Freesurfer

freesurfer@nmr.mgh.harvard.edu

19 participants
30088 discussions

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

2 2

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

13 Mar '14

2 1

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

2 3

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

2 2

'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

1 0

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!

3 16

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

1 0

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

4 6

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

2 1

glmfit with correlated covariates
by L. Schweren 12 Mar '14

12 Mar '14

Dear FreeSurfer experts, I am attempting to disentangle the effects of different features of pharmacological treatment on cortical thickness. I am running glmfit from the commandline, with multiple covariates (a.o. Z_Age, Z_TreatmentDuration and Z_StartAge) in the fsgd-file. These covariates are correlated up to approximately 0.6 , which to my understanding is not ideal yet not inducing collinearity. Running glmfit, I do not get any errors such as ill-designed matrix or so. My question regards the way the different regression weights are calculated in each voxel. If I test the variance in CT of voxel A explained by for example TreatmentDuration, and part of the variance in voxel A is explained by both TreatmentDuration and StartAge, will the regression weigth of TreatmentDuration than include the part that is also explained by StartAge? Or are all other covariates first "regressed out" of the variance, such that the variable I test can only explain the variance that was not explained by any of the other covariates? Thank you very much, your help is very much appreciated! Best wishes, Lizanne

2 1

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