Freesurfer

freesurfer@nmr.mgh.harvard.edu

18 participants
30066 discussions

Converting hyperfine MRI to nifti
by Fatima Karim 29 Aug '23

29 Aug '23

External Email - Use Caution Hello My lab is trying to analyze hyperfine acquired MRI using freesurfer. We are stuck at the step where freesurfer converts the dicom to nifti for analysis. Freesurfer cannot recognize the hyperfine as a manufacturer and exiting with this error. Can you please share the script you used to analyze hyperfine images starting from conversion till the end with me? Best Fatima Get Outlook for Android <https://secure-web.cisco.com/16jfFKrMp4E5uGCHCwQmLcL0M2XuJLc2D1i3F2Ezs1kUcA…>

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Password for extracting VM files
by TISSOT Ugo (NCPS) 29 Aug '23

29 Aug '23

External Email - Use Caution Hello, I am going through the installation of Freesurfer with VM and Ubuntu, could you provide me the password needed to finish it? Best regards, U.T

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[FreeSurfer] ValueError axes don't match array
by Cerri, Stefano,PHD 29 Aug '23

29 Aug '23

External Email - Use Caution Hi Krystal, Can you send your samseg command and the output of mri_info on both the T1 and coregistered FLAIR images? It seems that the two images have different image sizes. Stefano Subject: [Freesurfer] [FreeSurfer] ValueError axes don't match array Date: Tue, 22 Aug 2023 04:22:09 +0000 From: Krystal Xiwing Yau <krystaly(a)hku.hk><mailto:krystaly@hku.hk> Reply-To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu><mailto:freesurfer@nmr.mgh.harvard.edu> To: freesurfer(a)nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu> <freesurfer(a)nmr.mgh.harvard.edu><mailto:freesurfer@nmr.mgh.harvard.edu> External Email - Use Caution Dear FreeSurfer experts, I have completed the processes of coregistration of FLAIR to T1 image for the subject. As I ran samseg with lesion contrast, the following error message occurred: writing template transform to /home/admin1/freesurfer/subjects/103_samsegOutput/template.lta writing talairach transform to /home/admin1/freesurfer/subjects/103_samsegOutput/samseg.talairach.lta atlas registration complete: 0:00:17.614971 /home/admin1/freesurfer/python/lib/python3.8/site-packages/numpy/core/_asarray.py:83: VisibleDeprecationWarning: Creating an ndarray from ragged nested sequences (which is a list-or-tuple of lists-or-tuples-or ndarrays with different lengths or shapes) is deprecated. If you meant to do this, you must specify 'dtype=object' when creating the ndarray return array(a, dtype, copy=False, order=order) Traceback (most recent call last): File "/home/admin1/freesurfer/python/scripts/run_samseg", line 190, in <module> _, _, _, optimizationSummary = samseg.segment( File "/home/admin1/freesurfer/python/packages/freesurfer/samseg/Samseg.py", line 255, in segment self.preProcess() File "/home/admin1/freesurfer/python/packages/freesurfer/samseg/Samseg.py", line 318, in preProcess self.imageBuffers, self.transform, self.voxelSpacing, self.cropping = readCroppedImages( File "/home/admin1/freesurfer/python/packages/freesurfer/samseg/SamsegUtility.py", line 139, in readCroppedImages croppedImageBuffers = np.transpose(croppedImageBuffers, axes=[1, 2, 3, 0]) File "<__array_function__ internals>", line 5, in transpose File "/home/admin1/freesurfer/python/lib/python3.8/site-packages/numpy/core/fromnumeric.py", line 653, in transpose return _wrapfunc(a, 'transpose', axes) File "/home/admin1/freesurfer/python/lib/python3.8/site-packages/numpy/core/fromnumeric.py", line 55, in _wrapfunc return _wrapit(obj, method, *args, **kwds) File "/home/admin1/freesurfer/python/lib/python3.8/site-packages/numpy/core/fromnumeric.py", line 44, in _wrapit result = getattr(asarray(obj), method)(*args, **kwds) ValueError: axes don't match array Would somebody be kindly advise? Thank you. Regards, Krystal Tel.: +852 2255 5024 Fax: +852 2872 5828 Address: Room 304, 3/F, New Clinical Building, 102 Pokfulam Road, Hong Kong.

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Freesurfer Windows instalation
by Dominika Życka 29 Aug '23

29 Aug '23

External Email - Use Caution Hi, I'm having trouble installing Freesurfer on Windows. I want to use Virtual Machine to open FS_7_2_0_Ubuntu_18_04_06.ova.7z file. Could I get the password for this file please? Freesurfer would be very useful in my research on the analysis of brain symmetry in neurodegenerative and neuropsychiatric diseases. Best regards, Dominika Życka-Malesa Warsaw University of Technology, Faculty of Mathematics and Information Science

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Cerebellum ROI
by Gomar, Jesus 28 Aug '23

28 Aug '23

External Email - Use Caution Hello Freesurfer developers, I want to create a ROI in fsaverage space including only certain regions of the cerebellum cortex. Is it possible to use/extract the labels from the "# Cerebellar parcellation labels from SUIT" or "# Cerebellar lobule parcellations" in the FreeSurferColorLUT color table file? - FreeSurfer version freesurfer-linux-centos6_x86_64-7.2.0.tar.gz - Platform CentOS 6 x86_64 (64b) - Ubuntu 18.04.6 LTS I would appreciate any advice on how to proceed to achieve this. Thank you! Jesus The information contained in this electronic e-mail transmission and any attachments are intended only for the use of the individual or entity to whom or to which it is addressed, and may contain information that is privileged, confidential and exempt from disclosure under applicable law. If the reader of this communication is not the intended recipient, or the employee or agent responsible for delivering this communication to the intended recipient, you are hereby notified that any dissemination, distribution, copying or disclosure of this communication and any attachment is strictly prohibited. If you have received this transmission in error, please notify the sender immediately by telephone and electronic mail, and delete the original communication and any attachment from any computer, server or other electronic recording or storage device or medium. Receipt by anyone other than the intended recipient is not a waiver of any attorney-client, physician-patient or other privilege.

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CSF map
by Michael Mc Laughlin 28 Aug '23

28 Aug '23

External Email - Use Caution Hi, recon-all does not seem to produce a map of CSF. My research is especially interested in how CSF is distributed. Is there a way to get this? Michael McLaughlin,

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Questions about the different ways in which metrics such as the cortical surface area can be extracted in Freesurfer
by 1500787798 28 Aug '23

28 Aug '23

External Email - Use Caution Dear FreeSurfer developers,       When I extract the surface area of the brain regions corresponding to the DK atlas in fsaverage space with the following command, the corresponding DK atlas brain regions calculated after summation or averaging, whether using lh.area or lh.area.pial, do not match the values of the surface areas directly extracted from the lh.aparc.stats file. I'm curious to know why this is the cause?  mri_surf2surf --srcsubject $subject --sval area.pial --src_type curv \   --trgsubject fsaverage --trgsurfval $SUBJECTS_DIR/$subject/lh.area.pial.fsaverage.mgh --trg_type curv --hemi lh Best, Jinfeng Hou

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Re: [Freesurfer] Copy geometry (fov position) from one header to another while keeping voxel and matrix sizes unchanged
by Douglas N. Greve 28 Aug '23

28 Aug '23

External Email - Use Caution Sorry, I don't have your previous email so I don't know what the context is. Can you resend this email with the previous exchanges included at the bottom? Also, please remember to send to the FS list instead of us personally. thanks! doug On 8/24/2023 6:01 PM, Proulx, Jean Sebastien wrote: > Thanks for the suggestion! The two fov indeed don't align in freeview. > I played a little with the --no-resample option but did not acheive > what I wanted. > > Here I simplified the problem to two single-slice images (run1.nii.gz > and run2.nii.gz attached) acquired the same way (same resolution) but > in two different positions in scanner space. In freeview it looks like > this: > freeview anat.nii.gz run1.nii.gz run4.nii.gz > > > I need the fov to align, but the data to not change at all (because > the fov moved with the patient's head during the experiment). > > To get the transformation, I ran > tkregister2 --mov run4.nii.gz --targ run1.nii.gz --regheader --reg run4to1 > and clicked "save reg" without touching anything. It spits out the > following matrix > 0.99988 -0.01117 0.01053 -0.63259; > 0.01065 0.99879 0.04792 -0.70029; > -0.01105 -0.04780 0.99880 -3.93196; > 0.00000 0.00000 0.00000 1.00000; > Is this indeed the run4 to run1 transformation matrix? Do you know of > a way to get that transformation without user information? > > Then I thought > mri_vol2vol --mov run4.nii.gz --targ run1.nii.gz --reg run4to1 > --no-resample --o run4to1.nii.gz > would do the trick but no, the run1.nii.gz and run4to1.nii.gz don't > align, just like in the image above, as if the transformation is not > actually applied. > > Allowing resample > mri_vol2vol --mov run4.nii.gz --targ run1.nii.gz --reg run4to1 --o > run4to1.nii.gz > makes the two field of view align in freeview but the data is altered. > > It looks like the transformation is not actually applied so that only > the intersecting voxels are effectively resampled. > > There is no error message. > > I tried the dev environment and stable711. > > I tried renaming the run4to1 registration file to run4to1.lta and I > get the folloing error from mri_vol2vol: > regio_read_register: loading lta > error: Cannot allocate memory > error: LTAalloc(675792816): could not allocate xforms > > I tried renaming the run4to1 registration file to run4to1.xfm and > nothing changes (no error but the registration still does not seem to > be applied). > > Any idea what's going on? > > Thanks a lot for your help and > Good evening! > Sebastien

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Import Matlab SynthSeg labels to FS
by Haley O Higginbotham 28 Aug '23

28 Aug '23

External Email - Use Caution Hi, I experienced issues with segmentation (exclusion of large portion of cerebellum) and so used SynthSeg in Matlab (as the built-in mri_synthseg in freesurfer wasn’t working on my computer) to create the segmentation. Does anyone know how to import the resultant 3D categorical array containing the labels back into freesurfer (for the sake of further manipulating it in freeview and replacing the aseg file)? Best, Haley

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mri_watershed Error while running recon-all
by Iman Kianian 27 Aug '23

27 Aug '23

External Email - Use Caution Hi there, I was trying to extract the hippocampus parts of a T1 MRI dataset with 292 samples as it is mentioned in the documentation (" https://secure-web.cisco.com/1BAyhN9FdUHAAqUD8DOQTWc8CqCVlTa3xgiGxxFItgCG2A…"). when I was trying to use the recon-all command, after almost 1 hour of processing I encountered this error: """ mri_watershed Error: GLOBAL region of the brain empty ! Command exited with non-zero status 1 """ I appreciate your time for helping me. Note that I attached the recon-all.log for your review if it is needed.

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