[Freesurfer] fMRI-data mri_convert, missing header

Hello! I'm encountering a problem with converting fMRI-Data from dicom- to NIfTI-files (single file). The problem only occurs with data aquired on Siemens Vision, data from Siemens Trio work just fine. The Siemens ASCII header is missing (files have not been anonymized) and every dicom-file

Re: [Freesurfer] mri_surf2vol questions

Many Thanks Doug. Will try that out. Regards Koushik -Original Message- From: freesurfer-boun...@nmr.mgh.harvard.edu [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Douglas N Greve Sent: Monday, November 04, 2013 4:47 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re:

[Freesurfer] MRISread error

Hi everyone, I run into an error when I try to do the tutorial on ROI group analysis. I downloaded the tutorial set, but did not put it into FREESURFER_HOME/subjects, because my computer doesn't allow it. I made my own folder and copied everything in there. The error arises when I try to map a

Re: [Freesurfer] mri_segment WM/GM limits

Also, quick question . . . How exactly do you run a recon from scratch without nifti images? I’d always delete the directory and restart with mri_convert -i … Jon On Nov 5, 2013, at 10:40 AM, Louis Nicholas Vinke vi...@nmr.mgh.harvard.edu wrote: Hi Jon, I see the area you are talking

Re: [Freesurfer] expand GM label into white matter

I think that the first option you provided is more along the lines of what I'm looking for. Thanks Corinna On Mon, Nov 4, 2013 at 5:37 PM, Douglas N Greve gr...@nmr.mgh.harvard.eduwrote: Yes. As Bruce mentioned you can also use the program that creates the wmparc (mri_aparc2aseg). You can

[Freesurfer] fMRI postdoc, Center for Mind/Brain Sciences, University of Trento, Italy

*fMRI postdoc* At the Center for Mind/ Brain Sciences (CIMeC, www.unitn.it/en/cimec), University of Trento, Italy, there will soon be an opening for a postdoc position to work with Angelika Lingnau ( https://sites.google.com/site/angelikalingnau/) in collaboration with Carlo Marzi, University

Re: [Freesurfer] LGI path problem

Hi, Thank you very much, it works. I now however have another problem (sorry!). I have run the command on test subject and want to display using tksurfer. The file lh.pial_lgi has for sure been created, and i cd into correct subjects directory however when I try tksurfer lh inflated -overlay

Re: [Freesurfer] LGI path problem

Are you in the 'surf' directory? If not, then do -overlay $subject/surf/lh.pial_lgi On 11/05/2013 11:26 AM, Linn Mittlestein wrote: Hi, Thank you very much, it works. I now however have another problem (sorry!). I have run the command on test subject and want to display using tksurfer. The

[Freesurfer] Fwd: using matched pairs in QDEC?

Hi - Thank you for a fantastic piece of software :-) - I have en one question: - In the GUI-module QDEC, is it possible to adjust the GLM-model to account for a pair-matched cohort? (diabetes vs non-diabetes - matched pairwise by age, sex and bmi) Kind regards Christian, Denmark Christian

[Freesurfer] feat to qdec

Hi everyone, I am very new to freesurfer/qdec. What I would like to do is examine the results of a feat analysis in qdec and then perform further between-subject analyses with behavioural data (http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/FslFeatFreeSurfer). I've run against problems

[Freesurfer] Literature values of cortical thickness

Dear Freesurfers, I need to compare the cortical thickness values, obtained from a data set of 32 healthy subjects, with some reference literature values of cortical thickness. I'd like to check the values of mean and standard deviation for each one of the 32 cortical parcellations automatically

[Freesurfer] z-test differences from fscalc and mri_glmfit

Hi All, In a previous post Doug suggested two methods for generating voxel-wise z-score maps, one using glmfit with one subject in one group and the second using fscalc.fsl. Link to post: https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2010-June/014673.html I have tried both methods

Re: [Freesurfer] MRISread error

Hi Anita, I don't believe you have the complete path set to your SUBJECTS_DIR environmental variable, unless Desktop is in your root dir which I doubt is the case. Easy way to set the variable: cd /path/to/tutorial/data/ setenv SUBJECTS_DIR $PWD Also, check you have fsaverage symlinked to

Re: [Freesurfer] mri_segment WM/GM limits

Hi Jon, You can use the -clean flag, or you can just delete all the directories in the subject's recon directory except the mri folder, and then delete everything in the mri folder leaving the orig folder which contains the 001.mgz which is equivalent to the nifiti volume(s) initially passed

[Freesurfer] Grey Matter Mask

Hello, I was wondering what output from the recon-all freesurfer scripts would be best to make a grey matter only mask? Thanks, Emily ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu

Re: [Freesurfer] Grey Matter Mask

you can do this cd $SUBJECTS_DIR/subject/mri mri_binarize --i aparc+aseg.mgz --gm --o gmmask.mgz doug On 11/05/2013 03:45 PM, ebell...@uwm.edu wrote: Hello, I was wondering what output from the recon-all freesurfer scripts would be best to make a grey matter only mask? Thanks, Emily

[Freesurfer] visualizing a surface below the WM surface

Hi Freesurfer team We are sampling diffusion images below the WM surface , and would like to visualize with tkmedit or freeview the surface itself to see if it is appropriate to our analysis (not the surface overlay, but the surface as a line like the one that are on the surfs directory). I

[Freesurfer] Extract voxel time series from subcortical segmentation (without averaging)

Hi, I have fMRI data which has been co-registered with the FS reconstruction using bbregister. I would like to extract the voxel time series for the voxels in the subcortical labels from the aseg subcortical segmentation. I know that mri_segstats can be used with the --avgwf option to extract

Re: [Freesurfer] Fwd: using matched pairs in QDEC?

No sorry, you'll have to use the command line stream rather than QDEC (ie, mris_preproc, mri_surf2surf to smooth, and mri_glmfit). See the FSGD examples on our wiki for how to do the paired analysis doug On 11/05/2013 12:07 PM, christian buhl wrote: Hi - Thank you for a fantastic piece

Re: [Freesurfer] Extract voxel time series from subcortical segmentation (without averaging)

no, sorry, you'll have to do it with matlab. You can do something like mri_vol2vol --mov func.nii --reg register.dat --fstarg --o func.anat.nii aseg = MRIread('aseg.mgz'); indroi = find(aseg.vol == 17); % 17 = left hippo func = MRIread('func.anat.nii'); funcmat = fast_vol2mat(func); funcroi =

Re: [Freesurfer] Extract voxel time series from subcortical segmentation (without averaging)

hi martin, if you had one region you can use mri_segstats to extract for each voxel in that roi, but not for multiple rois. here is a snippet i use for timecourses in each roi. https://github.com/nipy/nipype/blob/master/examples/rsfmri_preprocessing.py#L219 cheers, satra On Tue, Nov 5, 2013

Re: [Freesurfer] Extract voxel time series from subcortical segmentation (without averaging)

Hi Doug, Thanks for your reply. I will do it in Python then ;). Is there a table somewhere with a list of values used for each label (17 = left hippo etc.)? Martin On 11/05/13 17:32, Douglas N Greve wrote: no, sorry, you'll have to do it with matlab. You can do something like mri_vol2vol

Re: [Freesurfer] visualizing a surface below the WM surface

Hi Celine we usually use mris_expand with a negative number to grow the surface inwards. Something like mris_expand lh.white -1 lh.interior would move the surfaces inwards by 1mm everywhere and save it in a file name lh.initerior. You could then visualize that in freeview or tkmedit as

Re: [Freesurfer] Extract voxel time series from subcortical segmentation (without averaging)

Thanks Satra, very helpful. On 11/05/13 17:34, Satrajit Ghosh wrote: hi martin, if you had one region you can use mri_segstats to extract for each voxel in that roi, but not for multiple rois. here is a snippet i use for timecourses in each roi.

Re: [Freesurfer] Extract voxel time series from subcortical segmentation (without averaging)

$FREESURFER_HOME/FreeSurferColorLUT.txt On 11/05/2013 05:42 PM, Martin Luessi wrote: Hi Doug, Thanks for your reply. I will do it in Python then ;). Is there a table somewhere with a list of values used for each label (17 = left hippo etc.)? Martin On 11/05/13 17:32, Douglas N Greve

Re: [Freesurfer] Seg fault with mri_segstats?

I am a bit stumped. Can you check that cache.th20.pos.sig.ocn.mgh and concat_output.nii.gz? I'm sure they most be. If so, send both to me on our file drop. doug On 11/04/2013 07:00 PM, Michael Waskom wrote: Hi Doug, I'm running into a strange seg fault when trying to use mri_segstats

Re: [Freesurfer] feat to qdec

Is reg-feat2anat in your path? It should be in $FREESURFER_HOME/bin/reg-feat2anat doug On 11/05/2013 12:15 PM, Christophe de Bezenac wrote: Hi everyone, I am very new to freesurfer/qdec. What I would like to do is examine the results of a feat analysis in qdec and then perform further

Re: [Freesurfer] convert (resample) fsaverage/mri/aseg.mgz into $FSLDIR Nifti with MNI152_T1_1mm target - aparc+aseg.mgz problem

Can you send your command lines for both aparc+aseg and aseg? doug ps. Please remember to post to the list and not to me personally. Thanks! On 11/05/2013 12:45 PM, Roderick McColl wrote: Actually does not display properly at least not in freeview. Slices are also upside down. Also the

Re: [Freesurfer] z-test differences from fscalc and mri_glmfit

When you say that you are getting very different results, what are you comparing exactly? I can't tell what your mri_glmfit command is because it is embedded in a script with lots of variables. Have mercy on me and just give me a simple command line that I don't have to struggle with:) doug

[Freesurfer] FW: convert (resample) fsaverage/mri/aseg.mgz into $FSLDIR Nifti with MNI152_T1_1mm target - aparc+aseg.mgz problem

Sure, no problem. Run from within the folder $SUBJECTS/fsaverage/mri :- mri_vol2vol --targ $FSLDIR/data/standard/MNI152_T1_1mm.nii.gz --mov aseg.mgz --reg transforms/reg.mni152.1mm.dat --o aseg_mni152.nii.gz mri_vol2vol --targ $FSLDIR/data/standard/MNI152_T1_1mm.nii.gz --mov aparc+aseg.mgz

Re: [Freesurfer] Creating group average ROI

Hi Bruce, The ROIs all on different subjects, but we've been able to put them all onto an average surface that we made using make_average_surface (using mri_label2label as explained in my previous email). We were hoping that now that they're all on a common average subject that we could some how

Re: [Freesurfer] A question as to subcortical volumetric measurement

Dear Drs. Bruce and Doug Thanks for the valuable comments. Discrepancy between FS and VBM lies in putamen and hippocampus. Would you please briefly comment regarding segmentation method of above structures in FS? I'm just wondering whether segmentation of grey matter in FS is largely different