Freesurfer December 2022

freesurfer@nmr.mgh.harvard.edu

75 participants
92 discussions

[WARNING: ATTACHMENT UNSCANNED]Volumetric extraction from volumetric mask in MNI space
by Beatriz Cavendish 23 Dec '22

23 Dec '22

External Email - Use Caution Hello, I would like to know the step by step to obtain volume (mm3) from a volumetric mask in the MNI space (follow the attached nifti file). I checked the forum but the tutorials are for surface extraction and cortical thickness. Yours sincerely, -- Beatriz Araújo Cavendish, MSc PhD student | Psychologist University of São Paulo São Paulo/SP - Brazil

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Re: [Freesurfer] lh.pial lh.pialT1n same file?
by Renew Andrade 22 Dec '22

22 Dec '22

External Email - Use Caution Dear Yujing: I wasn’t aware that there was an answer to my email that’s the reason it took me a while to write back. But I answer here. Yes I mean lh.pial.T1. I don’t have any other lh.pial. The recon-all command is properly correct like recon-all -all -i -s -openmp 8. Yes the freesurfer version is 7.1.1. Best, Rene Andrade. Hi Rene, Do you mean lh.pial.T1? Do you have any other lh.pial* files in the directory? What is your recon-all command line? And can you also provide the Freesurfer version you are running? Best, Yujing -----Original Message----- From: freesurfer-boun...(a)nmr.mgh.harvard.edu <freesurfer-boun...(a)nmr.mgh.harvard.edu> On Behalf Of Renew Andrade Sent: Tuesday, December 13, 2022 7:24 AM To: freesurfer(a)nmr.mgh.harvard.edu Subject: [Freesurfer] lh.pial lh.pialT1n same file? External Email - Use Caution Dear experts: I am wondering if lh.pial and lh.pialT1 are the same files. I don’t have lh.pial is that an error from recon-all? Should I rerun recon-all. Or just autorecon-pial? Would that change anything? Best, Rene Andrade. _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://secure-web.cisco.com/1LCc5ul3ZUaRdFDtH5um-8jSLqyO6Y34dKd_-lEHcjceUh… _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://secure-web.cisco.com/1LCc5ul3ZUaRdFDtH5um-8jSLqyO6Y34dKd_-lEHcjceUh… The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Mass General Brigham Compliance HelpLine at https://secure-web.cisco.com/1p9vuo0RkhGo0Iv6s95QbouvIcUud21_PCVthVxZ9GM4V6… <https://secure-web.cisco.com/1p9vuo0RkhGo0Iv6s95QbouvIcUud21_PCVthVxZ9GM4V6…> . Please note that this e-mail is not secure (encrypted). If you do not wish to continue communication over unencrypted e-mail, please notify the sender of this message immediately. Continuing to send or respond to e-mail after receiving this message means you understand and accept this risk and wish to continue to communicate over unencrypted e-mail.

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Asking for a password for my freesurfer
by Rana Fawzy 22 Dec '22

22 Dec '22

External Email - Use Caution Dear freesurfer team,Thanks for the great software with amazing details and capabilities.Thanks too for the help and the free registration code.Now, i am prompted for a pass code to expand the zip file to complete the installation process. Can you please send me the password for (FS_7_2_0_ubuntu_18_04_06.ova) zip file.. In order to be able to install the software on my virtual machine?? I am waiting for your help.Thanks alot Sent from Yahoo Mail on Android

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HELP! PASSWORD TO UNZIP FS_7_2_0_ubuntu_18_04_06.ova
by Ganeshkaran Mouralidaran 21 Dec '22

21 Dec '22

External Email - Use Caution Greetings, I am writing regarding the request to grant the password to unzip FS_7_2_0_ubuntu_18_04_06.ova file Thanks and regards, Ganeshkaran

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Freesurfer question about recon-all
by Rosalia Dacosta Aguayo 21 Dec '22

21 Dec '22

External Email - Use Caution Dear Freesurfer group, Could you tell me which is the flag I need to use to get all the brain parcellation when I run recon-all? It seems I am getting the tables with few volumes and I guess there is something wrong. Best wishes and Merry Christmas, Rosie

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questions about mri_glmfit
by James Brown 21 Dec '22

21 Dec '22

External Email - Use Caution Dear Freesurfer experts, I have 2 questions about the command mri_glmfit and I appreciate your help. 1- Are there any settings or flags that can be used in mri_glmfit to restrict statistical comparison of surface based analysis to specific ROIs rather than whole brain analysis. I would like to show the difference on the brain surface in lobes rather than in sub lobar labels. 2- I understand that the flag "--table" in command mri_glmfit allows for feeding spreadsheets instead of images. Can we restrict the number of columns in this spreadsheet to 8 columns for lobs (frontal, temporal, occipital and parietal) left and right? Also, is there any way to generate a statistical map from the spreadsheet statistics? Thank you and happy holidays :) James

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Tetrahedral mesh
by Donatas Sederevičius 21 Dec '22

21 Dec '22

External Email - Use Caution Hi, is there a tool to make a tetrahedral mesh of the brain from the MRI T1w image and/or its whole-brain segmentation? I need it for the finite elements method. -Don

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mri_sclimbic_seg patch issue?
by daedalus39＠aol.com 20 Dec '22

20 Dec '22

External Email - Use Caution Dear FreeSurfer Developers, We are interested in implementing " mri_sclimbic_seg " from FreeSurfer 7.3.2 and are having trouble getting it to finish processing. When I tried to runmri_sclimbic_seg. I keep getting a python error and the process never finishes.I searched through the forum and it said that this was a known error and thatthere was a patch. When I installed the patch I got the exact same error. The error message is: “ValueError: operands could not bebroadcast together with shapes (4,) (3,)” The link to the forum post is: https://secure-web.cisco.com/1BI_B41UWHwWJM3wQhzsqKLiN64Mdzk_AasgGunt7xAFi2… We tried running it on the test subject “bert” just to makesure the issue is not with our test scan and I got the same error. We are getting the erroreven after installing the patch. Here are the details of the commandline I used to run it and the error message: Command line: mri_sclimbic_seg --s bert --o/usr/local/freesurfer/7.3.2-1/subjects/bert/mri/mri_sclimbic_seg.mgz--write_volumes --write_qa_stat Error: Traceback (most recent call last): File "/usr/local/freesurfer/7.3.2-1/python/scripts/mri_sclimbic_seg",line 1049, in <module> main() File"/usr/local/freesurfer/7.3.2-1/python/scripts/mri_sclimbic_seg", line232, in main segmenter.process_files(**params) File "/usr/local/freesurfer/7.3.2-1/python/scripts/mri_sclimbic_seg",line 578, in process_files post, seg, vox_counts, volumes,mean_probs = self.segment(image) File"/usr/local/freesurfer/7.3.2-1/python/scripts/mri_sclimbic_seg", line498, in segment conformed = self.preprocess(image) File"/usr/local/freesurfer/7.3.2-1/python/scripts/mri_sclimbic_seg", line490, in preprocess processed =image.conform(shape=(*self.inshape, self.nchannels), voxsize=1.0,orientation='RAS', dtype='float32', copy=False) File "/usr/local/freesurfer/7.3.2-1/python/lib/python3.8/site-packages/surfa/image/framed.py",line 574, in conform conformed = conformed.reshape(shape,copy=False) File"/usr/local/freesurfer/7.3.2-1/python/lib/python3.8/site-packages/surfa/image/framed.py",line 515, in reshape delta = (np.array(shape) -np.array(self.baseshape)) / 2 ValueError: operands could not be broadcast together withshapes (4,) (3,) We are beginning to study professional and amateur fighters, and we suspect that shearing/disruptions to the septum pellucidum may have downstream consequences to the connectivity/DTI measures in the septal nuclei, mammilary bodies, etc. Thanks in advance for any help or comments you can provide. Sincerely -Randy

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Re: [Freesurfer] Freeview quit unexpectedly
by fsbuild 20 Dec '22

20 Dec '22

External Email - Use Caution By crashing from the GUI do you mean that you when you try to navigate to open a file, e.g.,   $SUBJECTS_DIR/bert/mri/brain.mgz,  using the freeview GUI Open-> pull down menu that you get the core dump listed below, but it works when your run “freeview  $SUBJECTS_DIR/bert/mri/brain.mgz” from the command line in the terminal window? The core dump shows a memory allocation error on MacOSX.  Some postings indicate setting MallocNanoZone to zero before running your program/command can remedy this, $ bash$ export MallocNanoZone=0 && freeview - but this may not work.   I don’t see any other workarounds for this right now.  I have not seen this error before with freeview on older versions of MacOS, so it may be related to running on MacOS 10.13. - R. On Dec 19, 2022, at 14:03, Addison, Reuben <RAddison(a)mghihp.edu> wrote:I updated the Xquartz yet still same issue. Freeview only works with the command line but the gui is till crashing.  Gkxgears seems to work fine I have attached images of both the crash report and the graphics information about my mac. Reuben A  

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Password to decrypt 7zip Virtualbox Image
by Jaron Shelow 20 Dec '22

20 Dec '22

External Email - Use Caution When I try to extract the 7zip containing the virtualbox image with freesurfer, it prompts me for a decryption password. I can't find it anywhere. Could you help?

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Freesurfer December 2022