Freesurfer March 2021

freesurfer@nmr.mgh.harvard.edu

106 participants
144 discussions

Re: [Freesurfer] Hippocampus subfield segmentation error on Ubuntu 20.04.1 LTS
by fsbuild 05 Mar '21

05 Mar '21

External Email - Use Caution Hello Ishi, After reviewing this thread, I made a *.deb installer from the 7.1.1 release.  I will send a download link to your private email so you can try it if you like.  You will need sudo privileges to run it.  If you try it, I suggest you first at least temporarily remove the soft link you made to fake having a libncurses.so.5 on your system. - R. On Mar 4, 2021, at 01:15, Ishi Tandon AIB, Jaipur <ishi.tandon(a)student.amity.edu> wrote:        External Email - Use Caution        Yes, the same error occurred again..It would be great if someone from the dev team could help me resolve it..On Thu, Mar 4, 2021 at 11:29 AM Horsng Junn <hsjunn(a)gmail.com> wrote:        External Email - Use Caution        You mean the following error occurred again?libncurses.so.5: cannot open shared object file: No such file or directorySorry but I ran out of ideas.Could anyone from the FreeSurfer dev team chime in?Please delete the file you just created with the following command, so it won't get in the way later.sudo rm /usr/lib/x86_64-linux-gnu/libncurses.so.5Best,HorsngOn Mar 4, 2021, at 2:46 PM, Ishi Tandon AIB, Jaipur <ishi.tandon(a)student.amity.edu> wrote:        External Email - Use Caution         Thanks alot.That seems to have executed without any errors.But segmentHA_T1.sh seems to display the same error again.On Thu, Mar 4, 2021 at 11:03 AM Horsng Junn <hsjunn(a)gmail.com> wrote:        External Email - Use Caution        Then installing libncurses5-dev doesn't seem like the solution we've been seeking after all.Could you try this instead?sudo ln -s /usr/lib/x86_64-linux-gnu/libncurses.so.6.2 /usr/lib/x86_64-linux-gnu/libncurses.so.5Regards,HorsngOn Mar 4, 2021, at 2:17 PM, Ishi Tandon AIB, Jaipur <ishi.tandon(a)student.amity.edu> wrote:        External Email - Use Caution         Upon running sudo apt-get install libncurses5-dev. This is what I get (attached below).On Thu, Mar 4, 2021 at 10:36 AM Horsng Junn <hsjunn(a)gmail.com> wrote:        External Email - Use Caution        Hi Ishi,The results suggest that libncurses5-dev isn't installed at all.(Listed files are all from the default libncurses 6)In your previous mail you said that:>> Also, I have tried sudo apt-get install libncurses5-dev. But that doesn't seem to resolve the issue.What exactly happened when you ran that command?Could you please re-run that command and attach the result?Best,HorsngOn Mar 4, 2021, at 1:58 PM, Ishi Tandon AIB, Jaipur <ishi.tandon(a)student.amity.edu> wrote:        External Email - Use Caution        Hello,Thanks for your response. I tried to look for libncurses5-dev in my home directory. It appears to be installed on usr/share/doc.Upon checking its permissions, it seemed to be owned by the root.Also, upon running the aforementioned commands this is what I get (attached below).On Thu, Mar 4, 2021 at 6:30 AM Horsng Junn <hsjunn(a)gmail.com> wrote:        External Email - Use Caution        Hi Ishi,Following are what I gathered:- You're running Freesurfer 7.1.1 on an ubuntu 20.04 box- Ubuntu 20.04 has libncurses 6 installed as default- Freesurfer 7.1.1 is linked against libncurses 5- So previously you were advised to install libncurses5-dev- And you followed the advice- But somehow your ubuntu is failing to find the shared object file of that libraryIt seems your installation of libncurses5-dev is somehow hosed.Could you please double check if libncurses5-dev is successfully installedby running the following commands one at a time?(You don't need to be root to run them.)apt list --installed *ncurses*find /lib -name 'libncurses*'find /usr/lib -name 'libncurses*'find /usr/local/lib -name 'libncurses*'BestHorsngOn Mar 3, 2021, at 1:53 PM, Ishi Tandon AIB, Jaipur <ishi.tandon(a)student.amity.edu> wrote:        External Email - Use Caution        Hello experts, With reference to my previous email, I am attaching the log file of segmentHA_T1.sh bert command.Please provide your feedback.Thanks in advance..On Mon, Mar 1, 2021 at 11:03 AM Ishi Tandon AIB, Jaipur <ishi.tandon(a)student.amity.edu> wrote:Hello experts, The recon-all command executed without any errors.However, on following the subsequent  command segmentHA_T1.sh bert, it gives me an error (even after modifying my .bashrc & .profile  with export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/usr/local/freesurfer/MCRv84/sys/os/glnxa64).Also, I have tried sudo apt-get install libncurses5-dev.. But that doesn't seem to resolve the issue.P.s - The error is attached below for reference.Thanks in advance.On Wed, Feb 24, 2021 at 4:51 PM Ishi Tandon AIB, Jaipur <ishi.tandon(a)student.amity.edu> wrote:Hello, Thanks for those suggestions.I already seem to have modified my bashrc with the same command. But I think running as root was a problem. But that's weird as earlier none of the Fs commands were executed without root. But now that seems to work. However, I still need to check with segmentHa_T1 if that works well after recon-all.Thanks for your help.On Wed, Feb 24, 2021 at 6:54 AM Horsng Junn <hsjunn(a)gmail.com> wrote:        External Email - Use Caution        And you seem to be running FreeSurfer as root.Since that could complicate matters, could you run it as a normal user?Best,HorsngOn Feb 24, 2021, at 9:36 AM, Horsng Junn <hsjunn(a)gmail.com> wrote:Hi Ishi,I'm actually not a FreeSurfer developer and this question seems beyond me, but my googling leads to this page:MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://secure-web.cisco.com/1LXYaQj802ML4iNIooz0zF3BuI01QLf1Hndk0T… seems to suggest that you add the following to your .bashrc, .profile or similar places and retry.export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/usr/local/freesurfer/MCRv84/sys/os/glnxa64Please try this and report your result.If this doesn't work, hopefully a FreeSurfer developer would chime in.Best,HorsngOn Feb 23, 2021, at 8:19 PM, Ishi Tandon AIB, Jaipur <ishi.tandon(a)student.amity.edu> wrote:        External Email - Use Caution        Hello, I am sorry for posting up another thread. Had an issue with subscription so had to post again (will keep it in mind now). I tried that out. And that worked well. But there's another error that pops up after I run (attached in the image): -recon-all -all -s bertI tried the following commands in order to update libstd. apt-get updateapt-get install libstdc++6But that didn't work. I am not able to trace the exact error. Thanks for the help.On Tue, Feb 23, 2021 at 11:56 AM Horsng Junn <hsjunn(a)gmail.com> wrote:        External Email - Use Caution        Hi Ishi,You apparently omitted an "n": it must be libncurses5-dev (please note the n after lib).And please try to keep previous correspondences intact,as otherwise the devs must hunt the mail archive for the detail.Best,HorsngOn Feb 23, 2021, at 3:10 PM, Ishi Tandon AIB, Jaipur <ishi.tandon@student..amity.edu> wrote:        External Email - Use Caution        Hello experts,In response to the previous email about matlab installation error while attempting to use hippocampal subfields. I tried the following command as suggested by you :- sudo apt-get install libcurses5-dev But I get the following error :- Reading package lists... Done Building dependency tree Reading state information... Done E: Unable to locate package libcurses5-dev Also, I am using fs version 7.1.1. I installed freesurfer-linux-centos7_x86_64-7.1.1.tar.gz file. Regards,Ishi TandonB.Tech + M.Tech - Cognitive NeuroscienceAmity University, RajasthanContact- +918239259846Email - ishi.tandon99@gmail.com_______________________________________________Freesurfer mailing listFreesurfer(a)nmr.mgh.harvard.eduMailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://secure-web.cisco.com/1v8o_5jhIAMg0L3iSZItnC_0xk-9gZHGY6urz6… mailing listFreesurfer(a)nmr.mgh.harvard.eduMailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://secure-web.cisco.com/1H2m2QbdJZtQi9A6j9BDmU-tU2cUAUp740BWzQ… 2021-02-23 at 4.36.59 PM.png>_______________________________________________Freesurfer mailing listFreesurfer(a)nmr.mgh.harvard.eduMailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://secure-web.cisco.com/1v8o_5jhIAMg0L3iSZItnC_0xk-9gZHGY6urz6… mailing listFreesurfer@nmr..mgh.harvard.eduMailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://secure-web.cisco.com/10bJFxTmrsfpTCVuNRCPcLDbakBuQB-T6EKJ2k… mailing listFreesurfer(a)nmr.mgh.harvard.eduMailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://secure-web.cisco.com/1v8o_5jhIAMg0L3iSZItnC_0xk-9gZHGY6urz6… mailing listFreesurfer(a)nmr.mgh.harvard.eduMailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://secure-web.cisco.com/1H2m2QbdJZtQi9A6j9BDmU-tU2cUAUp740BWzQ… 2021-03-04 at 10.27.31 AM.png>_______________________________________________Freesurfer mailing listFreesurfer(a)nmr.mgh.harvard.eduMailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://secure-web.cisco.com/1v8o_5jhIAMg0L3iSZItnC_0xk-9gZHGY6urz6… mailing listFreesurfer(a)nmr.mgh.harvard.eduMailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://secure-web.cisco.com/1H2m2QbdJZtQi9A6j9BDmU-tU2cUAUp740BWzQ… 2021-03-04 at 10.42.01 AM.png>_______________________________________________Freesurfer mailing listFreesurfer(a)nmr.mgh.harvard.eduMailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://secure-web.cisco.com/1v8o_5jhIAMg0L3iSZItnC_0xk-9gZHGY6urz6… mailing listFreesurfer(a)nmr.mgh.harvard.eduMailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to behttps://mail..nmr.mgh.harvard.edu/mailman/listinfo/freesurfer____________… mailing listFreesurfer@nmr.mgh.harvard..eduMailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to behttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer_____________… mailing listFreesurfer(a)nmr.mgh.harvard.eduMailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to behttps://mail..nmr.mgh.harvard.edu/mailman/listinfo/freesurfer____________… mailing listFreesurfer@nmr.mgh.harvard..eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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Re: [Freesurfer] ANNEX COMMAND NOT FOUND
by fsbuild 04 Mar '21

04 Mar '21

External Email - Use Caution Hello Donato, I think it should be “git-annex” and not “git annex”.  You can check where a command lives with the “which” command though your path could be different than mine. $ which git-annex/usr/local/bin/git-annex You can add an INSTALL_PREFIX to the cmake command with -DCMAKE_INSTALL_PREFIX=/path/to/installation_directory After you do the build under the ./fresurfer tree with the cmake and make commands, you would then type “make “install” and the built files will get installed to live under the /path/to/installation_directory. But we do not recommend building and installing the current source for public use since what you will get is not a tested release and could also be unstable.  You can instead download the latest release (freesurfer 7.1..1 from 7/2020) and earlier releases from the page https://secure-web.cisco.com/1gF066AaN_OzNBu1A3-GQNZIltUL8zt7uzu-… Someone with root/sudo privileges can install the *.rpm file which has the benefit of checking system packages needed to run freesurfer are installed on the system.  Otherwise you can download the *.tar.gz archive and expand it to live anywhere you have write permission. - R. On Mar 4, 2021, at 06:00, Donato Romano <d.romano20(a)studenti.uniba.it> wrote:        External Email - Use Caution        Hello FreeSurfer Developers,I'm trying to install FreeSurfer by source code on a distributed infrastructure. I'm following the FreeSurfer Builde Guide and when I run the command $ git annex get , the output is 'annex' isn't a command git.Can you send me a step-by-step guide to download and install FreeSurfer?Thank you._______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer On Mar 4, 2021, at 06:00, Donato Romano <d.romano20(a)studenti.uniba.it> wrote:        External Email - Use Caution        Hello FreeSurfer Developers,I'm trying to install FreeSurfer by source code on a distributed infrastructure. I'm following the FreeSurfer Builde Guide and when I run the command $ git annex get , the output is 'annex' isn't a command git.Can you send me a step-by-step guide to download and install FreeSurfer?Thank you._______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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ANNEX COMMAND NOT FOUND
by Donato Romano 04 Mar '21

04 Mar '21

External Email - Use Caution Hello FreeSurfer Developers, I'm trying to install FreeSurfer by source code on a distributed infrastructure. I'm following the FreeSurfer Builde Guide and when I run the command $ git annex get , the output is 'annex' isn't a command git. Can you send me a step-by-step guide to download and install FreeSurfer? Thank you.

1 0

Include T2 in recon-all command
by Rosalia Dacosta Aguayo 04 Mar '21

04 Mar '21

External Email - Use Caution Dear Freesurfer community, I would like to include the T2 image in the recon-all command to improve segmentation. Any idea how I should do this in the following command? recon-all -s Artico1 -i subj01_anat.nii.gz -all -qcache -3T Regards, Rosalia

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pial_lgi does not appear in QDEC
by Tien Pham 04 Mar '21

04 Mar '21

External Email - Use Caution Dear FreeSurfer Developers, I would like to measure LGI on my data, but pial_lgi option does not show in QDEC. I have tried to create .Qdecrc file with MEASURE1 = pial_lgi and put the file in both $SUBJECT_DIR/qdec dir and home directory. But It's still not worked. Can you help me please? Thank you. Best regards, Tien Pham

1 0

Re: [Freesurfer] longitudinal group analysis displaying results
by Agurne Sampedro Calvete 03 Mar '21

03 Mar '21

External Email - Use Caution Dear Freesurfer experts, In relation to the previous question, could I obtain a Z value of the significant cluster obtained by opening in freeview the z.mgh and place the cursor on the point with the highest value? Is there another way to obtain a Z value or alternatively, a t-value? Thank you very much in advance, Best regards, Agurne El mar, 23 feb 2021 a las 13:25, Agurne Sampedro Calvete (< a.sampedro(a)deusto.es>) escribió: > Dear Freesurfer experts, > > I am doing a longitudinal repeated measures analysis and after correcting > for multiple comparisons with Z Monte Carlo simulation (with the "mri_glmfit-sim > ... --cache 3 ..." command), I obtained a significant cluster for my > experimental group (pre-post). > > In order to obtain the information for displaying the results in the > paper, I am looking at the cluster summary table. I have seen that some > papers include the t value in addition to the p value, cluster size and > coordinates, but how can I obtain the t value? Does it appear in the > cluster summary table or elsewhere? > > Thank you very much in advance, > > Kind regards, > > Agurne > > > > >

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Hippocampal subfield segmentation
by Wei Shao 02 Mar '21

02 Mar '21

External Email - Use Caution Hi, Freesurfer expert I tried Hippocampal subfield segmentation with an additional T2 scan by using FS7.1.0 Here is the log error massage Attempted to access cropping(1); index out of bounds because numel(cropping)=0. Error in applyCropping (line 7) Error in segmentSubjectT1T2_autoEstimateAlveusML (line 950) MATLAB:badsubscript @#@FSTIME 2021:03:01:20:38:39 run_segmentSubjectT1T2_autoEstimateAlveusML.sh N 18 e 243.67 S 3.47 U 220.01 P 91% M 1248336 F 144 R 909119 W 0 c 49601 w 14948 I 320352 O 429920 L 30.66 34.91 35.10 @#@FSLOADPOST 2021:03:01:20:42:43 run_segmentSubjectT1T2_autoEstimateAlveusML.sh N 18 47.20 43.27 38.55 Linux gra813 3.10.0-1127.8.2.el7.x86_64 #1 SMP Tue May 12 16:57:42 UTC 2020 x86_64 GNU/Linux T2 hippocampal subfields exited with ERRORS at Mon Mar 1 20:42:43 EST 2021 For more details, see the log file /home/weishao//BAY11958/scripts/hippocampal-subfields-T2.T2.log Could you tell me how to fix this? Thanks. Best, Wei

2 3

Recon-all exiting with Errors during surface inflation
by Koch, Erin M. 01 Mar '21

01 Mar '21

External Email - Use Caution Hi all, The lab I work in recently upgrade to freesurfer-linux-centos7x_86_64-7.1.1 from freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0, and I am trying to use a series of shell scripts (that call freesurfer) which we successfully used to run to create flatmaps for non-human primate sessions. I am stuck when using recon-all to inflate the surface. Specifically, I am running the command: "recon-all -autorecon2-wm \ -subjid ${tmp_subj} ${corpcal_coord_string} ${pons_coord_string}\ -noaseg \ -mprage \ -xopts-use\ -debug\" This step runs for quite some time, seemingly making progress and then "Exits with errors" . In the terminal the error message that I can see is: "ERROR: need seg for ripping". This is followed by: "recon-all - s SUBJECTNAME exited with ERRORS." (Screen shot of this error is attached). I will also attach the recon-all.log. This issue does not seem to be a problem of quality of skull stripping or white matter segmentation, as the session can be completed with the older version of freesurfer, adn I get the same error with different sessions and subjects. Can you please shed some light on this? The machine I am using is running Linux 3.10.0-1127.18.2.e17.x86_64 . As an aside - Do you have any references or outline for flat map creation (specifically for non-human primates) with the newer versions of Free surfer? It is possible adapting our old pipeline is not ideal / there are more efficient or "better" ways to do this now. Thank you for your help. Best, Erin

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mri_vol2surf resolution warning
by Russo, Andrew William 01 Mar '21

01 Mar '21

Hello, I am moving a 6mm volume from MNI152 to fsaverage for group analysis and I get the following warning: mri_vol2surf --src MNI_6mm.nii.gz --out surf_sm4_lh.mgh --mni152reg --hemi lh --interp nearest --surf-fwhm 4 WARNING: the voxel resolution in the source volume (6,6,6) differs from that listed in the registration file (1,1,1) Do you know if this needs to be corrected or if there is a better method? Thanks for the help, Andrew Andrew Russo Clinical Research Coordinator Multiple Sclerosis Imaging Lab Massachusetts General Hospital 149 13th Street | Boston, MA 02129 617-726-7531

2 1

Talairach to RAS conversion
by Nasiriavanaki, Zahra 01 Mar '21

01 Mar '21

Hi Freesurferers I have some talairach coordinates on the cortical surface (extracted from a paper) and I need to see their location on my fmri maps. I used "tksurfer> go to saved point “ to see the location of that coordinate on my map. However, that coordinate is in talairach. Should I convert it to RAS and then save it as a point in tmp folder? If so, could you please let me know how I should convert them from talairach to RAS? Thanks MOna Zahra (Mona) Nasiriavanaki, M.D. Postdoctoral Research Fellow Department of Psychiatry Massachusetts General Hospital 149 13th Street, 149-2615 Boston, MA, USA, 02129

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Freesurfer March 2021