[Freesurfer] strangely low lhCorticalWhiteMatterVol estimate

Hi guys, We have a subject processed with FS v5.1 in which lhCorticalWhiteMatterVol in aseg.stats is much too low -- only 33781 mm^3. From what I see, the aseg.mgz looks fine. 'mris_volume lh.white' returns 287261 and running mri_segstats without the --excl-ctxgmwm option returns a

[Freesurfer] Overlaying a lesion map onto an inflated surface

Dear Freesurfer list, I did a group level thickness analysis in qdec with lesioned brains and I would like to overlay individual lesion map onto the group level results to check for overlap, etc. I was wondering if I could convert individual lesion maps and overlay them on the group level

Re: [Freesurfer] HELP!A problem of Oracle VM VirtualBox

BoBo, the root password is 'freesurfer', mentioned at the bottom on this page: http://surfer.nmr.mgh.harvard.edu/fswiki/Installation/FreeSurferVirtualImage you will have to use sudo to run root commands (or to change to root). N. On Mon, 2012-02-20 at 21:32 +0800, bowan...@mail.ustc.edu.cn

[Freesurfer] mri_vol2vol not downsampling when applying a morph and a rigid registration matrix

Hi Freesurfers, I am struggling to get mri_vol2vol to downsample when I apply an inverse morph and an inverse registration matrix. Specifically, I am bringing a volume in cvs_avg35 space back into an individual subject's functional space. I have already registered the subject's functional to

[Freesurfer] Nearst Cortical Label (Annotation) for the CVS space

Dear Doug, I wonder if you could get the chance to finish the work regarding the Nearest Cortical Label (Annotation) for the CVS space. Also, I have few questions and I will appreciate if anyone can help: 1) Can I get more clusters after I correct for multiple comparison than the number of

[Freesurfer] surface group analysis design matrix question

Dear freesurfer users, I have a question about a design matrx. I have read all your explications about the FSDG file. But I am not sure I can construct the design which corresponds to my study! I have two groups: control and patients. I want to compare their cortical thickness. I have have

Re: [Freesurfer] weird relabeling with mri_convert

Hi, Thanks for your response. When I tried that option I got the same results, and I looked at the output header file and it still said ‘float32.’ I tried removing the -nc option, but that messed it up worse. None of my other attempts at tweaking the command are working thus far. Is there

Re: [Freesurfer] weird relabeling with mri_convert

Hi folks, Sorry, I messed up – mri_convert is working fine. The error is actually occurring prior to that when I use ‘mri_label2vol’ to convert the annotation file to a volume. Here’s where it happens mri_label2vol --annot lh.Yeo_singles.annot --temp ../mri/orig.mgz --o Yeo_WMGM_lh.nii.gz

[Freesurfer] Trac-all -preproc cannot find cor-.info

Dear all, I'm trying to run trac-all (FS5.1, the updated trac-all) for a provided nii.gz DWI volume and it's bvals/bvecs. During the preprocessing mri_convert searches for dti/COR-.info, but cannot find it - see log below. Does anyone have a clue why it searches for this COR-.info file? Best,

Re: [Freesurfer] Trac-all -preproc cannot find cor-.info

Hi Martin, Are you including b0 correction in your preprocessing stream? I can see b0mag.nii.gz in your log file. Did you set dob0 = 1 in your configuration file? If so you have to set also the magnitude and phase maps (using set b0mlist and set b0plist in the configuration file,Check out

[Freesurfer] tksurfer error

Hi, I have been experiencing an error with tksurfer. It occurs when I am trying to generate an occipital patch, following these instructions: http://surfer.nmr.mgh.harvard.edu/fswiki/FreeSurferOccipitalFlattenedPatch I open a surface using: tksurfer SUBJ lh inflated -curv lh.curv Following the

[Freesurfer] How to only do spatial normalization in FreeSurfer.

Dear all, I had EPI images and T1 image and the EPI images are already co-registered to T1 image in their native space. I also run 'recon' on T1 image. I'd like to try surface-based spatial normalization in FreeSurfer, so how can I only do the spatial normalization of EPI images in FreeSurfer,

Re: [Freesurfer] OBJ conversion

Hi Darshan, If you'd like to go directly from FreeSurfer .asc to OBJ, the attached little script should do the trick... Hope it helps! All the best, Anderson On 21/02/12 16:59, Pedro Paulo de Magalhães Oliveira Junior wrote: There's a how-to in the FreeSurfer website:

[Freesurfer] Freesurfer and MATLAB

Dear All, Is there a way that I can open my rh.aparc.stats files (saved in stats after recon-all) in MATLAB as a matrix? I would like to concatenate all the rh.aparc.stats files from all my subjects. Many thanks, Antonella ___ Freesurfer mailing

Re: [Freesurfer] Freesurfer and MATLAB

You could store them as a table (aparcstats2table), you can open the resulting text file with matlab. Best, Martijn On Wed, Feb 22, 2012 at 6:59 PM, Antonella Kis ator...@yahoo.com wrote: Dear All, Is there a way that I can open my rh.aparc.stats files (saved in stats after recon-all) in

Re: [Freesurfer] Trac-all -preproc cannot find cor-.info

Hi Priti, Thanks for your notice. I thought I disabled dob0, but apparently I didn't... ;-) Now I disabled it and everything works fine! Best, Martijn On Wed, Feb 22, 2012 at 4:57 PM, Priti Srinivasan rspr...@nmr.mgh.harvard.edu wrote: Hi Martin, Are you including b0 correction in your

[Freesurfer] problems with dti data in magnetom skyra 3T

Hello all, I am trying to use a set of dti data from a Magnetom Skyra 3T. I use the dt_recon process with data from another siemens of 1.5T without problems. With the Skyra 3T I have the following error in the log file: MRIresample(): error inverting matrix; determinant is nan, matrix is: Can

Re: [Freesurfer] problems with dti data in magnetom skyra 3T

It sounds like something went wrong with the conversion to nifti. Do you use image compression? Are you sure that the series is the correct one? doug John Fredy wrote: Hello all, I am trying to use a set of dti data from a Magnetom Skyra 3T. I use the dt_recon process with data from another

[Freesurfer] memory and bus failure

I have three scans that exit with errors that I cannot comprehend. The first two indicate memory and bus failures, so I thought maybe my computer had choked during processing, but after running again I received the same errors. The third is too cryptic for me to understand at all. Can anyone

[Freesurfer] Cluster position

Dear All, Is there a way that I can get my clusters location (segmentation and/or annotation) inthe MNI space if I know the MNI coordinates? Many thanks. AK ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu

[Freesurfer] Vertex size and vertex value export

Hello Freesurfer's, What is the size of a vertex? Also, how do you define a vertex? Also, in the Qdec analyses, once you get a cluster and the maximum vertex, is there a way to export individual vertex value (for each subject)? Regards, Manish Dalwani Instructor Dept. of Psychiatry University

[Freesurfer] white matter edits

According to the tutorial at http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/WhiteMatterEdits, we should be looking for these holes in the white surface, but when I looked at my processed data using tkmedit SUBJECT brainmask.mgz -aux wm.mgz -surfs, I saw many such holes. They seem to be

[Freesurfer] Fixing talairach registration

After reading the tutorial at http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Talairach, I understand that I should be using tkregister2 --mgz --s SUBJECT --fstal --surf orig when editing my talairach transform. I have been somewhat successful at this, but I was wondering if there might

Re: [Freesurfer] Frontal signal drop out

Hi Bruce and Freesurfer Experts, I tried the suggestions below in these images but without complete resolution of the problem - there is an improvement but there is still stuff missing right at the front (last 3 to 4 slices). Is there anything else I can try in order to salvage these images ?

Re: [Freesurfer] problems with dti data in magnetom skyra 3T

Dear Douglas, I don't use image compression. The series are new to me, I see that the images uses a multiframe encoding, there is 63 directions each direction encoded in a sigle image like a BOLD EPI sequence I will check again all the series Thanks for the reply John Ochoa Universidad de