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30066 discussions

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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TRACULA cluster statistics visualization
by Makenna B McGill 19 Dec '22

19 Dec '22

External Email - Use Caution Hi Freesurfer Developers, I'm using FS v7.2 to conduct along-tract statistics using trac-all -stat, and I was wondering how to best visualize and interpret the results of the cluster-wise correction in freeview. I referenced this page ( https://secure-web.cisco.com/1rtane6ARuP3X8AuU2py8u1aHHy9K5qYs7DI1jVqCAg3GH…) which describes how to do this for uncorrected statistics, and used dmri_trk2trk to try to embed the *perm.th13.abs.sig.cluster.mgh files produced by mri_glmfit-sim into the template .trk files (--in $FREESURFER_HOME/trctrain/hcp/syn/"$tract".display.trk). I also embedded the *perm.th13.abs.sig.cluster.mgh files into the mean path .trk files (--in $FREESURFER_HOME/trctrain/hcp/syn/"$tract".mean.trk). However, I'm noticing inconsistencies in the location along the tract of significant clusters between the projection of the uncorrected statistics in freeview, projection of the corrected statistics in freeview, and the cluster location as indicated by the cluster summary file (*perm.th13.abs.sig.cluster.summary.txt). I've attached the cluster summary file for FA in the rh.cst tract as an example. My understanding is that for pathways with superior-inferior orientation, points along the tract are ordered from superior to inferior. Given that this significant cluster is at a VoxX of 68 (of 80 total points along the tract), I would have thought that this cluster would be located at a more inferior position along the right cst -- instead, the cluster appears to be located superiorly (trk files for uncorrected and corrected statistics for this pathway are attached). Similar to this FS user ( https://secure-web.cisco.com/1MD72Ga_1F-Q0FFmEMhYJe7s5dOdRHRhGL2ZDfR5AWgoRO…) I'm wondering: (1) Am I missing something regarding this embedding process? (2) Is it appropriate to embed the *perm.th13.abs.sig.cluster.mgh file to visualize the results of the cluster-wise correction? Please let me know if there is any other information or attachments you'd like me to provide. Any thoughts on where I might be going wrong would be greatly appreciated. Thank you! Best, Makenna *Makenna McGill *(she/her) Doctoral Student in Clinical Psychology The University of Texas at Austin

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Re: [Freesurfer] Freeview quit unexpectedly
by fsbuild 19 Dec '22

19 Dec '22

External Email - Use Caution I would downloaded and install the latest Xquartz (X-Windows for MacOS) which is version 2.8.3 from https://secure-web.cisco.com/1opXWtR1b08TpiSxuOjmZYBoO9MYN5pgHsuK…;  This was updated only a week ago and contains universal binaries. After you install Xquartz open a new terminal window and type “glxgears”.  An X-Window should pop up showing the spinning gears. % which glxgears /opt/X11/bin/glxgears % glxgears 303 frames in 5.0 seconds = 60.564 FPS 309 frames in 5.0 seconds = 61.607 FPS …... … close glxgears window to exit ... Then at least your X-Windows graphics will be up to date (which might affect the GUI).  Then try your image again. Do you see any warnings, error, info, etc., listed in the terminal window after the freeview command?   If so, please send that along. Maybe you could send along a screenshot of what “about this mac” displays.  That would tell us if you are using a graphics card or the built-in graphics - and also a screenshot of the freeview window. - R.

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cannot create directory freesurfer
by Nazanin Mirzaei 18 Dec '22

18 Dec '22

External Email - Use Caution Hello when i use recon-all, i get this message: mkdir: cannot create directory '/usr/local/freesurfer/7.2.0/subjects/name': Permission denied I did the solutions that were previously suggested on the site, but it still didn't work. Thank you in advance for your help. Best regards, Nazanin Mirzaei

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