Freesurfer

freesurfer@nmr.mgh.harvard.edu

19 participants
30088 discussions

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?

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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

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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

2 1

white matter edit
by Abazid, Leen 26 Feb '19

26 Feb '19

External Email - Use Caution ??Hello, I am a PhD student at the University of Texas in San Antonio. I am working on the PTSD project and we used the FreeSurfer to clean the MRI images of the patients. After we were done cleaning, the statistics analysis of the cingulate structure in the brain was not accurate, this part of the brain is one of the most important structure in the pathogenesis of PTSD. We believe that the FreeSurfer is messing the white matter with the gray matter and interpret what is supposed to be a gray matter as a white matter. So the values are not accurate which is affecting our results. We tried to use the command to edit the white matter but we are not sure if we are doing the correct thing. After the edit and re-running the FreeSurfer again on the white matter, the gray matter values are slightly increasing but the white matter values are increasing and decreasing, so we are not sure what the FreeSurfer is doing exactly and if our edit is correct. This is the command we are using to edit the white matter: freeview -v mri/brainmask.mgz \ mri/wm.mgz:colormap=heat:opacity=0.4 \ -f surf/lh.white:edgecolor=blue \ surf/lh.pial:edgecolor=red \ surf/rh.white:edgecolor=blue \ surf/rh.pial:edgecolor=red \ surf/rh.inflated:visible=0 \ surf/lh.inflated:visible=0 After done cleaning the white matter recon-all -autorecon2-wm -autorecon3 -subjid# Leen F. Abazid Ph.D. Student Neuroscience Imaging at the Research Imaging Institute UT Health Science Center at San Antonio (210) 823-3532

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MRISalloc error during automatic reconstruction
by Julia Ströhlein 26 Feb '19

26 Feb '19

External Email - Use Caution Dear experts, while running one of my subjects, I got this error: MRISalloc(732595, 480): could not allocate vertices Cannot allocate memory Linux xubuntu-VirtualBox 3.2.0-23-generic #36-Ubuntu SMP Tue Apr 10 20:41:14 UTC 2012 i686 i686 i386 GNU/Linux recon-all -s P_04 exited with ERRORS at Mon Feb 4 16:40:03 EST 2019 Do you know what went wrong and how I can fix this? Best regards, Julia

3 9

Alignment to ACPC
by Sadia Sheikh 26 Feb '19

26 Feb '19

External Email - Use Caution Hello Freesurfer experts Freesurfer preprocessed data by(recon-all) are ACPC aligned? If not how can I align my files to ACPC? I read the documents but I am still very confused about the alignment and coordinate system in freesurfer. Thanks in advance Regards Sadia Research Student

2 3

Freesurfer pre-processing on different operating systems
by Tim Schäfer 25 Feb '19

25 Feb '19

External Email - Use Caution Dear Freesurfer experts, we recently got access to a Linux-based cluster computer, and I need to run FreeSurfer pre-processing for several 100 subjects soon. We also have a Mac Pro with many cores that we used in the past and that could take part in the pre-processing. I found an older reference which suggests you should not run the pre-processing for one study on different architectures/operating systems [1] because this may affect the results. Does this still apply to Freesurfer 6? What are your recommendations in this regard? Also, out of curiosity: it is obvious why one should not use different Freesurfer versions, but what are the reasons for the reported differences between architectures/workstations? [1] https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0038234 Tim -- Dr. Tim Schäfer Postdoc Computational Neuroimaging Department of Child and Adolescent Psychiatry, Psychosomatics and Psychotherapy University Hospital Frankfurt, Goethe University Frankfurt am Main, Germany

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