Freesurfer October 2015

freesurfer@nmr.mgh.harvard.edu

142 participants
214 discussions

volume DTI metrics to sruface
by Victor Montal Blancafort 20 Oct '15

20 Oct '15

FS experts, I have seen several posts regarding volume-to-surface projections, but I am not 100% confident about which parameter should I use with mri_vol2surf that better fit my needs. Currently, my data are several DTI-metric volumes per subject already normalized to MNI152 space (both 1mm and 2mm voxel sizes). My intention is to move cortex values of those volumes into the fsaverage surface space. I know that mri_vol2surf will work, but I have some doubts on how this work. 1) If no extra commands are used (i.e projfrac or projdist), what will each value of the vertex mesh represent? A specific voxel value? 2) If my intention is to project the mean value across white and pial surface, which exact command should I use? 3) There exists any specific command to move from MNI152 volume (FSL) to fsaverage surface (avoiding bbregister)? 4) Statistically, smoothing my data at the surface for further VBM analyisis(i.e moving later the surface values to volumes), will introduce any bias? Thank you in advance for your time and help! Cheers, Victor Montal

2 1

error in FSL group analysis
by Park, Jung Mi 20 Oct '15

20 Oct '15

Hello FS expert While I ran higher level analysis using FSL feat, I received an error message. Does it mean this computer needs to update the FSL program? Computer: brain-vision at martinos center FS environment 5.3 FSL 5.0.7 /usr/pubsw/packages/fsl/current/bin/fsl_sub -T 60 -l logs -N feat4_post -j 4002 /usr/pubsw/packages/fsl/current/bin/feat /autofs/cluster/catanagp/users/jumi/jmi_analyses/2ndoutput/.gfeat/cope1.feat/design.fsf -D /autofs/cluster/catanagp/users/jumi/jmi_analyses/2ndoutput/.gfeat/cope1.feat -poststats 1 while executing "fsl:exec "${FSLDIR}/bin/feat ${fsfroot}.fsf -D $FD -poststats 1" -b 60 -N feat4_post -h $ID -l logs " invoked from within "if { $done_something == 0 } { if { ! $fmri(inmelodic) } { if { $fmri(level) == 1 } { for { set session 1 } { $session <= $fmri(multiple..." (file "/usr/pubsw/packages/fsl/current/bin/feat" line 389) 1445278890582 addons.update-checker WARN Update manifest for {972ce4c6-7e08-4474-a285-3208198ce6fd} did not contain an updates property thank you. Jung Mi

2 1

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. > >

2 1

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

3 3

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

1 0

MPRAGE SNR
by John Anderson 19 Oct '15

19 Oct '15

6 13

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

3 2

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

2 1

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

4 5

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

19 Oct '15

3 2

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Freesurfer October 2015