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30132 discussions

MD with dt_recon?
by Daniel Callow 28 Feb '19

28 Feb '19

External Email - Use Caution Hello, There is no mean diffusivity output with dt_recon. How would you suggest to create MD images? Could you simply divide the adc.nii.gz map by 3? 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

2 1

Correcting Defect error
by Miguel Ángel Rivas Fernández 28 Feb '19

28 Feb '19

External Email - Use Caution Dear Freesurfer devs, I ran the recon-all in one subject and and this process was stopped in the topology correction. In particular during the "CORRECTING DEFECT 36 (vertices=19847, convex hull=5892, v0=94733)". I reviewed the lh.inflated.nofix and the lh.orig.nofix files in Freeview and I noticed that the this error would be located in the lh.inflated.nofix file. How can I fix this problem? I sent to you a screenshot of the lh.inflated.nofix file as well as the recon-all.log file if you want take a look. Best regards, -- *Miguel Ángel Rivas Fernández*

2 1

problem with tkregister
by Barletta, Valeria 28 Feb '19

28 Feb '19

Dear Freesurfers, I am trying to do a registration with tkregister but am experiencing this type of issue: [cid:3aef6350-bea2-40fb-8e20-a58983ab0ce7] The image I should fit is the sagittal view instead of coronal. Is there some way to change it to coronal from the command window? Any other option? Thank you very much, Vale

2 1

Beta extraction
by Jahan, Bushra 28 Feb '19

28 Feb '19

I am wondering how to extract beta values from the clusters of task functional data, particularly output of the multiple comparisons correction? Aava Jahan

2 3

mri_coreg error
by Boris Rauchmann 28 Feb '19

28 Feb '19

External Email - Use Caution Hi FreeSurfer community, when I run mri_coreg I get the following error. /XYZ/2123/mri/brainmask.mgz is in the specified location. Can you help me with this? Thanks! Boris mri_coreg --s 2123 --mov /XYZ/2123.nii --reg 2123.reg.lta Could not set locale No such file or directory Could not set locale $Id: mri_coreg.c,v 1.27 2016/04/30 15:11:49 greve Exp $ cwd /home/demenzbild cmdline mri_coreg --s 2123 --mov /XYZ/2123.nii --reg 2123.reg.lta sysname Linux hostname XXX machine x86_64 user d dof 6 nsep 2 cras0 1 ftol 0.000000 linmintol 0.001000 bf 1 bflim 30.000000 bfnsamp 30 SmoothRef 0 SatPct 99.990000 MovOOB 0 optschema 1 Reading in mov /XYZ/2123.nii WARNING: 78694 NaNs found in volume /XYZ/2123.nii... No such file or directory Reading in ref /XYZ/2123/mri/brainmask.mgz mghRead(/XYZ/2123/mri/brainmask.mgz, -1): could not open file

2 1

Beta Extraction
by Jahan, Bushra 27 Feb '19

27 Feb '19

When I ran the following command (with our data), I got the average beta values for each segmentation i.e. only 5 beta values (as opposed to 5 beta values for each subject). mri_segstats --seg ocn.mgh --i beta.mgh --excludeid 0 --avgwf beta.clusters.dat That said, is it necessarily to run the previous command for each subject (in order to extract 5 beta values for each subject) or is there way to extract betas for each subject from the group analysis?

1 0

registration and resampling in native space
by Francesca Strappini 27 Feb '19

27 Feb '19

External Email - Use Caution Dear Freesurfer's experts, I would like to register some functional data to the T1, that were collected in separate days. I used bbregister: bbregister --s sub3 --mov func_data.nii.gz - --reg register.dat --init-coreg --t1 Now, I would like to resample the data based on the register.dat without upsampling and keeping the same FoV (3x3x3 mm; 64 64 50). Is it doable? Thanks! Best -- Francesca Strappini, Ph.D. Neurobiology Department Weizmann Institute of Science 234 Herzl Street, Rehovot 7610001 Israel Tel.: +972 58 444 2584 E-mail: francesca.strappini(a)weizmann.ac.il

3 17

mri_vol2surf for sampling spmT_0001.nii on pial surface
by Michael Jordan 27 Feb '19

27 Feb '19

External Email - Use Caution Hi, i would like to sample the t-values of a SPM output volume (spmT_0001.nii) onto the pial surface of the same subject. The volume is already aligned to the surface files (so if I view the volume as well as the surface files in Freeview they are already aligned). Therefore I am unsure how to use mri_vol2surf because from my point of view I do not need any registration (srcreg). Nevertheless the registration is required to run the command. I only found the --mni152reg option to avoid specifying a registration. How I should use the mri_vol2surf command to sample the volume onto the pial surface of the same subject under the condition that surface and volume are already aligned? Thank you!

2 3

mask-FA mri_vol2vol issue - followup
by Daniel Callow 27 Feb '19

27 Feb '19

External Email - Use Caution Hello, I am still having the same issue as in my previous post. I have successfully run dt_recon and upon looking at the images there seems to be no issue with the registrations of outputs including the FA, lowb and other images. I wanted to mask my FA images using the wmparc.mgz image from recon-all using mri_vol2vol --mov $subj_dir/dtrecon/${subj}.${cond}./lowb.nii.gz --targ $subj_dir/diffusion_recons/${subj}.${cond}/mri/wmparc.mgz --inv --interp nearest --o /Volumes/DANIEL/dti_freesurf/diffusion_recons/${subj}.${cond}/mri/wmparc2diff.mgz --reg $subj_dir/dtrecon/${subj}.${cond}./register.dat --no-save-reg This works perfectly for all of my subjects except 2 of them. These subjects seem to have normal lowb, wmparc, and FA images compared to the other 58 subjects. However, the wmparc2diff that is created from mri_vol2vol has significantly shifted away from the lowb and fa so that when I try to mask the fa with mri_mask $subj_dir/dtrecon/${subj}.${cond}./fa.nii.gz /Volumes/DANIEL/dti_freesurf/diffusion_recons/${subj}.${cond}/mri/wmparc2diff.mgz $subj_dir/dtrecon/${subj}.${cond}./fa-masked.nii.gz It cuts a large part of the brain off and masks incorrectly. Is there a way to troubleshoot the registration of wmparc to wmparc2diff? I am not sure why the registration is so off? Any troubleshooting help for why the registration of the segmentation to diffusion space is so poor (or if the issue is registration from diffusion space to anatomical space) would be greatly appreciated. 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

1 0

Question about Label
by 310913949 27 Feb '19

27 Feb '19

External Email - Use Caution Hi Freesurfer Pros， I want to know how the label file is generated?Is it the *h.cortex.label generated after mapping the vertices into the space of the fsaverage? If yes, why different subjects dont have the same vertices number of the lh.cortex.label after reconstruction? If not， i used the command line “mri_label2label --srcsubject mysubject --srclabel mysubject/label/lh.cortex.label --trgsubject fsaverage --trglabel lh.reg.cortex.label --regmethod surface --hemi lh” ,that i tried to map the vertices into the space of the fsaverage,but it still have the same vertices,why? I am looking forward to your reply!Thanks. Sincerely, KK

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