Freesurfer

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19 participants
30088 discussions

project locations from template to individual MRIs
by peng 17 Mar '14

17 Mar '14

Dear freesurfers, I have a set of dot locations (300~400) in a template brain, indicated by indices of a 3-D array of the template MRI data, which can be easily transformed to RAS coordinates. I wish to project these dot locations to individual MRIs, ideally also as indicated by indices in the 3-D array of the individual MRI data. Is it possible to do it in freesurfer? I guess the surface-based procedure shall work well for this. It might be a very junior question, if it was documented somewhere before, please let me know the link. Thank you very much for help. best Peng

2 5

SNR on DTI data
by Yuko Yotsumoto 17 Mar '14

17 Mar '14

Hello Freesurfers, I have DTI data for two groups of subjects, and were asked SNR for each group. I did ROI analysis on FA values, therefore, I do not have the averaged DTI data. I am wondering if there is any way to compute SNR from dt_recon output. It doesn't have to be the ROI specific SNR values, I just need SNR for the whole DTI data for each group. Any suggestions will be appreciated! Yuko Yotsumoto --- ------------------------------------------------------------- Yuko Yotsumoto, Ph. D. Associate Professor The University of Tokyo, Department of Life Sciences Bldg #2, 3-8-1 Komaba, Meguro-ku, Tokyo 153-8902 Japan phone : (+81)-3-5454-4332 E-mail: cyuko(a)mail.ecc.u-tokyo.ac.jp

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fMRI contrasts in Freesurfer
by Francesco Puccettone 17 Mar '14

17 Mar '14

Dear Freesurfer community: I have some (perhaps silly, but I think fundamental) questions about contrasts in functional analyses: 1. When wanting to see what regions are activated by exposure to a certain stimulus (blocked-design), what is the exact stats that is happening voxel-wise: (i) correlation between the time series of the HRF-convoluted BOLD and that of the behavioural stimulus that was used, or (ii) t-test between the BOLD signal during the stimulus and the BOLD signal during a resting baseline If ii) is the answer, then is "baseline" taken as an average of all non-stimulus (rest) periods in the scan, i.e. the "zero" periods in the block-design boxcar diagram? 2. When wanting, on the other hand, to see what regions are active in condition A but not in condition B (so a comparison this time), is it the case that i) is no longer a choice and a t-test always has to be used between condition A and condition B? If so, is the stimulus-vs-baseline situation from the previous question just a special case of this, where condition B = (passive) baseline? 3. Is it the case that a contrast probing the difference between two groups is using independent samples t-tests, whereas one probing the within-subject difference between two time-points is using paired-samples t-tests? Thank you for your help :-) --Francesco

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Fw: Re: convert sig.mgh into *.nii
by charujing123 17 Mar '14

17 Mar '14

Hi doug and other FS experts, Thanks doug. I have 2 new questions: 1,What you told me is generate a hemisphere. So there is only one hemisphere I can see in the AFNI? 2,After typing this code: "mri_surf2vol --surfval rh.36sb.10.mgh --hemi rh --fillribbon --subject fsaverage --template /mnt/sdb1/psylab16/BACKUP/freesurfer/freesurfer/subjects/fsaverage/mri/orig --o test.nii." the command window echo this error message: "gdiagno = -1 A volume registration file must be supplied" Thanks. All the best. Rujing Zha 2014-03-13 charujing123 发件人：Douglas Greve <greve(a)nmr.mgh.harvard.edu> 发送时间：2014-03-12 23:00 主题：Re: [Freesurfer] convert sig.mgh into *.nii 收件人："freesurfer"<freesurfer(a)nmr.mgh.harvard.edu> 抄送： Use mri_surf2vol to do this. Soemthing like mri_surf2vol --surfval rh.36...mgh --hemi rh --fillribbon --subject fsaverage --template $SUBJECTS_DIR/fsaverage/mri/orig --o yourvolume.nii doug On 3/11/14 10:10 PM, charujing123 wrote: Hi Bruce, Thanks Bruce. I knew that code, but I have no idea to deal with my problem after reading the help. Would you please tell me how to use mri_surf2vol after I describe my problem details? I have a file named rh.36sb.score.thickness.10.mgh which is created from the "mris_preproc --fsgd $FSGDFILE --target fsaverage --hemi $style --meas thickness --out ${style}.${FSGDFILE%_*}.00.mgh". I want to convert this file into nii format volume-based, so I can read it by AFNI. Thanks. All the best. Rujing Zha 2014-03-12 charujing123 发件人：Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> 发送时间：2014-03-12 09:44 主题：Re: [Freesurfer] convert sig.mgh into *.nii 收件人："charujing123"<charujing123(a)163.com> 抄送："freesurfer(a)nmr.mgh.harvard.edu"<freesurfer(a)nmr.mgh.harvard.edu> try mri_surf2vol with the output volume named .nii cheers Bruce On Wed, 12 Mar 2014, charujing123 wrote: > Hi doug, > Thanks doug. > I try this code, but it represent two dimension for each subject data when > loaded in the AFNI. Is there any code to volume-based conversion from mgh to > nii? > All the best. > Rujing Zha > > 2014-03-12 > > ____________________________________________________________________________ > charujing123 > > ____________________________________________________________________________ > 发件人：Douglas N Greve <greve(a)nmr.mgh.harvard.edu> > 发送时间：2014-03-12 00:16 > 主题：Re: [Freesurfer] convert sig.mgh into *.nii > 收件人："freesurfer"<freesurfer(a)nmr.mgh.harvard.edu> > 抄送： > > > mri_convert file.mgh file.nii > > doug > > On 03/11/2014 05:55 AM, charujing123 wrote: > > Hi FS experts, > > I want to extract time course from sig.mgh. But the *.y.ocn.mgh cannot > > be created. So I want to view it in other formats, such as nii. So how > > to convert it into nii format. > > Thanks. > > All the best. > > Rujing Zha > > 2014-03-11 > > ------------------------------------------------------------------------ ?? ?> charujing123 > > > > > > _______________________________________________ > > 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 i > s > addressed. If you believe this e-mail was sent to you in error and the e-ma > il > contains patient information, please contact the Partners Compliance HelpLi > ne at > http://www.partners.org/complianceline . If the e-mail was sent to you in e > rror > but does not contain patient information, please contact the sender and pro > perly > dispose of the e-mail. > > > _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

3 5

per-run and Native space
by SHAHIN NASR 17 Mar '14

17 Mar '14

I am trying to preproc-sess my data (fwhm 1.5, per-run, native space) with this command preproc-sess -fwhm 1.5 -fsd bold -per-run I expect it to generate fmcpr.sm1.5.nii.gz for each run of my dataset. Although preproc-sess finishes without any error, it only generates fmcpr.nii.gz and when I run selxavg3-sess, it returns an error that > cannot determine format of > test/bold/013/fmcpr.sm1.5 and exits. Would you tell me why those files are not generated? Regards -- Shahin Nasr PhD in Cognitive Neuroscience Martinos Imaging Center, MGH Harvard Medical School

2 1

Pial surface errors due to bad GM/WM contrast: What to do?
by Elijah Mak 17 Mar '14

17 Mar '14

Hello Freesurfer Community, I have a basic question about pial edits. I have a couple of subjects with very thin cortical measurements.Looking at the images, I think it could be an issue of weak intensity contrast between the GM and WM resulting in the erroneous pial surfaces? I have attached 2 screenshots in this email. In such a scenario, what can be done to correct the pial surfaces? Thank you very much for looking into this. Best Regards, Elijah

2 2

(no subject)
by Getaneh Bayu 15 Mar '14

15 Mar '14

1 0

dmri_motion
by Ruth Carper 15 Mar '14

15 Mar '14

Hi, I've been using dmri_motion to quantify motion in our DTI data. Can you give any guidance on selecting values for the -D and -T flags? I didn't see anything in the wiki or in your related papers and it can have a substantial effect on the outputs. Thanks.

2 3

Re: [Freesurfer] Fwd: converting to fsaverage space
by Barbara Weiland 14 Mar '14

14 Mar '14

Great - thanks for your help - got it all working now!

1 0

Consistent Dura issues
by Jonathan Holt 14 Mar '14

14 Mar '14

Hi all, I’m working with a particularly stubborn data set whose defining characteristic is dura along the posterior of the brain. It’s become so consistent that I’m hoping to find a way to perhaps tweak recon-all so as to take care of the issue in a more automated manner and save many many man hours of manual work. Is this possible? jon attached is an example of the general problem

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