Freesurfer November 2022

freesurfer@nmr.mgh.harvard.edu

80 participants
119 discussions

Extracting GWC values from mask
by Fulton, Travis 17 Nov '22

17 Nov '22

External Email - Use Caution Hello FreeSurfer Developers, I am trying to extract gray/white contrast stats for a specific area within a cortical region. I was able generate a mask of the significant area with: mri_binarize --i lh.RegionOfInterest.sig.mgh --o lh.SignificantAreaOfROI.sig.mgh --min 1.3 However, I'm not sure how to extract the values from this mask now. aparcstats2table doesn't have the --stats=lh.w-g.pct.stats option that asegstats2table uses and I'm not sure how to proceed. Is there a way to extract the gray/white contrast stats for this specific area for each of my subjects? Any help would be greatly appreciated! Thank you, Travis Fulton, MS Graduate Student Molecular and Systems Pharmacology Laney Graduate School | Emory University

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Re: [Freesurfer] VMWare: vmw_ioctl_command error
by fsbuild 17 Nov '22

17 Nov '22

External Email - Use Caution Hello Justina, The error message you list is from VMware and not from Virtualbox.  Those are 2 different virtualization applications which expect the Linux operating system virtual machine disk image file to be in different formats.   As far as I know, it will not work to run the Freesurfer VirtualBox VM as is using a VMware application.  The .vdi disk image file we provide as part of the Freesurfer VM download needs to run in the Virtualbox application. Do you have both a VMware application and the VirtualBox application installed on your machine?  If so -  and using VirtualBox to run the Freesurfer VM causes an error to be generated from the *VMware* software, then there is probably a conflict between the 2 applications.  In that case I would uninstall all the VMware software and try running VirtualBox again. - R. On Nov 17, 2022, at 07:38, Justina Lee <justinalee56(a)gmail.com> wrote:VMware: vmw_ioctl_command error Cannot allocate memory

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Password request
by Diana Kollenda 17 Nov '22

17 Nov '22

External Email - Use Caution Dear FreeSurfer team, Could you please provide me with the developer password (version 7.2.0) to open the image? Thank you!, Diana

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VMWare: vmw_ioctl_command error
by Justina Lee 17 Nov '22

17 Nov '22

External Email - Use Caution To the FreeSurfer supporters, Thank you for your time and efforts to help with this issue. I have installed Freesurfer through VirtualBox on Windows system with the following specifications: Processor: Intel(R) Xeon(R) W-2125 CPU @ 4.00 GHz 4.01 GHz Installed RAM: 32.0 GB (31.7 GB usable) System type: 64-bit operating system, x64-based processor The VM is accessing recon-all data stored in an external hard drive (named Local Media E:, space 342 GB free out of 931 GB). The data here is shared through mounting the external drive plugged into the Windows machine in the Ubuntu VM. The current task is to use Freeview through the VirtualMachine for control points to fix Intensity Normalization. I am freely able to access the data successfully run from the recon-all command (see recon-all.log for more information). For this specific data, I have run the command loaded into freeview: developer@developer-VirtualBox: ~/fs-subjects/sub-BE006-T0$ freeview -v meri/brainmask.mgz mri/T1.mgz -f surf/lh.pial:edgecolor=red suf/rh.pial:edgecolor=red surf/lh.white:edgecolor=yellow surf/rh.white:edgecolor=yellow This opens up the data into freeview successfully. I have followed the instructions to set up the Control points through *File -> New Point Set, *enter *control.dat*, and select template volume as *brainmask*. When I click *OK,* Freeview immediately shuts down and shows the following error message: VMware: vmw_ioctl_command error Cannot allocate memory. Aborted (core dumped). I am unable to find any existing issues other users may also have encountered regarding this. Could you provide me a reason as to why this happens? It would help immensely. Additionally, do you have any resources that would allow the parallel command to work on a Windows/Linux operating system? Any resources about this would be great. Thank you and I appreciate your time and efforts. Sincerely, You Na Lee

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mri_volcluster PDF multiple correction
by Vicente Ferrer 16 Nov '22

16 Nov '22

External Email - Use Caution Dear Freesurfer support, My name is Vicente and I have a question for you regarding mri_volcluster. I am interested in using mri_volcluster to correct for multiple comparison after generating a probability distribution function (pdf) via simulation testing. I know mri_glmfit-sim does this however in my study I am analyzing several tracts and therefore doing multiple comparisons that means that after obtaining the clusterwise pvalue I would need to correct for multiple comparisons. Instead of using Bonferroni (too conservative) there is an alternative method called MaxT (https://secure-web.cisco.com/13Z7rv-ZG0oGX2IKry8GaDvm3EW4QqaSUDpOASnWumxYbf…) Probably You already know how it works, basically you create a new distribution choosing the most extreme values in each iteration for your different tests (let’s say 20 different tracts). Usually you do this by selecting the largest Tstat in all of the subjects in each iteration ending up with a new probability distribution with the highest Tstats and therefore the p-value you obtain after comparing your original cluster tstat with the distribution can be considered corrected by multiple comparison. However I tried this and some of the p-values obtained where smaller than using the original pdf from mri_glmfit-sim.I would like to understand better how mri_volcluster does the test between the input file and the pdf file so I can create it properly. I gather that the size of the cluster has an influence both in the input and pdf file but I would like to understand better this.PD: Since I am testing different tracts the searchspace of each is different, could this affect also the testing? I know this is a very specific question, please let me know if I didn’t explain myself correctly. I look forward to your answer. Best, Vicente Vicente Ferrer Predoctoral Researcher BCBL http://secure-web.cisco.com/1Xh37aa15XLHMt4I6yT8yFkeiIiQU6DNsWruCXUSJJaD1w_… Legal disclaimer/Aviso legal/Lege-oharra: http://secure-web.cisco.com/11DVqQesiAlYYXw7EJ5u75OXNizu1qNUooOtomO025GeiRf…

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Tech Support removal
by penamarquezl95 16 Nov '22

16 Nov '22

External Email - Use Caution Hi, Can you please remove my email from FreeSurfer's email support. I don't want to keep receiving emails. Thank you, Sincerely, Luis Pena Marquez President of Graduate Students Association (GSA) [cid:638a6427-c72e-4c44-aebc-2e664d5d262f]

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Unsupported Datatype
by Rachel Wagner 16 Nov '22

16 Nov '22

External Email - Use Caution Hello, I’m getting the following error, not sure how to resolve! developer@developer-VirtualBox:~$ mri_convert dicom-series-005-t2_swi_tra_p2_3mm_Mag.nii dicom-series-005-t2_swi_tra_p2_3mm_Mag.mgz mri_convert dicom-series-005-t2_swi_tra_p2_3mm_Mag.nii dicom-series-005-t2_swi_tra_p2_3mm_Mag.mgz reading from dicom-series-005-t2_swi_tra_p2_3mm_Mag.nii... niiRead(): NIFTI_UNITS_UNKNOWN, assuming mm error: No such file or directory error: niiRead(): unsupported datatype 128 (with scl_slope = 0) in /home/developer/dicom-series-005-t2_swi_tra_p2_3mm_Mag.nii Thanks! Rachel Wagner

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Re: [Freesurfer] Issue with rotation during longitudinal base creation
by Andrew Beaudin 16 Nov '22

16 Nov '22

External Email - Use Caution Hi Nathan, I am reaching out because it looks like we are coming up against a similar issue with Freesurfer's 'mri_robust_template' and I was wondering if you have been able to figure out this error for your images. I am receiving the similar error message calling 'mri_robust_template' directly from the terminal (i.e., outside of Freesurfer's longitudinal pipeline) on our GE T1w images. I also posted my question to the Freesurfer mailing list a while ago (https://secure-web.cisco.com/1RpTwN8ji-OmV4wLBq2ngukhOIFRTuNMes-ZVlDOudKnAn…) but I still cannot find a solution to this problem. Any insights are greatly appreciated. Thanks for the help. Andrew ---- Andrew Beaudin, PhD | Postdoctoral Scholar University of Calgary | Cumming School of Medicine Department of Clinical Neurosciences HSC Rm 2935J, 3330 Hospital Drive N.W. | Calgary, AB | T2N 4N1 Phone: (403) 210-6273

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Original image and the mask file dimension mismatch
by priya padma 16 Nov '22

16 Nov '22

External Email - Use Caution Hello Team, I have a nifti file of dimension (256, 256, 156) but once I run the freesurfer recon-all the subregions mask "*aparc.DKTatlas+aseg.mgz*" has a dimension of (256,256,256) due to this I am unable to view the segmentation overlaid on the original image in any dicom viewer. May I know why freesurfer changes the dimension of the original image and the mask ? Is there any solution for this? Any help will be highly appreciated. Thank you. -- Best Regards Padma Priya *AI Developer * *PhenoMx, Inc.* *priya(a)phenomx.ai <priya(a)phenomx.ai> | (+82)10-5405-2685*

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about using -norandomness flag with recon-all
by Xin Qi 16 Nov '22

16 Nov '22

External Email - Use Caution Hello Freesurfer Team: Because of ensuring that results are exactly the same from run to run, norandomness flag is used with recon-all. To better understand the randomness, we have a few questions listed below. 1. Which algorithms inside the recon-all use the seeded random number? And what randomness is about? 2. Is there a way to use a seed value to ensure the same data can be reproduced? 3. Whether we are compromising anything by going with the non-random option? Thank you very much for your time and looking forward to hearing from you. Best regards Xin

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Freesurfer November 2022