Freesurfer September 2006

freesurfer@nmr.mgh.harvard.edu

37 participants
45 discussions

FW: field sign and colour lables
by kristofer kinsey 16 Sep '06

16 Sep '06

I have a question regarding colour labelling for the retinotopic maps generated by Freesurfer. I'm running Freesurfer-Linux-rh9-stable-pub-v3.0.2 and have successfully generated the polar, eccen, and field sign maps (no errors). The images seem to differentiate the occipital regions, except that the colour labelling appears to be incorrect. In the eccen image, for example, the order of the colours start out as red, green, blue and using the Configure Overlay Display Inverse it's green, blue, red. According to my notes one should see fovea=red, parafoveal=blue and periphery=green. Also, with the field sign image, the area that should be V1 shows up as blue instead of yellow (can't seem to invert the colours). I've since gone back to double check that my procedure is correct and re-checked my registration and can't seem to find my mistake. I was hoping to get some help to fix this problem. In case it helps, I've attached a few images of the maps that were generated. Cheers kk ______________________________ Kristofer Kinsey, PhD Neurosciences Research Institute School of Life and Health Sciences Aston University Birmingham B4 7ET Web Site: www.physiol.ox.ac.uk/~kk3/

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tksurfer marking nodes on "opposite" side of brain
by Johannes Klein 15 Sep '06

15 Sep '06

Hi everyone, I'm currently hand-drawing some labels using tksurfer. Unfortunately, quite often a node that I try to click will not be selected. Instead, the mark is placed on the surface "behind" the one I'm viewing, e.g. when trying to outline calcarine structures, the node mark will appear somewhere on the lateral surface. I wonder if anyone else has run into this? Is it possible to constrain tksurfer's node selection to the currently visible part of the cortex only? Alternatively, an undo feature to de-select the last point clicked would save me re-drawing the whole outline, but in my Edit menu, tksurfer consistently says "Nothing to Undo". Do I need to enalbe the Undo feature somewhere? I'm running FS 3.0.3 centos4. Thank you very much, Johannes

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resampling spm2 activations
by Kirk, Gregory 14 Sep '06

14 Sep '06

Hi, I think this is one for Doug, Thomas Witzel told me it is possible to resample the volume activation data from spm2 onto the cortical surface generated with freesurfer. Is their a blurb around that details the process or could you give me some instructions. thanks Greg.

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dicom to 4d nifti
by Aapo Nummenmaa 14 Sep '06

14 Sep '06

Hi, Referring to the mail-archive: http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg03460.html it is now possible to convert directly from dicom to 4d nifti in the dev-version of mri_convert, if i understand it correctly. Can one get the new version of mri_convert from somewhere for testing? Thanks, -Aapo

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Group analysis of curvature not running
by Per Alm 14 Sep '06

14 Sep '06

Hi, I have been running group analysis of thickness, with no problems. However, when trying to run a group analysis of curv.pial the mri_glmfit crashes. I'm basically using the same group descriptor file, contrast matrix, and command line as for thickness, but keep getting the error message: Matrix condition is 1 search space = 104352 ERROR: dimension mismatch between y and X. y has 1 inputs, X has 31 rows. I'm running a very simple analysis, with just two groups, 31 subjects, and no variables. Ideas? Thanks, Per

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Red Hat Linux Enterprise
by Juergen Haenggi 14 Sep '06

14 Sep '06

Dear FreeSurfer user which FreeSurfer version I have to use when running OS Red Hat Linux Enterprise? Red Hat Linux 9 or CentOS 4? Because there are many mails in the FreeSurfer archive that pose questions with respect to Red Hat Linux Enterprise, I concluded that FreeSurfer runs also on Red Hat Linux Enterprise! Right? Thanks in advance for helping Best regards Juergen ---------------------------------------------- Juergen Haenggi, Ph.D. student Neuropsychology and Imaging Division of Psychiatry Research Psychiatric University Hospital University of Zurich, Switzerland P.O. Box 1931 Lenggstrasse 31, 8032 Zurich 0041 44 384 26 10 (office phone) 0041 76 445 86 84 (mobile phone) 0041 44 384 26 86 (fax) H 115 (office room number) juergen.haenggi(a)bli.unizh.ch (division email) http://www.dpr.unizh.ch/ (division website) http://www.juergenhaenggi.ch (private website) ----------------------------------------------

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question about surface based segmentation...
by Shahabuddin Ansari 13 Sep '06

13 Sep '06

Hi, I have done volume-based segmentation using freesurfer and now am interested in surface-based segmentation. I have used the following set of commands in volume-based segmentation: #!/bin/csh # Shahab Ansari, August 22, 2006 #The following command creates a directory structure for the subject, and strip skull, normalize intesity and normalize coordinates recon-all -i /ensc/IMAGE/2998977_02/2998977_02.img -s 2998977_02 > 2998977_02.log recon-all -subjid 2998977_02 -autorecon1 >> 2998977_02.log #this command segments the subcortical brain and takes about 10 hrs recon-all -subcortseg -s 2998977_02 >> 2998977_02.log #this will translate the segmentation back to the original MRI space mri_convert -rl /ensc/IMAGE/opt/FREESURFER/subjects/2998977_02/mri/rawavg.mgz -rt nearest /ensc/IMAGE/opt/FREESURFER/subjects/2998977_02/mri/aseg.mgz /ensc/IMAGE/opt/FREESURFER/subjects/2998977_02/mri/aseg_raw.mgz >> 2998977_02.log I need some know what else I need to do to segment the cortical surface. I appreciate any help pointer. Thanks Shahab __________________________________________________ Do You Yahoo!? Tired of spam? Yahoo! Mail has the best spam protection around http://mail.yahoo.com

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Re: [Freesurfer] Odd brainmask.auto and brainmask data and behavior
by Graham Wideman 13 Sep '06

13 Sep '06

Jenni: Thanks for your reply and explanation of the brainmask logic and rationale. As for this: >> Question 1: Is there a rationale for 255 values? (in the brainmask volume) > >I'm not sure where these are coming from in your volume - I assume you >havent done any editting on this one. These subjects' data may well have been edited (not by me, hence my not knowing exactly what's what here). And I suppose it's the brainmask.mgz volume that would have been edited, and the act of editing it sets voxels to 255 perhaps? (The 255's are in the appropriate locations to add additional grey matter to the edges.) That leads me to believe that the answer to this: > Question 0: Is the detailed image data in brainmask.mgz ever used, or is > it simply a zero/not-zero mask? Ie: is the meaning "masked brain", or > "mask using non-zero values to show where brain is". ... is that brainmask.mgz is used by subsequent steps as a mask in combination with some other image volume providing the actual image. In that case the actual intensities of brainmask.mgz are ignored. And I now see in the script that mri_ca_normalize does indeed use brainmask.mgz with the mask flag, so I guess I'm probably right that the actual intensities are unimportant. (And nu.mgz provides the actual image). Phew, I think I now have that straight... for this week :-) Graham

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coordinates
by Frederick Klauschen 13 Sep '06

13 Sep '06

Hi, I have to bring up an issue again which we had some discussion about before, but which we haven't yet found a satisfying solution. I would like pose my question a little more precisely again: 1) I have a dataset that is in 181x217x181 coordinates. 2) I am processing it as follows: > mri_convert name.img name/mri/orig/001.mgz > recon-all -motioncor -subjid name 3) after step 2, the resulting dataset is somehow transformed to a 256x256x256 dataset, i. e. the 181x217x181 is embedded into the 256^3 array: it is rotated and the origin in 181x217x181 is not the origin in the 256x256x256 array. 4) Since I would like to do a voxelwise comparison between the recon-all result and my initial dataset 1), I need to backtransform the result into the 181x217x181 coordinates (and of course, the backtransformation should be the exact inverse of the transformation in 2). I haven't found any info about how this transformation is done by FS, mri_info does not provide it. Thanks, Frederick __________________________________________________ Do You Yahoo!? Tired of spam? Yahoo! Mail has the best spam protection around http://mail.yahoo.com

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Looking for older versions of mri_normalize
by Andrew H Bell 13 Sep '06

13 Sep '06

To FreeSurfer Community, I've looking for older versions of mri_normalize - in particular mri_normalize.041022 I am working with monkey volumes and have found that this version gives me the best results. Thanks Andy Andrew H. Bell, PhD Visiting Post-Doctoral Fellow Laboratory of Brain and Cognition National Institute of Mental Health 49 Convent Drive Building 49, RM 1B80 Bethesda, MD 20892 office: (301) 496-5625 ext.260 fax: (301) 402-0046 mobile: (202) 679-1279 bellah(a)mail.nih.gov

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Freesurfer September 2006