Freesurfer

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30099 discussions

R: Re: R: import FS-FAST results in FSL
by stdp82＠virgilio.it 20 Oct '15

20 Oct '15

I'd like to open with FSLview the sig.nii.gz which is produced by selxavg3-sess. If I use mri_surf2vol, which is the template to added in --template? It should be in Tailairach space? Where can I find the template that I should added? Thanks, Stefano subj/rest/fc.seed.surf.lh/L_seed/sig.nii.gz data_type FLOAT32 dim1 27307 dim2 1 dim3 6 dim4 1 datatype 16 pixdim1 1.000000 pixdim2 1.000000 pixdim3 1.000000 pixdim4 1100.000000 cal_max 49.1815 cal_min -12.3855 file_type NIFTI-1+ Thanks, Stefano >----Messaggio originale---- >Da: greve(a)nmr.mgh.harvard.edu >Data: 29-set-2015 22.09 >A: <freesurfer(a)nmr.mgh.harvard.edu> >Ogg: Re: [Freesurfer] R: import FS-FAST results in FSL > >Do you mean surface-based analysis? You'd have to put them back into the >volume using mri_surf2vol, write them out as nifti and then run fslview >on them > >On 09/29/2015 11:17 AM, stdp82(a)virgilio.it wrote: >> >> Hi list, >> >> I would like to import FS-FAST results (conjunction maps) in FSL, >> opening them by fslview. >> Could you provide me any suggestion? >> >> Thank you very much >> Best regards, >> >> >> Stefano >> >> >> >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer(a)nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > >-- >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/ > >_______________________________________________ >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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converting surfaces into volumes or integrating them into volumes
by Boris Shabash 19 Oct '15

19 Oct '15

Hello FreeSurfer group How are you? I have currently started working with FS and would like to visualize some of the volume results. I have no issue visualizing the .mgz volumes produced since I can use mri_convert to convert them to .nii format and then visualize them using my software. However, I'd like to know if there is a way to convert the resulting surface labels (e.g. my_output/surf/rh.white or my_output/surf/rh.pial) into .nii files that I can also visualize or combine them with a resulting .mgz file into a single .nii file that contains the information for both volumes and the surfaces. Ideally I'd like to know if there is a way to combine them into a single file via the terminal. Please let me know if FS comes with a tool the allows for this process or if you know of any external tool. Sincerely, Boris

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patching 5.1
by Aaron Tanenbaum 19 Oct '15

19 Oct '15

Hello All Several years ago Freesurfer 5.1 was patched to resolve some issues. I just remember the patch resolved issues plaguing 5.1 and earlier. how does one get the patch version. no where on the FTP server i can see patched versions and instruction on performing a patch. Aaron Tanenbaum

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MPRAGE SNR
by John Anderson 19 Oct '15

19 Oct '15

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Viewing vitamin E capsules?
by Hutton, Seth 19 Oct '15

19 Oct '15

Dear users, I have been using FreeSurfer for a while now, but am working in a new lab and their goals fall outside of my realm of experience. We are using both MRI imaging as well as FNIRs. We have multiple vitamin E capsules placed during both and would like to be able to view them in FreeSurfer so that we can better estimate the projected cortical localization of these capsules. Using the generic recon-all -s -i -all we are unable to see our capsules, as they are most likely eliminated during the skull strip step. I see that I can change the threshold with "-wsmore", but am wondering if this is really the best way to accomplish what we are trying to do. Is there any way to include our capsules without excluding the skull strip? If not could how would you recommend adjusting the threshold. I tried excluding the skulls trip step with recon-all -s -i -autorecon1 -noskullstrip but then when I tried to view it using free view it was unable to open due to the lack of the brain mask.mgz. Thank you so much for your time and consideration, Seth H ********************************************************** Electronic Mail is not secure, may not be read every day, and should not be used for urgent or sensitive issues

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BuildYourOwnMonteCarlo
by Joost Janssen 19 Oct '15

19 Oct '15

Hi, A question about building your own Monte Carlo. here: https://surfer.nmr.mgh.harvard.edu/fswiki/BuildYourOwnMonteCarlo it says: "If you want to restrict the correction to a smaller area to reduce the severity of the correction, you can specify a mask or a label and change the output folder". Thus, if i have 2 anatomically distant (e.g. 1 frontal and 1 occipital) but identically-sized (same # of vertices) cortical areas, only 1 MC for 1 area needs to be created and can then be used with both areas? That is, only the size of the area matters, not the location. Is that correct? Thanks, -joost

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Volumes differ in acquisition paramaters
by Kasper Jessen 19 Oct '15

19 Oct '15

Dear Freesurfer group, When looking through the log after running recon-all, i have noticed two different errors in the logs. The one being about 'volumes differ in acquisition parameters' and the other 'Image geometries differ across time, maybe due to aquisition changes?'. *Volumes differ in acquisition parametersv1acq fa=0.000000 tr=10.032000 te=0.000000 ti=0.000000v2acq fa=0.000000 tr=10.012000 te=0.000000 ti=0.000000WARNING: Image geometries differ across time, maybe due to aquisition changes?This can potentially bias a longitudinal study! Will continue in 10s.* What do the above errors mean and is it something we should be worried about? Best regards, Kasper Jessen MD, PhD Student

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recon-all stripped brains
by John Anderson 19 Oct '15

19 Oct '15

3 2

Re: [Freesurfer] recon-all pipeline for (sub-millimeter) 7T data
by Kendrick Kay 17 Oct '15

17 Oct '15

> Message: 1 > Date: Sat, 17 Oct 2015 11:09:08 -0400 (EDT) > From: Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> > Subject: Re: [Freesurfer] recon-all pipeline for (sub-millimeter) 7T > data > To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> > Message-ID: > <alpine.LRH.2.20.1510171108090.29644(a)gate.nmr.mgh.harvard.edu> > Content-Type: text/plain; charset="windows-1252" > > High resolution fMRI has always been supported. V6 beta has better support > for high-resolution structurals. If your fMRI is higher than 1mm isotropic > then having higher res structurals (and hence denser cortical meshes) might > be useful Is there a way to obtain denser cortical meshes using the standard FreeSurfer 5.3.0 reconstruction pipeline with 1mm anatomical data? I looked for a flag, but didn't find one.. -- Kendrick Kay, PhD Assistant Professor Center for Magnetic Resonance Research University of Minnesota, Twin Cities Web: http://cvnlab.net <http://cvnlab.net/> E-mail: kay(a)umn.edu <mailto:kay@umn.edu> Cell: 510-206-1059 Skype: kendrickkay

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Re: [Freesurfer] mri_convert with --like and -rt options
by Seung-Goo KIM 16 Oct '15

16 Oct '15

Hi Bruce, Thank you for response. This is the output message: > $ mri_convert -rt nearest --like template.nii.gz label.nii.gz label_nn.nii.gz > mri_convert -rt nearest --like template.nii.gz label.nii.gz label_nn.nii.gz > $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ > reading from label.nii.gz... > TR=1000.00, TE=0.00, TI=0.00, flip angle=0.00 > i_ras = (-1, 0, 0) > j_ras = (0, 1, 0) > k_ras = (0, 0, 1) > INFO: transform src into the like-volume: template.nii.gz > writing to label_nn.nii.gz... It doesn’t print out interpolation method for reslicing, which I see when running mri_convert without “—like” switch. And the output (label_nn.nii.gz) has mixed labels due to linear interpolation. Just in case, please find the attached for the header information of the two image files. Best, -SG > Hi Seung-Goo > > I would have that that your command line would work as is. Can you send us the full screen output? > cheers > Bruce > On Fri, 16 Oct 2015, Seung-Goo KIM wrote: > >> Dear all, >> I wish to know whether mri_convert provide a nifty way to reslice and crop a NIFTI >> image with labels (positive integers) with “—like” and “-rt” options. It seems like >> “—like” option overrides “-rt” option, thus the result from such a command: >> >> mri_convert -rt nearest —like ${referenceImage} ${inputImage} >> ${outputImage} >> is resampled with trilinear interpolation. I don’t know if I did something wrong >> (maybe file format?) or this is a bug in mri_convert. >> Of course, one can write a script that creates binary images for each label values, >> transforms it (using "mri_convert —like"), threshold it (like value>0.1), and finally >> finds the label with the highest value (probability) for each voxel in the reference >> space. But I believe there should be a simpler and faster way to do this with >> mri_convert or any other program in freesurfer :) >> FIY, the version of freesurfer package I use is >> "Linux-centos6_x86_64-stable-pub-v5.3.0”. >> Best regards, >> -- >> Seung-Goo KIM -- Seung-Goo KIM

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