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30083 discussions

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

2 1

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

2 1

Corpus Callosum area
by Fernanda Hansen P. de Moraes 07 Oct '19

07 Oct '19

External Email - Use Caution Dear Freesurfer experts, how can I extract the corpus callosum cross sectional area for each hemisphere? Thank you very much in advance, Fernanda Hansen P. de Moraes fernandahmoraes(a)gmail.com Física Médica | Rede D'Or São Luiz Doutoranda em Ciências Médicas | Instituto D'Or de Pesquisa e Ensino

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mri_surf2vol -lost cluster
by Albrecht, Daniel S. 07 Oct '19

07 Oct '19

Hello everyone, I've been using mri_vol2surf to move some activation data in MNI space to the fsaverage surface with the following command: mri_vol2surf --mov MNIvol.nii --projfrac-max 0 1 0.1 --hemi rh --o rh.out.mgz --mni152reg This works well, but I'm losing a small temporal gyrus cluster that sits close to pial surface. I was assuming this was due to the proximity to the pial surface and resampling, but are there any other options or flags I could use to get this to project successfully? Thanks very much, Dan

2 1

What's the difference between FSFAST and SPM in the 1-st level GLM?
by Zhi Li 07 Oct '19

07 Oct '19

External Email - Use Caution Dear Freesurfer experts, May I ask what's the difference between FSFAST and SPM in the 1st level GLM? Now I use fsfast to pre-process my task-based imaging data, then model the data with FSFAST and SPM respectively. I expected to get very similar results from FSFAST and SPM in the whole brain volume-based analysis. Although there is some overlap between FSFAST and SPM on the whole brain activation, however, there is a lot of difference. Activation in some regions based on SPM was not found in that based on FSFAST. Please see below for my mkanalysis information: mkanalysis-sess \ -fsd Num -mni305 2 -fwhm 8 \ -event-related -paradigm Num.par -nconditions 18 \ -spmhrf 0 -TR 2 -refeventdur 16 -nskip 0 -polyfit 0 \ -hpf 128 -mcextreg \ -analysis Num.sm08.mni305 -per-run -force Any suggestions? In addition, I am not clear if I convert the volume data from FSFAST to SPM in a right way. I replace the mask of subcortical mask with the whole brain mask. Then I convert the pre-processed data from mni305 to mni152 and model it with SPM. However, there is a lot of loss in the prefrontal and subcortical regions. Seems like the whole brain data shrinkage in SPM (please see attached figure). Looking forward to your kind reply. Thanks and best, Li Zhi

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