Freesurfer

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30099 discussions

Which Volume is the one in Qdec measures?
by amirhossein manzouri 17 Mar '14

17 Mar '14

Hi All, Would please let me know about the origin of volume in the measures menu of Qdec, so I can interpret the results from group comparisons. Is it Gray Matter volume? Best regards, Amirhossein Manzouri

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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

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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

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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

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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

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(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.

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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!

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