Freesurfer

freesurfer@nmr.mgh.harvard.edu

18 participants
30131 discussions

White matter normalization
by James Brown 16 Sep '22

16 Sep '22

External Email - Use Caution Dear Freesurfer experts, In order to normalize white matter intensity of T1 images and correct for bias field. I do the following steps: mri_convert T1.nii.gz T1.mgz mri_nu_correct.mni --i T1.mgz --o T1_N3.mgz --n 2 mri_normalize -g 1 T1_N3.mgzT1_norm.mgz mri_convert T1_norm.mgz T1_norm.nii.gz I would like to apply bias field correction on FLAIR images then normalize white matter intensity. I tried N4biasfieldcorrection from ANTS but it didn't work as expected. Reviewing documents about N4biasfieldcorrection I realize that the algorithm has been developed to correct bias field correction in T1. Are the steps above valid for FLAIR images or it can only be applied on T1 images. We appreciate any feedback about the proper way to correct FLAIR images for bias field and normalize white matter intensity. Thank you JamesB

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Virtual Machine password request
by Dakota Graham 16 Sep '22

16 Sep '22

External Email - Use Caution Dear Admins, I've installed VirtualBox and am now at the stage of extracting the 7zip Ubuntu image that includes freesurfer. Could you please send the password for extracting this encrypted file? Thanks, Dakota

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password for the Ubuntu virtual machine zip file
by STACEY M SCHAEFER 14 Sep '22

14 Sep '22

External Email - Use Caution Could I get the password for the Ubuntu virtual machine zip file? If you also have the license file to include as well, that would be great! Thank you, Stacey Stacey M. Schaefer, Ph.D. Center for Healthy Minds University of Wisconsin-Madison 625 W Washington Ave Madison WI 53703 ________________________________ From: freesurfer-bounces(a)nmr.mgh.harvard.edu <freesurfer-bounces(a)nmr.mgh.harvard.edu> on behalf of freesurfer-request(a)nmr.mgh.harvard.edu <freesurfer-request(a)nmr.mgh.harvard.edu> Sent: Tuesday, September 13, 2022 2:04 PM To: freesurfer(a)nmr.mgh.harvard.edu <freesurfer(a)nmr.mgh.harvard.edu> Subject: Freesurfer Digest, Vol 223, Issue 22 Send Freesurfer mailing list submissions to freesurfer(a)nmr.mgh.harvard.edu To subscribe or unsubscribe via the World Wide Web, visit https://secure-web.cisco.com/1ryvJ3kIC4pQAjIIyQdqR6JgVQJZfYjU4jKC1pPr9LKeoL… or, via email, send a message with subject or body 'help' to freesurfer-request(a)nmr.mgh.harvard.edu You can reach the person managing the list at freesurfer-owner(a)nmr.mgh.harvard.edu When replying, please edit your Subject line so it is more specific than "Re: Contents of Freesurfer digest..." Today's Topics: 1. Re: Follow Up License Freesurfer 5.3 Ubuntu (Wighton, Paul) 2. Re: Freesurfer: fs_install_mcr: Unzip command not found (Justina Lee) 3. Re: Follow Up License Freesurfer 5.3 Ubuntu (fsbuild) 4. Re: Freesurfer: fs_install_mcr: Unzip command not found (Wighton, Paul) 5. Re: Follow Up License Freesurfer 5.3 Ubuntu (Wighton, Paul) 6. Re: Freesurfer: fs_install_mcr: Unzip command not found (Justina Lee) 7. Re: Freesurfer: fs_install_mcr: Unzip command not found (Wighton, Paul) 8. Re: Freesurfer: fs_install_mcr: Unzip command not found (Justina Lee) 9. Re: Freesurfer: fs_install_mcr: Unzip command not found (Wighton, Paul) 10. Re: Freesurfer: fs_install_mcr: Unzip command not found (Justina Lee) 11. Re: Freesurfer: fs_install_mcr: Unzip command not found (Wighton, Paul) ---------------------------------------------------------------------- Message: 1 Date: Tue, 13 Sep 2022 17:28:39 +0000 From: "Wighton, Paul" <PWIGHTON(a)mgh.harvard.edu> Subject: Re: [Freesurfer] Follow Up License Freesurfer 5.3 Ubuntu To: "freesurfer(a)nmr.mgh.harvard.edu" <freesurfer(a)nmr.mgh.harvard.edu> Message-ID: <BN8PR04MB57952410B3C48F5F89851D4382479(a)BN8PR04MB5795.namprd04.prod.outlook.com> Content-Type: text/plain; charset="iso-8859-1" Hi R?diger, This is really interesting.. I'm able to reproduce this issue in a docker container. Anyone else who would like to reproduce or look into this issue can use the following containers - The container `pwighton/freesurfer:5.3.0-HCP` is based off of ubuntu 16.04 (glibc v2.23) and everything works as expected in this container. - The container `pwighton/freesurfer:5.3.0-HCP-focal` is based off of ubuntu 20.04 (glib2 v2.31) and I am experiencing the same issue you describe. - The container `pwighton/freesurfer:7.3.2-focal` is based off of ubuntu 20.04 and has the latest version of FreeSurfer installed. Everything works as expected in this container. So the issue seems to be some interaction between the v5.3 license checking code and the crypt() function provided by different versions of glibc, but that is just speculation at this point. I'm sorry I don't have any solution for this at the moment. You mention you are using lmod, would it be possible to define LD_LIBRARY_PATH inside the FreeSurfer 5.3 module to point to an older version of glibc? -Paul ________________________________ From: freesurfer-bounces(a)nmr.mgh.harvard.edu <freesurfer-bounces(a)nmr.mgh.harvard.edu> on behalf of Ludwig, R?diger <r.ludwig(a)eni-g.de> Sent: Tuesday, September 13, 2022 11:32 AM To: freesurfer(a)nmr.mgh.harvard.edu <freesurfer(a)nmr.mgh.harvard.edu> Subject: [Freesurfer] Follow Up License Freesurfer 5.3 Ubuntu Hello again, I realized I might have missed some important information in my question about freesurfer 5.3 license files a few days ago: We use Ubuntu 20 with lmod. FREESURFER_HOME is ''/opt/apps/freesurfer/5.3/'' for freesurfer 5.3 When we try ''mri_convert sample-001.mgz sample-001.nii.gz'' without a proper license file we get the Error: ERROR: Invalid FreeSurfer license key found in license file /opt/apps/freesurfer/5.3/license.txt After we copy the license file to the proper position we get: ERROR: Invalid FreeSurfer license key found in license file /opt/apps/freesurfer/5.3/license.txt So the file is obviously read but rejected. We get the same result it with a brand new license file, and one that still works for freesurfer 5.3 on our CentOS 7 node. We do not have any problems reading the license file in freesurfer 7.2 or freesurfer 7.3 If you need any further information to help us, we am more than willing to provide that. Thank you so much in advance Ruediger --- R?diger Ludwig (he/him) IT-Service European Neuroscience Institute A Joint Initiative of the University Medical Center G?ttingen and the Max Planck Society Grisebachstr. 5 37077 G?ttingen Tel: +49 551-39 61308 Email: r.ludwig(a)eni-g.de Office: 0.051

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Virtual Machine Password?
by Ty Christian 14 Sep '22

14 Sep '22

External Email - Use Caution Hello! Could I please get the password for the Ubuntu virtual machine zip file? (And possibly the license.txt as well?) Thanks very much! -Ty Christian Brain Imaging/CHM Systems Administrator 1500 Highland Ave. Room T131 and/or 625 W. Washington Ave Madison, WI 53705-2280 (608) 890-0142

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Re: [Freesurfer] sclimbic sometimes does not detect left basal forebrain
by Miriam Taza 13 Sep '22

13 Sep '22

External Email - Use Caution Hello, Im wondering if there is an update regarding etiv differences between recon all and using sclimbic. I want to divide the volumes extracted from using sclimbic on t1s by etiv. Im not sure given the discrepancy if I should use etiv extracted from recon all command or from sclimbic. Thanks, Miriam ________________________________ From: Miriam Taza <miriam.taza(a)mail.mcgill.ca> Sent: Thursday, August 11, 2022 6:01 PM To: Greve, Douglas N.,Ph.D. <dgreve(a)mgh.harvard.edu> Subject: Re: [Freesurfer] sclimbic sometimes does not detect left basal forebrain Hello, I just wanted to follow up about etiv, if you had the chance to look into if your recon all vs sclimbic also does simithing similar on the subjs i sent? I am also attaching another graph that depicts the difference between etivs extracted from sclimbic and from recon all. [cid:89abfbda-77b0-4a5c-ade3-c4d18cc274d6] Thanks for all your help, Miriam ________________________________ From: Miriam Taza <miriam.taza(a)mail.mcgill.ca> Sent: Wednesday, August 3, 2022 4:59 PM To: Douglas N. Greve <dgreve(a)mgh.harvard.edu> Subject: Re: [Freesurfer] sclimbic sometimes does not detect left basal forebrain Hello, Attached are a few subjects, where YA denotes younger adults and OA older adults. I also included the stats file when I run sclimbic for reference. Please let me know if this mode of transfer works. Thank you, Miriam P.S. I also sent a previous email regarding etiv values "etiv value differs if using recon all vs freesurfer dev". Are you able to also see if your sclimbic etiv values differ much from recon all? For example, sub1221084 etiv greatly differs between sclimbic, old recon all, and new recon all. ________________________________ From: Douglas N. Greve <dgreve(a)mgh.harvard.edu> Sent: Friday, July 29, 2022 12:29 PM To: Miriam Taza <miriam.taza(a)mail.mcgill.ca> Subject: Re: [Freesurfer] sclimbic sometimes does not detect left basal forebrain yes, you can try sending it to me. if they are too big for email, then we have other solutions On 7/29/2022 12:19 PM, Miriam Taza wrote: External Email - Use Caution Hello, Thank you for your quick response! I can certainly share a few participants data with you but I would prefer not to share with the entire mailing list if possible. If so, should I attach it to this email? I could send you more than one if you prefer. Thank you, Miriam ________________________________ 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 Douglas N. Greve <dgreve(a)mgh.harvard.edu><mailto:dgreve@mgh.harvard.edu> Sent: Friday, July 29, 2022 12:06 PM To: freesurfer(a)nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu> <freesurfer(a)nmr.mgh.harvard.edu><mailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] sclimbic sometimes does not detect left basal forebrain Can you send us a sample case? On 7/28/2022 8:58 PM, Miriam Taza wrote: Nothing strange about them. They’re T1w scans 1x1x1mm3 ________________________________ 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 Douglas N. Greve <dgreve(a)mgh.harvard.edu><mailto:dgreve@mgh.harvard.edu> Sent: Thursday, July 28, 2022 1:25 PM To: freesurfer(a)nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu> <freesurfer(a)nmr.mgh.harvard.edu><mailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] sclimbic sometimes does not detect left basal forebrain Have you looked at the input volume to see if there is anything strange about them? What kind of scans are you passing to it? What is the resolution? On 7/25/2022 9:03 PM, Miriam Taza wrote: External Email - Use Caution Hello, I noticed 20 out of ~240 subjects left basal forebrain volumes were not picked up after running ScLimbic. These are healthy adults and their scans look good. Also, I noticed often when this occurs NAcc is also 0 or other regions. I am concerned if there is a systematic issue with left volumes ending up smaller than they should relative to right. Thanks, Miriam _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu> https://secure-web.cisco.com/1aHP51Gh4Z1uAdfXJyh4F87Sk47MLeA_21xYnLafTh6DU-…<https://secure-web.cisco.com/1X7C66SKfMm3Xi_QjnUKOg1Tq7kCF9P3CBqvauyRAAu47A…> _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu> https://secure-web.cisco.com/1aHP51Gh4Z1uAdfXJyh4F87Sk47MLeA_21xYnLafTh6DU-…<https://secure-web.cisco.com/1X7C66SKfMm3Xi_QjnUKOg1Tq7kCF9P3CBqvauyRAAu47A…> 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://secure-web.cisco.com/1jo15xReilwGxW9qbUhvkTFFMMv0ahF7rIqkSJv2eL5mI7… . Please note that this e-mail is not secure (encrypted). If you do not wish to continue communication over unencrypted e-mail, please notify the sender of this message immediately. Continuing to send or respond to e-mail after receiving this message means you understand and accept this risk and wish to continue to communicate over unencrypted e-mail.

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Re: [Freesurfer] Follow Up License Freesurfer 5.3 Ubuntu
by fsbuild 13 Sep '22

13 Sep '22

External Email - Use Caution The glibc version has changed in newer versions of Ubuntu.  That and/or changes to encryption related functions is likely preventing the license decoding from working.   Binary backwards compatibility cannot assure old binaries will indefinitely run on newer releases of the operating system., e.g., CentOS6 binaries may not run on CentOS8.  Freesurfer 5.3 was released in 2013 at the time of Ubuntu 12 so I would not assume it will run on Ubuntu 18 and/or newer versions.  I don['t think LD_LIBRARY_PATH will help with statically linked binaries - and sertting it to point to a version could break dynamically linked binaries with RPATH strings.  In general it is a bad idea to be running with different versions of glibc on the same system. There is an Ubuntu 12 VM running Freesurfer 5.3 available from https://secure-web.cisco.com/1X4Gyy7SfMYdVSIKIWMlCS7GCLmcJfLLRdLZ…;  That VM still runs in VirtualBox on todays operating systems.  - R. On Sep 13, 2022, at 13:28, Wighton, Paul <PWIGHTON(a)mgh.harvard.edu> wrote:Hi Rüdiger,This is really interesting..  I'm able to reproduce this issue in a docker container.  Anyone else who would like to reproduce or look into this issue can use the following containers- The container `pwighton/freesurfer:5.3.0-HCP` is based off of ubuntu 16..04 (glibc v2.23) and everything works as expected in this container.- The container `pwighton/freesurfer:5.3.0-HCP-focal` is based off of ubuntu 20.04 (glib2 v2.31) and I am experiencing the same issue you describe.- The container `pwighton/freesurfer:7.3.2-focal` is based off of ubuntu 20.04 and has the latest version of FreeSurfer installed.  Everything works as expected in this container.So the issue seems to be some interaction between the v5.3 license checking code and the crypt() function provided by different versions of glibc, but that is just speculation at this point.I'm sorry I don't have any solution for this at the moment.  You mention you are using lmod, would it be possible to define LD_LIBRARY_PATH inside the FreeSurfer 5.3 module to point to an older version of glibc?-PaulFrom: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces(a)nmr.mgh.harvard.edu> on behalf of Ludwig, Rüdiger <r.ludwig@eni-g.de>Sent: Tuesday, September 13, 2022 11:32 AMTo: freesurfer@nmr.mgh.harvard.edu <freesurfer@nmr.mgh.harvard.edu>Subject: [Freesurfer] Follow Up License Freesurfer 5.3 Ubuntu Hello again,I realized I might have missed some important information in my question about freesurfer 5.3 license files a few days ago:We use Ubuntu 20 with lmod. FREESURFER_HOME  is  ''/opt/apps/freesurfer/5.3/''  for freesurfer 5.3When we try ''mri_convert sample-001.mgz sample-001.nii.gz'' without a proper license file we get the Error:ERROR: Invalid FreeSurfer license key found in license file /opt/apps/freesurfer/5.3/license.txtAfter we copy the license file to the proper position we get:ERROR: Invalid FreeSurfer license key found in license file /opt/apps/freesurfer/5.3/license.txtSo the file is obviously read but rejected. We get the same result it with a brand new license file, and one that still works for freesurfer 5.3 on our CentOS 7 node.We do not have any problems reading the license file in freesurfer 7.2 or freesurfer 7.3If you need any further information to help us, we am more than willing to provide that.Thank you so much in advanceRuediger---Rüdiger Ludwig (he/him)IT-ServiceEuropean Neuroscience InstituteA Joint Initiative of the University Medical Center Göttingen and the Max Planck SocietyGrisebachstr. 537077 GöttingenTel: +49 551-39 61308Email: r.ludwig(a)eni-g.deOffice: 0.051_______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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Follow Up License Freesurfer 5.3 Ubuntu
by Ludwig, Rüdiger 13 Sep '22

13 Sep '22

Hello again, I realized I might have missed some important information in my question about freesurfer 5.3 license files a few days ago: We use Ubuntu 20 with lmod. FREESURFER_HOME is ''/opt/apps/freesurfer/5.3/'' for freesurfer 5.3 When we try ''mri_convert sample-001.mgz sample-001.nii.gz'' without a proper license file we get the Error: ERROR: Invalid FreeSurfer license key found in license file /opt/apps/freesurfer/5.3/license.txt After we copy the license file to the proper position we get: ERROR: Invalid FreeSurfer license key found in license file /opt/apps/freesurfer/5.3/license.txt So the file is obviously read but rejected. We get the same result it with a brand new license file, and one that still works for freesurfer 5.3 on our CentOS 7 node. We do not have any problems reading the license file in freesurfer 7.2 or freesurfer 7.3 If you need any further information to help us, we am more than willing to provide that. Thank you so much in advance Ruediger --- Rüdiger Ludwig (he/him) IT-Service European Neuroscience Institute A Joint Initiative of the University Medical Center Göttingen and the Max Planck Society Grisebachstr. 5 37077 Göttingen Tel: +49 551-39 61308 Email: r.ludwig(a)eni-g.de Office: 0.051 External Email - Use Caution

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Grey matter was not included in pial surface
by DINGLAN TANG 13 Sep '22

13 Sep '22

External Email - Use Caution Hi, I ran recon-all for my participants (T1 and T2, DICOM*.nii). but for some of my participants (3 out of 15), the grey matter was not correctly traced. Its overlapping with the white matter boundary. See image below. I have searched the list and no similar errors have been reported. Does anyone have any thoughts or suggestions on how to trouble-shoot this? [cid:image001.jpg@01D8C75F.1EE738C0] Best wishes dinglan

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Extract Fetal Brain MRI
by Xuchu Liu 13 Sep '22

13 Sep '22

External Email - Use Caution Hi Dear, We are a research team at Rush University Medical Center. We are working on the Fetal MRI data. In this step,*we need to extract the "Fetal Brain MRI" from our images, which have "mother and other tissues"* as well. One of our options is using "FreeSurfer" Software. But before that, we want to make sure that "Freesurfer" is able to extract the "Fetal brain", from other tissues in the MRI. Could you guide us that this software can help us for this problem? Thanks, Xuchu, Rush University Research Team

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MNI coordinates of minimal thickness in ROI
by Olga Kepinska 13 Sep '22

13 Sep '22

External Email - Use Caution Dear Experts, I am looking for a way to extract information on the location (xyz coordinates in MNI space) of a vertex with the lowest thickness value within an ROI (label) for a group of subjects. I have previously ran recon-all and qcache on the data. Any insights will be welcome! Thank you in advance and kind regards, Olga Kepinska -- Olga Kepinska, PhD  she/her Postdoctoral Researcher Brain and Language Lab (http://secure-web.cisco.com/1sChCMMb6dwvPKcri0GopC5Le8_9OomfgYJzxDh8yt_dSgy…) University of Vienna @olgakepinska

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