Freesurfer

freesurfer@nmr.mgh.harvard.edu

4 participants
30076 discussions

Pass code
by Wei 12 Apr '22

12 Apr '22

External Email - Use Caution Dear professors, I have downloaded the FreeSurfer Vitrual VM images and a pass code is needed for this 7z archieve. Would you please send me the pass code for help? wzh

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Pass code for FreeSurfer VitrualBox VM Images
by Wei 12 Apr '22

12 Apr '22

External Email - Use Caution Dear professors, I have downloaded the FreeSurfer Vitrual VM images and a pass code is needed for this 7z archieve. Would you please send me the pass code? wzh

1 0

Re: [Freesurfer] Request passcode VirtualBox image archive
by fsbuild 11 Apr '22

11 Apr '22

External Email - Use Caution Sending the info to your email shortly. - R. On Apr 10, 2022, at 05:36, Caterina Trainito <caterina.trainito(a)synlab.it> wrote:        External Email - Use Caution        Hello,I would like to request the passcode for the VirtualBox image archive "FS_7_2_0_ubuntu_18_04_06.ova.7z", as described in the wiki page: MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to behttps://surfer.nmr.mgh.harvard.edu/fswiki/VM_67Thank you!Best regards,Caterina Trainito, MScResearcherIRCCS Synlab SDNVia Gianturco 113 / Via Brin 55, Naples, Italy_______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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[IMPORTANT MESSAGE] Subfields & MCR problems solved
by Iglesias Gonzalez, Juan E. 10 Apr '22

10 Apr '22

Dear all, We have recently fixed two problems in the subfield modules using the Matlab runtime: 1. We have moved on from MatlabR2014b to MatlabR2019b, which enables users to run the code in more modern versions of Mac OS. 2. A bug in the the longitudinal hippocampal subfield (& amygdala) segmentation was fixed, where the volumes reported in the text files did NOT account for linear deformations across timepoints, thus greatly underestimating change (I would *really* like to apologize for this). Kind regards, Juan Eugenio Iglesias http://www.jeiglesias.com

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Request passcode VirtualBox image archive
by Caterina Trainito 10 Apr '22

10 Apr '22

External Email - Use Caution Hello, I would like to request the passcode for the VirtualBox image archive "FS_7_2_0_ubuntu_18_04_06.ova.7z", as described in the wiki page: https://secure-web.cisco.com/18CS92dSpHzbEbaM7FWv6m5pnsisNkx8qwe4hCCmONAupm… Thank you! Best regards, Caterina Trainito, MSc Researcher IRCCS Synlab SDN Via Gianturco 113 / Via Brin 55, Naples, Italy

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recon-all error
by cooperr1＠student.unimelb.edu.au 09 Apr '22

09 Apr '22

External Email - Use Caution Dear FreeSurfer developers, I'm attempting to run recon-all on a set of T1-weighted images acquired in the 1980s-1990s and am having trouble with the recon-all pipeline. I have used the original dicom files in the recon-all using the command below. Command: recon-all -s 1003156_dicom -i 2008-11-13_GE_001910/13.39_-_PACE/Ax_3D_512x256/002/I.001 -all Error message: /Applications/freesurfer_v6/bin/mri_convert: line 3: 8196 Segmentation fault: 11 mri_convert.bin "$@" The recon-all.log is also attached. I've also explored using dcmunpack and obtain the following result: Command: dcmunpack -src 2008-11-13_GE_001910/13.39_-_PACE/Ax_3D_512x256 Message: cat: /tmp/dcmdir-all.89439: No such file or directory Found 0 unique series: Patient: Undefined variable. Do you have any idea what might be the problem? Freesurfer version: freesurfer-Darwin-OSX-stable-pub-v6.0.0-2beb96c Platform: Mac OS X 10.13.3 Recon-all.log: attached. With warm regards, Rebecca Cooper

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Re: [Freesurfer] mkheadsurf error: mris_smooth and mris_inflate synthesized bizarre output paths
by Megan Schendel 09 Apr '22

09 Apr '22

External Email - Use Caution Hello, I am also trying to use mkheadsurf and getting the same errors described in the January topic by user Yong-Jun Lin. https://secure-web.cisco.com/1gWrCRE26r6WP8WhRpdFnJDHSFKaCpEOt6y_UEivpQG5fG… 1. The first error message is "subjdir: Undefined variable.". I followed the thread and also manually defined subjdir 2. Same problems with mris_smooth -n 10 -b /.. resulting in error: MRISwriteCurvature: could not open lh./... and mris_inflate -n 10 -sulc /... resulting in error: MRISwriteCurvature: could not open /... Lastly, I followed the response from Douglas N. Greve <https://secure-web.cisco.com/1ahbUvtJEJ2YIzAb-v2Vq6dQ8vxhI4tzwwkf_H3Yz4GyLG…> to try the new mkheadsurf. When I tried that, the subjdir error went away, but the output paths errors with the mris_smooth and mris_inflate persisted. The end result output files that I need were created, however, so I can go on with my work. But I thought I'd reply to the list and let you know that I'm also getting these path errors. Thanks for any help, Megan MEG Technician Pronouns: she/her The Mind Research Network 1101 Yale Blvd. NE Albuquerque, New Mexico 87106

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Freesurfer stats output meaning
by Rafael Navarro 09 Apr '22

09 Apr '22

External Email - Use Caution Hello Freesurfer developers, I am attempting to build a brain age estimator with FreeSurfer output. However, I am having some problems disentangling Freesurfer stats output. I will be using only the Desikan-Killiany atlas cortical segmentation. I have identified these files as useful: aseg.stats -> subcortical segmentation features lhaparc.stats -> DK cortical segmentation left hemisphere features rhaparc.stats -> DK cortical segmentation right hemisphere features lh.w-g.pct.stats -> DK cortical segmentation left hemisphere grey matter - white matter contrast features rh.w-g.pct.stats -> DK cortical segmentation right hemisphere grey matter - white matter contrast features wmparc.stats -> white matter close to DK cortical segmentation areas features However, I checked these two files too: lh.curv.stats rh.curv.stats But I don't have a clear idea of the meaning of the features in those files. For what I understand the features are the mean and standard deviation of the white matter surface and the pial surface. However, these measurements would be redundant if I include the features from xhaparc.stats, wouldn't they? Thanks for your help! ___________________________________ ----------------------------------- || Rafael Navarro González || Ph.D. Student || ETSI Telecomunicación || Universidad de Valladolid || Campus Miguel Delibes || 47011 Valladolid, Spain || e-mail: rafael.navarro(a)uva.es || Phone: +34 672 394 294 ||_________________________________ -----------------------------------

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Medial prefrontal cortex
by Patricia Schwery 09 Apr '22

09 Apr '22

External Email - Use Caution Hi there, I would like to know if someone could tell me how i can measure the medial prefrontal cortex (mPFC) with freesurfer as i see it is displayed within the superior frontal but i would need only the mPFC. I thank you so much for your help. Patricia

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recon-all error in a specific data
by Lee, Jeungchan 09 Apr '22

09 Apr '22

Hi freesurfer team, I collected an MPRAGE in Bay2 scanner (0.75 x 0.75 x 0.75 mm resolution), and the recon-all procedures with freesurfer version 6.0.0 and 7.1.1 were both failed. I'm not sure if this is due to the participant's large CSF or motion or something else. I have attached the log files (recon-all.log and talairach.log from both versions), which I noticed a warning/error in the recon-all.log : (version6.0.0) WARNING: only one run found. This is OK, but motion correction cannot be performed on one run, so I'll copy the run to rawavg and continue. (version6.0.0 and 7.1.1) ERROR: talairach_afd: Talairach Transform: transforms/talairach.xfm ***FAILED*** (p=0.0000, pval=0.0000 < threshold=0.0050) mritotal -verbose -debug -clobber -modeldir /space/lyon/9/pubsw/Linux2/packages/mni/current/bin/../share/mni_autoreg -protocol icbm transforms/tmp.talairach.7133/src.mnc transforms/talairach.auto.xfm Can't locate shellwords.pl in @INC (@INC contains: /autofs/cluster/pubsw/1/pubsw/Linux2/packages/mni/1.4/bin/../lib/mni_autoreg /usr/local/freesurfer/stable6_0_0/mni/share/perl5 /usr/local/lib64/perl5 /usr/local/share/perl5 /usr/lib64/perl5/vendor_perl /usr/share/perl5/vendor_perl /usr/lib64/perl5 /usr/share/perl5 .) at /space/lyon/9/pubsw/Linux2/packages/mni/current/bin/mritotal line 460. ERROR: mritotal failed, see transforms/talairach.log I have tested the recon-all with another Bay2 data (from different project in our group), and it worked perfectly (with version 6.0.0) with the same script. Thus, I did not think this is due to my script or FS version.. Thanks, Jeungchan

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Freesurfer