Freesurfer November 2016

freesurfer@nmr.mgh.harvard.edu

120 participants
214 discussions

GM = SurfArea x Thick
by Daya P 09 Nov '16

09 Nov '16

Hi all, I grey matter volume supposed to be equal to surface area x average thickness in each ROI when looking at mris_anatomical_stats for individual subjects? Thank you, Daiana

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GM ROI list?
by P Taylor 09 Nov '16

09 Nov '16

Is there an available list of GM regions within the list of regions in the FreeSurferColorLUT.txt? (In particular, I am interested in a list of GM regions output in a default run of recon-all, which seems to have a maximum regionnumber of 2035. But a full list is great, too-- I'm not sure which might be already available or easier to generate.) I had thought of using the segmentation volumes to help me differentiate ROIs. For example, I could get rid of regions that overlap with the WM volume, but I think that the segmentation might come from a slightly different bit of information than the sum of segmented regions. As shown in the attached slice image, if I underlay the WM segmentation volume (color = white), and overlay a "recon-all" parcellation+segmentation map (color = red for GM on right, yellow for GM on left, and green for non-GM) to look for overlap, I see that some of the WM seg volume overlaps with GM ROIs (overlaps are isolated pink-ish voxels and light yellow voxels; one highlighted in cross hairs). I guess this difference occurs because the segmentation volume comes from the surfaces themselves? Anyways, this makes me think that I can't automate finding the GM, and I would rather go from LUT numbers, and hence the above question. Thanks, pt

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latest version of mri_glmfit-sim?
by Elijah Mak 09 Nov '16

09 Nov '16

H <ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mri_glmfit-si…>ello Freesurfer Team, Where may I download the latest version of mri_glmfit-sim and QDEC to run the mri_surfcluster? I am having errors on mri_glmfit-sim and monte-carlo simulations in QDEC (dev version that was released quite awhile back). A snippet of the error below after MC correction in QDEC Searching for Clusters ... thmin=2.000000 (2.000000), thmax=-1.000000 (-1), thsignid=0, minarea=0.000000 Found 36 clusters Max cluster size 2817.874756 INFO: fixing MNI talairach coordinates Pruning by CW P-Value 0.05 ERROR! Error in Monte Carlo simulation: Error running mri_surfcluster! Many thanks for your help. Best Wishes, Elijah

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mri_convert scaling
by Funk, Quentin 09 Nov '16

09 Nov '16

All, I have some DICOM files from a pet scan and an MRI. I viewed the files in three different ways: 1. Opened the DICOM's directly in a viewer (Pmod) 2. Used mri_convert to change the DICOMs to a .nii, and opened them. 3. Used dcm2nii to change the DICOMS to a .nii and opened them. It's my intuition that the raw intensity values are displayed when I directly open the DICOM images. However, both step (2) and (3) give images with intensity values scaled--(2) scales by different factors depending on the modality, anywhere from 16 to 50; (3) scales by a fixed amount (two orders of magnitude, possibly understandable). The images are indistinguishable when the levels are set properly, so this scaling would appear to be a flat linear multiplier. I'd like to know where it comes from--is there some information in the DICOM headers that mri_convert is using to scale things? I checked the archives of this mailing list and found the tag -ns 1, but this didn't change the output file at all. Any help is appreciated. -- Quentin Funk, PhD Houston Methodist Research Institute 713-363-9003 Houston Methodist. Leading Medicine. U.S. News & World Report has recognized Houston Methodist as one of the nation’s top 20 hospitals, placing it for the second time on the magazine’s prestigious Honor Roll. It is also designated as a Magnet hospital for excellence in nursing. Visit us at houstonmethodist.org. Follow us at twitter.com/MethodistHosp and facebook.com/HoustonMethodist. ***CONFIDENTIALITY NOTICE*** This e-mail is the property of Houston Methodist and/or its relevant affiliates and may contain restricted and privileged material for the sole use of the intended recipient(s). Any review, use, distribution or disclosure by others is strictly prohibited. If you are not the intended recipient (or authorized to receive for the recipient), please contact the sender and delete all copies of the message. Thank you.

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1st level fMRI analysis maps looking strange
by Tuominen, Lauri Johannes 09 Nov '16

09 Nov '16

Dear freesurfer, I’m trying to do resting state fMRI analysis in freesurfer. Most of the 1st level analyses look ok, but for few subjects the mas looks strange. Please find an example attached. Could you give me suggestions how to trouble shoot the problem. Thank you! Lauri Tuominen [cid:B7649807-0689-4BEC-A949-1B5D92A4D7C1@partners.org]

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Re: [Freesurfer] mri_gtmpvc error: failed tissue type check
by Donatas Sederevicius 09 Nov '16

09 Nov '16

I followed the processing workflow as described in PETSurfer wiki and gtmseg.mgz was created using gtmseg script as described. I ran this processing for over 100 subjects and only one has failed.

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Recon reprocessing control points error
by Sarah Finnegan 09 Nov '16

09 Nov '16

Hi Bruce, Thanks for your email. I have uploaded the two examples. The first subj001_fs.zip has the control points added but has not been rerun yet. The second subj001_fs_cp.zip has been rerun and the segmentation looks incorrect. Thanks for your input! Sarah ________________________________________

1 0

Area after fsaverage resample
by Lachlan Strike 09 Nov '16

09 Nov '16

Dear FreeSurfer Developers I have a question regarding the area measures for subjects following registration to fsaverage (produced through the qcache flag – lh/rh.area.fsaverage.mgh). What do the values for each vertex represent? Is it correct to state that these measures are in mm2, or are these measures now somehow relative to the corresponding vertex values within fsaverage? Best regards Lachlan

2 1

mri_gtmpvc error: failed tissue type check
by Donatas Sederevicius 09 Nov '16

09 Nov '16

Dear Freesurfer community, An error has occured while applying PET partial volume correction using mri_gtmpvc. A snippet from the log file: Reading /projects/PET/recon/ID247/mri/gtmseg.lta Replacing 18 ERROR: CheckSegTissueType() tissue type for seg 29 Left-undetermined not set Failed tissue type check gtmseg was run as: gtmseg --s ID247 and completed without errors. mri_gtmpvc was run as: mri_gtmpvc --i /projects/PET/processed/ID247/ID247_PIBStatic.nii.gz --psf 2 --no-rescale --seg /projects/PET/recon/ID247/mri/gtmseg.mgz --reg /projects/PET/processed/ID247/PET2MRI.lta --default-seg-merge --o /projects/PET/processed/ID247/gtmpvcYES.output/SGTM/non_scaled --save-input --km-ref 8 47 --km-hb 11 12 13 50 51 52 How could this problem be solved? Thank you. Best regards, Donatas

2 1

nuisance dichotomous variables
by Dominic Dwyer 09 Nov '16

09 Nov '16

Dear FS experts, Sorry for my confusion here, but I'm wondering why dichotomous nuisance variables (e.g., gender) can't be used in qdec? I was thinking that if it uses a generalized linear model then it should be ok? I read other posts and understand why discrete factors can't be used with more than 2 levels, but was thinking that dichotomous variables should be different. NB. we're trying to run a simple two group comparison, but we two dichotomous variables that we want to control for. Many thanks for your help, Dom -------------------------------------------------------------------- Dom Dwyer, PhD Psychiatry & Psychotherapy LMU Munich A: Nußbaumstr. 7, Munich, 80336 E: dominic.dwyer(a)med.uni-muenchen.de T: +49 (0)89 4400 55880

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Freesurfer November 2016