Freesurfer November 2020

freesurfer@nmr.mgh.harvard.edu

107 participants
149 discussions

Mean Curvature
by Letitia Schneider 29 Nov '20

29 Nov '20

External Email - Use Caution Dear Freesurfer team, When I analyse the mean curvature value of a particular ROI, do I have to control for overall brain curvature, to make sure the results are not driven by individual differences in overall brain curvature? Best wishes, Letitia Schneider

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mri_segstats question
by RENXI LI 29 Nov '20

29 Nov '20

External Email - Use Caution Hi Freesurfer experts: I am trying to extract the mean-time series from the functional image using mri_segstats. However, the cerebral white matter signals were cropped out in my functional images, and the regions that I am trying to extract signal from are close to the cerebral white matter that some voxels at the boundary may not contain any signals. Is there any arguments in mri_segstats that I can use to only extract voxels that has non-zero time-series? Best, Renxi

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Re: [Freesurfer] error: MatrixMultiply: m1 is null
by Hoopes, Andrew 29 Nov '20

29 Nov '20

Hi Noam, Do the volumes look okay? I’m seeing a lot of ‘non-orthogonal axes’ warnings in the log. If that’s not the issue, this could be a bug that’s randomly occurring with parallel recons in v7. Although, I’ve never seen it fail during mri_convert. Can you try to rerun? It might succeed the second time. If not, can you send us the input scan and try again without the -parallel flag. best Andrew From: <freesurfer-bounces(a)nmr.mgh.harvard.edu> on behalf of "Peled, Noam" <NPELED(a)mgh.harvard.edu> Reply-To: FS Help <freesurfer(a)nmr.mgh.harvard.edu> Date: Tuesday, November 24, 2020 at 10:10 PM To: FS Help <freesurfer(a)nmr.mgh.harvard.edu> Subject: [Freesurfer] error: MatrixMultiply: m1 is null Dear FreeSurfer community, I encountered a recon-all error where I couldn’t find on the web. The error message is: “error: MatrixMultiply: m1 is null!”. You can find the complete log attached. I used the stable7.1.1 version. Thanks, Noam

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(no subject)
by Sara Lyn 29 Nov '20

29 Nov '20

External Email - Use Caution Hi Freesurfer experts, I'm doing a surface based volume analysis and wanted to know if there was a flag to regress out eTIV in the model. Thank you

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Mean Curvature for whole hemisphere
by Josue Luiz Dalboni Da Rocha 29 Nov '20

29 Nov '20

External Email - Use Caution Dear FreeSurfer, Why an average whole hemispherical value for mean curvature is not provided by Qdec? Is there geometrical reason? Best regards, Josue

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PETSurfer voxelwise statistic
by Boris Rauchmann 29 Nov '20

29 Nov '20

External Email - Use Caution Dear all, How can I run a voxelwise statistic using grey and white matter uptake? mgx.ctxgm.nii.gz and the other files in output all only include gm as I understand. My goal is to run whole brain volume-based analysis. Like in this example for subcortical analysis: mri_vol2vol --mov subctxgm.nii.gz --reg aux/bbpet2anat.lta --tal --talres 2 --o subctxgm.mni305.2mm.sm00.nii.gz Thanks, Boris

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Splitting a label region?
by Hyon, Justin J. 29 Nov '20

29 Nov '20

External Email - Use Caution Hello, I am wondering whether there is a way to split a labeled region in a volume into 2 labels, perhaps by using the Freeview gui? I just need to roughly split one region generated via one of the default atlases into 2 custom labels. I tried using the tools in Freeview, but I can only seem to edit 1 layer of the volume at a time. Thank You!

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group analysis
by Ambulatorio SNA FEDERICO II 29 Nov '20

29 Nov '20

External Email - Use Caution Dear Freesurfer team, I'm running a group analysis where I'd like to compare myelination between two groups regressing out cortical thickness, age and sex. My FSGD file is: GroupDescriptorFile 1 Title Func Class HC Class CMT Variables Age gender Input fs_VF HC 46 Female Input fs_RF HC 24 Female ....... My group.diff.mtx is: 1 -1 0 0 0 0 0 My command line: mri_glmfit.bin --y rh.t1t2ratio_30_fmed_3sm_decurv.fsavg.mgh --fsgd age_gender.fsgd --pvr rh.thickness_30.fsavg.mgh --C group.diff.mtx --surf fsaverage rh --cortex --glmdir rh_allbrain_t1t2_group_thickness_age_gender.glmdir *But unfortunately I get this wrong message: * RROR: matrix is ill-conditioned or badly scaled, condno = 1e+08 -------------------------------- Possible problem with experimental design: Check for duplicate entries and/or lack of range of continuous variables within a class. If you seek help with this problem, make sure to send: 1. Your command line: mri_glmfit.bin --y rh.t1t2ratio_30_fmed_3sm_decurv.fsavg.mgh --fsgd age_gender.fsgd --pvr rh.thickness_30.fsavg.mgh --C group.diff.mtx --surf fsaverage rh --cortex --glmdir rh_allbrain_t1t2_group_thickness_age_gender.glmdir 2. The FSGD file (if using one) 3. And the design matrix above Attempting to diagnose further SumSq: Min=0.000000 (col 5), Max=146.140350 (col 3) The scale is much different between columns 5 and 3, you may want to normalize by subtracting the mean and dividing by the standard deviation. Column 5, all values are 0 Column 6, all values are 0 Columns 5 and 6 are the same Can you please help me? Thank you very much Raf

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Manual ROIs in PETSURFER
by Jessica Cooperrider 29 Nov '20

29 Nov '20

External Email - Use Caution Hello, I would like to draw a volume of interest on T1 images and then evaluate metabolism changes in this region. Is this possible to accomplish using PETSURFER? Thank you for your time,Jess

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mri_surf2surf (and mri_preproc) clarification
by Daniel Leopold 29 Nov '20

29 Nov '20

External Email - Use Caution Dear Freesurfer experts, The mri_surf2surf example 1 specifies that lh thickness is resampled onto the 7th order icosahedron. Does it place the lh.thickness curv into freesurfer space, or is it still in the subject's native space (i.e., pre-transformation to the fsaverage template)? I used a similar process to downsample subjects' thickness to fs5 resolution, which I then concatenated and used as input for PALM. What I'm now wondering is whether results may be due to misalignment between individual subjects because they were not transformed to the fsaverage template and space. Do the inputs below (-srcsurfval) need to be thickness.fsaverage.mgh (already mris_preproc'd in the recon-all pipeline) instead? mri_surf2surf --hemi lh --srcsubject 1001 --srcsurfval thickness --src_type curv --cortex --trgsubject ico --trgicoorder 5 --trgsurfval ./mgh/1001_lh_fs5_thick.mgh --trg_type mgh –fwhm-trg 10 **Note: My apologies if this re-posts, but it doesn't seem like my initial submission went through** With gratitude, Dan

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Freesurfer November 2020