Freesurfer June 2023

freesurfer@nmr.mgh.harvard.edu

75 participants
107 discussions

Recon-all v.7.1.1 and TRACULA 7.3.2 compatible?
by Blujus, Jenna 28 Jun '23

28 Jun '23

External Email - Use Caution Hi all, I am using TRACULA for a longitudinal analysis of WM integrity. I used the longitudinal stream from freesurfer v7.1.1 to process the T1w images via recon-all. I'd like to use TRACULA v7.3.2 to process the DWI data and generate 42 WM tracts. Can I feed in the recon-all outputs from v7.1.1 to v7.3.2 or should they be reprocessed with v7.3.2? Thank you, Jenna

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mris_label2annot
by Maria Czarnecka 28 Jun '23

28 Jun '23

External Email - Use Caution Dear Sisters and Brothers in neuroscience, I am trying to make my own annotation file that will include only occipital cortex labels from the a2009s atlas. Is it possible? I am trying to do that with: mris_label2annot --ctab lh.my-color-table.txt --a my-annot-name --h lh --s fsaverage --l lh.S_calcarine.label --l lh.S_parieto_occipita.label --l lh.G_cuneus.label --l lh.G_oc-temp_med-Lingual.label --l lh.S_collat_transv_post.label --l lh.G_and_S_occipital_inf.label --l lh.Pole_occipital.label --l lh.G_occipital_middle.label --l lh.S_oc_middle_and_Lunatus.label --l lh.S_oc_sup_and_transversal.label --l lh.G_occipital_sup.label --l lh.S_oc-temp_med_and_Lingual.label --l lh.G_oc-temp_lat-fusifor.label --l lh.S_oc-temp_lat.label If i run it i get: 0 0 1 -1 NOT_FOUND 2 -1 NOT_FOUND 3 -1 NOT_FOUND 4 -1 NOT_FOUND 5 -1 NOT_FOUND 6 -1 NOT_FOUND 7 -1 NOT_FOUND 8 -1 NOT_FOUND 9 -1 NOT_FOUND 10 -1 NOT_FOUND 11 -1 NOT_FOUND 12 -1 NOT_FOUND 13 -1 NOT_FOUND Writing annot to... The file is saved and it is empty. Where is my mistake? I will be grateful for your help, Best, Maria Czarnecka

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Re: [Freesurfer] Error running hippocampus subfields and amygdala nuclei segmentation pipeline
by Mengjie Huang 27 Jun '23

27 Jun '23

External Email - Use Caution Hi FreeSurfer experts, I am writing to follow up on the ‘invalidMEXFile’ error. I have tried to run the segmentation pipeline with both 7.1.1 and the dev version, but the problem persists. Unfortunately I don't have access to the Python version. Could you please provide any guidance on how to resolve the error? Many thanks for your time and help. Best regards, Mengjie > On 14 Jun 2023, at 2:56 am, freesurfer-request(a)nmr.mgh.harvard.edu wrote: > > Message: 8 > Date: Tue, 13 Jun 2023 16:07:34 +0000 > From: "Iglesias Gonzalez, Juan E." <JIGLESIASGONZALEZ(a)mgh.harvard.edu> > Subject: Re: [Freesurfer] Error running hippocampus subfields and > amygdala nuclei segmentation pipeline > To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> > Message-ID: > <BL0PR04MB65315BAA0800424C60740C87FD55A(a)BL0PR04MB6531.namprd04.prod.outlook.com> > > Content-Type: text/plain; charset="windows-1252" > > External Email - Use Caution > > I?ll defer to our software engineering experts, but in the meantime, you could maybe try the Python version? > https://secure-web.cisco.com/1Cv_49AxchVd_2vIYynJ4qP6kfmnE5Dy5Tw3AuuGeUNzzO… > Cheers, > /E > > -- > Juan Eugenio Iglesias > http://secure-web.cisco.com/1QfGfcEcTkVF9fEP1hlZPh1BIK3eVs0WEnf3b34X1Z7TR0_… > > From: freesurfer-bounces(a)nmr.mgh.harvard.edu <freesurfer-bounces(a)nmr.mgh.harvard.edu> on behalf of Mengjie Huang <mhua0773(a)uni.sydney.edu.au> > Date: Tuesday, June 13, 2023 at 8:12 AM > To: freesurfer(a)nmr.mgh.harvard.edu <freesurfer(a)nmr.mgh.harvard.edu> > Subject: [Freesurfer] Error running hippocampus subfields and amygdala nuclei segmentation pipeline > > External Email - Use Caution > Hello FreeSurfer developers, > > I am writing to seek help regarding an issue I encountered when trying to run the hippocampus subfields and amygdala nuclei segmentation pipeline (please see the error message attached below). > I am running FreeSurfer V.7.1.1 on my university?s high performance computing (HPC) system. I have Matlab R2014b installed in '/usr/local/freesurfer/MCRv84?). I greatly appreciate any suggestions on how to resolve this issue. Many thanks for your time and help. > > > ------------------------------ > USER mhua0773 > HOST hpc008 > PROCESSID 3344 > PROCESSOR x86_64 > OS Linux > ITK_GLOBAL_DEFAULT_NUMBER_OF_THREADS 1 > Linux hpc008 2.6.32-696.16.1.el6.x86_64 #1 SMP Wed Nov 15 16:51:15 UTC 2017 x86_64 x86_64 x86_64 GNU/Linux > pbsjob 6889001.pbsserver > ------------------------------ > > freesurfer-linux-centos6_x86_64-7.1.1-20200723-8b40551 > > setenv SUBJECTS_DIR /scratch/Amy_FTD/controls_2_base/Preprocessing > cd /scratch/RDS-FSC-Amy_FTD-RW/controls_2_base/Preprocessing > /usr/local/freesurfer/7.1.1//bin/segmentHA_T1.sh 501_MRI1 > > #-------------------------------------------- > #@# Hippocampal Subfields processing (T1) left Tue Jun 13 13:59:28 AEST 2023 > ------------------------------------------ > Setting up environment variables > --- > LD_LIBRARY_PATH is .:/usr/local/freesurfer/7.1.1//MCRv84//runtime/glnxa64:/usr/local/freesurfer/7.1.1//MCRv84//bin/glnxa64:/usr/local/freesurfer/7.1.1//MCRv84//sys/os/glnxa64:/usr/local/freesurfer/7.1.1//MCRv84//sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/usr/local/freesurfer/7.1.1//MCRv84//sys/java/jre/glnxa64/jre/lib/amd64/server:/usr/local/freesurfer/7.1.1//MCRv84//sys/java/jre/glnxa64/jre/lib/amd64/client:/usr/local/freesurfer/7.1.1//MCRv84//sys/java/jre/glnxa64/jre/lib/amd64:/usr/local/freesurfer/7.1.1//lib/vtk/lib > Invalid MEX-file '/tmp/MCR_65032579/.mcrCache8.4/segmen0/autofs/space/panamint_005/users/iglesias/software/freesurfer.GEMS2.terrier/bin/kvlGEMSMatlab.mexa64': /tmp/MCR_65032579/.mcrCache8.4/segmen0/autofs/space/panamint_005/users/iglesias/software/freesurfer.GEMS2.terrier/bin/kvlGEMSMatlab.mexa64: failed to map segment from shared object: Operation not permitted > > Error in kvlClear (line 11) > > > > Error in segmentSubjectT1_autoEstimateAlveusML (line 115) > > > > MATLAB:invalidMEXFile > @#@FSTIME 2023:06:13:13:59:28 run_segmentSubjectT1_autoEstimateAlveusML.sh N 14 e 6.47 S 0.57 U 4.19 P 73% M 201140 F 0 R 61507 W 0 c 189 w 3872 I 0 O 84184 L 18.03 17.42 13.59 > @#@FSLOADPOST 2023:06:13:13:59:34 run_segmentSubjectT1_autoEstimateAlveusML.sh N 14 18.03 17.43 13.61 > Linux hpc008 2.6.32-696.16.1.el6.x86_64 #1 SMP Wed Nov 15 16:51:15 UTC 2017 x86_64 x86_64 x86_64 GNU/Linux > > T1 hippocampal subfields exited with ERRORS at Tue Jun 13 13:59:34 AEST 2023 > > Best regards, > Mengjie > >

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EPI Factor generated by dmri_bids_config
by Blujus, Jenna 27 Jun '23

27 Jun '23

External Email - Use Caution Hi all, I am using TRACULA (v7.3.2) to examine longitudinal changes in WM integrity by diagnostic groups. For preprocessing, I did not use topup because my data have a single acquisition (i.e., I do not have two acquisitions with opposing polarities of the phase-encode blips). But I did utilize the Eddy command for eddy current and motion correction. To do so TRACULA requires information regarding the epi factor, echo spacing, and phase encoding direction. My data are in BIDS format and so I used the dmri_bids_config script to extract these factors. While the echo spacing and PE direction match the information in my json files, I am finding that I am getting a large EPI factor (e.g., 115001.0273). I looked at the acqp.txt file generated for use with Eddy and the correct values are stored in the file for each subject (PE direction [0 1 0] and total readout time) so I believe the command was executed properly despite the large magnitude EPI factor. My questions are: 1. How is the EPI factor used in preprocessing by TRACULA? 2. Will the magnitude difference in the EPI factor affect the preprocessing of the DWI data if topup is turned off and only eddy is used? Thanks, Jenna

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Re: [Freesurfer] FS_7_2_0_ubuntu_198_04_06 root password
by fsbuild 27 Jun '23

27 Jun '23

External Email - Use Caution You were already sent the login credentials. If you have unzipped the archive, setup and started the VM and successfully logged in as the user shown in the login screen, then you can run system commands via "sudo".  No other login is needed to run Freesurfer in the VM.   We don't support otherwise modifying the VM, setting up other userids, etc. - R. On Jun 27, 2023, at 02:58, marco.muti(a)tin.it wrote:        External Email - Use Caution        Would you please send me the root password for FS_7_2_0_ubuntu_18_04_06?   Thanks!!! _______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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Missing file colortable_BA_thresh.txt for recon-all-clinical
by Michael Mc Laughlin 27 Jun '23

27 Jun '23

External Email - Use Caution I finally was able to run recon-all-clinical.sh without errors! There is a file in the development fork on Github called *colortable_BA_thresh.txt* in the *average* directory that is not present in the 7.4.1 release. When I downloaded this and put it into the 7.4.1 release, the replacement recon-all-clinical.sh ran without any errors. I also solved the mystery of the missing lateral ventricles. The file mri/brainmsk.mgz in the clinical version is a synthetic file that doesn't contain any ventricles. The equivalent to brainmsk.mgz in the clinical version is synthSR.mgz. This has the missing ventricles and indeed all the other brain components like the cerebellum etc. Alas, despite running error free, there is still no stats/aseg.stats file. I hope that this is on the TODO list for the developers. In the meantime I will write a matlab function to extract the aseg stats from mri/aseg.mgz, which seems to have all the necessary data. If anyone wants a copy of this please email me. Michael McLaughlin,

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removal
by Pavlina.Pokosova＠fnmotol.cz 27 Jun '23

27 Jun '23

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FS_7_2_0_ubuntu_198_04_06.ova unzip password
by marco.muti＠tin.it 27 Jun '23

27 Jun '23

External Email - Use Caution Would you please send me the unzip pass for FS_7_2_0_ubuntu_198_04_06.ova? Thanks!

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F mgh file
by Adriana Cannizzaro 26 Jun '23

26 Jun '23

External Email - Use Caution Dear FreeSurfer team, We would like to extract the F value from the group effect. Based on previous posts, we should use the file F.mgh in order to achieve that. How can this method be used without a matlab licence ? Is there any possibility to start a matlab terminal using FreeSurfer's matlab libraries ? Thank you in advance ! Adriana Cannizzaro

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Ubuntu unzip password request
by 朱宣龙 26 Jun '23

26 Jun '23

External Email - Use Caution Hi, I am attempting to install Ubuntu following the tutorial provided on the wiki, but it requires a passcode to open the image. Can I ask for the password for the FS_7_2_0_ubuntu_18_04_06.ova.7z? Thanks. Best, Xuanlong

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Freesurfer June 2023