Freesurfer

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30083 discussions

recon all
by 郑凤莲 01 Feb '21

01 Feb '21

External Email - Use Caution Hi experts, We have segmented hippocampus using Freesurfer 6.0. I have a question that is there "head motion correct" in this step? If yes, how does it examined? I am looking forward to your reply. Thanks very much. Sincerely, Zheng | | 郑凤莲 | | 邮箱：zhengfenglian0105(a)163.com | 签名由网易邮箱大师定制

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the T2.mgz in subject/mri should be skull stripped or not?
by shan chen 01 Feb '21

01 Feb '21

External Email - Use Caution Hi all, I encountered a problem about the T2.mgz in subject/mri. I ran my data using recon-all -all -i T1path -s name -T2 T2path -T2pial(7.1.1 or 7.1.0), but the results were inconsistent, sometimes the mri/T2.mgz had skull sometimes it didn't. That is weird. I read the recon-all.log T2.mgz with skull, the code is: %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% writing normalized volume to /xx/subject/mri/T2.norm.mgz #VMPC# mri_normalize VmPeak 978796 mri_normalize done @#@FSTIME 2021:01:31:21:55:47 mri_normalize N 18 e 42.55 S 2.36 U 40.16 P 99% M 723884 F 0 R 925502 W 0 c 78 w 4 I 0 O 78480 L 62.01 61.65 61.48 @#@FSLOADPOST 2021:01:31:21:56:29 mri_normalize N 18 61.84 61.65 61.49 mri_mask -transfer 255 -keep_mask_deletion_edits /xx/subject/mri/T2.norm.mgz /xx/subject/mri/brain.finalsurfs.mgz /xx/subject/mri/T2.mgz transfer mask voxels=255 to dst vol Transferring mask edits ('1' voxels) to dst vol DoAbs = 0 MRImask(): AllowDiffGeom = 1 MRImask(): AllowDiffGeom = 1 Writing masked volume to /xx/subject/mri/T2.mgz...done. %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% when it comes to no skull, the code is: writing normalized volume to /xx/subject/mri/T2.norm.mgz mri_mask /xx/subject/mri/T2.norm.mgz /xx/subject/mri/brainmask.mgz /xx/subject/mri/T2.mgz DoAbs = 0 Writing masked volume to /xx/subject/mri/T2.mgz...done. %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% it seems that the pial is not refined by the T2 image if the T2.mgz is with-skull. anybody know what's going on here? Thanks, Yijun.

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report results
by Marina Fernández 01 Feb '21

01 Feb '21

External Email - Use Caution Dear experts, In addition to t and p-value, I would like to report the beta coefficient of the fixed effects in the following regression equation for the vertex showing the max statistic within the cluster that survived multiple comparison correction: y = β0 + β1*sex + β2*age + β3*(sex+age) + e I know that beta.mgh contains the beta estimates corresponding to the intercepts of male and female and the slopes of age for each sex. However, what I need is the beta corresponding to the intercept (β0), and the beta for the slope of sex (β1), age (β2) and sex*age interaction (β3). I also need the residual variance of the model (e), but rvar.mgh contains 4 values, 2 for the intercepts and another two for the slopes. I would really appreciate if you could help me to obtain this information. Thanks a lot in advance Marina

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FW: Re: SAMSEG questions
by Stefano Cerri 01 Feb '21

01 Feb '21

External Email - Use Caution Forwarding Koen's and my answers ________________________________ From: Koen Van Leemput <leempko(a)gmail.com> Sent: 01 February 2021 10:22 To: Stefano Cerri Cc: David Kamson Subject: Re: SAMSEG questions Hi Stefano and David, Regarding GPU/tensorflow issues, Andrew recommended running fspython -c 'import tensorflow' to diagnose what the problem is. Koen On Mon, Feb 1, 2021 at 3:04 AM Stefano Cerri <stce(a)dtu.dk<mailto:stce@dtu.dk>> wrote: Hi David, 1a) It depends on what analysis you are doing, but in general I would correct with SBTIV the longitudinal analysis as well. 1b) I assume you are computing volumes on the seg.mgz file with 3D slicer. The samseg.stats file is computed from "soft segmentations", i.e. probabilistic maps of each individual structure. These maps can be obtained by adding the flag --save-posteriors. 1c) This file is a scaling factor to obtain a certain average intensity in a target structure. It is used later on in the FreeSurfer pipeline for creating the wm mask and surfaces. It is unrelated to volume analysis/correction. 2) On this page (http://secure-web.cisco.com/1VcMQfGu6N_o0lPCGE8rKcisZZBWi7SnvF0e_eGMHnEZteu…) there is a link for downloading the development version. Installation is then similar to Freesurfer 7.1, you just need to change the name of the downloaded file. Remember that it is essential to process all your subjects with the same version of FreeSurfer. 3) If you have both Tensorflow versions, the latest installed version is used. If you have the GPU version installed and the CPU is used, it means that Tensorflow has some problems locating your cuda/cudnn libraries. Unfortunately, I can't help much here. The specific cuda/cudnn libraries depend on your specific OS and GPU graphic card. Also note that the GPU is used only in the last part of the algorithm, during the sampling phase. Hope this helps. Best, Stefano ________________________________ From: David Kamson <dkamson1(a)jhmi.edu<mailto:dkamson1@jhmi.edu>> Sent: 30 January 2021 20:45 To: Stefano Cerri; freesurfer(a)nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu> Cc: leempko(a)gmail.com<mailto:leempko@gmail.com> Subject: SAMSEG questions Hey Stefano, Thanks for the quick responses! Your arxiv.org<http://secure-web.cisco.com/1fCw1M5LHKguprGZaKGYWYPrl-nXSWhkOsGqvsvmcZq9aDp…> paper is very helpful! I was wondering if you could help me with some of the follow up questions: 1) SAMSEG long should compute more consistent longitudinal structural volumes than SAMSEG while detecting better volumetric group differences (cf. Table 1 and Fig 3 of https://secure-web.cisco.com/1GQa4CGwElUY2mW4Sq82w19at83-bnSN-rjbzKNFRS6VfQ…) Yes, using SBTIV for correcting volume changes from different scanners would be beneficial and most probably necessary. * Do you recommend using the SBTIV correction for the longitudinal analyses as well? * The volumes I get if I look at the statistics for SEG in 3D slicer, they differ by up to 2%. Is there another scaling factor applied in the samseg.stats file? * What is the the SUBJ_scaling.txt file referring to? Should I use that to make corrections? 2) The lesion version of SAMSEG long is available in the development version. Enabling the lesion extension can be done by adding the same flag(s) as for the cross-sectional lesion version (--lesion, see the Wiki for details: https://secure-web.cisco.com/1zxjznTdMuBEIc1Dx0NZk6wpPdZ8iSQLZ2MiValYSz09WG…) Thank you! Unfortunately the wiki doesn’t specify how I could get access to the development version? 3) We never conducted extensive experiments for the number of burn-in and samples for the MCMC scheme, but we found that 50 burn-in and 50 samples lead to robust and replicable lesion segmentation results. Increasing these two numbers might increase the lesion segmentation performance, although differences might be minimal and the overall computational cost high. We suggest to not decrease these two numbers as lesion performance could potentially decrease. This is very very helpful! Is there a way to force CUDA for the in the lesion segmentation? In order for me to be able to run the lesion segmentation under Ubuntu, I had to install both the CPU and the GPU tensorflow, and it does not seem to use the GPU at all (TensorFlow puts out the CPU specs but not the GPU and GPU utilization % doesn’t change during the processing). Thank you for the help! David Hi FreeSurfers, Thank you for sharing the new SAMSEG tool, which I consider a major breakthrough in image processing! I have a few questions about using SAMSEG vs SAMSEG_Long: 1. What volumetric differences should I expect between running SAMSEG on individual images, vs. using SAMSEG_Long for the longitudinal analysis? Could I use SBTIV to adjust differences between scans? (all images are FLAIRs preprocessed using mrI_robust_template) 2. Is there currently a way to integrate lesion segmentation into the SAMSEG_long?s longitudinal analysis? 3. What is the expected impact of increasing or decreasing -Burn-In and -Sample numbers for lesion segmentation? Thank you for all the help! Best, Dave Kamson

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Voxel-wise volumes vs APARC volumes
by Mark Wagshul 31 Jan '21

31 Jan '21

External Email - Use Caution Dear Freesurfer experts, I'm stuck on something which I think has to do with how Freesurfer calculates volumes, but can't quite wrap my head around it, hopefully you can enlighten me. I have already produced robust results for our data using region-based cortical volumes, using aparcstats2table. This is in a group of 55 healthy older adults, modeling is using linear mixed effects models. All volumes were normalized with the eTIV. We were hoping on exploring the same models with voxel-wise analyses, and are getting wildly different results. Data were created using mri_preproc, resampled onto fsaverage, and my assumptions was that because of this resampling, we should NOT be normalizing these values to the eTIV. The same regions which were highly significant on the region-based analyses and now not significant at all, and other regions are now showing up as significant. Just as a sanity check, I attempted to reproduce the region-based analyses with these data using the following simple (I thought!) procedure: 1) Created an mgz mask of the region I'm interested in, using mri_annotation2label and mri_label2label 2) Read my volume data (#subjects x #vertices) into Matlab 3) Read my mask into Matlab (yes, I know I can probably do this in Freesurfer, but I'm more comfortable with Matlab!) 4) Multiply them together and take the sum across vertices. 5) Feed the resultant data back into my LME model. Two things are puzzling to me. 1) The highly significant results from the old LME are no longer significant (at the moment, only checked for two of the cortical regions), and 2) The correlation between these new data and the aparc volume are OK, although far from perfect (R2 ~ 0.86). So, I'm obviously missing something here. What is the difference between the two volume calculation methods which could explain these discrepancies? Any help with this would be MOST appreciated! Best, Mark [cid:image004.jpg@01D6F59B.DA0205F0] ____________________ Mark Wagshul, PhD Associate Professor Gruss Magnetic Resonance Research Center Albert Einstein College of Medicine Bronx, NY 10461 Ph: 718-430-4011 FAX: 718-430-3399 Email: mark.wagshul(a)einsteinmed.org<mailto:mark.wagshul@einsteinmed.org> [einstein-logo-rgb] This email message and any accompanying attachments may contain privileged information intended only for the named recipient(s). If you are not the intended recipient(s), you are hereby notified that the dissemination, distribution, and or copying of this message is strictly prohibited. If you receive this message in error, or are not the named recipient(s), please notify the sender at the email address above, delete this email from your computer, and destroy any copies in any form immediately.

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Tkregister2 resolution difference
by Shi, Yuelin 31 Jan '21

31 Jan '21

External Email - Use Caution Dear FreeSurfer, Hi, I'm Yuelin, a graduate student from Caltech. I came across an issue using the Tkregister2 registration GUI: the target scan are always rendered with much lower resolution than the movable scan. This difference in resolution makes it almost impossible to registering details. I wonder if this is a known issue and is there any way to solve that? Any information will be very helpful! Our lab currently uses version "freesurfer-local-build-dev-20200114" (this is what's shown with the "recon-all version" command, but should be 7.0 or 7.1), I also checked some older versions we used before and the same issue exists. Thanks, Yuelin

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Fw: Freesurfer recon all
by Paul, Rahul 29 Jan '21

29 Jan '21

________________________________ From: Paul, Rahul Sent: Thursday, January 28, 2021 3:52 PM To: freesurfer(a)nmr.mgh.harvard.edu <freesurfer(a)nmr.mgh.harvard.edu> Subject: Freesurfer recon all Hi, I just started working on the freesurfer software. I was trying to use recon-all command but there was an output saying XL error detected, and it remained same for more than 6 hours or so. Any idea how I can fix it? Bdw i stopped it running after 8 hours or so. I am using a T1-MRI scan. I am using a MacBook pro (8GB RAM). I am attaching a screenshot and the command I used can be seen in the bottom of the screenshot. Thank you, Rahul Paul

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Parallel computing for recon-all
by Wei Shao 29 Jan '21

29 Jan '21

External Email - Use Caution Hi, Freesufer experts My name is wei shao, I have a few questions regarding the parallel computing of recon-all 1 According to documents, freesurfer is OpenMP code , I use -openmp 8 flag like: recon-all -alli -i input.file -s output.file -openmp 8 to tun the recon command on a server, but it doesn't work for me (the running time is very similar for the same subject). Cloud you tell me what is wrong? 2 Can Freesufer take advantage of several GPUs? 3 Is it possible to open few threads to run recon-all on different sections parallelly? Best, Wei

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FW: T1 Recon-all error: CTABWriteFileASCII; could not open file for writing
by Loreto, Flavia 29 Jan '21

29 Jan '21

External Email - Use Caution Dear FreeSurfer Experts, I am writing to kindly follow-up on my below query. Is there any chance you could assist me? Thank you. Kind regards, Flavia From: "f.loreto(a)imperial.ac.uk" <f.loreto(a)imperial.ac.uk> Date: Monday, 18 January 2021 at 13:19 To: "Freesurfer(a)nmr.mgh.harvard.edu" <Freesurfer(a)nmr.mgh.harvard.edu> Subject: Recon-all error: CTABWriteFileASCII; could not open file for writing Dear FreeSurfer Experts, Version: FreeSurfer 7.0 Platform: Bash remotely through High Performance Computing (HPC) on a MacOS Mojave We are trying to run recon-all on T1 images but the job stops with the following error: Reading annotation /rds/general/project/imperialapc/live/freesurfer/APC001/label/lh.aparc.annot reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/tanha_002/users/greve/fsdev.build/average/colortable_desikan_killiany.txt) Seg base 1000 error: Permission denied error: CTABwriteFileASCII(/tmp/mri_segstats.tmp.APC001.lh.176.ctab): could not open for writing Could you please help us figuring out where is the problem? I am attaching the script we are running and the recon-all log for one of our analysed subjects. Thank you for your help. Kind regards, Flavia

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Re: [Freesurfer] Using mri_surf2surf to split files
by Douglas N. Greve 29 Jan '21

29 Jan '21

Sorry, can you include the previous correspondence so that I have context. Also, please remember to post to the list On 1/28/2021 12:07 PM, Karan Desai wrote: > > External Email - Use Caution > > My bad, I meant to say surfaces. Right now the files are downsampled on > fsaverage4 space and I need to now split it into the respective left/right > hemispheres. For context, these are .nii.gz files currently. Is there a way to > easily do this in Freesurfer? > > Best, > > Karan Desai > Morey Lab - Duke

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