Freesurfer September 2013

freesurfer@nmr.mgh.harvard.edu

124 participants
243 discussions

Reading surface features into a vector
by Joy-Loi Chepkoech 27 Sep '13

27 Sep '13

Dear FreeSurfer experts, I am looking for a way to read a subject's cortical thickness and volume, and surface area at each vertex into a vector that is readable by matlab. How should I go about doing this? Thanks, Joy-Loi

2 1

group pcc maps for functional connectivity
by Caspar M. Schwiedrzik 27 Sep '13

27 Sep '13

Hi Freesurfer Experts, I am trying to calculate group pcc maps for resting state functional connectivity analyses. Unfortunately, the walkthrough does not cover this. I found several posts regarding this on the mailing list, but I am not sure which one is the right way to go: There is -m pcc in isxconcat-sess ( http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg30456.html) and there is also fast_glm_pcc (e.g., http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg22648.html) however, the various posts on the later functional all seem to differ in how to properly use it. This is in version 5.1. Please advise. Thanks, Caspar

2 5

Extracting SUV values from Freesurfer ROIs
by Alexander Lebedev 27 Sep '13

27 Sep '13

*Dear Freesurfers,* I apologize if this question has already been asked somewhere - I didn't manage to find the answer in the archives. I have my T1 images processed in FS_5.3 and corresponding PET images co-registered with rawavg.nii-images in SPM (converted from mgz). Now I would like to extract standardized uptake values from the Freesurfer's ROIs (aparc.a2009s+aseg.mgz) in native space. Is there a straightforward way to do this? (preferably, in one command without creating multiple labels from the parcellation) Thank you very much in advance. *=======* *Best Regards,* *Alexander Lebedev* University of Bergen, Norway

1 0

freesurfer map with low efftive size
by Knut J Bjuland 27 Sep '13

27 Sep '13

How to detect group differences between groups with low group size like for instant n=8 vs n=50? Are there any statistics measures I could use like looking at interaction between group and gender, or should I use doss? Is it feasible to design a custom based design matrix? Knut J

1 0

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. > > > > >

1 0

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

4 4

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/

1 0

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

2 1

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Freesurfer September 2013