Freesurfer February 2024

freesurfer@nmr.mgh.harvard.edu

58 participants
83 discussions

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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creating a cortical label using a 3D image ROI and calculating its volume and average thickness
by Yakupov, Renat /DZNE 23 Feb '24

23 Feb '24

External Email - Use Caution Dear Freesurfer users, I would like to do the following: - there is an ROI mask image file in the same space as the T1-weighted image - I would like to use that mask to define the borders of a cortical area - and then calculate volume and average thickness of the above defined cortical area I know that I can get a rough estimate of the volume by applying the ROI mask to the the aparc* file and calculating the number of voxels, but what I would really like to do is use the ROI mask to constrain the WM and pial surfaces to the volume inside the ROI and then calculate statistics using the surfaces approach. I also know that I can combine existing labels, but unfortunately this custom ROI contains parts of various cortical regions, not whole regions. Any advice would be appreciated! Best wishes, Renat.

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How to write rh.w-g.pct from recon-all stats output into a table
by ERNEST KISSI 23 Feb '24

23 Feb '24

External Email - Use Caution I processed several items of data. And I have rh.w-g.pct file in my stats folders. How can I get process this file to get table reading file? I tried to use asegstats2table and aparcstats2table but it didn’t work. Could you provide me with necessary information about getting of stats from rh.w-g.pct to table file like asegstats2table? Thank you.

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Using MRI_segstats to calculate grey matter intensity
by ERNEST KISSI 23 Feb '24

23 Feb '24

External Email - Use Caution Hello freesurfer Team, I have the grey matter segmentation from FSL and I have freesurfer recon-all output but the recon-all outputs do not have regional grey matter intensities. Can I use MRI_segstats to calculate the regional grey matter output using the FSL grey matter segmentation and the recon-all subject hemi parc and subject hemi labels to get the various brain parts and labels for the grey matter?

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Freesurfer February 2024