Freesurfer

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Re: [Freesurfer] Fwd: converting to fsaverage space
by Douglas N Greve 13 Mar '14

13 Mar '14

Hi Barbara, please post to the list. Thanks! the vol2surf command output should be .mgh or .mgz, not .mg (or maybe that is just a typo in the email). If it is, then you should load the mgh file as an overlay, not as a surface, eg tksurfer [subj] lh inflated -overlay file.mgh -fminmax .5 1000 setting the min threshold to .5 assures that you can see the ROI doug On 03/13/2014 05:10 PM, Barbara Weiland wrote: > Hi - > > Sorry to not have been clearer. > > I have /functional ROIs defined by the Greicius > lab// (http://findlab.stanford.edu/functional_ROIs.html) just as in > this post to the Freesurfer list from //Mon Dec 2 15:22:08 EST 2013:/ > / > / >> Doug, Thank you for your very helpful suggestion. Indeed, doing so >> made it so I could quickly take any parts (or all) of each Greicius >> network and put them in individual subject space. In case this may >> help anyone else, the final series of commands were (in this case, >> for the whole anterior salience network): *mni152reg --s [subj]* >> mri_label2vol *--seg anterior_Salience.nii.gz \* --reg >> $SUBJECTS_DIR/[subj]/mri/transforms/reg.mni152.2mm.dat \ --invertmtx >> --o anterior_Salience_[subj].nii.gz \ --temp >> $SUBJECTS_DIR/[subj]/mri/orig.mgz Cheers, Paul > > These ROIs were originally in MNI space and I used the commands listed > above from Paul to move them to subject space first creating the > reg.mni152.2mm.dat for each subject. LECN….nii is one of these > network ROIs. I can see this ROI using free view and it looks > correct. What I want is to extract volume and thickness for this ROI. > As outlined below,I thought I needed to first convert this to a > surface and tried: > >>> mri_vol2surf --src $SUBJECTS_DIR/[subj]/label/LECN_subjXXX.nii --out >>> $SUBJECTS_DIR/[subj]/label/LECN_subjXXX_lh_surf.mg --srcreg >>> $SUBJECTS_DIR/[subj]/mri/transforms/reg.mni152.2.dat --hemi lh >> > > I tried to look at the output (LECN_subjXXX_lh_surf.mg) by using > tksurfer [subj] lh inflated and then load the it from the GUI onto the > inflated surface -- this says that the > file (LECN_subjXXX_lh_surf.mg) "has 0 vertices! > Probably trying to use a scalar data file as a surface!" > > Do I need to move the LECN….nii to be a surface or should I just be > able to make a label from it? I assumed I need the ROI information to > be a label to use mris_anatomical_stats? > Thank you, > Barbara > > > Barbara Weiland, Ph.D. > Research Asst. Professor > CU Change Lab > Dept. of Psychology & Neuroscience > University of Colorado Boulder > barbara.weiland(a)colorado.edu <mailto:barbara.weiland@colorado.edu> > > > > On Mar 13, 2014, at 1:14 PM, Douglas N Greve > <greve(a)nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> wrote: > >> >> Can you give more details? What is LECN_...nii? Where did it come from? >> What space is it in? MNI152 I assume? What does it mean you can't load >> it? Load it with what? What is your command line? >> doug >> >> >> >> >> >> On 03/13/2014 01:36 PM, Barbara Weiland wrote: >>> Hi - >>> >>> I am trying to extract volumes & thickness stats of networks and >>> followed the commands from the post in the subject line to create >>> network .nii files in each subject's space. Based on some other >>> postings, I thought I needed to first move the volumes to surf for >>> each hemisphere, i.e.: >>> >>> mri_vol2surf --src $SUBJECTS_DIR/[subj]/label/LECN_subjXXX.nii >> >>> --out $SUBJECTS_DIR/[subj]/label/LECN_subjXXX_lh_surf.mgh >> >>> --srcreg $SUBJECTS_DIR/[subj]/mri/transforms/reg.mni152.2.dat --hemi lh >> >> >>> But this does not seem to create the surf correctly - I am unable to >>> load it. >>> I have also tried to use mri_cor2labels to create labels directly >>> front the .nii files but found that the first column in the label >>> files were all -1 (which I found in a previous posting meant the >>> volumes needed to be moved to surface first as I tried above)?? >>> I ultimately want to use mris_aatomical_stats with these labels to >>> output stats. Any help would be appreciated, >>> thanks, >>> Barbara >>> >>> Barbara Weiland, Ph.D. >>> Research Asst. Professor >>> CU Change Lab >>> Dept. of Psychology & Neuroscience >>> University of Colorado Boulder >>> barbara.weiland(a)colorado.edu <mailto:barbara.weiland@colorado.edu> >>> <mailto:barbara.weiland@colorado.edu> >>> >>> >>> >>> >>> >>> _______________________________________________ >>> 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 >> 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. >> > -- 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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fsaverage_sym in xhemi commands
by Markus Gschwind 13 Mar '14

13 Mar '14

Dear all, I have a question concerning the xhemi commands as explained here: http://surfer.nmr.mgh.harvard.edu/fswiki/Xhemi 2. The command surfreg --s $subject --t fsaverage_sym --lh is absolutely searching for fsaverage_sym in the $SUBJECTS_DIR. Do I really have to copy the whole fsaverage_sym folder from $FREESUERFER_HOME/subjects into each subject's directory once again? Thank you very much! Markus

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Re: [Freesurfer] Fwd: converting to fsaverage space
by Barbara Weiland 13 Mar '14

13 Mar '14

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Combining scans with different scanning parameters
by Ashley Shurick 13 Mar '14

13 Mar '14

Hi, I'm interested in comparing CT differences between 2 different groups, and in order to increase my sample size I'm contemplating combining 3 datasets with different scanning parameters. Some scans were collected with a 3T1 with fmri head coil, while others were collected with a 3T2 magnet with 8 channel head coil. The scans also differ in FOV (25.6 vs 22cm) and resolution. Thank you in advance for your support. Ashley -- Ashley A. Shurick Ph.D. Candidate Department of Psychology Stanford University

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Error mri_label2label
by _andreia_＠sapo.pt 13 Mar '14

13 Mar '14

Hello list, When running the following command : mri_label2label --srcsubject fsaverage --srclabel /home/user/visao/Freesurfer/fsaverage/label/lh.BA1.thresh.label --trgsubject subjid --trglabel ./lh.BA1.thresh.label --hemi lh --regmethod surface I get the error "INFO: found 1014 nlabel points Performing mapping from target back to the source label ERROR: SRCVTXNO = -1 < 0 trgvtxno = 122050, dmin = 1000 trgregxyz = 0, 0, 0 This means that a vertex in the target surface could not be mapped to a vertex in the source surface because the xyz of the target is outside of the range of the hash table." I have used this command in several subjects and never got this error. What went wrong? As far as I'm aware I did all the processing in the same way for every subject. How can I fix this this? Thank you! Andreia

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'patching' the base template with additional runs
by Govindarajan, Koushik Athreya 13 Mar '14

13 Mar '14

Dear FS experts, I am trying to add a 6th and 7th timepoint to my longitudinal analysis that already has a base template from 5 timepoints. I saw an earlier response on the mailing list about doing this using a 'patch' script but there was no further information on this. Is this script available in FreeSurfer now ? Thanks Koushik

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Resting State Networks on Cortical Surface
by Xuelong Zhao 13 Mar '14

13 Mar '14

Hi, I am trying to display the 20 ICA components in this nifti file http://brainmap.org/icns/maps.zip onto anatomical template they've provided here http://brainmap.org/icns/colin_tlrc_1x1x1.nii My question is: How do I extract only the cortical surface from the anatomical template and overlay it with only parts of each ICA component that intersects with the surface? Thanks!

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Longitudinal stream
by Eduard Vilaplana Martinez 13 Mar '14

13 Mar '14

Dear Freesurfer experts, I would like to perform a longitudinal analysis with freesurfer 5.1 and I have some questions regarding the whole processing stream. I have BL and 1Y follow-up from all patients (110), and moreover I have 2Y follow-up from only some patients (more or less 50). Do you recommend using the 2Y when available in the whole stream? Or, on the other hand, it would be better to perform a BL and 1Y analysis in the whole sample and then, separately, do a second analysis only with those subjects that have 2Y follow-up? My idea is to study rates of change (cortical and ventricles, mainly). I have another more technical question. When running the base (recon-all -base <templateid> -tp <tp1id> -tp <tp2id> ... -all), does the order of the time points matter? In Reuter et al., 2012 says that all scans are treated the same, so I guess it doesn't matter if tp1 is the 1Y and tp2 is the BL. Am I wrong? Finally, to look at ventricle changes, do you also recommend using the longitudinal stream or rather the cross-sectional one? It seems that the longitudinal stream is more cortical specific, but maybe I would be wrong... Thanks Best, Eduard

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convert sig.mgh into *.nii
by charujing123 12 Mar '14

12 Mar '14

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

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12 Mar '14

Hi everybody, I would like to ask a question about trac-preproc, because I'm new to Tracula and I'm studying how the entire trac-all process works. I want to know which is the specific structural image (I mean the name of the file) that is registered to the dwi volume during trac-preproc, and at which point of the process this is done. I'm doing this because I want to track down all the movements of the files used by Tracula. Thanks, Francesco Baldacchini

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