -- 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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talaiarch labels to fsaverage
by Maryam Vaziri Pashkam 26 Sep '13

26 Sep '13

Hi Doug, I have a bunch of label files donlowded from talairach Daemon website that I would like to upload to freesurfer and I am having trouble with it: http://www.talairach.org/nii/gzip/ I could read the files to matlab using MRI_read and they are volume masks of zeros and ones with the size: 172x141x110 Now I would like to import these into freesurfer and visualize them on the fsaverage suface or volume. The volume size in the mri folder of fsaverage is 256*256*256 and even though there is a transform function I am not sure how to match two volumes with very different sizes. Is this even possible? Thanks, Maryam

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Fwd: Brainhack 2013 Stipend Program (DEADLINE TO APPLY: 11:59PM EST SEPTEMBER 27, 2013)
by MCLAREN, Donald 26 Sep '13

26 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) To apply, please send the above details to Donald McLaren ( mclaren.donald(a)gmail.com) This change is being made due to technical difficulties of the website. I will email everyone on Saturday morning to confirm that their application is being considered. If you do not receive and email on Saturday morning, please resend your application. 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. Good luck. Best Regards, Donald McLaren ================= D.G. McLaren, Ph.D. Research Fellow, Department of Neurology, Massachusetts General Hospital and Harvard Medical School Postdoctoral Research Fellow, GRECC, Bedford VA Website: http://www.martinos.org/~mclaren Office: (773) 406-2464 ===================== This e-mail contains CONFIDENTIAL INFORMATION which may contain PROTECTED HEALTHCARE INFORMATION and may also be LEGALLY PRIVILEGED and which is intended only for the use of the individual or entity named above. If the reader of the e-mail is not the intended recipient or the employee or agent responsible for delivering it to the intended recipient, you are hereby notified that you are in possession of confidential and privileged information. Any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited and may be unlawful. If you have received this e-mail unintentionally, please immediately notify the sender via telephone at (773) 406-2464 or email.

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Re: [Freesurfer] Surface to nifti prime vertices
by Douglas N Greve 26 Sep '13

26 Sep '13

I would actually put the data straight onto fsaverage, smooth there, and do the FSL analysis there. You will need to put it on fsaverage eventually for group analysis, and you're better off doing that before doing the FEAT analysis. Remember to turn off temporal pre-whitening when running FEAT. For nifti1, there is no solution to the prime number of vertices problem. The problem is fixed in nifti2, so, assuming that FSL is reading nifti2, you could write a mgh to nifti2 converter. But I would do it on fsaverage anyway doug On 09/26/2013 01:53 PM, Connor Lane wrote: > Hmm, that's unfortunate. > > The reason I'm interested in this surface to nifti conversion is that I'm trying to incorporate surface based pre-stats smoothing into my FSL fMRI analysis stream. My strategy has been: preprocess with FSL --> map to surface space and smooth --> convert mgh surface to nifti surface and continue with FSL analysis. > > Do you think the surface smoothing benefits of this kind of stream justify the trouble associated with either a) modifying the data as you suggest every time this factoring issue shows up, or b) writing an mgh <-> nifti utility that avoids the issue? > > Some other possible answers I've thought of are: > -After surface smoothing, map the functional data to fsaverage and then convert back to nifti (since we know there's no factoring problem with fsaverage). The drawback here is we never get to see statistics in subject-specific space. > -Switch from FSL to FsFast, where surface smoothing is built in. > > Or maybe I should forget about surface based smoothing altogether, and actually volumetric smoothing works just fine? > > I would really appreciate hearing your overall recommendation on this. > > Connor > > > > -- 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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Demean Covariates Qdec
by Erik Lindberg 26 Sep '13

26 Sep '13

Dear Doug and Freesurfers, I noticed that the DOSS option no longer exists in qdec and that Doug said there was a bug related to it. If i want to assess the differences in cortical thickness between groups while covariating for age and gender, since i don't expect any interactions, can i just demean the covariates and make my analysis in qdec with dods? Thanks!

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Re: [Freesurfer] [FreeSurfer] multiple sets of control points
by Bruce Fischl 26 Sep '13

26 Sep '13

Hi Francesco please cc the list so that others can answer! This isn't the way recon-all works, but I think you can achieve what you want by copying the control.dat to control.1.dat or some such before you add additional control points so you can always go back to a previous version cheers Bruce On Thu, 26 Sep 2013, Francesco Siciliano wrote: > Hi Bruce, > > When I edit a brain a second and third time, it is helpful to create new control point files while maintaining the old ones. Because edits are not an exact science, I've noticed that sometimes new problems arise after a first edit. In my experience, creating a new control.dat file and overwriting the old one will undo the edits of the original set of control points (hence why it is useful to have multiple sets such that the original set remains in place and the second set can adjust new errors that have arisen). I understand what you mean - I try to place all of the control points I need in one sweep - however I cannot anticipate with certainty the combined effect of my edits, thus some situations call for multiple sets of control points on subsequent edits. Is it not possible to have multiple sets of control points recognized during a recon-all? > > Thanks, > Francesco > ________________________________________ > From: Bruce Fischl [fischl(a)nmr.mgh.harvard.edu] > Sent: Thursday, September 26, 2013 12:06 PM > To: Francesco Siciliano > Cc: freesurfer(a)nmr.mgh.harvard.edu; Louis Nicholas Vinke > Subject: Re: [Freesurfer] [FreeSurfer] multiple sets of control points > > Hi Francesco > > recon-all assumes that all the control points are in the single file > <subject>/tmp/control.dat. Why are you separating them? Can you combine > them? > > cheers > Bruce > On Thu, 26 Sep 2013, Francesco Siciliano wrote: > >> Hello, >> I am currently having an issue getting my recon's to recognize multiple sets >> of control points. When I create a control point set, I make sure I select >> "control points", place them on the brainmask, and save them in the "tmp" >> folder as control.dat, control2.dat, control3.dat, etc. >> >> I have been using the command recon-all -autorecon2 -autorecon3 -s Subject1 >> >> There does not seem to be a problem when I just have one set of control >> points. However, when I have multiple sets, I can see where control points >> have not been taken into account and have not altered the intensity of the >> voxels at all. I currently have them re-running with the command recon-all >> -autorecon2-cp -autorecon3 -s Subject1 to see if that makes a difference. >> >> However, as I said before, one set of control points was previousy effective >> simply using the command recon-all -autorecon2 -autorecon3 -s Subject1 >> >> Any ideas? >> >> Thanks, >> Francesco >> >> >> >> Francesco Siciliano, B.A. Research Assistant >> Department of Child and Adolescent Psychiatry >> The New York State Psychiatric Institute >> Columbia University >> 1051 Riverside Drive, Unit 74 >> New York, NY 10032 >> (212) 543-6155 >> >> > > > 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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