Freesurfer April 2012

freesurfer@nmr.mgh.harvard.edu

123 participants
192 discussions

Identifying meridia in retinotopic maps
by Greg Burgess 10 Apr '12

10 Apr '12

HI freesurfers, I have a few questions that were asked previously, but I don't seem to be able to find (or possibly understand) the answers. 1) I'm displaying polar and eccentricity maps using the rtview script. However, no color wheel appears, and I do not seem to be able to find an option to display it in the tksurfer menus. What colors correspond to the horizontal and vertical meridia? Is there a way to display the color wheel as a legend? 2) If, instead of using rtview, I display the heat maps in tksurfer, how do I know what values correspond to the horizontal and vertical meridia? 3) My fieldsign maps appear very speckled, like red and blue polka dots across all of cortex. However, as far as I can determine, the polar and eccentricity maps look reasonable. As suggested elsewhere, I've applied various amounts of smoothing in the fieldsign-sess call. More smoothing makes it look better, but even with 10mm of smoothing, it's unclear if the fieldsigns are correct. How can I track down the problems with the fieldsign maps? Thanks in advance! --Greg ____________________________________________________________________ Greg Burgess, Ph.D. Staff Scientist, Human Connectome Project Washington University School of Medicine Department of Anatomy and Neurobiology Email: burgessg(a)pcg.wustl.edu

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How to let fsfast process the data not named f.nii.gz?
by Zhen Zonglei 10 Apr '12

10 Apr '12

My raw BOLD data is named func.nii.gz in each run directory. It preprocess-sess reported the ERROR: could not determine format for S0001/obj/004/f, even I provide the –i func option. Is there an easy way to let fsfast process the data not named f.nii.gz ? The version I used is FS 5.1. Thanks Zonglei

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recon-all processing stages
by Ed Gronenschild 10 Apr '12

10 Apr '12

Hi I'm not sure but does the Talairach stage precede the nu-correct stage in version v5.1.0? If so, is there an option to switch these two stages? Cheers, Ed

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mapping label from fsaverage LH to fsaverage RH
by Ritobrato Datta 10 Apr '12

10 Apr '12

Hi All, In the fig attached, I have an area of activation in the LH fsaverage. I have created a label from it. I am wondering if there is a way to map this label to the RH fsaverage surface ? Please let me know. Thanks Ri

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Possible underestimation of eTIV ?
by Cheryl McCreary 09 Apr '12

09 Apr '12

Dear Freesurfer experts, I have recently processed a group of subjects and am interested in the eTIV and brain volume to estimate the brain parenchymal fraction. The values that eTIV from the asegstats seem to be underestimated. I understand that the eTIV is based on an atlas scaling factor determined from determinant of the affine transform to the Talairach atlas. Is the transform to Talairach space completed after the skull has been removed? If CSF surround the brain is missing from the brainmask, would this result in a smaller estimate of total intracranial volume? Our subject population is older with the presence of atrophy. Would you recommend manual editing of the brainmask and reprocessing to include CSF surrounding the brain to get a better representation of the intracranial volume? Thanks for your advice and any clarification of the method can offer. Regards, Cheryl

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Middle Frontal Region
by Vina Goghari 09 Apr '12

09 Apr '12

Hi, Would anyone be able to share some papers that suggest different functions (or the reason for this differentiation) of the caudal and rostral middle frontal region as parcellated by FreeSurfer? Many thanks, Vina Goghari

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Longitudinal Template Edits
by Tate, David Franklin 09 Apr '12

09 Apr '12

We have been using the version 5.1 to do some longitudinal processing on a Mac computer using Lion. Our template results have several areas that concern us and we are wondering the best approach for editing. We believe it is edit the pial surfaces in tkmedit. However, the tutorials are a bit confusing as they seem to contain slightly different steps and in neither place do they provide the kind of detail (i.e., which editing tool to use in tkmedit and if there are any configuration changes needed). We have posted the following screen captures. The first shows is from free view and shows that strange lines in the hippocampus. The last two show attempts at editing but in the posterior part of the brain in the inter hemispheric fissure. Any help would be greatly appreciated. Thanks, [cid:3A68F9FB-CA43-46B6-8D1B-8F0F42243677@v3.uthscsa.edu] [cid:4483FB3B-AB38-4350-973B-A800BD6FD3CA@v3.uthscsa.edu] [cid:220E38D7-5796-47E4-BDE5-DDB75CB6E2AE@v3.uthscsa.edu]

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Reading/loading posterior_* files from hippocampal subfield segmentation
by Irwin, William 09 Apr '12

09 Apr '12

Hi- This is probably a question for Koen, but perhaps others could help me out. I want to read into Matlab the 'posterior_*.mgz' files generated by the subfield segmentation. I'm not exactly sure the format/content of these files, but in addition to any information (e.g., some coordinate reference), I'm assuming it contains the posterior probability (0 - 255, scaled) for each (sub) voxel for each of the regions/fields. I tried the obvious Matlab file (i.e., load_mgh.m), but that results in an error (the current Matlab directory contains the files and if I include the full path the same error obtains): >> [vol M] = load_mgh('hippoposterior_right_CA4-DG.mgz'); gzip: hippoposterior_right_CA4-DG.mgz.gz: No such file or directory ERROR: problem reading fname SWITCH expression must be a scalar or string constant. Error in load_mgh (line 156) switch type Given what I know (or think I know) about the procedure by which the subfields are labeled, it likely isn't surprising the genearl Matlab scripts don't properly deal with the posterior subfield files. My objective is to be able to evaluate the distribution of voxels values (posterior probabilities) which exist for each of the subfields/regions. Thanks, Wil

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mpr2mni305 failed for 2 subjects.
by Zheng Hui 09 Apr '12

09 Apr '12

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grid overlay?
by Phiroz Tarapore 06 Apr '12

06 Apr '12

Hello, I have been trying to figure out if it is possible to overlay a grid on a surface (such as the regular non-inflated pial surface). I would like the grid to ignore the cortical convolutions and follow just the overall curvature of the cortex. I am trying to represent a grid of electrodes on the surface of the cortex, as would be placed in the operating room for surface cortical recordings (ECOG). Is there a way for me to do this? Thanks for your help. Phiroz

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Freesurfer April 2012