Freesurfer March 2014

freesurfer@nmr.mgh.harvard.edu

147 participants
247 discussions

Re: [Freesurfer] Displaying ROI's from Destrieux atlas (aparc.a2009s)
by Douglas N Greve 17 Mar '14

17 Mar '14

Hi Laura, please make sure to post to the list. Thanks! This is possible. Run mri_annotation2label to break the annotation up into labels, then use mris_label2annot to recombine only the ones you want back into an annotation doug On 03/17/2014 03:55 PM, Laura Taylor wrote: > Sorry, I will try to explain better. > > I have used the average thickness (ThickAvg) stats from the > rh/lh.aparc.a2009s.stats file in my data analysis comparing cortical > thickness in different patient groups. > > For my results, I have say 10 areas from the rh/lh.aparc.a2009s.stats > that are thicker in one patient group than in another. I would like > to visually display these specific areas of cortex that are thicker in > one group than another on a whole/half brain. > > I can load the annotation file in freeview with all of the 74 regions > per hemisphere in different colors, but I'd like to make it so that my > 10 regions of interest are say red and the rest of the brain (64 other > regions) are, e.g. grey. > > Is this possible? > > Thank you, > > Laura > > > On Mon, Mar 17, 2014 at 12:24 PM, Douglas N Greve > <greve(a)nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> wrote: > > I'm not sure what you mean, can you elaborate? > doug > On 03/17/2014 03:02 PM, Laura Taylor wrote: > > Hi there, > > > > I am looking to somehow display a handful of cortical areas from the > > Destrieux atlas (aparc.a2009s). Is there a way to do this? > > > > Thanks, > > > > Laura > > > > > > > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer(a)nmr.mgh.harvard.edu > <mailto:Freesurfer@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 <mailto:greve@nmr.mgh.harvard.edu> > Phone Number: 617-724-2358 <tel:617-724-2358> > Fax: 617-726-7422 <tel:617-726-7422> > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 > www.nmr.mgh.harvard.edu/facility/filedrop/index.html > <http://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 <mailto:Freesurfer@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. > > -- 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/

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Segmentation fault:11 with mris_anatomical_stats
by Rupa Sabbineni 17 Mar '14

17 Mar '14

Good morning! I was trying to run the mris_anatomical_stats command and for some subjects I keep getting Segmentation fault:11 error. Some of the posts in the archive suggested that I run the recon-all command since it usually means that subjects surfaces are out of sync SO I RERAN RECON_ALL(which created the stats). Then I reran the mris_anatomical_stats command and got the segmentation fault again. The command im using is mris_anatomical_stats -l new.label -a aparc.a2009s.annot -log outSUB1_lhVOL2 SUB1 lh A little background on the new.label. We got the label by doing a regression in qdec at FDR 0.05 which created cluster and peak cluster label. Can anyone please provide me some insight on how to trouble shoot this problem? Thank you! Rupa

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Displaying ROI's from Destrieux atlas (aparc.a2009s)
by Laura Taylor 17 Mar '14

17 Mar '14

Hi there, I am looking to somehow display a handful of cortical areas from the Destrieux atlas (aparc.a2009s). Is there a way to do this? Thanks, Laura

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[Label] Extract coordinate of Corpus Callossum
by Thomas PAUL 17 Mar '14

17 Mar '14

Dear FreeSurfer experts, I've been using FreeSurfer for 2 months now, and I have a question on how to proceed to do the following thing: My goal is to obtain the CRS coordinates of the corpus callossum. Here is what I was thinking to do, based on what I read: 1. Annotation to segmentation: mri_annotation2label --seg --hemi ?? --subject bert volume_annot.mgh => I need to provide an hemisphere, which one should I use, should I do this for both ? 2. Binarize the volume, keeping the label we want: mri_binarize --i volume_annot.mgh --match 86 --o corpusCallossum.mgh => I use the number 86 based on the LUT table... 3. Execute: mri_surfcluster --in corpusCallossum.mgh --thmin 0.5 --subject bert --hemi ?? --o outputfile.mgh Am I on the right path? I am not sure on how to use the outputfile.mgh after. Did I miss any arguments in the command line? Thank you in advance for your help Thomas Paul.

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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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Freesurfer March 2014