Freesurfer

freesurfer@nmr.mgh.harvard.edu

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30064 discussions

Updated instructions for running Freesurfer in a Linux VM (virtual machine)
by fsbuild 26 Feb '24

26 Feb '24

External Email - Use Caution  Instructions about how to setup a VM running Ubuntu 22.04 LTS Linux have been updated on the wiki page,  https://secure-web.cisco.com/1-hfMzPT3UMB77kyvVjV7UDTVoojwvFmLCgo5iFkfwXwZ25LXFS9Roz8W9yuwq3ZMgs5tjQSEKQlcqIQbRxJ1rps2AabjEIivAzU8ekg5AsJLT6mntG2Nc4NnzZYDPJZG2wf_aLnz6uKLNaustProbSHYKiMbskeae7cLki3u_nSnw4xu4chaYhm-Z5kLiuCwcqECsDkdCMoITT-JKqqCHPkmz-brMCz3F9oCcmaqFMirOwqvqcbah9n7ycsFnHd3RDgkGDoMo6zuiX8aecB8B0MO5X6QvJKUslOgGjkBUQ4W4ItrfjjElVnPeg2YV9CgmgVdxPZUx-arGQMnQ7ZyPg/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FVM_67The instructions include how to install and run the current Freesurfer release (7.4.1 from June 2023). Please keep in mind that while the VirtualBox virtualization application runs on hosts with Intel processors, it does not run on arm64 machines (including silicon Macs with M1, M2, M3 chips). - R.

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Segmentation White matter bad
by lejia2011411409 26 Feb '24

26 Feb '24

External Email - Use Caution Dear freesurfer experts, A large amount of subjects got segmentation white matter bad (some dark white matter cannot be recognition below 57 slices). Attachment show this problem. I used 'kvlEMSegment brainmask.mgz 3 4 4 ' to segment white matter again. while there reported kvlEMSegment: command not found. Do you have any solutions for this? Thanks in advance. Best wishes, Lejia

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Re: [Freesurfer] Permission denied error from -localGI
by Douglas N. Greve 26 Feb '24

26 Feb '24

That is weird -- ft_read_mri is not one of our files. Can you send the command line and the *full* terminal output? The lGI stuff is pretty old and does not have a maintainer. On 2/26/2024 1:40 PM, Michael Ruvalcaba wrote: > > External Email - Use Caution > > Hi Douglas, > > Yes I can definitely do that! > > After I run the recon -all part for a specific subject using > freesurfer 7.2.0 in MATALB, I then run the below code: > > %% 4c. Load Freesurfer Pre-Op MRI (do not edit) > addpath('/usr/local/freesurfer_x86_64-7.2.0/matlab'); > fsmri_pre_acpc = ft_read_mri([subdir > '3D_Images/freesurfer_pre-op/freesurfer/mri/T1.mgz']); > > Which gives me the following error: > > /bin/bash: > /scratch/tp0a8d7d21_790a_4945_a04d_b0cc7d38be4f.load_mgh.m.mgh: > Permission denied > > ERROR: could not open > /scratch/tp0a8d7d21_790a_4945_a04d_b0cc7d38be4f.load_mgh.m.mgh for reading > ERROR: loading > /home/knight/ecog/DATA_FOLDER/UCSD/SD11/3D_Images/freesurfer_pre-op/freesurfer/mri/T1.mgz > as MGH > Dot indexing is not supported for variables of this type. > > Error in ft_read_mri (line 401) > ndims = numel(size(tmp.vol)); > > Error in SD11_Recon_Pipeline (line 197) > fsmri_pre_acpc = ft_read_mri([subdir > '3D_Images/freesurfer_pre-op/freesurfer/mri/T1.mgz']); > > > I don't get this error when using freesurfer 6.0.0 and using those > above commands. So I'm guessing it's because freesurfer 7.2.0 is > trying to write something to a scratch file that doesn't even exist? > > Thank you for your help! > > Best, > Michael Ruvalcaba > Knight Lab > Helen Wills Neuroscience Institute > University of California, Berkeley > > > On Fri, Feb 23, 2024 at 10:26 AM Douglas N. Greve > <dgreve(a)mgh.harvard.edu> wrote: > > Can you send more info? Eg, command line, all terminal output, > version of FS you are using? > > On 2/6/2024 6:18 PM, Michael Ruvalcaba wrote: >> >> External Email - Use Caution >> >> Hello, >> >> I had a similar question you had in the past thread >> (https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg72609.html >> <https://secure-web.cisco.com/1zJkMv9aRmMM6PokM8jDCRUGLybtdGCgeH3ZTgzjLrgSV_…>) >> but I cannot seem to access the link where you solved this issue. >> It looks like Tashrif helped you and he informed me to ask you >> >> Can you help me with this by chance? I tried opening an account >> and logging in but it says my account hasn't been approved yet :( >> and I'm not sure who to contact to get it approved. It's been >> months. >> >> Thank you! >> >> Best, >> Michael Ruvalcaba > > The information in this e-mail is intended only for the person to > whom it is addressed. If you believe this e-mail was sent to you > in error and the e-mail contains patient information, please > contact the Mass General Brigham Compliance HelpLine at > https://www.massgeneralbrigham.org/complianceline > <https://secure-web.cisco.com/1NtHoQ5l2JOZE9k3SI7BCp1fNSP7MoxRtpOqh63C_iPwsC…> > . > > > Please note that this e-mail is not secure (encrypted). If you do > not wish to continue communication over unencrypted e-mail, please > notify the sender of this message immediately. Continuing to send > or respond to e-mail after receiving this message means you > understand and accept this risk and wish to continue to > communicate over unencrypted e-mail. >

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if: Expression Syntax - preproc-sess
by Stefano Delli Pizzi 26 Feb '24

26 Feb '24

External Email - Use Caution Hello FreeSurfer Developers, I'm attempting to run preproc-sess with -nomc option preproc-sess -s subj -surface fsaverage lhrh -fwhm 0 -nomc -mni305 -fsd rest -per-run -sliceorder up -force if: Expression Syntax. This error occurred before to create the file with slice timing correction The error did not occur when I run the preproc-sess command line without the -nomc option. I've searched the list and no similar errors have been reported. Does anyone have any thoughts on how to trouble-shoot this one? FreeSurfer version: freesurfer-macOS-darwin_x86_64-7.4.1-20230614-7eb8460 Platform: Darwin Kernel Version 21.6.0

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Re: [Freesurfer] Freesurfer white matter overestimated
by Douglas N. Greve 26 Feb '24

26 Feb '24

It looks like the volume has very poor contrast. What volume are you displaying it on? Can you take a pic on the nu.mgz? On 2/26/2024 2:53 AM, Luisa Klahn wrote: > > External Email - Use Caution > > Dear Douglas, > Please find attached the pictures for the following issue: > I am processing structural data from a 3T scanner using Freesurfer > version 7.3.2. For some subjects, the grey matter looks very thin, and > the white matter looks overestimated. I'll attach screenshots of the > brainmask, wm mask, and T1 including wm and pial surface lines. > I have tried to set control points into the wm but this did not change > the results. > Does anyone have an idea? Would it be possible to change the intensity > settings in the recon-all command? > > Thanks for helping! > Best, > Luisa

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7.4.1 release archive has extra directory prepended
by fsbuild 25 Feb '24

25 Feb '24

External Email - Use Caution  The leading ./ in the path looks like a by-product of needing to use various/different options now in creating the tar archives and also the tar command running may be from a different system.  Not sure that can be reverted. - R.Hi Freesurfer, Wasn’t sure where to post this as the github is more for source code issues.The 7.4.1 archives all have ‘./’ prepended to them (i.e., ‘./freesurfer/’ vs ‘freesurfer/’). This is causing an issue with neurodocker as the definition file it creates  strips the first directory when building images. Thus, containers built on the 7.4.1 archives need to have their paths changed compared to prior versions or they need to strip the first 2 levels of the path. It’s not a big deal and easy to fix in the def files once it's figured out, but given that it’s a departure from prior releases and is breaking some of the downstream tools, perhaps the next releases can go back to just 1 level deep (i.e. ‘freesurfer’)?  Cheers,Dylan Wagner<Attached Message Part.txt>

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recon-all-clinical synthseg error
by Agata Wolna 25 Feb '24

25 Feb '24

External Email - Use Caution Hi! I'm trying to run recon-all-clinical but I'm running into an error with the SynthSeg at the very beginning. Do you have any hints what the problem might be here? Here's the full error message: the following problem occured with image [mypath]/mri/native.mgz : Traceback (most recent call last): File "/usr/local/freesurfer/python/scripts/mri_synthseg", line 303, in predict image, aff, h, im_res, shape, pad_idx, crop_idx = preprocess(path_image=path_images[i], File "/usr/local/freesurfer/python/scripts/mri_synthseg", line 554, in preprocess im, _, aff, n_dims, n_channels, h, im_res = get_volume_info(path_image, True) File "/usr/local/freesurfer/python/scripts/mri_synthseg", line 1456, in get_volume_info im, aff, header = load_volume(path_volume, im_only=False) File "/usr/local/freesurfer/python/scripts/mri_synthseg", line 1377, in load_volume x = nib.load(path_volume) File "/usr/local/freesurfer/python/lib/python3.8/site-packages/nibabel/loadsave.py", line 110, in load img = image_klass.from_filename(filename, **kwargs) File "/usr/local/freesurfer/python/lib/python3.8/site-packages/nibabel/dataobj_images.py", line 503, in from_filename return klass.from_file_map(file_map, mmap=mmap, keep_file_open=keep_file_open) File "/usr/local/freesurfer/python/lib/python3.8/site-packages/nibabel/freesurfer/mghformat.py", line 526, in from_file_map header = klass.header_class.from_fileobj(mghf) File "/usr/local/freesurfer/python/lib/python3.8/site-packages/nibabel/freesurfer/mghformat.py", line 171, in from_fileobj + int(klass._data_type_codes.bytespervox[tp]) * np.prod(hdr_str_to_np['dims']) KeyError: 10 resuming program execution ERROR: some problems occured for the following inputs (see corresponding errors above): [mypath]/mri/native.mgz Error in SynthSeg Best, Agata

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consistency in recon-all parallel pipeline
by Horn, Mitchell Jacob 24 Feb '24

24 Feb '24

Hi FS Devs, I'm experiencing unreproducible thickness results when running any 7+ version with parallelization enabled. Running recon-all without parallelization produces consistent thickness results. I'm running this in AlmaLinux8 (a library-equivalent downstream OS to CentOS8). I'm attaching a table (table1) of 12 recons with bert: * 3 parallelized with CentOS8-compiled 7.4.1 * 3 non-parallelized with CentOS8-compiled 7.4.1 * 3 parallelized with CentOS7-compiled 7.4.1 * 3 non-parallelized with CentOS7-compiled 7.4.1 I suspected the downstream CentOS8 libm was the culprit (because of testing I did this last 2023 summer). I ran 3 more recons parallelized with the CentOS7-compiled 7.4.1, but before running the recon-all command, set LD_PRELOAD to a copy of the CentOS7 libm libraries. The thickness results were then consistent, see the second table below (table2). I could not run this experiment on the CentOS8-compiled version, as that one is obviously not backward compatible with CentOS7 libm. As a quick test of the OS-dependency, I submitted 3 parallel recons on MLSC with 7.3.3. Each reported different thickness. See table 3 (table3). I'm asking if you can please confirm whether running any 7.+ version with parallelization is generating reproducible results for you in CentOS8 (or equivalent)? P.S. - I tested 6.0 (CentOS6-compilation) with parallelization, and the results were consistent. Best, Mitch

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Temporal lobe mask
by Camargo, Aldo 23 Feb '24

23 Feb '24

External Email - Use Caution Hi there, I would like to know where I can find a mask in MNI space for the temporal lobe. Thanks a lot in advance for your help, Aldo Camargo

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overlay activation map on flattened surface
by Atena Akbari 23 Feb '24

23 Feb '24

External Email - Use Caution Hello Freesurfer team, I have flattened the occipital patch using "mris_flatten -w 10 subj04/surf/lh.occip.patch.3d subj04/surf/lh.occip.flattened" and it worked without any error and I can load the flattened patch in freeview. However, I have difficulty overlaying the activation map onto the flattened surface. Is the following command correct for this purpose? (mri_vol2surf --mov spmT_0001.nii --out subj04/surf/lh.bold.flat.mgz --reg fsl_reg.dat.lta --surf occip.flattened --hemi lh) Many thanks, Atena

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