Freesurfer October 2022

freesurfer@nmr.mgh.harvard.edu

89 participants
132 discussions

MRI skewness
by Peled, Noam,PhD 24 Oct '22

24 Oct '22

Dear group, I have a T1 dicoms that looks like that: [cid:image001.png@01D8E7D5.31FD8C20] But the T1.mgz recon-all produces looks like that: [cid:image002.png@01D8E7D5.31FD8C20] How can I fix this skewness? Here is the dicoms info: type: MGH dimensions: 640 x 640 x 243 voxel sizes: 0.390625, 0.390625, 1.000000 type: SHORT (4) fov: 250.000 dof: 1 xstart: -125.0, xend: 125.0 ystart: -125.0, yend: 125.0 zstart: -121.5, zend: 121.5 TR: 700.00 msec, TE: 15.00 msec, TI: -1.00 msec, flip angle: 120.00 degrees nframes: 1 PhEncDir: ROW FieldStrength: 3.000000 ras xform present xform info: x_r = -1.0000, y_r = -0.0000, z_r = -0.4231, c_r = -55.4712 : x_a = -0.0000, y_a = 0.0377, z_a = 0.9059, c_a = 29.9016 : x_s = 0.0000, y_s = -0.9993, z_s = 0.0165, c_s = -19.3352 talairach xfm : Orientation : LIA Primary Slice Direction: coronal voxel to ras transform: -0.3906 -0.0000 -0.4231 120.9404 -0.0000 0.0147 0.9059 -84.8789 0.0000 -0.3903 0.0165 103.5695 0.0000 0.0000 0.0000 1.0000 voxel-to-ras determinant -0.138228 ras to voxel transform: -2.5600 -1.1949 -0.0451 212.8522 -0.0000 0.0467 -2.5601 269.1053 0.0000 1.1031 0.0416 89.3201 -0.0000 -0.0000 -0.0000 1.0000 Thanks! Noam The information in this e-mail may be privileged and confidential, intended only for the use of the addressee(s) above. Any unauthorized use or disclosure of this information is prohibited. If you have received this e-mail by mistake, please delete it and immediately contact the sender.

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mri_segment
by James Brown 24 Oct '22

24 Oct '22

External Email - Use Caution Dear Freesurfer experts, I would like to inquire about the flags "-whi" and "-ghi" in the command "mri_segement". According to FS wiki, the command "mri_normalize" sets white matter voxels around ~110 and gray matter around ~70. - The default white matter high limit in the command mri_segemnt is 125, what is the highest value to consider white matter voxels in an image? Is it 125? - What are the situations where we need to set the gray and white matter voxels at a high limit of 100 and 125 respectively in the command mri_segment? Does the brightness of the image or motion play a role in the decision of choosing high limits values? Thank you, James

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Question about sclimbic
by Zeng, Victor (BIDMC - Keshavan - Psychiatry) 24 Oct '22

24 Oct '22

External Email - Use Caution I receive an error when I try to run the sclimbic module, do you have any suggestions on why this might be happening? : Loaded input image from /mnt/V/Datasets/BSNIP2/Processing/Finished_q2/GP1462~1/mri/nu.mgz Traceback (most recent call last): File "/usr/local/freesurfer/7.3.2/python/scripts/mri_sclimbic_seg", line 1048, in <module> main() File "/usr/local/freesurfer/7.3.2/python/scripts/mri_sclimbic_seg", line 232, in main segmenter.process_files(**params) File "/usr/local/freesurfer/7.3.2/python/scripts/mri_sclimbic_seg", line 577, in process_files post, seg, vox_counts, volumes, mean_probs = self.segment(image) File "/usr/local/freesurfer/7.3.2/python/scripts/mri_sclimbic_seg", line 497, in segment conformed = self.preprocess(image) File "/usr/local/freesurfer/7.3.2/python/scripts/mri_sclimbic_seg", line 489, 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/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/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 with shapes (4,) (3,) Segmentation fault Victor Zeng Beth Israel Deaconess Medical Center Keshavan Lab --

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B0 distortion correction (a clearer question)
by Addison, Reuben 24 Oct '22

24 Oct '22

I sent a question earlier on but I do don’t think I was clearer the first time. I am trying to do a distortion correction using (epidewarp.fsl) epidewarp.fsl \ --mag mag.nii.gz \ --dph dphase.nii.gz \ --tediff YOUR_TE_DIFF --esp YOUR_ESP \ --vsm bold/b0dcmap.nii.gz The issue we collected two field maps one in the AP direction and one in the PA direction (hence I have two different mag and phase volumes). I am not quite sure how if I should create two different maps and keep them in my bold folder for my FSFAST pipeline

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White Matter Hypointensities Not Calculating for Left and Right
by Atwater, Emanuel R 24 Oct '22

24 Oct '22

External Email - Use Caution Hello Freesurfer Team, My issue is within the aseg.stats information. There is WM-hypointensities volumetric data present, however, there are "0's" for Left and Right WM-hypointensities. Why are the hypointensities not being calculated/separated for the left and right hemisphere? FS version: freesurfer-linux-centos7_x86_64-7.2.0-20210720-aa8f76b Aseg.stats: see attached for sample V/r, Emanuel Atwater

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aparcstats2table command
by eso 24 Oct '22

24 Oct '22

External Email - Use Caution Hi Freesurfer experts, I am new to the Freesurfer world ! My question is how to use aparcstats2table to extract data for a large number of subjects (approximately 700 subjects). I have tried to paste the folder path that included all the pre-processed images, but it has not worked. Anything will help Thanks Esraa

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Re: [Freesurfer] Upgrading Operating System (OS)
by fsbuild 24 Oct '22

24 Oct '22

External Email - Use Caution Hello Nárlon, The caveat we post on the web page for the current 7.X releases at https://secure-web.cisco.com/1SH9723fOHUEJDTPhOh9cxPtQV83D227ju0p39…, mentions longitudinal processing should not be adversely affected when switching to a different OS and/or newer version of freesurfer.   Important Note: When processing a group of subjects for your study, it is essential to process all your subjects with the same version of FreeSurfer, on the same OS platform and vendor, and for safety, even the same version of the OS. While we continue to work to ensure that results match across platforms, there are none-the-less system-level libraries that are OS dependent. An exception to this rule is that you may view and edit files across any platform or version, and run some post-processing tools (outside the recon-all stream) if you check with us first (for instance you may run the longitudinal processing with newer versions). Recon-all output can show differences in the floating point output when the compilers we use change or an existing release is run on a different OS. - R. On Oct 19, 2022, at 12:42, Boa Sorte Silva, Narlon <narlon.silva(a)ubc.ca> wrote:        External Email - Use Caution        Dear FreeSurfer team: I just wanted to confirm the potential issues of upgrading the OS. We are running FreeSurfer 7.1.1 on MacOS 10.4.6 and wanted to upgrade to MacOS 10.15. Our data have been analyzed cross-sectionally and we’ll soon run longitudinal analysis. Would upgrading the MacOS on the same machine and same version of FreeSurfer be detrimental to the analysis results of the same data? In particular, would it bias longitudinal analysis results?Thank you for your helpBest regards,Nárlon CássioNárlon Cássio Boa Sorte Silva PhD (He, Him, His)CIHR and MSHR BC/PARF Postdoctoral Research FellowAging, Mobility, and Cognitive Health LabDjavad Mowafaghian Centre for Brain HealthDepartment of Physical Therapy, Faculty of MedicineUniversity of British ColumbiaVancouver, CanadaTwitter: @BoaNarlon_______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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Resmoothing subjects that have already been standardised to fsaverage space
by Akansha Mahesh Naraindas 24 Oct '22

24 Oct '22

External Email - Use Caution Hi I have a query about resmoothing subjects after they have already been standardised to fsaverage space. We were thinking of using the normal steps for smoothing as specified below mri_surf2surf --hemi lh \ --s fsaverage \ --sval lh.gender_age.thickness.00.mgh \ --fwhm 10 \ --cortex \ --tval lh.gender_age.thickness.10B.mgh We are unsure if there is any influence of using fsaverage target as input, as our data is already in this space. As we ran smoothing earlier. Best Akansha

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Getting recon-all stats from SynthSeg 2.0 segmentations
by Young, Jenna M 24 Oct '22

24 Oct '22

External Email - Use Caution Hello all, I'm trying to perform a comparison of the global and regional phenotype statistics produced by `recon-all` with the outputs of SynthSeg 2.0. Based on the wiki, it looks like I should be able to pass the segmentation from SynthSeg to recon-all (somehow) and run it through steps further down the pipeline. My current best guess at a command to do this is: recon-all -autorecon2-pial -autorecon3 -s SUBJECTID -i INPUT_IMAGE.nii.gz At this point, I have 2 questions: 1. Is -autorecon2-pial the correct step to insert the SynthSeg segmentations into the recon-all pipeline? 2. What is the correct way to pass an existing segmentation file to recon-all, and how do you also pass it the original brain image? Thanks in advance for your suggestions. Jenna

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7.2.0 CentOS7 and Ubuntu 18.04
by Alexopoulos, Dimitrios 24 Oct '22

24 Oct '22

External Email - Use Caution We've made system software upgrades recently and of some our data was run using the FS 7.2.0 CentOS 7 build but on Ubuntu 18.04 servers. The outputs look good and there no output errors. Should these data be rerun? Jim ________________________________ The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail.

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Freesurfer October 2022