Freesurfer August 2022

freesurfer@nmr.mgh.harvard.edu

85 participants
120 discussions

primary diffusion direction & surface normal vector
by Zeng, Qi 28 Aug '22

28 Aug '22

External Email - Use Caution Hi Freesurfer experts, After DTI tensor fitting, usually we obtain primary, secondary, and tertiary eigenvectors (V1, V2, V3) and eigenvalues (L1, L2, L3). So what do we use to describe the primary diffusion direction, FA or AD(=L1)? I read the term "surface normal vector" from a paper and the formula r=[Vn * e1|. V presents the surface normal vector, which can be computed using the cross-product between edges. Where can I find this information? The paper named: "Surface-based analysis of diffusion orientation for identifying architectonic domains in the in vivo human cortex" Thank you so much! Best, Qi -- Ph.D. candidate Icahn School of Medicine at Mount Sinai

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Gyrification Index
by Steger Celine 28 Aug '22

28 Aug '22

External Email - Use Caution Dear FreeSurfer experts, I try to explore the Gyrification Index of both hemispheres in a population. For this I computed the LGI using the Freesurfer pipeline and used the command suggested in previous mails: mri_segstats --slabel subject lh $SUBJECTS_DIR/subject/label/lh.cortex --i $SUBJECTS_DIR/my_subject_id/surf/lh.pial_lgi -excluded 0 --sum lh.aparc.pial_lgi.stats Based on:(https://secure-web.cisco.com/1_9wsKWw32_G-UJUtVnh9GwxfZh3NF5eNv2TMJEx0j… With this I get one line of results for this hemisphere in this subject in the file lh.aparc.pial_lgi.stats .... # NRows 1 # NTableCols 10 # ColHeaders Index SegId NVertices Area_mm2 StructName Mean StdDev Min Max Range 1 1 115191 82607.4 Seg0001 3.5515 0.8629 2.1340 5.9443 3.8103 I would like to clarify, which variable is reporting the gyrification index? Thank you for your help and time. Kind regards, Céline Steger

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mris_sphere - cortex incomplete coverage
by Jayashree Chandrasekaran 28 Aug '22

28 Aug '22

External Email - Use Caution Hello, I'm working with the spherical surface generation for the NMT template brain using freesurfer (using NHP-freesurfer pipeline as a guide). I run into the following issue where the spherical surface generated doesn't engulf the entire cortical surface as seen in the screenshot attached. I couldn't find documentation for this command so I'm hoping to get your help. 1) FreeSurfer version: freesurfer 6.0-2017 2) Platform: CentOS Linux 7 (Core) 3) uname -a: Linux 3.10.0-1160.6.1.el7.x86_64 #1 SMP Tue Nov 17 13:59:11 UTC 2020 x86_64 x86_64 x86_64 GNU/Linux [image: Screen Shot 2022-08-04 at 9.38.19 AM.png] Thanks, Jayashree

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mri_fill error : *** Error in `mri_fill': double free or corruption (!prev): 0x00000000014aab70 ***
by 丁晴 28 Aug '22

28 Aug '22

External Email - Use Caution Hello FreeSurfer Developers, I'm attempting to generate filled.mgz using the mri_fill -a */ponscc.cut.log -xform */talairach.lta -segementation aseg.auto_noCCseg.mgz wm.mgz filled.mgz Error : *** Error in `mri_fill': double free or corruption (!prev): 0x00000000014aab70 *** And before the error: INFO: Using /home/qding/FBIP/pipeline/KM_test/2//KM002/mri/transforms/talairach.lta and its offset for Talairach volume ... using segmentation /home/qding/FBIP/pipeline/KM_test/2//KM002/mri/aseg.auto_noCCseg.mgz... reading input volume...done. searching for cutting planes...voxel to talairach voxel transform 1.26345 -0.00883 0.01215 -37.76160; 0.05445 1.62947 0.37797 -140.90414; -0.00773 -0.25421 1.23906 -2.18153; 0.00000 0.00000 0.00000 1.00000; reading segmented volume /home/qding/FBIP/pipeline/KM_test/2//KM002/mri/aseg.auto_noCCseg.mgz voxel to talairach voxel transform 1.26345 -0.00883 0.01215 -37.76160; 0.05445 1.62947 0.37797 -140.90414; -0.00773 -0.25421 1.23906 -2.18153; 0.00000 0.00000 0.00000 1.00000; segmentation indicates cc at (125, 108, 153) --> (3.0, 25.0, 20.0) Looking for area (min, max) = (350, 1400) area[0] = 2589 (min = 350, max = 1400), aspect = 1.11 (min = 0.10, max = 0.75) need search nearby using seed (125, 108, 153), TAL = (3.0, 25.0, 20.0) The details of bug is attached in the attachment. The data come from a macaque.But I can use ""mri_fill" with -CV -PV to generate filled.mgz I've searched the list and no similar error have been reported. Looking forward to your reply.

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R: SAMSEG estimation error
by Cerri, Stefano 28 Aug '22

28 Aug '22

Hi Giulio, This is odd. I've run your scan on my computer two times using both a single thread and 8 threads with the default FS 7.2 and obtained the same results within the same number of threads. Regarding the np.random functions, these are called only by the lesion version -- which, by the way, we have fixed in version 7.3 the seed to obtain reproducible results. Are you sure you're running these commands on the same machine? Stefano ________________________________ Da: giulio siracusano <giuliosiracusano(a)gmail.com> Inviato: sabato 27 agosto 2022 14:15 A: Cerri, Stefano <SCERRI(a)mgh.harvard.edu> Cc: giulio siracusano <siracusanogiulio(a)gmail.com>; freesurfer(a)nmr.mgh.harvard.edu <freesurfer(a)nmr.mgh.harvard.edu> Oggetto: Re: [Freesurfer] SAMSEG estimation error External Email - Use Caution Hi Stefano, thanks a lot for the reply. Unfortunately, I've realized that even when you run the same command with a single-thread (see attached results 1 and 3) you get slighly different results, which are also different against the multi-thread execution (result 2). I've checked the code in Python for samseg (in /usr/local/freesurfer/7.2.0/python/packages/samseg) and I can see there are several calls to np.random, without setting the pseudonumber generator (such as with np.random(1234)). This of course might have implications on the reproducibility of the results, although I think most of the code is in a compiled library. You can check yourself using the file I've shared with you on google drive. I agree with you that, based on the implementation, running SAMSEG with a multi-thread execution (i.e. using --threads flag) causes a non-deterministic behaviour and the results will not be reproducible. Of course, we are talking about very very small variations (<0.1%) among results, but it is something disappointing (at least when using default settings which imply a single-thread execution). Thanks for letting me know about this option when compiling the source code. Regards Giulio On Sat, 27 Aug 2022 at 17:38, Cerri, Stefano <SCERRI(a)mgh.harvard.edu<mailto:SCERRI@mgh.harvard.edu>> wrote: Hi Giulio, Although SAMSEG is a deterministic algorithm the default version might give you different results when executed with a different number of threads. These are small differences when looking at seg.mgz (a few voxels with swapped labels), but they are more visible when looking at volumes computed from soft segmentations like the stats files. Note that you will obtain the same exact results when running SAMSEG with the same number of threads. If you want to have cross-thread reproducible results with SAMSEG you can download the source files of FS 7.2 and build FS with the flag (GEMS_CROSS_THREAD_REPRODUCIBLE ON when doing cmake). Note that this version of SAMSEG will run slower than the original version. Source files can be downloaded here: https://github.com/freesurfer/freesurfer/tags?after=v7.3.1<https://secure-web.cisco.com/1f6_OrrMtkirHO7dyqPm2qDT9b28pekhPVqQDcrIico18J…> and instructions on how to build FS are here: https://surfer.nmr.mgh.harvard.edu/fswiki/BuildGuide<https://secure-web.cisco.com/1CaXd2_aFCyTRvuzpyKfKWpi8AQAZcUmyziYiFtuz41i6X…> Hope it helps, Stefano ________________________________ Da: giulio siracusano <siracusanogiulio(a)gmail.com<mailto:siracusanogiulio@gmail.com>> Inviato: sabato 27 agosto 2022 04:22 A: freesurfer(a)nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu> <freesurfer(a)nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>> Cc: Cerri, Stefano <SCERRI(a)mgh.harvard.edu<mailto:SCERRI@mgh.harvard.edu>> Oggetto: Re: [Freesurfer] SAMSEG estimation error External Email - Use Caution Hi Stefano, I've investigated the use of SAMSEG for AD/MCI patients. I'm using the 7.2 version of Freesurfer and I've realized that I get different results using the same data but when I run the SAMSEG multiple times. Differently from using ASEG, SAMSEG provides also the chance to execute the code using multiple threads. In the first run I've executed SAMSEG on ADNI patient id 002_S_0685 using the MP-RAGE series having ID I18211 (the link below provides the NIFTI version of the series which has been used for the processing). https://drive.google.com/drive/folders/15oghna17Qz-OSuo9E3-rldOt935AEEuO?us…<https://secure-web.cisco.com/1kjcQ6V-ZSEdfK2uygax7NBB93ggYjLmfqbPpwSpeHhQev…> The first execution of SAMSEG was with default settings (1 thread) and results are attached, the second was using --threads 6. These results from the SAME series are similar but they are NOT the same. How can we explain that? Regards Giulio 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/1F9iopsAcv81Y5jnzKuZoZPRhV3AbjEr6rKYyE8cQbZEG5…> .

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Re: [Freesurfer] SAMSEG estimation error
by giulio siracusano 27 Aug '22

27 Aug '22

External Email - Use Caution Hi Stefano, I've investigated the use of SAMSEG for AD/MCI patients. I'm using the 7.2 version of Freesurfer and I've realized that I get different results using the same data but when I run the SAMSEG multiple times. Differently from using ASEG, SAMSEG provides also the chance to execute the code using multiple threads. In the first run I've executed SAMSEG on ADNI patient id 002_S_0685 using the MP-RAGE series having ID I18211 (the link below provides the NIFTI version of the series which has been used for the processing). https://secure-web.cisco.com/1iXLPU1Pah9fJGAnXTC3r119YX5fn9IazKSNeP15n5H0Ek… The first execution of SAMSEG was with default settings (1 thread) and results are attached, the second was using --threads 6. These results from the SAME series are similar but they are NOT the same. How can we explain that? Regards Giulio

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FW: mri_cvs_register on sub mm brain
by Elizabeth Haris 27 Aug '22

27 Aug '22

External Email - Use Caution Hi developers! I am using v7.2.0 recon-all and mri_cvs_register to preprocess and normalise to MNI152. When I use recon-all with the -cm flag to preprocess at min voxel size (0.7mm), recon-all is fine; however, the final output from mri_cvs_register is deformed. When I complete recon-all without the -cm flag, mri_cvs_register seems fine (I assume because these both run in 1mm). Is there any way to use mri_cvs_register to correctly normalise a sub mm brain preprocessed with recon-all? I’ve attached the mri_cvs_register logs in case they’re of use. I did notice a previous thread on this which was incomplete, so I was hoping to get some further clarification (https://secure-web.cisco.com/1vPiA7tLYYfSCOisjKe6jKEkNpqpDKFmnzqRtM0mX1ess6…) Thanks, Elizabeth

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SAMSEG and statistics
by k3ops＠free.fr 27 Aug '22

27 Aug '22

External Email - Use Caution Hi FreeSurfer community, I recently discovered the SAMSEG application in the FreeSurfer 7.2.0 release and started to give a try on few subjects were FreeSurfer was having a hard time to segment brain structures (due to poor contrast). So I have few questions to harmonize the SAMSEG and FreeSurfer statistical files: 1. "samseg.stats" file is not compliant with the "asegstats2table" application so I was not able to generate a final CSV file with volumetric results Is there another solution? 2. "samseg.stats" file does not provide large brain structures like "BrainSegNotVent" or "SupraTentorialNotVent", is there a way to get them calculated? 3. "samseg.stats" file does not provide left/right or global cortical thickness, is there a command line to execute to get these extra values? Thanks. Best, Florent

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Pass code to unzip file
by Noam Khayat 24 Aug '22

24 Aug '22

External Email - Use Caution Hello, I can't find the code to open the zipped file of the freesurfer virtualbox version. Can you help me with this? Thanks you, Noam

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Freeview quitted unexpectedly
by Danesh kajbaf 23 Aug '22

23 Aug '22

External Email - Use Caution Dear support team, After installing Freeview, I tried to load a volume, while checking how it works with samples, from the subject folder in the Freesurfer folder. Unfortunately after choosing the file, Freeview crashed out and popped up an error message “Freeview quitted unexpectedly!”. I tried with other files and the same happened again, while all these files could be loaded by FSLeyes, so the problem was not with data. I run Apple Diagnostics to find if the problem was with the hardware or OS and there was no issue. Attached is the text file of the error as I copied and pasted it so it might help to tackle the problem. Freeview 2.0 is installed ,via the Freesurfer 7.3.2 package installer, on macOS Catalina 10.15.7, and my MacBook Pro’s part number is A1706. Regards, Danesh

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Freesurfer August 2022