Freesurfer

freesurfer@nmr.mgh.harvard.edu

19 participants
30132 discussions

autorecon2
by Mareen Kussatz 13 Aug '10

13 Aug '10

Hi to all, after correcting white matter problems, we saved the wm as aux volume and we tried also to save it as main volume. And than, we started recon-all -autorecon2-wm -subjid (subject file name). The process ends without any error for both conditions but after checking the tkmedit, there weren´t any corrections visible and actually there were no change at all.??? We just want to know if it is a syntax problem or if there is something wrong with the freesurfer itself. thanks and best regards. Mareen Kussatz -- Neu: GMX De-Mail - Einfach wie E-Mail, sicher wie ein Brief! Jetzt De-Mail-Adresse reservieren: http://portal.gmx.net/de/go/demail

2 1

Talairach xform problem
by Tricia Merkley 13 Aug '10

13 Aug '10

Hi Freesurfers, Is there a solution for fixing a bad talairach transform as shown in the attached figures? Recon-all completed without error (with the -notal-check included, v4.5.0), and the output looks pretty good. However I'm concerned that the 'IntraCranialVol' value will be off since it is based on the tal xform. I've tried to fix it as described at http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Talairach, but to no avail. I'd appreciate any suggestions. Thanks, Tricia

3 4

overlaying surfaces on volumes in freeview
by ythomas 12 Aug '10

12 Aug '10

Hi, when we load a mri volume and a surface at the same time, such as: freeview -v mri/norm.mgz -f surf/lh.white should we expect to see the lh.white surface be on top of the norm.mgz volume? I certainly do not see the surface unless I "unhighlight" the volume. Thanks, Thomas

2 1

activity time course
by Shahin 12 Aug '10

12 Aug '10

Hi, Would you tell me how can I see time-course of activities within one ROI (averaged over voxels) for each experiment condition? Should I use matlab commands? Shahin Nasr PhD in Cognitive Neuroscience Martinos Imaging Center, MGH Harvard Medical School

2 1

Coordinates for DTI tractography
by Lena Palaniyappan 12 Aug '10

12 Aug '10

Hi all I want to use a freesurfer parcellation as a seed point in DTI analysis using a non-FSL DTI tractography tool. I have the raw DTI images for around 40 subjects (20 scz 20 controls). From the structural MPRAGEs that correspond to these subjects, I have an average image where I have my defined ROI (which is a freesurfer atlas based parcellation). The ROI has numerous vertices whose MNI coordinates are available to me. Please correct me if I have understood this properly 1. I have to process the raw DTI images to obtain FA/trace images first for each subject 2. each FA/trace image should be registered to the average structural MPRAGE of the group How do I then go on to obtain the coordinates for my label on the DTI space? Many thanks Lena > > _______________________________________________________ Lena Palaniyappan Clinical Lecturer & Honorary StR | Division of Psychiatry ( University of Nottingham) South Block 'A' floor| Queens Medical Centre | Nottingham | NG7 2UH This message has been checked for viruses but the contents of an attachment may still contain software viruses which could damage your computer system: you are advised to perform your own checks. Email communications with the University of Nottingham may be monitored as permitted by UK legislation.

2 3

Transferring surface coordinates to functional data coordinates
by Patrik Ahvenainen 12 Aug '10

12 Aug '10

Dear FreeSurfer experts, For the past few days I have been struggling with how to transform points in FreeSurfer surface coordinates to points in functional data (SPM t-values) coordinates. I can coregister the functional data with FreeSurfer anatomical image using tkregister2. What I'm having trouble with is how to transform FreeSurfer surface coordinates to (any) volume coordinates that can be coregistered with the anatomical image. I have looked at the FreeSurfer wiki page about the coordinates, but I have not been able to understand fully which transformations are needed and where the related matrices are. I believe that the center of the RAS-coordinate systems (mri_info spmT_0001.img --cras; mri_info wm.mgz --cras) could be helpful as well as a transformation from voxel (volume) coordinates to RAS-coordinates (mri_info spmT_0001.img --vox2ras). What I'm looking for is the matrix-multiplication that would transform the FreeSurfer surface coordinates (such as those in ?h.white) to the functional data volume coordinates (in spmT_0001.img). I need to know what these matrices are (and where to get them) and in which order to apply the transformation matrices. I would like to do this with Matlab as much as possible. I have a large number of points and therefore I cannot do it manually for each point. Any help would be greatly appreciated. Sincerely, Patrik Ahvenainen AMI centre Helsinki University of Technology

1 0

registering a segmentation from one time-point to another
by Mehul Sampat 12 Aug '10

12 Aug '10

Hi Folks, I have two MR scans per subject. Lesions (white matter hypo-intensities) have been manually outlined for the first time-point. I would like to create a lesion mask for the 2nd time-point. But instead of starting from scratch, I would like to use the lesion-mask from the 1st time-point as a starting point for the lesion mask for time-point 2. for this task, I think I can use the following steps: Step 1) Register 1st time-point to the 2nd scan (using 2nd timepoint as reference) with flirt Step 2) Use mri_convert to apply the transformation matrix from flirt to the lesion mask and create a lesion mask for time-point 2. Step 3) make corrections to the lesion mask for time-point 2 if required. Would you suggest to do it in this manner or is an alternative approach recommended ? thanks Mehul ps: I thought of using the longitudinal freesurfer pipeline but i dont know how to compute the transformation matrix from time-point 1 to time-point 2 use the pipeline...

3 2

Curvature of the Corpus Callosum in Schizophrenia
by Alan Francis 11 Aug '10

11 Aug '10

Hi All: Does a lower score on the curvature of the CC (as done by FreeSurfer) imply that the Corpus Callosum is more curved or is it the other way around? If I am not making any sense in my previous statement, a simpler question would be : What do the scores on the curvature index mean for the shape of the CC? thank you so much, A

1 0

FSFAST Users Group Meetings
by Douglas N Greve 11 Aug '10

11 Aug '10

Hi All, I have scheduled a series of three meetings to talk about FSFAST, particularly the new version that is coming out with FreeSurfer 5.0 (due out "soon"). THIS IS NOT A HANDS-ON COURSE ON HOW TO USE FS-FAST!!! The purpose of these meetings is to give an overview of FSFAST, including the changes from version 4.5 to 5.0. So it is going to be mostly useful for people who already know some FSFAST. For others, it will serve as an introduction to FSFAST but you will not likely come out of a meeting knowing how to use FSFAST. I'm preparing on-line documentation and tutorials, and their might be a class in the future. These meetings will be held in 2204 (where the Brain Map lectures usually are) on the following dates and times: Mon Jul 12 3-4pm Tue Jul 27 3-4pm Wed Aug 11 4-5pm doug

1 5

LGN and Heschl's gyrus in freesurfer
by ridatta＠mail.med.upenn.edu 11 Aug '10

11 Aug '10

Hello All, I have two questions - 1) Is there an LGN label or ROI in freesurfer ? 2) Is this implemented in freesurfer ? Mapping an intrinsic MR property of gray matter in auditory cortex of living humans: a possible marker for primary cortex and hemispheric differences. Sigalovsky IS, Fischl B, Melcher JR. If I am not wrong, this is similar to the Hinds and Fischl method of demarcating V1. So is this a separate step like the V1 demarcation or is it integrated in the recon-all pipe ? Please let me know. Thanks Ri

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