Freesurfer June 2017

freesurfer@nmr.mgh.harvard.edu

116 participants
186 discussions

Nonlinear CVS registration into average brain for coordinates
by Zhou, David Wei 10 Jan '18

10 Jan '18

Hi all, I have a data set of 14 subjects with intracranial (both cortical and subcortical) electrode implants, already recon'ed in Freesurfer, with an average brain + surface computed of these subjects. I would like to map each subject's electrode coordinates (a set of RAS points) into the average brain using a nonlinear transformation to account for individual deviations in surface topology. I'm trying to figure out the steps that must be taken to achieve this. With my average brain as a template, it seems like I would use mri_cvs_register to produce each subject warped onto the template. After generating those warps, how does one apply the same warp to a set of coordinates, for example to find out where my electrodes end up in the template brain? Which output file in .../cvs contains the data necessary to compute the coordinates in the template? I'd appreciate any instruction, thanks! David

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How to output particular area from stats subdir
by Jing Gu 09 Jan '18

09 Jan '18

Dear FreeSurfer Developers, By using the following code, we can get volume data of different areas from stats file. asegstats2table --subjects N01 --meas volume --tablefile aseg_stats.txt How can I get information of one or two areas, such as hippocampal? thanks Best, Gina

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Re: [Freesurfer] [tracula] error running trac-all -prep
by Borsodi Florian 20 Dec '17

20 Dec '17

Hi Anastasia, Yes, i am running this on ubuntu 12.04. Sincerely, Florian >>> Anastasia Yendiki 20.08.13 17.38 Uhr >>> Hi Florian - Are you running this on an ubuntu system by any chance? a.y On Tue, 20 Aug 2013, Borsodi Florian wrote: > Hi Anastasia, > > Thank you for your help. > I changed the commas in "/dmri/bvecs" to dots and reran trac-all. But the command "xfmrot" changed the dots back to > commas. So, I changed our system language from de_AUT.UTF-8 to en_US.UTF-8 and reran trac-all. After changing the > system language everything was genereted correctly and trac-all -prep ran without any errors. > I'm so glad. > > Then, I started the next step "trac-all -bedp" and got a syntax error "/usr/local/freesurfer/bin/bedpostx_mgh: 131: > /usr/local/freesurfer/bin/bedpostx_mgh: Syntax error: "(" unexpected. " I also attached the the logfile. I was reading > about this error in the mail archive. Would I have to run "bedpostx" outside of tracula ? > > Sincerely, > Florian > > >>> Anastasia Yendiki 19.08.13 17.54 Uhr >>> > > Hi Florian - Can you please change the decimal commas to points and try > again? > > a.y > > On Mon, 19 Aug 2013, Borsodi Florian wrote: > > > Hi Anastasia, > > > > Here are the bvec and bval files you asked me about. > > > > Sincerely, > > Florian > > > > >>> Anastasia Yendiki 18.08.13 22.52 Uhr >>> > > > > Hi Florian - Can you please also attach the bvecs/bvals files from the > > dmri directory? > > > > Thanks, > > a.y > > > > On Sun, 18 Aug 2013, Borsodi Florian wrote: > > > > > Hi Anastasia, > > > > > > Thanks for your help. I renamed the directories and reran trac-all. It > > > worked for the moment. > > > However, then I got another error: "bvecs and bvals don't have the same > > > number of entries." > > > I don't know why, because they actually have the same number of entries. > > > > > > I attached the logfile so that you may see what is going on. The error > > > occours at line 1463. > > > > > > Thank you in advance for your help. > > > > > > Sincerely, > > > Florian > > > > > > > > > >>> Anastasia Yendiki 15.08.13 18.01 Uhr >>> > > > > > > Hi Florian - I see what's going on. Can you please rename the directory > > > /data/physics/florian/nii into something that doesn't include "nii", and > > > rerun? Because "nii" is a file extension, this confuses some of the > > > scripts. > > > > > > Thanks, > > > a.y > > > > > > On Thu, 15 Aug 2013, Borsodi Florian wrote: > > > > > > > Hi Anastasia > > > > > > > > I ran the command you sent me and it runs without any errors. > > > > I also attached the command line for you. > > > > > > > > Furthermore i ran data with 12 diffusion directions and i keep getting the > > > > same kind of problems. > > > > > > > > sincerely > > > > Florian > > > > > > > > >>> Anastasia Yendiki 02.08.13 19.59 Uhr > > > >>> > > > > > > > > Hi Florian - Can you please run this command directly on the command line > > > > and see if there are any errors? > > > > > > > > flip4fsl > > > > /data/physics/florian/nii/1020000485074_20080319/dmri/dwi_orig.nii.gz > > > > /data/physics/florian/nii/1020000485074_20080319/dmri/dwi_orig_flip.nii.gz > > > > > > > > Thanks, > > > > a.y > > > > > > > > On Fri, 2 Aug 2013, Borsodi Florian wrote: > > > > > > > > > Hi Anastasia > > > > > > > > > > Thank you for your answer. > > > > > > > > > > Yes, those files exist. > > > > > I also extracted the bvec an bval files with anotther software then > > > > dcm2nii > > > > > and i keep getting the same kind of error. > > > > > Also, about the 6 diffusion direction, those data i sent you, are just > > > > > testdata for running tracula. > > > > > > > > > > sincerely > > > > > Florian > > > > > > > > > > >>> Anastasia Yendiki 02.08.13 0.41 Uhr > > > >>> > > > > > > > > > > Hi Florian - Do these files exist? > > > >>/data/physics/florian/nii/1020000485074_20080319/dmri/dwi_orig.mghdti.bvec > > > s > > > > > > > > > > > > >>/data/physics/florian/nii/1020000485074_20080319/dmri/dwi_orig.mghdti.bval > > > s > > > > > > > > > > > > > > > > > > > The format of the bvecs and bvals that you sent seems fine, but (and > > > this > > > > > has nothing to do with the error you're getting) I have to warn you that > > > > > you may not be able to get good results running probabilistic > > > tractography > > > > > on this data. It looks like you're acquiring the same 6 diffusion > > > > > directions, repeated 8 times. Six directions is the absolute minimum for > > > > > reconstructing the tensor model, but will probably not be sufficient for > > > > > the crossing fiber model that bedpostx reconstructs (and is used by > > > > > tracula). Your scan time is better spent acquiring 48 different > > > > > directions, rather than the same 6 directions 8 times. > > > > > > > > > > a.y > > > > > > > > > > On Mon, 29 Jul 2013, Borsodi Florian wrote: > > > > > > > > > > > Hello, > > > > > > > > > > > > I have been trying to run tracula on my data and i keep getting the > > > same > > > > > > kind of error repeatedly. > > > > > > For my imput I am using dicoms from a Siemens scanner with a stadard > > > > > > diffusion protocol. However, tracula cannot read the bvec and bval > > > data > > > > > out > > > > > > of the dicom header. Therefore, I implemented bvec and bval files into > > > > the > > > > > > config file. > > > > > > After doing so, I got the error which says that tracula cannot find > > > the > > > > > > "dwi_orig_flip.mghdti.bvecs" and "dwi_orig_flip.mghdti.bvals" files. > > > > > > I have tried many options, but still cannot find a solution. > > > > > > I am hoping to get some troubleshooting help. > > > > > > > > > > > > I have atteched my log- and config- files, as well as my bvec and bval > > > > > > files. > > > > > > To uphold patient confidentiality, I have encode the name patient's > > > data > > > > > as > > > > > > "AAAAAA". > > > > > > > > > > > > I believe the problems are the bvec and bval files or their > > > structures. > > > > > The > > > > > > log-file lete me assume this, especially the lines 202 - 205, 264 - > > > 268 > > > > > and > > > > > > 1480 - 1484. > > > > > > > > > > > > Thank you in advance for your help, and your speedy response. > > > > > > > > > > > > With kind regards, > > > > > > > > > > > > Florian Borsodi > > > > > > Department of Neurology > > > > > > Medical University of Graz > > > > > > > > > > > > > > > > > > > > > > > > > > > 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 > > > > > > > > > > > > > > > > > > > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > >

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A note about the Freesurfer license file
by Z K 14 Dec '17

14 Dec '17

Hello All, Users on newer linux distributions who upgrade from Freesurfer version 5.3 to version 6.0 may get the following error message: -------------------------------------------------------------------------- GNU libc version: 2.17 ERROR: Systems running GNU glibc version greater than 2.15 require a newly formatted license file (it's free). Please download a new one from the following page: http://surfer.nmr.mgh.harvard.edu/registration.html -------------------------------------------------------------------------- This is a known issue, and as the message says, it is resolved by downloading a newly formatted license file from our registration page: http://surfer.nmr.mgh.harvard.edu/registration.html Simply overwrite the old license file with the newly formatted one. Sorry for any inconvenience this may have caused. -The Freesurfer team

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mri_cvs_register: how to read/import .m3z warp file
by Stefano Zappalà 06 Nov '17

06 Nov '17

Dear FreeSurfer Developers, I am trying to visualize and modify the output warp field (in .m3z) of a mri_cv_registration call aimed at aligning a T1w scan to the MNI space. I was wondering how file format .m3z is organized, in order to read it with, for example, matlab. Or if there are simpler file format to convert the warp field to. No information about it seems to be reported in the website. Moreover, I've searched the list and a similar question was not answered. I was wondering if you have some suggestions in reading the output warp field of mri_cvs_register. 1) FreeSurfer version: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c 2) Platform: ubuntu 16.04 LTS Many thanks, Stefano.

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Contrast matrix for PVR
by Sahil Bajaj 05 Sep '17

05 Sep '17

Hi everyone, >From FreeSurfer manual and discussion forum, I found that volume and LGI can be correlated using mri_glmfit command with -pvr flag. For that, my fsgd file has age, gender as covariates and the file is as following: GroupDescriptorFile 1 Class Male Class Female Variables Age Input zerek1 Male 21 Input zerek2 Male 25 etc. My concern is: To run mri_glmfit command, I am not sure how to define my contrast matrix if I am interested in removing the effect of age and sex. 1st option I tried is: 0 0.5 0.5 0 1 Here, I think first 0 regresses out age, 0.5 0.5 should be averaging over males and females and last 0 1 correlates between volume and LGI. But this looks like it is not giving me correct correlations maps, although there is no error. 2nd option I tried is: 0 0 0 0 1 This looks like its working and maps look correct to me but I want to make sure this is the correct contrast matrix and I am not sure how this matrix is regressing out age and gender or 1st option is correct contrast matrix? Thank you so much ! Best, Sahil

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Version 6.0 - ?h.white.preaparc vs. ?h.white for determining the need to edit brainmask.mgz, wm.mgz, add control points, etc.
by Mira Michelle Raman 04 Sep '17

04 Sep '17

Hi, My main question to the 6.0 experts is: Is the lh.white.preaparc close enough to the lh.white to determine whether editing is needed (brainmask.mgz, wm.mgz,control points) or do we need to run the full pipeline and get ?h.white? Here's the reasoning behind this question. In previous versions of Freesurfer we have run -autorecon1 -autorecon2, then checked surfaces, made edits if needed, and then only after we were satisfied with the surfaces we ran -autorecon3. Primarily we have done this for 2 reason, first is to save processing time, on both the initial pass and running -autorecon2-cp or -autorecon2-wm. We also use this as a quality control method, in which ONLY subjects whose surfaces have been verified, have been through -autorecon3, those that haven't, don't have stats files, and thus can't get inadvertently included with finished data. If ?h.white.preaparc doesn't topologically differ from the ?h.white could we use it for determining what edits to do? if it does differ obviously we will have to run the whole pipeline. Thank you in advance for your guidance. Sincerely, Mira _______________________________________________ Mira Michelle Raman Lead Scientific Programmer The Center for Interdisciplinary Brain Sciences Research Stanford University 401 Quarry Rd, Ste. 1356

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Freesurfer with infarct patients
by Budge, Mariana 03 Sep '17

03 Sep '17

Hi Freesurfer experts, I am running FS on a patient with a chronic right occipital lobe infarct as part of a larger study. The program does not recognize the area around the lesion as brain matter, and I am wondering how best to treat this situation. I am worried that adding Control Points will incorrectly label the region as white matter. I am attaching some pictures of slices where this is apparent. Thank you so much for your help! Best, Mariana

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Using own parcellation atlas
by Julie Hall 17 Aug '17

17 Aug '17

Hi experts, I would like to use a different atlas other than the 'default' Freesurfer atlases, namely the Gordon Parcellation (surface based parcellation of 333 ROIs of the cortex) to segment my T1 datasets. So I can go on to use these segmentations for DTI connectome analysis using MRTrix (or MatLab). I have two questions: - I have this atlas as a nifti file. Do I need to transform this atlas into a different file for it to run in freesurfer? - Can I run this step in autorecon3 (step 28)? Or should I rerun recon-all all together? If so, could you help me with what commands I need to run (mris_ca_train?)” Thank you, Julie

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Re: [Freesurfer] [Announcement] Freesurfer v6.0 beta release and testing
by Elijah Mak 03 Aug '17

03 Aug '17

Hi ZK, Thanks. It is great news! I would like to report the following. asegstats2table seems to be acting strangely. File "/Applications/freesurfer_b6/bin/asegstats2table", line 195 print 'ERROR: subjects are not specified (use --subjects SUBJECTS)' Even typing asegstats2table --help leads to the same error message. It was not found in a prev dev built or in 5.3. Thanks. Also, not sure if it's placebo, but freeview seems to be running quicker now. Best Wishes, Elijah

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Freesurfer June 2017