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30087 discussions

Segmentation problems
by Tetiana Dadakova 02 Feb '11

02 Feb '11

Dear FreeSurfer users, I run a <recon-all -all> for one of my subjects. When I check the segmentation, it looks incorrect (see attached picture). What can be the problem? At which step can I change something? Should I do manual correction? Thank you, Tetiana.

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Surface area intepretation problem
by Jürgen Hänggi 02 Feb '11

02 Feb '11

Dear FS experts We divided the superior temporal sulcus derived from the aparc.a2009s.annot into parcellations of 300mm2 (using mris_divide_parcellation) and computed the mean cortical thickness within each parcellation. So far so good. But we noticed that each parcellation has a unique surface area that deviates largely from 300mm2 (96-480mm2). We defined the parcells on the fsaverage template and transformed them back into the native space of each individual. Therefore, we expected some variation in the surface area, but not such large differences. How to explain it? Thanks in advance Regards Jürgen ---------------------------------------------------------------------------- Jürgen Hänggi, Ph.D. Division Neuropsychology Institute of Psychology University of Zurich Binzmuehlestrasse 14, PO Box 25 8050 Zurich, Switzerland 0041 44 635 73 97 (phone office) 0041 76 445 86 84 (phone mobile) 0041 44 635 74 09 (fax office) BIN 4.D.04 (office room number) j.haenggi[at]psychologie.uzh.ch (email) http://www.psychologie.uzh.ch/neuropsy/ (website) http://www.juergenhaenggi.ch (private website) This e-mail (and any attachment/s) contains confidential and/or privileged information. If you are not the intended recipient (or have received this e-mail in error) please notify the sender immediately and destroy this e-mail. Any unauthorised copying, disclosure or distribution of the material in this e-mail is strictly forbidden. ----------------------------------------------------------------------------

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Manual editing of skull strip and mri_segstats
by Cheryl McCreary 01 Feb '11

01 Feb '11

Hi, I'm new to Freesurfer and am trying to process some data for the first time. I have two questions: 1. I have done some manual editing of the brainmask for skullstripping, saving the edits using 'Save As' and the default names. This seems to create a new group of files separate from the brianmask, in the mri subdirectory. Are these edits incorporated in the brainmask when autorecon2 and autorecon3 are run? I ask because the pial surfaces viewed using tkmedit after processing is complete often extends into the dura and unstripped skull that remains visible on the brainmask, even though it was removed in manual editing. Should I be using 'Save' instead of 'Save as' after editing? 2. For then initial analysis of my data, I would like to create a table of intracranial volume, brain parenchymal volume, gray matter volume and white matter volume. I've tries using the following command line: mri_segstats --sum TableFileName.sum --pv $SUBJECTS_DIR/Subject/mri/norm.mgz --ctab-default --surf-ctxgmwm --etiv $SUBJECTS_DIR/Subject/mri/transforms/talairach.xfm However, this fails with the error: unknown option --surf-ctxgmwm. What have I missed? Can you recommend another way to get this information? I have also tried asegstats2table as well, but intracranial volume was not included in the table. Thank you for any assistance or suggestions. Kind regards, Cheryl

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How to cite DOSS / DODS?
by Christian Scheel 01 Feb '11

01 Feb '11

Dear all, does anyone know one or two good method papers to cite when describing the difference of DOSS and DODS? I have already screened Pubmed and Co. but did not really find anything convincing. Any help greatly appreciated! Best wishes, Christian Scheel

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mri_convert problem
by Gabriel Go.Es. 01 Feb '11

01 Feb '11

Dear FS users I'm using FS v5 to convert some dicom images to mgz running the comand: mri_convert -it dicom -ot mgz 000001.DCM 001.mgz And get the error: ERROR: /root/trabajo/freesurfer/subjects/sujeto1/mri/orig/MPRAGE1/000001.DCM is not a dicom file But when I try to open the file in MRIcro it is a dicom (philips) file (see attached file), can any one help me with this? Regards, Gabriel

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Spikes in the inflated surface
by Nikolas Borrel-Jensen 01 Feb '11

01 Feb '11

Hi everybody. I have done all the auto-recon steps on my data, and I have some questions about the quality of the resulting images. I am aware of the troubleshooting tutorials, but I don't think these are covering my questions. I have uploaded some images of the surfaces and segmentations of a subject to http://freesurfer.nikolasborrel.com, and my question is about the spikes in the inflated surfaces. I have selected two spikes on the surface (green mark), one for each hemisphere, and have found the corresponding location in tkmedit in each of the three directions (s,h,c). For the spike in the left hemisphere (spike1_lh), I can't see what should be causing the spike. The segmentation looks correct. For the spike in the right hemisphere (spike_rh), it seems like there are many 'isles of segmentations, but are these causing the spike? If yes, how should these isles be corrected? Finally, how smooth is the inflated surface expected to be in a 'correct' case? Should a small amount of spikes be allowed, as long as they are not 'too severe'? I can upload more images if needed, thanks in advance! Kind regards Nikolas

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loading data to matlab?
by Léoné, F.T.M. (Frank) 01 Feb '11

01 Feb '11

Hi everyone, A sort of continuation of an old topic: I am able to load data into matlab (actually, I now plot the patches in Matlab, in order to be able to control the color myself, works great), but now I want to be able to get the x, y, z coordinates of the original data back. For example, if my functional was 64 x 64 x 18, I want to know the mapping from that space to my flattened/inflated brain. The reason I want to know this is because I have some additional info per voxel, which I want to be able to show/pop up if I click at a spot in the flattened/inflated representation. So, I have all the files already in matlab, now I just need to know how this conversion works. Specifying -noreshape apparently isn't the entire story. Thanks a lot in advance, kind regards, Frank

2 1

Phantom data
by Alan Francis 31 Jan '11

31 Jan '11

Hi Bruce, Nick, Doug and others: I have Phantom data from around 900 scans collected across 5 sites in the US. Does FS have a way of processing Phantom data. Thanks much, Alan Alan Francis Beth Israel Deaconess Medical Center

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white matter volume and qdec
by tulu＠ms36.hinet.net 31 Jan '11

31 Jan '11

2 1

postmortem analysis
by Sarah Whittle 30 Jan '11

30 Jan '11

Hi, I have some post-mortem MR images that I'd like to run through FreeSurfer to obtain thickness estimates. I've had a look at the instructions on http://surfer.nmr.mgh.harvard.edu/fswiki/ExVivo. The images were obtained with a T1-weighted fast gradient echo sequence (1.5-mm slice thickness, FOV = 25 cm; NEX = 1; matrix = 256 x 192; TR = 35 ms; FA = 60). Although the images are T1-weighted, they appear to look like T2-weighted images (ie, dark WM, white GM). I haven't worked with post-mortem MRI before, and my knowledge of MR physics isn't great, so I'm not sure why that is. So, my questions are, 1) can I use these images in the processing stream described on the wiki? 2) Is it possible to do the automated atlas-based cortical and subcortical parcellations? Thanks, Sarah

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