Freesurfer

freesurfer@nmr.mgh.harvard.edu

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30070 discussions

Error Sourcing Freesurfer
by Turco, Isabella 02 May '23

02 May '23

External Email - Use Caution Hello, When trying to source Freesurfer version 7.1.1 using the command below, I'm getting the error "No such file or directory." source /usr/local/freesurfer/fs-stable711-env-autoselect Any guidance on potential solutions would be much appreciated! Thanks, Isabella Isabella Turco, B.S. Senior Clinical Research Coordinator Massachusetts General Hospital Department of Anesthesia, Critical Care and Pain Medicine 617-643-2896 iturco(a)mgh.harvard.edu<mailto:iturco@mgh.harvard.edu>

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Re: [Freesurfer] mri_normalize error MP2RAGE
by Douglas N. Greve 02 May '23

02 May '23

External Email - Use Caution The current versions of FS require an intensity normalization step be run on 7T data prior to running it through FS. I have used SPM VBM for this, but I think samseg should work too, eg, samseg --i t1.mgz --o samseg Then use samseg/mode01_bias_corrected.mgz as input to FS. On 5/2/2023 10:28 AM, Jastrzebowska, Maya Anna wrote: > > External Email - Use Caution > > Dear Doug, > > I'm having the same issue as numerous others have described: a failure > to run the Intensity Normalization step of recon-all on a single > subject's skull-stripped T1-MP2RAGE 7T data, with the following error > displayed in the log file: > > mri_normalize -g 1 -seed 1234 -mprage -noconform nu.mgz T1.mgz > > [...] > > 3d normalization pass 1 of 2 > > error: MRInormFindControlPoints: could not find enough control points > > error: MRInormFindControlPoints failed > > I am attaching the log file here. > > I am able to run recon-all without errors for other subjects with the > same sequence and preprocessing steps (removing MP2RAGE background > noise as suggested by Marques et al., bias correction and > skull-stripping). > > Please let me know if a solution has been found for this issue. Thank > you in advance for your help! > > Best, > > Maya Jastrzebowska > > >

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mri_synthseg problem with CT... freesurver v 7.3.2
by Gonzalo Rojas Costa 02 May '23

02 May '23

External Email - Use Caution Hi: I downloaded some CT from OASIS 4 database... I tried to segment it using mri_synthseg (freesurfer v 7.3.2)... But I got bad results... Only I got the segmentation of one region of the brain... Also, I do the crop of the image, and the threshold from 0-80 hounsfield units... Sincerely, Gonzalo Rojas Costa Department of Radiology Clínica las Condes Lo Fontecilla 441, Las Condes, Santiago, Chile. Tel: 56-2-2105170 Cel: 56-9-97771785

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QDEC Alternative
by Lauren Stephens 02 May '23

02 May '23

External Email - Use Caution Dear Freesurfers, We are looking to do a voxel-wise analysis on cross sectional and longitudinal data. We wanted to use QDEC but see that it is no longer maintained and has been removed in version 7.3.2 which we are using. Is there going to be a GUI replacement released in the near future? Are there alternatives for QDEC besides the command-line analysis, or potential third-party alternatives that are compatible with freesurfer? Thank you, Lauren

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covariates in 2nd level anaysis
by Maria Czarnecka 01 May '23

01 May '23

External Email - Use Caution Dear Sisters and Brothers in neuroscience I am analyzing functional data in FSfast in Freesurfer. I define my conditions in an osgm file, then I create contrasts. On the second level, I would like to add two covariates (scanning facility and handedness). I don't need contrasts, I just need the model to account for the variance. Can I define both osgm and fsgd files? How do I construct the fsgd? I will be grateful for your suggestions. Best, Maria Czarnecka

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VirtualBox VM
by Aqeel Mohamed 01 May '23

01 May '23

External Email - Use Caution Hi, I have recently downloaded Freesurfer and am planning on using VirtualBox VM. I was wondering if I could please have the password to open the .7z file of the Freesurfer image? Many thanks! Aqeel

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Pass code for FS_7_2_0_Ubuntu_18_04_06.ova.7z
by Nathan Santana Schunk 30 Apr '23

30 Apr '23

External Email - Use Caution Hi, I would like to request the pass code needed to extract the FS_7_2_0_Ubuntu_18_04_06.ova.7z archive. Thanks in advance.

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Fwd: questions about mri_normalize
by Fischl, Bruce R.,PHD 28 Apr '23

28 Apr '23

External Email - Use Caution Hi John 1. We empirically set it at 2, but that was a long time ago, but the optimal number is dependent on a lot of things, mostly image CNR. If the gray/white contrast is good enough you can run it for more, but you have to make sure that the normalization doesn’t start creeping into the gray matter. It is essentially a coarse segmentation that tries to find the bulk of the wm, then normalize it to 110. In regions of low gray/white CNR it would sometimes start normalizing the deeper layers to 110 at which point the thickness and surface placements will of course be wrong. 2. Yes, if the wm is not around 110 then something went wrong. You can also just put a single control point in the body of the wm, but I don’t think I’ve seen it not center most of the wm on 110, so maybe something else is going on? Cheers Bruce External Email - Use Caution Dear experts, I have been using the mri_normalize in FSv7.3.2 to standardize the intensity of FLAIR images , and I've observed that increasing the sigma parameter up to 25 is effective in improving the quality of the normalized images for noisy datasets. mri_normalize -sigma 25 -g 1 FLAIR_skullstripped.nii FLAIR_skullstripped_norm.mgz However, I have questions about the n argument, which is set to 2 by default. For noisy images, white matter intensity after normalization is around 140-150. When using n=10, I noticed that the white matter intensity decreased from 140-150 to around 110-120, resulting in better quality normalized images. 1) I'm wondering if there is a cut-off value for the number of iterations, or if a higher number of iterations always yields better results. 2) Also, if the intensity of the white matter after normalization is not around 110, but instead around 140 or 150, does that indicate that the normalization was not effective and that we need to increase the number of iterations? Thank you for your assistance. John

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substantia nigra
by Lund, Anina 28 Apr '23

28 Apr '23

External Email - Use Caution Hi, Is it currently possible to extract metrics (volume, thickness, or area) of the substantia nigra with freesurfer?

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parallel recon-all using T1,T2 images
by Toshiharu Kamishikiryo 28 Apr '23

28 Apr '23

External Email - Use Caution Hello Freesurfer experts I am trying to recon-all using T2 images as well to improve pial surfaces. Does anyone know how to use GNU Parallel in bash to run the following commands in parallel? recon-all -subject subjectname -i /path/to/T1w.nii -T2 /path/to/T2w.nii -T2pial -all -qcache Thanks in advance. Regards Kamishikiryo Research Student

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