[Freesurfer] Freesurfer Version

Gentleman Which Version of Freesurfer should I download for use with the OS X Yosemite 10.10.1? Thanks Cristian ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in t

[Freesurfer] [FreeSurfer] Version

Is this the 5.3.0 version for snowleopard? [image: File:]freesurfer-Darwin-snowleopard-i686-dev.tar.gz 4355640 KB 7/31/15 3:31:00 AM terminal outputs freesurfer-Darwin-snowleopard

[Freesurfer] FreeSurfer Version

Is there any other way I can find the FreeSurfer version I am using? According to https://surfer.nmr.mgh.harvard.edu/fswiki/UserContributions/FAQ#Q.HowdoIknowtheversionofFreeSurferI.27mrunning.3F I have to run: recon-all -version, but I get the output below. Now the stable FreeSurfer Version is

[Freesurfer] FreeSurfer version

External Email - Use Caution Hi! I am re-running all recon-all using version 6.0. I was running a full list of subjects when our server crashed - and I would like to begin where it stopped. How do I check which subjects have been run on the latest version (v. 6)? Thanks so!

[Freesurfer] Freesurfer version

Hi freesurfer experts, I was using FreeSurfer v6 for my research. Recently, I started move to FreeSurfer v7.2. I encountered the following issue: Some patients, that had extra large error (xL error), were running fine (recon-all) in freesurfer 6 (it took time, but the process finished, and the

[Freesurfer] Freesurfer version

External Email - Use Caution Hi, I was wondering if you could help me or give me more information. I have pre-processed my MRI data using FreeSurfer version 7.0, which has been recalled. I used the same version for the thalamic segmentation. I have elaborated my data one year ago.

[Freesurfer] Freesurfer Version

External Email - Use Caution Good afternoon, I have run recon-all for my subjects, however I just realised I am using the ver devel-2019128, I wonder which version is this? Is it recommended to re-run the recon-all using the newer updates? (At present we have the option of Freesu

Re: [Freesurfer] Freesurfer Version

The 64bit Lion version. It should probably be made a little more clear that that version is for 10.7 and higher. Ill fix that. https://surfer.nmr.mgh.harvard.edu/fswiki/Download -Zeke > Gentleman > Which Version of Freesurfer should I download for use with the OS X > Yosemite 10.10.1? > Thanks

Re: [Freesurfer] Freesurfer Version

Thanks, Zeke!!! On Tue, Nov 25, 2014 at 10:59 AM, wrote: > > The 64bit Lion version. It should probably be made a little more clear > that that version is for 10.7 and higher. Ill fix that. > > https://surfer.nmr.mgh.harvard.edu/fswiki/Download > > -Zeke > > > > Gentleman > > Which Version of Fr

[Freesurfer] Freesurfer version compatibility

Hi everyone, We have a number of Freesurfer segmentations performed with version 5.0. Some of these will need to be corrected, most likely with adding control points. The question is we currently have version 5.3 running on our server. Is it okay to add the control points and run the segmentation

Re: [Freesurfer] [FreeSurfer] Version

No its not version 5.3, its the development version (most up-to-date daily build). Its not officially supported but is available for download. -Zeke On 07/31/2015 05:14 PM, joseph veliz wrote: > Is this the 5.3.0 version for snowleopard? > > File:freesurfer-Darwin-snowleopard-i686-dev.tar.gz >

Re: [Freesurfer] FreeSurfer Version

look at $FREESURFER_HOME/build-stamp.txt doug On 7/25/13 11:45 AM, Rodrigo Perea wrote: Is there any other way I can find the FreeSurfer version I am using? According to https://surfer.nmr.mgh.harvard.edu/fswiki/UserContributions/FAQ#Q.HowdoIknowtheversionofFreeSurferI.27mrunning.3F I

[Freesurfer] FreeSurfer Version 6

Dear Freesurfers, At long last, the new version of Freesurfer v6.0 is available for download! For a list of what it contains, see this page: http://surfer.nmr.mgh.harvard.edu/fswiki/ReleaseNotes To download it, see this page: http://surfer.nmr.mgh.harvard.edu/fswiki/DownloadAndInstall We are w

[Freesurfer] Freesurfer version 6.0

Dear Freesurfer experts, How may I get Freesurfer v 6 ? Thank you very much, Best wishes, Barbara ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is

Re: [Freesurfer] FreeSurfer version

look in subject/scripts/build-stamp.txt you should see something like freesurfer-Linux-centos7_x86_64-stable-v6-20161229-80ac5eb On 7/29/2019 6:40 PM, FAST Study wrote: External Email - Use Caution Hi! I am re-running all recon-all using version 6.0. I was running a full list of subje

[Freesurfer] Freesurfer version confusion

Hi freesurfer experts, I was using FreeSurfer v6 for my research. Recently, I started move to FreeSurfer v7.2. I encountered the following issue: Some patients, that had extra large error (xL error), were running fine (recon-all) in freesurfer 6 (it took time, but the process finished, and the

Re: [Freesurfer] Freesurfer version

un...@nmr.mgh.harvard.edu On Behalf Of Paul, Rahul Sent: Wednesday, September 22, 2021 10:35 AM To: freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] Freesurfer version Hi freesurfer experts, I was using FreeSurfer v6 for my research. Recently, I started move to FreeSurfer v7.2. I encounte

[Freesurfer] Freesurfer version help

External Email - Use Caution Hi, I was wondering if you could help me or give me more information. I have pre-processed my MRI data using FreeSurfer version 7.0, which has been recalled. I used the same version for the thalamic segmentation. I have elaborated my data one year a

Re: [Freesurfer] Freesurfer version

The 7.0.0 release was recalled because the intensity normalization *sometimes* did the wrong thing. It would not surprise me if you were not seeing any of these effects, but I can't guarantee that it won't happen in your data. If it was happening, you would see some big differences in the thick

Re: [Freesurfer] Freesurfer Version

External Email - Use Caution Hello Jacob, It looks like some digits at the end of "devel-2019128” are missing, but I read that to be a development build from December of 2019. If you look at the dates on the 7.X releases under https://secure-web.cisco.com/1UnwnrVRzttVZt3syMWUb0Da

[Freesurfer] Freesurfer version 4.5

Hi Freesurfer experts, Thanks for Jesse's recent posting which raises my question. I am in the process of compiling a series of control patients with freesurfer version 4.5. Is it possible to save the output after autorecon1( with version 4.5), and use it to continue autorecon2 when versio

[Freesurfer] freesurfer version difference

Hello, We used Freesurfer version 4.0.0 for a many of our subjects and version 4.0.1 for the other subjects. Will there be a difference between both the versions. We are comparing individual subjects brain (aseg stats) at 2 different instances. It so happens we are comparing the same subject's b

[Freesurfer] freesurfer version 3.0 ?

Hi, We have a dataset that was processed (by somebody else) with an old freesurfer version and we need to find out exactly which version was used. We have a freesurfer_3.0 directory (and a freesurfer-Linux-centos4-stable-v3.0-full.tar.gz download) with a build-stamp.txt that says: freesurfer-Linux-

Re: [Freesurfer] Freesurfer version compatibility

Hi Deniz if you rerun them all with 5.3 that should be ok Bruce On Fri, 12 Dec 2014, Deniz Ozgen wrote: Hi everyone, We have a number of Freesurfer segmentations performed with version 5.0. Some of these will need to be corrected, most likely with adding control points.  The question is we c

[Freesurfer] FreeSurfer version for subjects

Hello everyone, isthere a method to verify which was the last version of FreeSurfer that was used to perform the recon-all ? For. ex. in /subjects/subject_name/scripts/build-stamp.txt/I can see that this subject was registered the first time with FS version 5.0but after that, an additional r

Re: [Freesurfer] FreeSurfer Version 6

Congratulations! I just updated the FreeSurfer BIDS App to version 6.0.0: https://github.com/BIDS-Apps/freesurfer It's already on Docker Hub. All you need to do to grab it is to run: docker run -ti --rm bids/freesurfer:v6.0.0-1 Best, Chris On Mon, Jan 23, 20

Re: [Freesurfer] Freesurfer version 6.0

We don't have a v6 ready. You can get a development version, you just have to keep in mind that it is a snapshot and that the software will change without notice. On 02/16/2016 02:12 PM, Barbara Kreilkamp wrote: > Dear Freesurfer experts, > > How may I get Freesurfer v 6 ? > > Thank you very muc

Re: [Freesurfer] Freesurfer version 6.0

Dear Douglas, Thanks a lot, I found the version. Best wishes, Barbara On 16/02/2016 20:44, Douglas N Greve wrote: > We don't have a v6 ready. You can get a development version, you just > have to keep in mind that it is a snapshot and that the software will > change without notice. > > On 02/16/2

Re: [Freesurfer] Freesurfer version 6.0

Dear all, Sorry to bother you again. I am a bit confused as others seem to use a 'version 6.0' but I cannot find reference inthe nightly development ( ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/dev ) of it being called a version 6.0. Am I missing something? I don't know where I got t

Re: [Freesurfer] Freesurfer version 6.0

hello Barbara, A freesurfer v6.0-beta was released some months ago. But after various rounds of QA testing it was decided that additional significant development was required. So the beta version was withdrawn and active development remains ongoing in the dev version. You can download the late

Re: [Freesurfer] Freesurfer version 6.0

Dear Zeke, Great, thanks for the clarification! All the best, Barbara On 17/02/2016 16:53, Z K wrote: > hello Barbara, > > A freesurfer v6.0-beta was released some months ago. But after various > rounds of QA testing it was decided that additional significant > development was required. So the be

Re: [Freesurfer] Freesurfer version confusion

Did the size of the defect change? On 9/19/2021 8:36 PM, Paul, Rahul wrote: Hi freesurfer experts, I was using FreeSurfer v6 for my research. Recently, I started move to FreeSurfer v7.2. I encountered the following issue: Some patients, that had extra large error (xL error), were running fi

Re: [Freesurfer] Freesurfer version 4.5

Hi Toh, if you did manual skull stripping within FS we will retain your edits when you reapply the latest version. cheers Bruce On Tue, 27 Jul 2010, Toh Hock Wong wrote: > Hi Freesurfer experts, > Thanks for Jesse's recent posting which raises my question. I am in > the process of compiling

Re: [Freesurfer] freesurfer version difference

Hi Mithra, yes, there might be. You should rerun the 4.0.0 subjects with 4.0.1 (it should preserve all manual edits so you won't need to intervene). cheers, Bruce On Mon, 11 Feb 2008, Mithra wrote: Hello, We used Freesurfer version 4.0.0 for a many of our subjects and version 4.0.1 for

Re: [Freesurfer] freesurfer version difference

Mithra, We highly recommend using the same version of freesurfer to perform recon-all processing on a group of subjects. Processing with different versions introduces an extra level of variability in your study. However, in looking at the ReleaseNotes page: https://surfer.nmr.mgh.harvard.edu/fs

Re: [Freesurfer] freesurfer version 3.0 ?

Lars, It is v3.0.0. The date should be March 2006. You can find out release dates to tie to version numbers here: https://surfer.nmr.mgh.harvard.edu/fswiki/ReleaseNotes Nick On Tue, 2008-05-27 at 16:27 +0200, Lars M. Rimol wrote: > Hi, > We have a dataset that was processed (by somebody else)

[Freesurfer] Freesurfer version and Installation

External Email - Use Caution Dear Freesurfer developers, Previously, I downloaded the freesurfer-linux-centos7_x86_64-dev-20230331-e304091 version and successfully analyzed some data using this version. Now, I find myself in the need to reinstall Freesurfer, but I am unable to

[Freesurfer] Freesurfer version for processed data

Hello, Is there any way to find out which Freesurfer version I used to process data? Thanks, Krista ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail

[Freesurfer] freesurfer version vs cvs version

Hello, I have 80 subjects' MRIs that were segmented in 2009 with a version of freesurfer that included this (cvs_version $Id: mri_segstats.c,v 1.11.2.5 2006/04/13 18:57:07 nicks Exp $) in the aseg.stats output. The other 19 of my subjects segmented in 2013 display this (cvs_version $Id: mri_seg

[Freesurfer] Freesurfer: Version of development version?

External Email - Use Caution Dear Sir or Madam, first of all, thanks a lot for providing such a great tool like Freesurfer! I only have a minor question regarding the version I used: As I am writing a Paper for a Journal right now, I also wanted to quote the Freesurfer Version I

Re: [Freesurfer] Freesurfer version and Installation

External Email - Use Caution Development builds are continually updated and may not be stable, i.e., so the March 31st development build is no longer available.  I suggest using one of the release builds listed on the release page.  The 7.4.1 build from this June is the most rec

Re: [Freesurfer] Freesurfer version and Installation

...@nmr.mgh.harvard.edu on behalf of hmarz...@student.ubc.ca Sent: Monday, July 31, 2023 11:38:48 AM To: freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] Freesurfer version and Installation [CAUTION: Non-UBC Email] External Email - Use Caution Dear Freesurfer developers, Previously

Re: [Freesurfer] Freesurfer version and Installation

stion: I am utilizing Synthsr version 2.0. Is this particular version included in The 7.4.1 version of freeusrfer?RegardsHengamehFrom: freesurfer-boun...@nmr.mgh.harvard.edu <freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of hmarz...@student.ubc.ca<hmarz...@student.ubc.ca>Sent: 

[Freesurfer] freesurfer version 6 on Debian

External Email - Use Caution Is there a way to install freesurfer6 on Debian? I see only CentOS packages available for freesurfer6. Or, is there a way to build from source on Debian? ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard

Re: [Freesurfer] Freesurfer version for processed data

look in the subject/scripts/build-stamp.txt Note that if you set this environment variable setenv REQUIRE_FS_MATCH 1 it will require that a re-running of recon-all use the same version as previous runs doug On 02/12/2013 12:35 PM, krista kelly wrote: > Hello, > > Is there any way to find out whic

Re: [Freesurfer] freesurfer version vs cvs version

Joel, The 'recon-all.log' file in the 'scripts' directory of the subject should have the version of freesurfer used. Also, the file 'build-stamp.txt' in that same directory will show the version used. N, On Tue, 2014-08-26 at 18:31 +, Joel R Pieper wrote: > Hello, > > I have 80 subjects'

Re: [Freesurfer] freesurfer version vs cvs version

: Freesurfer support list Subject: Re: [Freesurfer] freesurfer version vs cvs version Joel, The 'recon-all.log' file in the 'scripts' directory of the subject should have the version of freesurfer used. Also, the file 'build-stamp.txt' in that same directory will show the ve

[Freesurfer] freesurfer version update issue in MacOS

Hello! I'm Joonyoung Kang, a graduate student in neuroscience. I've been using freesurfer over an year and I realized that I've used an old version of it. So I decided to update freesurfer and I couldn't find a way to do that. Do I just have to re-install the new version of freesurfer? If so,

Re: [Freesurfer] Freesurfer: Version of development version?

the 7.1.1 and 7.2 releases. Anastasia. From: freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Tobias Ruzok Sent: Wednesday, September 29, 2021 11:26 AM To: freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] Freesurfer: Version of development version?

Re: [Freesurfer] Freesurfer: Version of development version?

reesurfer@nmr.mgh.harvard.edu> Betreff: Re: [Freesurfer] Freesurfer: Version of development version? Hi Tobias - You can see the dates of official version releases here: https://secure-web.cisco.com/1sY88wu32DUCQV1vqZMVub

[Freesurfer] FreeSurfer version 7.0.0 is now available

We are pleased to announce the release of FreeSurfer version 7. You can get the new software from here https://surfer.nmr.mgh.harvard.edu/fswiki/DownloadAndInstall You can find the release notes here https://surfer.nmr.mgh.harvard.edu/fswiki/ReleaseNotes Let us know how it goes best doug and th

[Freesurfer] Freesurfer version 7.0.0 and hippocampal segmentation

External Email - Use Caution Hello Freesurfer team, I have just become aware of the release notes concerning v7.0.0 being recalled and not to be used, with the recommendation to use v7.1.0 instead: https://surfer.nmr.mgh.harvard.edu/fswiki/ReleaseNotes I have a couple of questio

Re: [Freesurfer] Freesurfer version 6.0 and 7.2

you will have to be more specific than "totally different" On 5/24/2022 8:33 AM, Lexuri Fernández de Gamarra Oca wrote: External Email - Use Caution Good afternoon, I have both versions (i.e., version 6.0 and 7.2) downloaded and for the analyses to run only with the newer version I w

Re: [Freesurfer] freesurfer version 6 on Debian

External Email - Use Caution  Debian 9 looks like it was the current version when Freesurfer 6 was released in 2017 for CentOS6 and MacOS.    But even if Freesurfer 6 runs on Debian 9, it’s not expected to run on current versions of Debian or CentOS because of system library cha

[Freesurfer] Freesurfer version from recon-all output files

Hi everyone, How can I find the freesurfer version used (recon-all) from the resulting files? This would be necessary for keeping freesurfer versions consistent. Thank you, Diogo ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nm

[Freesurfer] Freesurfer version after 5.3.0 from May 2013?

Hi all, I am a little confused about what the latest Freesurfer version is. I thought that v5.3.0 from May 15, 2013 would be the latest, but today I saw in the Tracula update list that there is apparently a version from December 9, 2013. Could you please clear that up for me? Thanks, Janosch

Re: [Freesurfer] freesurfer version update issue in MacOS

Hi Joonyoung you can just install the new version in a new location and point your path at it instead of the older version. cheers Bruce On Tue, 12 Dec 2017, 강준영 wrote: Hello! I'm Joonyoung Kang, a graduate student in neuroscience. I've been using freesurfer over an year and I realized tha

Re: [Freesurfer] freesurfer version update issue in MacOS

Hi Bruce! Thank you for your fast and kind answer. I have one more detailed question that I forgot to ask.. The main reason I want to update freesurfer is to use better hippocampal subfield and I want to make the subfield based on my previous data (in the older version freesurfer path) I expect

Re: [Freesurfer] freesurfer version update issue in MacOS

Hi Joonyoung. I'll leave this for Eugenio, but I think the answer is yes cheers Bruce On Tue, 12 Dec 2017, 강준영 wrote: Hi Bruce! Thank you for your fast and kind answer. I have one more detailed question that I forgot to ask.. The main reason I want to update freesurfer is to use better hip

Re: [Freesurfer] freesurfer version update issue in MacOS

The answer is yes, indeed. Just be careful when you report your results, specifying which version you used for what. Cheers, /Eugenio -- Juan Eugenio Iglesias ERC Senior Research Fellow Translational Imaging Group University College London http://www.jeiglesias.com http://cmictig.cs.ucl.ac.uk/

Re: [Freesurfer] freesurfer version update issue in MacOS

Thank you for your answer, Bruce and Eugenio. Then the way to do that might be,, 1. Install new version of freesurfer to a new location. 2. Move previous data from old version freesurfer path to the new location. 3. Do what I want (hippo subfield) Right..? Thanks. Sincerely, Joonyoung. 2017

Re: [Freesurfer] Freesurfer version 7.0.0 and hippocampal segmentation

Juan Eugenio Iglesias Senior research fellow CMIC (UCL), MGH (HMS) and CSAIL (MIT) http://www.jeiglesias.com From: on behalf of Vanessa Cropley Reply-To: Freesurfer support list Date: Wednesday, May 20, 2020 at 01:35 To: "freesurfer@nmr.mgh.harvard.edu" Subject: [Freesurfer]

Re: [Freesurfer] Freesurfer version 7.0.0 and hippocampal segmentation

0:44 PM To: Freesurfer support list Subject: Re: [Freesurfer] Freesurfer version 7.0.0 and hippocampal segmentation Dear Vanessa, 1. No changes were made in the hippocampal module between 7.0 and 7.1, so you don’t need to rerun (as the subjects were reconned-all with 6.0, which doesn’t have any prob

Re: [Freesurfer] Freesurfer version from recon-all output files

There is a file called scripts/build-stamp.txt. Also, if you set setenv REQUIRE_FS_MATCH 1 It will compare the current version with the version in the build stamp and exit with error if they don't agree On 4/25/17 5:14 PM, Diogo Duarte wrote: Hi everyone, How can I find the freesurfer versi

Re: [Freesurfer] Freesurfer version from recon-all output files

Thank you for your answer! For future reference, info about the machine can be found in the scripts/recon-all.done. Diogo On 25 April 2017 at 22:24, Douglas Greve wrote: > There is a file called scripts/build-stamp.txt. Also, if you set > setenv REQUIRE_FS_MATCH 1 > > It will compare the curre

[Freesurfer] [freesurfer] version differences for pial matter / skull strip?

Hello, I have posted several times about problems with skull-stripping with our dataset. We have tried gcut and multiple other options in other packages (AFNI, FSL, ANTS) to remove skull from structural images in our dataset with little success. Recently, a colleague suggested this may be due to

Re: [Freesurfer] Freesurfer version after 5.3.0 from May 2013?

Hi Janosch - The December 9th tracula update is just that, an update to the tracula code without any changes to the rest of freesurfer. a.y On Tue, 1 Apr 2014, Janosch Linkersdörfer wrote: Hi all, I am a little confused about what the latest Freesurfer version is. I thought that v5.3.0 fr

Re: [Freesurfer] Freesurfer version after 5.3.0 from May 2013?

Thanks, Anastasia! Am 01.04.2014 um 17:36 schrieb Anastasia Yendiki : > > Hi Janosch - The December 9th tracula update is just that, an update to the > tracula code without any changes to the rest of freesurfer. > > a.y > > On Tue, 1 Apr 2014, Janosch Linkersdörfer wrote: > >> Hi all, >> >>

Re: [Freesurfer] Freesurfer version 7 reconall -autorecon2-wm error

Hi Jewelia, Can you try running without the -parallel flag to see if that’s the issue? Best Andrew From: freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Jewelia K. Yao Date: Tuesday, May 4, 2021 at 11:06 AM To: freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] Freesurfer version 7

Re: [Freesurfer] [freesurfer] version differences for pial matter / skull strip?

Hi Michelle are you doing anything out of the ordinary? Do you want to send us a dataset and we will take a look? I don't think 6.0 is very different from 5.3 in regard to skull stripping, although it is probably a bit better Bruce On Fri, 17 Nov 2017, Michelle VanTieghem wrote: Hello,  I

Re: [Freesurfer] [freesurfer] version differences for pial matter / skull strip?

Hi, Yes I can send you the data - should I just attach the mprage file in the email, or is there another way to share the data with freesurfer? Also, should I send one scan or multiple scans? Thanks, Michelle On Sat, Nov 18, 2017 at 10:37 AM, Bruce Fischl wrote: > Hi Michelle > > are you doing

Re: [Freesurfer] [freesurfer] version differences for pial matter / skull strip?

Hi Michelle probably best to tar and gzip the entire subject directory and ftp it to us: https://surfer.nmr.mgh.harvard.edu/fswiki/FtpFileExchange cheers Bruce On Sat, 18 Nov 2017, Michelle VanTieghem wrote: Hi,  Yes I can send you the data - should I just attach the mprage file in the

Re: [Freesurfer] [freesurfer] version differences for pial matter / skull strip?

Hi, I am confused by the instructions for the ftp. Once I am logged into the ftp and have navigated to the transfer/incoming directory, how am I supposed to find / access the file that I would ike to send through? Does terminal still recognize my working directory before I logged into the ftp? Th

Re: [Freesurfer] [freesurfer] version differences for pial matter / skull strip?

yes, it should. You should just be able to do a "put" On Fri, 1 Dec 2017, Michelle VanTieghem wrote: Hi,  I am confused by the instructions for the ftp. Once I am logged into the ftp and have navigated to the transfer/incoming directory, how am I supposed to find / access the file that I woul

Re: [Freesurfer] [freesurfer] version differences for pial matter / skull strip?

Hi, I am unsure whether this worked: see attached screenshot. Thanks! M On Fri, Dec 1, 2017 at 4:26 PM, Bruce Fischl wrote: > yes, it should. You should just be able to do a "put" > > On Fri, 1 Dec 2017, Michelle VanTieghem wrote: > > Hi, >> I am confused by the instructions for the ftp. Once I

Re: [Freesurfer] [freesurfer] version differences for pial matter / skull strip?

can you paste the full session text into the email (not as a screen shot)? On Fri, 1 Dec 2017, Michelle VanTieghem wrote: Hi, I am unsure whether this worked: see attached screenshot. Thanks! M On Fri, Dec 1, 2017 at 4:26 PM, Bruce Fischl wrote: yes, it should. You should just be able

Re: [Freesurfer] [freesurfer] version differences for pial matter / skull strip?

yn-128-59-230-36:structural michellevantieghem2$ ftp surfer.nmr.mgh.harvard.edu Connected to surfer.nmr.mgh.harvard.edu. 220-This is the Martinos Center Anonymous FTP service. Use of this site 220-shows implicit consent to our Acceptable Use Policy outlined at 220-http://www.nmr.mgh.harvard.e

Re: [Freesurfer] [freesurfer] version differences for pial matter / skull strip?

try cd'ing to incoming not outgoing (the names are from our perspective I think :) On Fri, 1 Dec 2017, Michelle VanTieghem wrote: yn-128-59-230-36:structural michellevantieghem2$ ftp surfer.nmr.mgh.harvard.edu Connected to surfer.nmr.mgh.harvard.edu. 220-This is the Martinos Center Anonymou

Re: [Freesurfer] [freesurfer] version differences for pial matter / skull strip?

Ok that worked. I sent the data for a subject with the skull stripping issue that is common in most of our dataset. Thanks, Michelle On Fri, Dec 1, 2017 at 4:56 PM, Bruce Fischl wrote: > try cd'ing to incoming not outgoing (the names are from our perspective I > think :) > > > On Fri, 1 Dec 201

Re: [Freesurfer] [freesurfer] version differences for pial matter / skull strip?

Hi, I am just following up on my prior posts regarding skull strip issues and whether using freesurfer 6.0 would improve over freesurfer 5.3 . I sent the data over the ftp and would greatly appreciate it if you could take a look to see if there is a way to improve the skull strip since we have thi

Re: [Freesurfer] [freesurfer] version differences for pial matter / skull strip?

Hi, I am following up again -- on my prior posts regarding skull strip issues and whether using freesurfer 6.0 would improve over freesurfer 5.3 . I sent the data over the ftp on Dec 1 and would greatly appreciate it if you could take a look to see if there is a way to improve the skull strip si

Re: [Freesurfer] [freesurfer] version differences for pial matter / skull strip?

Hi Michelle, sorry about not getting to this before. It looks like Bruce was helping you out, but he's just left and won't be back until the new year. To answer your first question, I don't think that v6 performs much differently on skull stripping than v5.3. What is the nature of the skull str

Re: [Freesurfer] [freesurfer] version differences for pial matter / skull strip?

Hi Michelle sorry you are having so much trouble! Can you give us some details of you acquisition? We don't usually see this kind of persistent issues cheers Bruce On Fri, 22 Dec 2017, Michelle VanTieghem wrote: Hi Douglas,  I have reported many problems with the skull stripping and result

Re: [Freesurfer] [freesurfer] version differences for pial matter / skull strip?

that's good to hear, thanks for letting us know Michelle Bruce On Mon, 22 Jan 2018, Michelle VanTieghem wrote: Hi,  I went ahead and re-processed all of our data with the newest version (6.0) of freesurfer (I didn't hear back from anyone on this issue for over a month). It does make a signific

[Freesurfer] Freesurfer Version mismatch between Subject and Control Stamp in autorecon2 and autorecon3

Hi all, I'm sorry if this is a silly question, but what might cause the version of Freesurfer to be different in the Subject and Current Stamps of the output following autorecon2 and autorecon3? And is this a problem? The relevant lines of output are as follows: INFO: FreeSurfer build stamps do

Re: [Freesurfer] Freesurfer Version mismatch between Subject and Control Stamp in autorecon2 and autorecon3

Hi Amy looks like you processed them on different machines that use different version of freesurfer. One is centos4 with FS 5.0 and one is centos 6 with 5.3. You definitely don't want to mix these. Bruce On Thu, 3 Dec 2015, Amy L wrote: > Hi all, > > I'm sorry if this is a silly question, b