Freesurfer October 2019

freesurfer@nmr.mgh.harvard.edu

111 participants
180 discussions

Re: [Freesurfer] ERROR gtmseg
by Marina Fernández 07 Oct '19

07 Oct '19

External Email - Use Caution Dear Douglas, Thank you for the replay. I think so, I can't find the code 229 in any subject. I can't see anything strange in the aparc+aseg.mgz. The cerebral voxels have the normal segmentation and labels. Could it be a problem with the extracerebral voxels? Best regards, Marina.

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Confidence interval for Cohen's d from gamma/rstd
by Caspar M. Schwiedrzik 07 Oct '19

07 Oct '19

External Email - Use Caution Hi! I have an OSGM from a fixed effects group analysis with mri_glmfit. I would like to calculate the effect size and the 95% confidence intervals. I see from various threads on the mailing list that Cohen's d can easily be obtained from the outputs of mri_glmfit by dividing gamma by rstd. I am wondering now how to compute the 95% CIs for Cohen's d from the outputs of mri_glmfit? Thank you very much! Caspar

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Comparing effects between voxels in a FFX GLM
by Caspar M. Schwiedrzik 07 Oct '19

07 Oct '19

External Email - Use Caution Hi Doug, I would like to test whether an effect that I observed in a given voxel is larger than in other voxels (this is fMRI data). The additional complication is that I would like to stick as close as possible to the original analysis that yielded these effects, which were fixed effects. I am wondering whether that is somehow possible using selxavg3 and mri_glmfit? Thank you! Caspar

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question about aparcstats2table
by chen 07 Oct '19

07 Oct '19

External Email - Use Caution Hi FreeSurfer experts, I want to converts a cortical stats file into a table by the aparcstats2table command. However, there are totally 500 subjects. And it is really hard to input subject numbers one by one. The Numbers are arranged in a regular way. So, can you give me some advices? Thanks a lot. Cheers, Chen

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Vertex by Vertex Analysis
by WON JONG CHWA 07 Oct '19

07 Oct '19

External Email - Use Caution Hello, I would like to perform a group difference analysis with gray-white matter contrast between healthy controls and patients, covarying for the cortical thickness at each vertex throughout the entire brain surface. How would we go about doing this? Thank you.

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question on mris_calc - re-submitting
by Barletta, Valeria 07 Oct '19

07 Oct '19

________________________________ From: Barletta, Valeria Sent: Friday, September 27, 2019 12:30 PM To: freesurfer-bounces(a)nmr.mgh.harvard.edu <freesurfer-bounces(a)nmr.mgh.harvard.edu> Subject: question on mris_calc Dear Freesurfers, I am trying to perform an operation with .mgh files by using mris_calc. This is my operation: (image1 - image2) _______________ (image2) First I am using the command: mris_calc -o $hemi.FILE1.mgh $hemi.image1.mgh sub $hemi.image2.mgh And then: mris_calc -o $hemi.FILE2.mgh $hemi.FILE1.mgh div $hemi.image2.mgh Is this procedure correct? Also, I have read this information about the command mris_calc functions: "Note: <file1> and <file2> should typically be generated on the same subject" But actually, my image1 belongs to a single subject, while image2 is a mean of images from many different subjects (obtained using mri_concat --mean). Is mris_calc going to work in this case? Thank you very much for your help, Valeria

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Error in glmfit-sim cache
by Renew Andrade 07 Oct '19

07 Oct '19

External Email - Use Caution Dear FreeSurfer experts: I have an issue when running correction for multiple comparisons. I enter this (mri_glmfit-sim --glmdir lh.IXI.glmdir --cache 4 abs —cap 0.05 --2spaces) in the terminal and I only receive messages of this sort (ERROR: thresh = 4,0 must be 1.3, 2.0, 3.0, 4.0) What can I do to fix this? Sincerely, Andrade.

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Question about settig up FS-FAST file hierarchy
by Hossein Sanjari Moghaddam 07 Oct '19

07 Oct '19

External Email - Use Caution Dear officer, Greetings. We are working on a set of resting-state fMRI data using Freesurfer. However, in the course of fMRI preprocessing, we are wondering how to correctly set up the FS-FAST file hierarchy. Should be done manually or there is a specific way to automatically manage the FS-FAST file hierarchy. We really appreciate your time and help. Bests, HSM

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TRACULA - input Nifti instead of DICOM?
by Daniel Callow 07 Oct '19

07 Oct '19

External Email - Use Caution Hello Anastasia, I am following up on my previous email about running TRACULA on my subject's NIFTI DWI images instead of dicoms and am running into the following issues which I have had before when trying to use NIFTI files instead of dicoms. Too many ('s. ERROR: must specify as many DWI dicoms as subjects The number of subjects and dwi's listed should all be the same? I have included the dmrirc file to this email as a reference. Any ideas what could be leading to this issue? Is it the way I am naming or referencing the DWI images? Best, *Daniel Callow* *PhD Student, Neuroscience and Cognitive Science* Exercise for Brain Health Lab University of Maryland, College Park *ddcc2442(a)gmail.com <ddcc2442(a)gmail.com>* 443-254-6298

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mask of premotor cortex and primary cortex
by sang ho shin 07 Oct '19

07 Oct '19

External Email - Use Caution Dear Freesurfer Developers, I have analyzed connectivity between striatum and different brain cortex with diffusion weighted MRI. I completed recon-all on all participants. *SHINui-iMac:~ shinsangho$ recon-all -s NOR86_AHJ -i ~/sangho/NOR86_AHJ/NOR86_AHJ_T1/coT1.nii –all* And I processed to get seed mask of DLPFC as follows and got the mask. *SHINui-iMac:nor86_ahj shinsangho$ mri_binarize --i nor86_ahj_fs/mri/aparc+aseg.mgz --match 1027 --o nor86_ahj_dlpfc/nor86_ahj_rostalmiddlefrontal.nii.gz* However, I can't get the mask of both premotor and motor cortex. According to FreeSurferColorLUT, matching numbers are as follows, Premotor - 9002 ctx_lh_premotor, 9502 ctx_rh_premotor Primotor - 9001 ctx_lh_primary motor, 9501 ctx_rh_primary motor While I put any other mgz files(*ex, aparc.a2009s+aseg.mgz, * *aparc.DKTatlas+aseg.mgz..*) in mri folder instead of aparc+aseg.mgz, I was not able to get the mask. The command lines and results are as follows, SHINui-iMac:dti_analysis_kings shinsangho$ mri_binarize --i nor82_pji/nor82_pji_fs/mri/*aparc.a2009s+aseg.mgz* --match *9002* --o nor82_pji/nor82_pji_dlpfc/NOR82_PJI_LH_PREMOTOR.nii.gz $Id: mri_binarize.c,v 1.43 2016/06/09 20:46:21 greve Exp $ cwd /Users/shinsangho/sangho/DTI_analysis_kings cmdline mri_binarize.bin --i nor82_pji/nor82_pji_fs/mri/aparc.a2009s+aseg.mgz --match 9002 --o nor82_pji/nor82_pji_dlpfc/NOR82_PJI_LH_PREMOTOR.nii.gz sysname Darwin hostname SHINui-iMac.local machine x86_64 user shinsangho input nor82_pji/nor82_pji_fs/mri/aparc.a2009s+aseg.mgz frame 0 nErode3d 0 nErode2d 0 output nor82_pji/nor82_pji_dlpfc/NOR82_PJI_LH_PREMOTOR.nii.gz Binarizing based on matching values nMatch 1 0 9002 binval 1 binvalnot 0 fstart = 0, fend = 0, nframes = 1 Found 0 values in range Counting number of voxels in first frame *Found 0 voxels in final mask* Count: 0 0.000000 16777216 0.000000 mri_binarize done Can you tell me how to get the mask of premotor cortex and primary motor cortex? I am looking forward to your help. Best wishes, Sangho ᐧ

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Freesurfer October 2019