Freesurfer November 2022

freesurfer@nmr.mgh.harvard.edu

80 participants
119 discussions

acompcor in fsfast
by Addison, Reuben 09 Nov '22

09 Nov '22

Hi, I am running resting State functional connectivity and I want to run everything in freesurfer and fsfast. I wanted to know is it is possible to run acompcor in fsfast. If so, how do I go about it. Thanks. Get Outlook for iOS<https://aka.ms/o0ukef>

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Help: Vertex Properties
by Sarah Lavelle 09 Nov '22

09 Nov '22

External Email - Use Caution Hi, I’m wondering if there’s a way to get the properties of individual vertices such as: 1)Coordinates 2)Surface area 3)angles 4) Side lengths 5) distance matrix from other vertices And can you get these properties for individual surfaces/ transformations (eg. On the spherical map or flatmap) ? On the FreeSurfer application or else through matlab? Any help would be greatly appreciated, Thanks, Sarah

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Question about freesurfer default settings.
by Katrina Simon 09 Nov '22

09 Nov '22

External Email - Use Caution Hi, I have a dataset i have run with the default settings of Freesurfer 6.0. A reviewer for a paper recently raised the question "Were T1 images warped with the grey matter preserved? Were volumetric images for the amygdala and hippocampus smoothed?" I have tried to look through the archives and freesurfer papers but dont see anything that directly addresses these aspects, and some help would be appreciated. Thank you! Katrina -- Katrina Simon

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FreeSurfer Hippocampus Segmentation Question
by Jun Yeon Won 09 Nov '22

09 Nov '22

External Email - Use Caution Dear Freesurfer experts, I have a question about hippocampal segmentation. For the hippocampal mask after completing recon-all, is it purely gray matter or does it also include some aspects of white matter and others? Please advise. Best, JW

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Calculating Distortion in mris_flatten()
by Sarah Lavelle 08 Nov '22

08 Nov '22

External Email - Use Caution Hi freesurfers, Does anyone know how to measure the distortion of your inflated surface -> flatmap transformation (using mris_flatten)? When being run, the function outputs "final distance error ...%" in the terminal. What exactly does this mean? and how is this calculated? I would like to research optimal cuts for flatmaps, depending on the region of interest (ROI), so we can minimize the distortion of the ROI itself on the 2D map. If anyone has any ideas on how this can be done or is interested in working with me on this, please contact me via < lavells1(a)tcd.ie> Kind regards, Sarah

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Convert image in native coordinate space
by Haiyun Chen 08 Nov '22

08 Nov '22

External Email - Use Caution Hello FreeSurfer Experts, Could you help to tell how can we convert the file lh.pial.native to Nifti file or Dicom file? The file lh.pial.native is generated by FreeSurfer as mentioned in your website: https://secure-web.cisco.com/1OqLwwMukRA3gBsB4xIyWu7jYzQnxoAsxTmCFH4BX5vUNN… <https://secure-web.cisco.com/1ADHgS0v8L4KAY_-4Q1wqkSQ0S5tB-9JDHvuOQr01nK4OE…> Thank you in advance for your help! Best regards Haiyun

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design is ill-conditioned
by Loeffler, Martin 08 Nov '22

08 Nov '22

External Email - Use Caution Dear experts, I’m running into an error when running selxavg3. It says the design is ill-conditioned. I’m a bit stuck, because the same pipeline works in most subjects, but not all. Also, if I exchange the functional scan (f.nii.gz) with a scan from a working session of the same subject (same number of volumes etc.) I don’t get any errors. I’m grateful for any advice that helps to track down the mistake I’m doing. Here the content of the selxavg3.log file: cd /home/hector/SENS_MAPPING_BLOCK/sessions /opt/software/freesurfer/fsfast/bin/selxavg3-sessbc -s HEC_035_1 -analysis MPBDandefs_orig_lhrh_revd11.5_sm2.lh -no-preproc -fwhm -force Found 42449/139130 (30.5) voxels in mask Creating Design Matrix ... creation time = 0.004 sec DoMCFit = 1 ntptot = 500, nX = 33, DOF = 467 XCond = 2.63784e+16 (normalized) ERROR: design is ill-conditioned Before the error it gives a warning that the design matrix is singular or badly scaled: [Warning: Matrix is close to singular or badly scaled. Results may be inaccurate. RCOND = 1.271035e-17.] [> In fast_selxavg3bc (line 318)] norm(inv(XtX),2) = [14601308845709730.0] Saving X matrix to /home/hector/SENS_MAPPING_BLOCK/sessions/HEC_035_1/bold/MPBDandefs_orig_lhrh_revd11.5_sm2.lh/Xtmp.mat XCond = 2.63784e+16 (normalized) ERROR: design is ill-conditioned >> ------------------------------------------ ERROR: fast_selxavg3bc() failed\n Many thanks in advance, Martin

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Cutting an occipital patch
by Noam Khayat 08 Nov '22

08 Nov '22

External Email - Use Caution Hello, I need to cut the occipital pole in order to make a retinotopy analysis. I read that tksurfer no more exists, and with freeview I only succeed in cutting the plane but I'm having trouble with separating it into a patch with the occipital part only. Do you know if there is a way to do this? Thanks! Noam

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Question about color look up table
by Yoshito Saito 08 Nov '22

08 Nov '22

External Email - Use Caution Hello. I would like to ask a question about the color look-up table. I want to change the opacity of color on a brain atlas in Freeview. I changed the number in a column of opacity in the Color Lookup Table file by following the instructions on this website ( https://secure-web.cisco.com/1DQQao3VQ454IQKL-p8fj3rK0Jciinx1EwjIuNuRgfloa5…) but I could not change the opacity at all. I am using a bit old version of FreeSurfer (ver 6.0) on the HPC of my university, but is this the reason I couldn't change it? I am looking forward to hearing from you. Sincerely, Yoshito -- Yoshito Saito MBBS Master's candidate (Master of Philosophy - Medicine) Melbourne Neuropsychiatry Centre The University of Melbourne

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intensity statistics in aseg.stats
by Zeng, Qi 08 Nov '22

08 Nov '22

External Email - Use Caution Hi Freesurfer scholars, The output of recon-all "aseg.stats" file contains information on volume and intensity statistics of each segmentation of subcortical brain regions. May I ask what is this intensity measurement (e.g. intensity mean)? How is it different from volume? What characteristics of the brain did it try to explain? Thank you! Best, QZ

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Freesurfer November 2022