Freesurfer July 2023

freesurfer@nmr.mgh.harvard.edu

93 participants
130 discussions

Ubuntu Image Password
by Marmol, Sarah E. 25 Jul '23

25 Jul '23

External Email - Use Caution To whom it may concern: I downloaded the following file, but am unable to extract the image without the password, can you please provide me with the password? Ubuntu 18.04.06 compressed image with the FreeSurfer<https://secure-web.cisco.com/10USfDpNqoFHfi0K-jim8ctXwBwgoZU9bmC1529XXu1Ick…> 7.2.0 release Thank you

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Re: [Freesurfer] Any chance at all for an official proper fix for Freesurfer on FIPS?
by fsbuild 25 Jul '23

25 Jul '23

External Email - Use Caution My understanding is no environment variable setting like OPENSSL_FIPS=0 will allow md5 or other algorithms found in linux open source code to run which are not allowed under FIPS, e.g., see list, docs.oracle.com/cd/E36784_01/html/E54953/fips-notok-1.html Barring any environment override to turn off FIPS, and assuming you can’t boot into a non-FIPS enabled kernel to run Freesurfer, then one alternative could be to run a container or VM that is not FIPS enabled and in turn run Freesurfer in that.  That container/VM could be constrained with specific userids,  limited mount points, limited network connections, etc. There are examples of users running (even cloud based) container instances where they need to disable FIPS in order to run software/services, http://secure-web.cisco.com/1YPySRXdxKA8W9FNheIf6NOl70aLbr0Kl0TeGnNEk89j6ZU… We currently don’t have resources to test Freesurfer in a FIPS environment.  But I would not expect FS to run under FIPS given the list in the above link.. - R. On Jul 24, 2023, at 12:26, Salomon, Ryan <rsalomon(a)upenn.edu> wrote:        External Email - Use Caution        Hello!I'm trying to support our users who use Freesurfer on our systems, but we are trying to keep to a rollout of FIPS, without the need to employ any hacks or the like, and I don't believe non-FIPS is an option on our systems. We still encounter the crypt() error on Freesurfer versions greater than 7.1.1, and again, non-FIPS is likely not an option. There is an environment variable workaround that has been mentioned elsewhere and it doesn't seem to be working for me for mri_deface at least, and again, I really would like to see a word about a proper solution. _______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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Questions for the estimated brain volume based on new version of FreeSurfer
by Yoonho Hwang 25 Jul '23

25 Jul '23

External Email - Use Caution Dear FS developers, Hi, I am very happy that we can use new features of FreeSurfer (e.g., recon-all-clinical.sh, SynthSeg, SynthSR, etc.) While using a variety of functions from FreeSurfer (v7.3.2 and v7.4.1), we would like to hear the answers to the following questions. 1-1. Compared to the recon-all stream, using SynthSeg seems to overestimate the volume in many subregions of the brain including eTIV? Can you explain why this happens? 1-2. The estimated volume of the entorhinal cortex is different between recon-all/SynthSeg and recon-all-clinical.sh. There is a 3-4 times difference. Can you tell me why the result is? 2. Can the functions (segment_subregions, segmentThalamicNuclei.sh, segmentBA.sh, segmentHA.sh, etc.) used in recon-all be used in recon-all-clinical.sh? Please let me know if there is anything you don't understand. Looking forward to your feedback. Thank you very much. Best, Yoonho -- *Hwang, Yoonho* *Research professor* *Institute of Human Genomic Study,* *College of Medicine, Korea University* *#123, Jeokgeum-ro, Danwon-gu, Ansan-si, Gyeonggi-do, **15355, Republic of Korea.* *Email: ken.lmstar11(a)gmail.com <ken.lmstar11(a)gmail.com>*

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pass code for FS_7_2_0_Ubuntu_18_04_06.ova.7z
by Geng Liu 25 Jul '23

25 Jul '23

External Email - Use Caution Dear freesurfer developer: I am writing to ask for the pass code for FS_7_2_0_Ubuntu_18_04_06.ova.7z. Could you kindly provide it? Many Thanks! Best, ---------------------------------------------- Geng UESTC school of Life Science University Of Electronic Science and Technology of China Shahe Campus: No.4, Section 2, North Jianshe Road Chengdu, Sichuan, P.R China Zip/Postal Code:611731

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FS 7.2.0 VM pass code
by Dina V. Popovkina 24 Jul '23

24 Jul '23

External Email - Use Caution Hi Freesurfer team, I'm looking for the pass code for the VM image with the 7.2.0 version of FreeSurfer. Many thanks, Dina Dina V. Popovkina, Ph.D. Postdoctoral Scientist, Vision + Cognition Group Department of Psychology, University of Washington

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Any chance at all for an official proper fix for Freesurfer on FIPS?
by Salomon, Ryan 24 Jul '23

24 Jul '23

External Email - Use Caution Hello! I'm trying to support our users who use Freesurfer on our systems, but we are trying to keep to a rollout of FIPS, without the need to employ any hacks or the like, and I don't believe non-FIPS is an option on our systems. We still encounter the crypt() error on Freesurfer versions greater than 7.1.1, and again, non-FIPS is likely not an option. There is an environment variable workaround that has been mentioned elsewhere and it doesn't seem to be working for me for mri_deface at least, and again, I really would like to see a word about a proper solution.

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Possible bug: recon-all -i $T1 -T2 $T2 -autorecon1 attempts to run -T2pial
by Christopher Markiewicz 24 Jul '23

24 Jul '23

External Email - Use Caution Hi all, This is a reproduction of GitHub issue 1010. There is a section of recon-all (L5927-5930 in current dev) that states: # MOD: turn on T2/FLAIR pial editing when FLAIR specified # This can backfire, eg, if not all the preceeding steps # are included set DoT2pial = 1; This seems an intentional decision to make -T2 activate -T2pial (and similar for -FLAIR), which I suppose is a response to people running `recon-all -i $T1 -T2 $T2 -all` without `-T2pial`. However, it also activates with -autorecon1 and -autorecon2, which will not run -pial before -T2pial. Would you all consider this a bug or a caveat emptor kind of situation? Would it make sense to add the following to -autorecon1 and -autorecon2 (hopefully this formats okay)? diff --git a/scripts/recon-all b/scripts/recon-all index 4b98118264..0655097ab9 100755 --- a/scripts/recon-all +++ b/scripts/recon-all @@ -6869,6 +6869,7 @@ while( $#argv != 0 ) breaksw case "-autorecon1": + set DoT2pial = 0; set DoCreateBaseInput = 1; set DoMotionCor = 1; set DoTalairach = 1; @@ -6911,6 +6912,7 @@ while( $#argv != 0 ) set DoRemoveNeck = 0; set DoSkullLTA = 0; set DoSegStats = 0; + set DoT2pial = 0; set DoCANormalize = 1; set DoGCAReg = 1; set DoCALabel = 1; In any case, I am now adding -noT2pial and -noFLAIRpial to -T2 calls that aren't -all as well, which seems safe for writing commands that will work for both FreeSurfer 6 and 7. Thanks, Chris

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PetSurfer analisis whit another atlas
by Matteo Parodi 24 Jul '23

24 Jul '23

External Email - Use Caution Good morning. I try to use surfer analysis with another atas instead of the built-in one. I have an atlas in nifti or mgz format. I tried using it in gtmseg's --head option and it doesn't work, maybe due to normalization issues but I'm not sure. I tried to build the atlas with the utilities in https://secure-web.cisco.com/1npKm2rw7ypoDV5y3qkt0Aa0W2d4IRkHhrWfsjK3gU03P8… but i have problems to interfacing whit gca, gcs and annot file. I searched the mail archive and found no answer. Thank you very much for any input, Parodi.

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Request for 7 zip password VM_67
by Ynze Hokken 24 Jul '23

24 Jul '23

External Email - Use Caution Dear freesurfer expert, I just need a passcode to archive the zip folder for file FS_7_2_0_ubuntu_18_04_06.ova so that i can install a FreeSurfer vitual disk. Thanks, Ynze Hokken

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Re: [Freesurfer] Longitudinal pipeline for FreeSurfer (v7.3.2)
by Jackson Lee 23 Jul '23

23 Jul '23

External Email - Use Caution Hi Yujing, Thanks for your reply – I have a follow up query (see email thread below): I have both a cross-sectional aim and a longitudinal aim I am hoping to explore with FreeSurfer. While they are separate aims, some participants are present in both the cross-sectional and longitudinal arm. Currently I have run recon-all on all participants for my study using the standard recon-all command. As mentioned, I am hoping to do hippocampal subfield analysis (both cross-sectional and longitudinal). I have read both the hippocampal subfield and longitudinal pipelines available from FreeSurfer (linked below): https://secure-web.cisco.com/1_iq2Ortiz8d4uJhrtEXKZ_Row3SgFJsQNSJUW3b3hm3Fp… https://secure-web.cisco.com/1K3vQAJc_XjPimaagPX_W_n-ig3v4kt3fgvsYNoj9HGxxF… I was planning on running the longitudinal recon-all pipeline as it seems that running longitudinal pipeline allows for greater reliability as "the subject is used as their own control". But if I do this, then the subjects that are also in the cross-sectional arm will potentially have different outputs (even though they are the same scan) compared to outputs from the longitudinal pipeline. This would be the same for the subfield analysis. What is the best approach here? Would I be better off running all participants (even those with one T1-weighted scan) with the longitudinal pipeline so that every participant is treated the homogenously? Let me know if I need to clarify anything! Warm regards, Jack Hi Jack, Longitudinal recon-all pipeline is available in Freesurfer 7.3.2. To do longitudinal segmentation using the hippocampal subfield pipeline, it is a requirement that the data have been processed with the longitudinal stream Freesurfer. Best, Yujing From: freesurfer-bounces(a)nmr.mgh.harvard.edu<mailto:freesurfer-bounces@nmr.mgh.harvard.edu> <freesurfer-bounces(a)nmr.mgh.harvard.edu<mailto:freesurfer-bounces@nmr.mgh.harvard.edu>> On Behalf Of Jackson Lee Sent: Wednesday, July 12, 2023 10:25 PM To: freesurfer(a)nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu> Subject: [Freesurfer] Longitudinal pipeline for FreeSurfer (v7.3.2) External Email - Use Caution Hi there, I am hoping to process some longitudinal data using the longitudinal recon-all pipeline available in FreeSurfer: MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to behttps://surfer.nmr.mgh.harvard.edu/fswiki/LongitudinalChangeLog<https://secure-web.cisco.com/1Y9uqixBqGC2B0XHSMg2zr4QS96oUVSkkZcMdhRqdEkVD1…> Will this pipeline work for FreeSurfer v7.3.2? I cannot see any resources to suggest this is the case. Additionally, I am hoping to conduct some longitudinal analysis using the hippocampal subfield pipeline: MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to behttps://surfer.nmr.mgh.harvard.edu/fswiki/HippocampalSubfieldsAndNucleiOf…<https://secure-web.cisco.com/1ILqdmv74otr5LeRS7UQz83p5UDddkh5pv-Luvs5PHnW-6…> Would the best course of action be to run recon-all with the longitudinal pipeline first (assuming it is applicable for freeSurfer v7.3.2) and then use the longitudinal command for post-hoc subfield analysis?: segmentHA_T1_long.sh <baseID> [SUBJECTS_DIR] Thank you, Jack

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Freesurfer July 2023