Freesurfer

freesurfer@nmr.mgh.harvard.edu

11 participants
30080 discussions

lme_mass_F error
by Emmanuel Nwosu 24 Sep '21

24 Sep '21

External Email - Use Caution Dear All I am running the longitudinal post processing statistical analysis and this error comes up each time I run the lme_mass_F. Does anyone have an idea of why this is happening and how to resolve it. Any help will be appreciated *************************************************************************************************** F_lstats = lme_mass_F(tlstats,CM); Computing F statistics, degrees of freedom and P-values ... Error using lme_mass_F (line 92) The source code (/matlab filepath/lme_mass_F.m) for the parfor-loop that is trying to execute on the worker could not be found. Caused by: Undefined function 'fcdf' for input arguments of type 'double'. Error using remoteParallelFunction (line 84) Worker unable to find file. Undefined function 'fcdf' for input arguments of type 'double' **************************************************************************************************** Kind regards Emmanuel

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fsaverage nifti to gifti
by Tom Vanasse 24 Sep '21

24 Sep '21

External Email - Use Caution Hello, I have a question regarding the conversion of functional fsaverage lh and rh files (created from the Yeo lab MNI to fsaverage projection software: https://secure-web.cisco.com/1nRJbdVDTJHwxxGMU9q1fmvcPt_Df0AIfr6uIaGGD96UkP…) to a *gifti file*. For example, 'rh.sub-13_ses-fmri1_task-awak_run-1_space-MNI152NLin2009cAsym_desc-preproc_bold_cleaned.allSub_RF_ANTs_MNI152_orig_to_fsaverage.nii.gz' This is necessary because my end goal is to then transform that gifti file, using wb_command, to the fs_LR HCP surface. Any help would be greatly appreciated, Tom

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Error in Analyze: Couldn't open PATH/sub_01/surf/lh.thickness.fwhm10.fsaverage.mgz or .mgh file.
by Fabiola Macruz 24 Sep '21

24 Sep '21

External Email - Use Caution Dear FreeSurfer experts: I am processing in qdec 25 subjects (each with 3 MRIs studies) and I have this terminal output: Error in Analyze: Couldn't open PATH/sub_01/surf/lh.thickness.fwhm10.fsaverage.mgz or .mgh file. I have executed the following qcache command for each subject: long_mris_slopes --qdec qdecfile --meas thickness --hemi > lh --do-avg --do-rate --do-pc1 --do-spc --do-stack --do-label --time > months --fwhm 10 --qcache fsaverage --sd SUBJECTS_DIR All the bases subjects have the specific files after this cmd: lh.long.thickness-avg[pc1/rate/spc].fwhm0[5, 10, 15, 20, 25].fsaverage.mgh. However, the file that qdec asks for - is missing in all the bases subjects. I have also created a qdec/.Qdecrc file in the qdec directory that contains the following lines: MEASURE1 = long.thickness-avg MEASURE2 = long.thickness-rate MEASURE3 = long.thickness-pc1 MEASURE4 = long.thickness-spc Could you please help out? I have found another person with exactly the same problem in the freesurfer forum and the person assisting him, couldn't explain why this happen. Just went around about a bunch of other things that could be and didnt solve the guy's problem. I honestly found the tutorials for longitudinal analysis in the website very frustrating and poorly explained. Even in regard to the .Qdecrc file that we need to create, it wasn't clear to me what extension it was and if we were only suppose to copy paste the following in any terminal editor: EASURE1 = long.thickness-avg MEASURE2 = long.thickness-rate MEASURE3 = long.thickness-pc1 MEASURE4 = long.thickness-spc Thanks, Fabiola

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Re: [Freesurfer] freesurfer running error at start
by fsbuild 23 Sep '21

23 Sep '21

External Email - Use Caution Your output shows you should you should be ready to work with freesurfer version 6.0 which is an older release from ~2017.  So people there may have used version 6 for quite some time.   If there was something missing on the system that freesurfer 6 needed to run, it’s probably been remedied by now.  If you are just starting out with freesurfer then I would not be too concerned with using version 6. Just keep in mind the current release is version 7.2.0 from this year (2021).  Browsing the 7.X release notes (at the top of the page) and comparing then with the 6.0 release notes (at the bottom of the page) can help you decide if version 7 offers improvements depending upon what you need to do - see  https://secure-web.cisco.com/1BDXGUYepZSu-OnlNwiqwjMw9yYjoVH9lFYYgCyki-ZNot8TkGmaIVwTD9K5BQZzvk4HPvMrJ70VW_4L4LS4YCgONmrFbWrWSrr1SNqCc5eBh9Dkgm6gXT5a6iILq6cs4QyT0bhqBlK3UNMV7iayEbLgUxXWayiDLf0uImbHIg44Fs9ZY3h23oKWKU68tDgSkNZQiHtSz7k_uP8qWWVg3p1hRr3Sl0vZBeZEb3O6d3rEVs_ugFAfUBbbHaE6ey9MK2zgpKB3RxWjRpsiRBloIdQ/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FReleaseNotes.  For ongoing work it’s recommended to stick with the version of freesurfer you started with  -  see the “Important Note” on this page, https://secure-web.cisco.com/1PMV3hWYoa71yGCIFhXRqSneCKhKc1Kl4cv…. - R. On Sep 23, 2021, at 18:25, Banik, Rana <rana.banik(a)vanderbilt.edu> wrote:        External Email - Use Caution                External Email - Use Caution        banikr2@banikr:~$ bashbanikr2@banikr:~$ export FREESURFER_HOME=/usr/local/freesurferbanikr2@banikr:~$ source SFREESURFER_HOME/SetUpFreeSurfer.shbash: SFREESURFER_HOME/SetUpFreeSurfer.sh: No such file or directoryInstead, I changed the command as: banikr2@banikr:~$ source /usr/local/freesurfer/SetUpFreeSurfer.shgives the following: banikr2@banikr:~$ source /usr/local/freesurfer/SetUpFreeSurfer.sh-------- freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c --------Setting up environment for FreeSurfer/FS-FAST (and FSL)FREESURFER_HOME   /usr/local/freesurferFSFAST_HOME       /usr/local/freesurfer/fsfastFSF_OUTPUT_FORMAT nii.gzSUBJECTS_DIR      /usr/local/freesurfer/subjectsMNI_DIR           /usr/local/freesurfer/mniFSL_DIR           /usr/local/fslHow do I check the installation is done properly? FYI, I have used mri_convert from python script.Rana BanikFrom: fsbuild <fsbuild@contbay.com>Sent: Thursday, September 23, 2021 4:11 PMTo: freesurfer@nmr.mgh.harvard.edu <freesurfer@nmr.mgh.harvard.edu>Cc: Banik, Rana <rana.banik@vanderbilt.edu>Subject: Re: [Freesurfer] freesurfer running error at start OK, then try setting FREESURFER_HOME and setting the environment in a terminal window with the commands,$ bash$ export FREESURFER_HOME=/usr/local/freesurfer$ source $FREESURFER_HOME/SetUpFreeSurfer.shThen you should see what the output reports for the freesurfer version.- R.On Sep 23, 2021, at 15:30, Banik, Rana <rana.banik(a)vanderbilt.edu> wrote:        External Email - Use Caution                External Email - Use Caution        Hello, There is no directory called /7.2.0 rather the directory i am finding the files is: <pre>banikr2@banikr:/usr/local/freesurfer$ pwd/usr/local/freesurfer</pre>Trying the same in the /freesurfer folderRana BanikFrom: fsbuild <fsbuild@contbay.com>Sent: Wednesday, September 22, 2021 7:11 PMTo: freesurfer@nmr.mgh.harvard.edu <freesurfer@nmr.mgh.harvard.edu>Cc: Banik, Rana <rana.banik@vanderbilt.edu>Subject: Re: [Freesurfer] freesurfer running error at start Hello Rana,Running that script (or any other freesurfer commands/binaries) assumes you’ve setup the freesurfer environment by,1) setting FREESURFER_HOME in your shell to point to the top of the freesurfer tree2) source’ing a shell init file to set PATH and other environment variables in order to run freesurfer commandsThere is info on the wiki about this for linux,MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to behttps://surfer.nmr.mgh.harvard.edu/fswiki/SetupConfiguration_Linux- and the Mac,MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to behttps://surfer.nmr.mgh.harvard.edu/fswiki/SetupConfiguration_MacJust find the absolute path to the top of the freesurfer tree.  For the latest 7.2.0 release installed by the package installers the version number is already in the absolute pathname to the top of the freesurfer tree.  On linux that path would be /usr/local/freesurfer/7.2.0 and on the Mac that path would be /Applications/freesurfer/7.2.0For that linux path using bash you would do,$ bash$ export FREESURFER_HOME=/usr/local/freesurfer/7.2.0$ source $FREESURFER_HOME/SetUpFreeSurfer.shWhen you run the source command to read the SetUpFreeSurfer script for the shell you are using, the version of freesurfer will get printed out automatically for you.Using the 7.2.0 linux release you would see the string between the dashes no matter what the absolute path is to FREESURFER_HOME on your system.tmp$ export FREESURFER_HOME=/usr/local/freesurfer/7.2.0tmp$ source $FREESURFER_HOME/SetUpFreeSurfer.sh-------- freesurfer-linux-centos7_x86_64-7.2.0-20210720-aa8f76b --------Setting up environment for FreeSurfer/FS-FAST (and FSL)FREESURFER_HOME   /usr/local/freesurfer/7.2.0FSFAST_HOME       /usr/local/freesurfer/7.2.0/fsfastFSF_OUTPUT_FORMAT nii.gzSUBJECTS_DIR      /usr/local/freesurfer/7.2.0/subjectsMNI_DIR           /usr/local/freesurfer/7.2.0/mniFSL_DIR           /usr/pubsw/packages/fsl/current… now run any freesurfer commands …- ROn Sep 22, 2021, at 18:04, Banik, Rana <rana.banik(a)vanderbilt.edu> wrote:        External Email - Use Caution                External Email - Use Caution        Running freesurfer from terminal with the following error: banikr2@banikr:~/freesurfer/bin$ ./freesurfer FreeSurfer is a set of tools for the analysis and visualization of structural and functional brain imaging data. FreeSurfer also refers to the structural imaging stream within the FreeSurfer suite. Users should consult the online documentation available at:   MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be http://secure-web.cisco.com/12K27iXExmAVdiVJTTUsxnZc3CWcIk9z0PWXun_LFxlG1Lp… Alternatively, the 'recon-all' command help-text provides adequate information to begin processing subject data, such as the sample subject 'bert' found in the 'freesurfer/subjects' directory.  Type 'recon-all --help' to view this help-text. Direct comments and questions to:   freesurfer(a)nmr.mgh.harvard.edu You are running this version of FreeSurfer: cat: /build-stamp.txt: No such file or directory Any idea what went wrong or how to fix it? Rana BanikGraduate StudentDept. of Biomedical Engineering Vanderbilt University, Nashville, TN_______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://secure-web.cisco.com/1OK46XhJ4f_3Ospz1-ee0_xWo4bRUc2OoqTABw2Ah_pe27RdS-aW_pQibZAl974Pt0PYOjUCLJT08iSBJwOy6FkDfGIKfPAZJvrEb-GG4HlOoKmGJMj2V-gnQbGbxXbtVxxpQoXTWcLQn7m7cisnAWyh_xUTKuSmFr-ecgOAENC8xA_cpcBL982rkplEg2kgVAt--kwwzQSi8ocDZ5LOJkI5ulY2HiNfAIUe8X_dvuN797OzEM5V45r0DW-llL6qeJabxGSUsj3JljdC9xOCqmQ/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer_______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://secure-web.cisco.com/1BELKLcx6vgPMRdbYs-4tYZraPJcxSMRMxvDPgZ6p3a19TxnKVgkfMht9L_2VlznjdQDFxez5HBbIyXgrXkWk_Lc6S2ghMN25SNzHEo5jakTOjKVR1vXcR2zKWVVmVYgvD31PbL99JuXSTXIQk2Jq1REbdeDeXUawe6UFm7-IxrcoCnkmlgYIaC8Dg2rlzCxHrbacEqizESsgVtSde41PUjRMLJOoveJOe7cYqS5ndpqfY9g1UorY4kIuVgJjDUmk4xXbl037m0GcYyizM05PpQ/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer_______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://secure-web.cisco.com/1O0Y-A9a1QmlEQo8otOOhFrUi49KsM6gWNLejHjGUSI2lsBAF750WEBRQIL3BLRG3LzGH8tJohR9HiYOH510la_I4CbO0Bq_k7GTRgavQJi1obMeez1PmtNNjxE03xvq-7MPKAzvFTzbr42gnRt4m16jvPXunP2CGUlLhkKCsdsOWg6JtunHvFcpTF4_nRShaXoL2GlH01XwQlbPKdWJGSd-pBEaTSFBpokVMrwTyqM2qeFYP6HlqTFqPCYI3zpFQ8hex_uoHo-zt9_e3TcCqmQ/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer

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Re: [Freesurfer] freesurfer running error at start
by fsbuild 23 Sep '21

23 Sep '21

External Email - Use Caution OK, then try setting FREESURFER_HOME and setting the environment in a terminal window with the commands, $ bash $ export FREESURFER_HOME=/usr/local/freesurfer$ source $FREESURFER_HOME/SetUpFreeSurfer.sh Then you should see what the output reports for the freesurfer version. - R. On Sep 23, 2021, at 15:30, Banik, Rana <rana.banik(a)vanderbilt.edu> wrote:        External Email - Use Caution                External Email - Use Caution        Hello, There is no directory called /7.2.0 rather the directory i am finding the files is: <pre>banikr2@banikr:/usr/local/freesurfer$ pwd/usr/local/freesurfer</pre>Trying the same in the /freesurfer folderRana BanikFrom: fsbuild <fsbuild@contbay.com>Sent: Wednesday, September 22, 2021 7:11 PMTo: freesurfer@nmr.mgh.harvard.edu <freesurfer@nmr.mgh.harvard.edu>Cc: Banik, Rana <rana.banik@vanderbilt.edu>Subject: Re: [Freesurfer] freesurfer running error at start Hello Rana,Running that script (or any other freesurfer commands/binaries) assumes you’ve setup the freesurfer environment by,1) setting FREESURFER_HOME in your shell to point to the top of the freesurfer tree2) source’ing a shell init file to set PATH and other environment variables in order to run freesurfer commandsThere is info on the wiki about this for linux,MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to behttps://surfer.nmr.mgh.harvard.edu/fswiki/SetupConfiguration_Linux- and the Mac,MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to behttps://surfer.nmr.mgh.harvard.edu/fswiki/SetupConfiguration_MacJust find the absolute path to the top of the freesurfer tree.  For the latest 7.2.0 release installed by the package installers the version number is already in the absolute pathname to the top of the freesurfer tree.  On linux that path would be /usr/local/freesurfer/7.2.0 and on the Mac that path would be /Applications/freesurfer/7.2.0For that linux path using bash you would do,$ bash$ export FREESURFER_HOME=/usr/local/freesurfer/7.2.0$ source $FREESURFER_HOME/SetUpFreeSurfer.shWhen you run the source command to read the SetUpFreeSurfer script for the shell you are using, the version of freesurfer will get printed out automatically for you.Using the 7.2.0 linux release you would see the string between the dashes no matter what the absolute path is to FREESURFER_HOME on your system.tmp$ export FREESURFER_HOME=/usr/local/freesurfer/7.2.0tmp$ source $FREESURFER_HOME/SetUpFreeSurfer.sh-------- freesurfer-linux-centos7_x86_64-7.2.0-20210720-aa8f76b --------Setting up environment for FreeSurfer/FS-FAST (and FSL)FREESURFER_HOME   /usr/local/freesurfer/7.2.0FSFAST_HOME       /usr/local/freesurfer/7.2.0/fsfastFSF_OUTPUT_FORMAT nii.gzSUBJECTS_DIR      /usr/local/freesurfer/7.2.0/subjectsMNI_DIR           /usr/local/freesurfer/7.2.0/mniFSL_DIR           /usr/pubsw/packages/fsl/current… now run any freesurfer commands …- ROn Sep 22, 2021, at 18:04, Banik, Rana <rana.banik(a)vanderbilt.edu> wrote:        External Email - Use Caution                External Email - Use Caution        Running freesurfer from terminal with the following error: banikr2@banikr:~/freesurfer/bin$ ./freesurfer FreeSurfer is a set of tools for the analysis and visualization of structural and functional brain imaging data. FreeSurfer also refers to the structural imaging stream within the FreeSurfer suite. Users should consult the online documentation available at:   MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be http://secure-web.cisco.com/1BX9WO2ZIUDU9BmWuM0YkMFQ5KPQ0N_6lDMeyaiAbyQnDa-… Alternatively, the 'recon-all' command help-text provides adequate information to begin processing subject data, such as the sample subject 'bert' found in the 'freesurfer/subjects' directory.  Type 'recon-all --help' to view this help-text. Direct comments and questions to:   freesurfer(a)nmr.mgh.harvard.edu You are running this version of FreeSurfer: cat: /build-stamp.txt: No such file or directory Any idea what went wrong or how to fix it? Rana BanikGraduate StudentDept. of Biomedical Engineering Vanderbilt University, Nashville, TN_______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://secure-web.cisco.com/1OK46XhJ4f_3Ospz1-ee0_xWo4bRUc2OoqTABw2Ah_pe27RdS-aW_pQibZAl974Pt0PYOjUCLJT08iSBJwOy6FkDfGIKfPAZJvrEb-GG4HlOoKmGJMj2V-gnQbGbxXbtVxxpQoXTWcLQn7m7cisnAWyh_xUTKuSmFr-ecgOAENC8xA_cpcBL982rkplEg2kgVAt--kwwzQSi8ocDZ5LOJkI5ulY2HiNfAIUe8X_dvuN797OzEM5V45r0DW-llL6qeJabxGSUsj3JljdC9xOCqmQ/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer_______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://secure-web.cisco.com/1BELKLcx6vgPMRdbYs-4tYZraPJcxSMRMxvDPgZ6p3a19TxnKVgkfMht9L_2VlznjdQDFxez5HBbIyXgrXkWk_Lc6S2ghMN25SNzHEo5jakTOjKVR1vXcR2zKWVVmVYgvD31PbL99JuXSTXIQk2Jq1REbdeDeXUawe6UFm7-IxrcoCnkmlgYIaC8Dg2rlzCxHrbacEqizESsgVtSde41PUjRMLJOoveJOe7cYqS5ndpqfY9g1UorY4kIuVgJjDUmk4xXbl037m0GcYyizM05PpQ/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer

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Customising overlay
by Worker, Amanda 23 Sep '21

23 Sep '21

External Email - Use Caution Dear FreeSurfer Developers, I am attempting to create some figures which display regional (Destrieux atlas) values which are typically in the range of 0-10. I would like to have an inflated brain with those regional values overlaid, for both patients and healthy controls. In total there will be four independent figures. The problem I am having is that the range of values is different for each overlay e.g. overlay 1 regional value range from 0-3, overlay 2 regional values range from 0-8, which means that the colour scales are on different scales. I would like to find a way to manually set the scale to 0-10 for each overlay, regardless of the actual values that exist within the overlay file. I am currently using the below command to load the overlay and then manually configuring the colour scale via the custom option, but I cannot add a point that is outside the range of values that exist in that overlay. I hope this makes sense and I would appreciate any advice you can give on how to achieve consistent colour scales for different overlays. freeview -f /software/system/freesurfer/freesurfer-6.0.0/subjects/fsaverage/surf/rh.inflated:overlay=rh_pcnt_neg_control_01.mgz:overlay_method=linearopaque:overlay_threshold=0,5,10 Kind regards, Amanda

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Re: [Freesurfer] freesurfer running error at start
by fsbuild 23 Sep '21

23 Sep '21

External Email - Use Caution Hello Rana, Running that script (or any other freesurfer commands/binaries) assumes you’ve setup the freesurfer environment by, 1) setting FREESURFER_HOME in your shell to point to the top of the freesurfer tree2) source’ing a shell init file to set PATH and other environment variables in order to run freesurfer commands There is info on the wiki about this for linux,https://secure-web.cisco.com/1U_tQcIreV6NPEuFeulfUWAOPFCaUe8vUQglXkIl… and the Mac,https://secure-web.cisco.com/1lLrW0TVmBeBE-XNNGyud8WDh5s2-DkWIjI41lqr-K… Just find the absolute path to the top of the freesurfer tree.  For the latest 7.2.0 release installed by the package installers the version number is already in the absolute pathname to the top of the freesurfer tree.  On linux that path would be /usr/local/freesurfer/7.2.0 and on the Mac that path would be /Applications/freesurfer/7.2.0 For that linux path using bash you would do,$ bash$ export FREESURFER_HOME=/usr/local/freesurfer/7.2.0$ source $FREESURFER_HOME/SetUpFreeSurfer.sh When you run the source command to read the SetUpFreeSurfer script for the shell you are using, the version of freesurfer will get printed out automatically for you. Using the 7.2.0 linux release you would see the string between the dashes no matter what the absolute path is to FREESURFER_HOME on your system.. tmp$ export FREESURFER_HOME=/usr/local/freesurfer/7.2.0tmp$ source $FREESURFER_HOME/SetUpFreeSurfer.sh-------- freesurfer-linux-centos7_x86_64-7.2.0-20210720-aa8f76b --------Setting up environment for FreeSurfer/FS-FAST (and FSL)FREESURFER_HOME   /usr/local/freesurfer/7.2.0FSFAST_HOME       /usr/local/freesurfer/7.2.0/fsfastFSF_OUTPUT_FORMAT nii.gzSUBJECTS_DIR      /usr/local/freesurfer/7.2.0/subjectsMNI_DIR           /usr/local/freesurfer/7.2.0/mniFSL_DIR           /usr/pubsw/packages/fsl/current … now run any freesurfer commands … - R On Sep 22, 2021, at 18:04, Banik, Rana <rana.banik(a)vanderbilt.edu> wrote:        External Email - Use Caution                External Email - Use Caution        Running freesurfer from terminal with the following error: banikr2@banikr:~/freesurfer/bin$ ./freesurfer FreeSurfer is a set of tools for the analysis and visualization of structural and functional brain imaging data. FreeSurfer also refers to the structural imaging stream within the FreeSurfer suite. Users should consult the online documentation available at:   http://secure-web.cisco.com/12yYZnrgAMX9gDsyIH0PviXj24zc_BpPcACqoCQE3uVFASO… Alternatively, the 'recon-all' command help-text provides adequate information to begin processing subject data, such as the sample subject 'bert' found in the 'freesurfer/subjects' directory.  Type 'recon-all --help' to view this help-text. Direct comments and questions to:   freesurfer(a)nmr.mgh.harvard.edu You are running this version of FreeSurfer: cat: /build-stamp.txt: No such file or directory Any idea what went wrong or how to fix it? Rana BanikGraduate StudentDept. of Biomedical Engineering Vanderbilt University, Nashville, TN_______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://secure-web.cisco.com/1OK46XhJ4f_3Ospz1-ee0_xWo4bRUc2OoqTABw2Ah_pe27RdS-aW_pQibZAl974Pt0PYOjUCLJT08iSBJwOy6FkDfGIKfPAZJvrEb-GG4HlOoKmGJMj2V-gnQbGbxXbtVxxpQoXTWcLQn7m7cisnAWyh_xUTKuSmFr-ecgOAENC8xA_cpcBL982rkplEg2kgVAt--kwwzQSi8ocDZ5LOJkI5ulY2HiNfAIUe8X_dvuN797OzEM5V45r0DW-llL6qeJabxGSUsj3JljdC9xOCqmQ/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer

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Announcing FreeSurfer version 7.2
by Douglas N. Greve 23 Sep '21

23 Sep '21

We are please to announce version 7.2. Mostly bug fixes and behind-the-scenes enhancements. But there are a few new goodies and one new "known issue" about defacing. Check out https://surfer.nmr.mgh.harvard.edu/fswiki/ReleaseNotes doug

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How to get cortical volume from a particular atlas?
by DRON Noramon 23 Sep '21

23 Sep '21

External Email - Use Caution Dear Freesurfer Team I have a very naive question. I am in urgent need to get a cortical region volume base on the Harvard-Oxford Cortical Atlas(from FSL). I have T1 images in nifti files, brain extracted. How can I get the cortical volume using Freesurfer, and regions based on the Harvard-Oxford Cortical Atlas? Please, I am very new to Freesurfer and in the middle of installing Freesurfer to linux server. Can you tell me the steps or a link to your tutorial page? I am trying to find it on your wiki page and have trouble navigate around. Thank you in advance, Best regards Noramon The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336. Is e buidheann carthannais a th' ann an Oilthigh Dhùn Èideann, clàraichte an Alba, àireamh clàraidh SC005336.

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Migrating data from v6 to v7
by Amanda Boyes 23 Sep '21

23 Sep '21

External Email - Use Caution Hi fellow FreeSurfer users, I am part of a longitudinal project and have a large dataset that has been processed in v6. I have now upgraded to v7 and would like to update my processed data, retaining the existing manual masks and pial edits. I found an old ReconAllChanges page (January 27, 2006, last updated 2012) referring to this as a “legacy data set” https://secure-web.cisco.com/1MoVgZUSO9R-A8IjZAHqOzDT9Py5A4Mq4VNrsSGB5Dphed… I have also found a recon-all wiki page (https://secure-web.cisco.com/1EqY5oKya3ZRmkvhBV2hjYD2yCLyZAOJUT5Hd_RXPDPt5m… last updated 2017) suggesting the use of the following command for legacy datasets: recon-all -subject subjectname -all -legacy Unfortunately, the -legacy flag is not recognised in v7. I would be grateful for any advice on how to update my existing data from v6.0.0 to v7.2. Thank you in advance, Amanda Amanda Boyes My pronouns are she/her/hers PhD Candidate and Research Assistant (Youth Mental Health) Thompson Institute USC  Tel: +61 7 5456 3886 amanda.boyes(a)usc.edu.au | usc.edu.au<http://secure-web.cisco.com/1otQ0N4r7tGUgtK8BkwMQjmBlIsM1lQpsIY-owcgNEj3Pph…> [Logo, company name Description automatically generated] I acknowledge the Traditional Custodians of the lands and waters upon which the University’s campuses are located. I acknowledge their continuing connections to country and pay my respects to Elders past, present and emerging. University of the Sunshine Coast | CRICOS Provider Number: 01595D

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