Freesurfer September 2019

freesurfer@nmr.mgh.harvard.edu

93 participants
143 discussions

Hippocampal and Amygdala Segmentation Error - Incorrect Path and Missing Files
by Chen, Christine 16 Sep '19

16 Sep '19

External Email - Use Caution To whom it may concern, I am attempting to run the hippocampal and amygdala segmentation (https://surfer.nmr.mgh.harvard.edu/fswiki/HippocampalSubfieldsAndNucleiOfAm…) on the development version of FreeSurfer. However, I am running into a couple errors when running the segmentHA_T1.sh script. The first error is that the script is looking for segmentSubjectT1_autoEstimateAlveusML in the wrong directory. It is currently looking for this command in /usr/local/freesurfer/bin/ however I need to change this path to /g5/dcn/freesurfer_testing/HippoSegment_Test/freesurfer/bin/. I couldn't find where to change this path in run_segmentSubjectT1_autoEstimateAlveusML.sh. Where is this path defined so I can change it? Secondly, the error output states that I am missing the following files in the subject's mri folder: lh.hippoSfVolumes-T1.v21.txt lh.amygNucVolumes-T1.v21.txt rh.hippoSfVolumes-T1.v21.txt rh.amygNucVolumes-T1.v21.txt I believe these files are created using recon-all -all -s [subjectname]. I ran this command before segmentHA_T1.sh using MPRAGE dicoms, and it seemed to have run without noticeable error, but these four files are still missing. How would I go about resolving this to create these files? Thank you in advance for the help! Best, CC ---------------------------------------------------------------------- Disclaimer: The materials in this e-mail are private and may contain Protected Information. Please note that e-mail communication is not encrypted by default. You have the right to request further emails be encrypted by notifying the sender. Your continued use of e-mail constitutes your acknowledgment of these confidentiality and security limitations. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying, distribution, or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this e-mail in error, please immediately notify the sender via telephone or return e-mail.

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Re: [Freesurfer] Longitudinal stream finalsurfs misalignment?
by Douglas Merkitch 16 Sep '19

16 Sep '19

External Email - Use Caution Hey Martin, Sounds like a logical approach. I'll give it a try and let you know how it ends up. I am using version 6.0 by the way. Thanks, Doug -----Original Message----- From: Martin Reuter <mreuter(a)nmr.mgh.harvard.edu> Sent: Monday, September 16, 2019 2:39 AM To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> Cc: Douglas Merkitch <dmerkitch(a)sralab.org> Subject: Re: [Freesurfer] Longitudinal stream finalsurfs misalignment? Hi Doug, probably something went wrong during the editing. E.g maybe you edited files in the cross sectional or base directories and copied/saved these to the longitudinals or vice-verca. There should be no mis-alignments. I would recommend this: 1. run one such subjects without edits through cross, base and long locally 2. if that looks good, run cross do finalsurf edits if necessary and complete cross runs. Then run base, do finalsurf edits and complete base run. Finally run long. All should be fine. Depending on the type of problem you are editing, usually it is sufficient to edit these only in the base. And make sure you use fs60 (not sure which version you used). Best, Martin On Fri, 2019-09-13 at 16:41 +0000, Douglas Merkitch wrote: > External Email - Use Caution > Hey all, > > I have a group of subjects with 2 time points that I've run thru the > longitudinal processing stream. All goes OK until I run the recon-all > -long and the resulting .long. subject dirs have the finalsurfs > misaligned (i.e. one subject has the edits moved inferior and the > other has them moved superior, causing drastic consequences to the > pial/wm surfaces). > > FYI these subjects were processed on a Linux-based high performance > computing cluster and edits were made locally on a Linux virtual > machine with subject dirs being transferred back and forth via scp. > Not sure if this is relevant, but thought I’d mention it just in case. > > I’ve uploaded a .tar file containing one of these longitudinal > subject’s directories (i.e. both cross tps, base, and both resulting > long tps) called ‘merkitch_upload_201980913.tar’ via the filedrop > website. > > Any help would be appreciated! > > Thanks, > > Doug > > Douglas Merkitch > Clinical Research Coordinator > > 355 E. Erie St, Chicago, IL 60611 > 312-238-5911 office > dmerkitch(a)sralab.org > > > sralab.org > > Facebook | Twitter | YouTube > > Confidentiality Notice: This message and any attachments are only for > the intended recipient(s) and may contain confidential, privileged > and/or protected health information. If you are not the intended > recipient of this message, please: 1) be advised that unauthorized > review, use, copying, disclosure, or distribution is strictly > prohibited and may be unlawful; 2) notify the sender of the delivery > by reply e-mail or contact Shirley Ryan AbilityLab's Privacy Officer > at 312.238.0766 or privacyofficer(a)sralab.org; and 3) delete and > destroy all copies of the message and its attachments. Thank you. > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer Confidentiality Notice: This message and any attachments are only for the intended recipient(s) and may contain confidential, privileged and/or protected health information. If you are not the intended recipient of this message, please: 1) be advised that unauthorized review, use, copying, disclosure, or distribution is strictly prohibited and may be unlawful; 2) notify the sender of the delivery by reply e-mail or contact Shirley Ryan AbilityLab's Privacy Officer at 312.238.0766 or privacyofficer(a)sralab.org<mailto:privacyofficer@sralab.org>; and 3) delete and destroy all copies of the message and its attachments. Thank you.

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Longitudinal stream finalsurfs misalignment?
by Douglas Merkitch 16 Sep '19

16 Sep '19

External Email - Use Caution Hey all, I have a group of subjects with 2 time points that I've run thru the longitudinal processing stream. All goes OK until I run the recon-all -long and the resulting .long. subject dirs have the finalsurfs misaligned (i.e. one subject has the edits moved inferior and the other has them moved superior, causing drastic consequences to the pial/wm surfaces). FYI these subjects were processed on a Linux-based high performance computing cluster and edits were made locally on a Linux virtual machine with subject dirs being transferred back and forth via scp. Not sure if this is relevant, but thought I'd mention it just in case. I've uploaded a .tar file containing one of these longitudinal subject's directories (i.e. both cross tps, base, and both resulting long tps) called 'merkitch_upload_201980913.tar' via the filedrop website. Any help would be appreciated! Thanks, Doug Douglas Merkitch Clinical Research Coordinator 355 E. Erie St, Chicago, IL 60611 312-238-5911 office dmerkitch(a)sralab.org [cid:image002.jpg@01D56A28.22DB2140] sralab.org<http://www.sralab.org/> Facebook | <https://www.facebook.com/ShirleyRyanAbilityLab/> Twitter | <https://twitter.com/AbilityLab> YouTube<https://www.youtube.com/c/ShirleyRyanAbilityLab> Confidentiality Notice: This message and any attachments are only for the intended recipient(s) and may contain confidential, privileged and/or protected health information. If you are not the intended recipient of this message, please: 1) be advised that unauthorized review, use, copying, disclosure, or distribution is strictly prohibited and may be unlawful; 2) notify the sender of the delivery by reply e-mail or contact Shirley Ryan AbilityLab's Privacy Officer at 312.238.0766 or privacyofficer(a)sralab.org<mailto:privacyofficer@sralab.org>; and 3) delete and destroy all copies of the message and its attachments. Thank you.

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Error in running make_average_subject
by Himanshu Aggarwal 15 Sep '19

15 Sep '19

External Email - Use Caution Hello Freesurfer Developers I am trying to create an average subject for 20 subjects using the function make_average_subject. But I keep running into a segmentation fault. I have attached the recon-all.log file. I found a few other posts about the same problem which direct the users to the following patch: https://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/6.0.0-patch/ (https://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/6.0.0-patch/) But this patch does not have a readme file which can instruct the users about the steps that need to be followed to get rid of this bug. However, I have replaced the files in /usr/local/freesurfer/bin/ (i.e. the $FREESURFER_HOME) with the files given in this patch directory. But the problem still persists. Kindly provide the steps that need to be followed to make use of this patch properly. Regards Himanshu

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Downsampling from fsaverage to fsaverage6
by Matthieu VANHOUTTE 14 Sep '19

14 Sep '19

External Email - Use Caution Dear FS's experts, I am trying to downsample some surface data from fsaverage to fsaverage6 with the following command: mri_surf2surf --hemi lh --srcsubject fsaverage --sval ./lh.fsaverage.s8mm.mgh --trgsubject fsaverage6 --tval ./lh.fsaverage6.s8mm.mgh --cortex However, the output surface data is a binary file contrary to the source one (please see attached). Would anyone have an idea of the problem? Best, Matthieu

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Postdoc position at MGH/Harvard
by Jacobs, H (NP) 13 Sep '19

13 Sep '19

External Email - Use Caution Postdoctoral Opportunity at Mass General Hospital – Harvard Medical School The Gordon Center for Medical Imaging (GCMI) in the Department of Radiology at Massachusetts General Hospital (MGH) and Harvard Medical School (HMS) in Boston, Massachusetts, has an opening for highly qualified individuals at the post-doctoral level to work on research related to multi-modal 7T (f)MRI imaging of the brainstem in aging under the mentorship of Dr. Heidi Jacobs. This exciting multi-modal project involves dedicated imaging of the brainstem nuclei, high-resolution fMRI (possibility to go to layer-fMRI) with physiological monitoring, HCP sequences for diffusion imaging and PET-imaging. Most of the work in this project will be performed at the Athinoula A. Martinos Center for Biomedical Imaging. The Department of Radiology at MGH is equipped with the first mobile PET/CT, the first brain PET/MRI, the first whole-body PET/MRI in the USA and several MRI scanners, including two 7T ultra-high-field scanner. It is also equipped with a substantial large scale shared memory computing facility for parametric image analysis, tomographic reconstruction, Monte Carlo simulation, and other computationally intensive research applications. Applicants must have obtained or anticipate soon receiving a Ph.D. in biomedical, computer or electrical engineering, medical physics, cognitive neuroscience or a related field. Strong analytical, quantitative and programming skills are essential (e.g., QSM, fMRI-physiological data analyses). Prior experience in medical imaging, signal/image processing, and physiological investigation is advantageous. The successful candidate will have joint appointments at MGH and HMS and will be closely interacting with the Harvard Aging Brain Study team, the HCP team and the high-field MRI group. If interested, please send your CV, letter describing interests, background, qualifications and 3 references (including contact details). MGH & HMS are equal-opportunity, affirmative action employers. Women and minority candidates are encouraged to apply. Heidi Jacobs, Ph.D. Email: hjacobs(a)mgh.harvard.edu<mailto:hjacobs@mgh.harvard.edu> [cid:image001.png@01D56AA0.20580A50] Gordon Center for Medical Imaging MGH – Nashua 6606; Radiology, MGH 125 Nashua Street Boston, MA 02114

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Re: [Freesurfer] c_ras for HCP compatibility
by Glasser, Matthew 13 Sep '19

13 Sep '19

External Email - Use Caution Were the images acquired with the animal in a funny position relative to humans? That might be the issue. I would convert DICOMs to NIFTI prior to FreeSurfer, make sure the image is oriented as RPI or LPI and that the labels match the brain (e.g. in a tool like FSLView) and then run FreeSurfer. Matt. From: <freesurfer-bounces(a)nmr.mgh.harvard.edu> on behalf of Robert Austin Bruce Benn <robertaustinbruce.benn(a)cnic.es> Reply-To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> Date: Friday, September 13, 2019 at 7:06 AM To: "freesurfer(a)nmr.mgh.harvard.edu" <freesurfer(a)nmr.mgh.harvard.edu> Subject: [Freesurfer] c_ras for HCP compatibility External Email - Use Caution Hi Y’all, I was wondering if Y’all could tell me how c_ras is calculated in the x_form matrix for orig.mgz? I’ve been using some animal brains, and the pipeline works very well at creating surfaces and aligning them to their coresponding image for freeview. Post pipeline I’ve been applying the cras matix as derived from the orig.mgz to remove the offset for use in wb_view. The commands for applying the transforms work fine. However I end up getting a surface that is either inverted, or perpendicular to the nifti volume in wb_view. The animal image does have a large field of view, with a relatively small brain. I think the cras matrix isn’t getting calculated correctly, but that the images I’m using may not have a standered cras so I may need to hack around that. Could you explain to me how c_ras is calculated? Also if I need to edit c_ras how would I go about doing it? is it derived from the q and s forms? thanks! austin ________________________________ *************** AVISO LEGAL *************** Este mensaje va dirigido, de manera exclusiva, a su destinatario y contiene información confidencial y sujeta al secreto profesional, cuya divulgación no está permitida por la ley. En caso de haber recibido este mensaje por error, le rogamos que, de forma inmediata, nos lo comunique mediante correo electrónico remitido a nuestra atención o a través del teléfono (+34 914531200) y proceda a su eliminación, así como a la de cualquier documento adjunto al mismo. Asimismo, le comunicamos que la distribución, copia o utilización de este mensaje, o de cualquier documento adjunto al mismo, cualquiera que fuera su finalidad, están prohibidas por la ley. Le informamos, como destinatario de este mensaje, que el correo electrónico y las comunicaciones por medio de Internet no permiten asegurar ni garantizar la confidencialidad de los mensajes transmitidos, así como tampoco su integridad o su correcta recepción, por lo que el CNIC no asume responsabilidad alguna por tales circunstancias. Si no consintiese la utilización del correo electrónico o de las comunicaciones vía Internet le rogamos nos lo comunique y ponga en nuestro conocimiento de manera inmediata. ________________________________ *************** LEGAL NOTICE ************** This message is intended exclusively for the person to whom it is addressed and contains privileged and confidential information protected from disclosure by law. If you are not the addressee indicated in this message, you should immediately delete it and any attachments and notify the sender by reply e-mail or by phone (+34 914531200). In such case, you are hereby notified that any dissemination, distribution, copying or use of this message or any attachments, for any purpose, is strictly prohibited by law. We hereby inform you, as addressee of this message, that e-mail and Internet do not guarantee the confidentiality, nor the completeness or proper reception of the messages sent and, thus, CNIC does not assume any liability for those circumstances. Should you not agree to the use of e-mail or to communications via Internet, you are kindly requested to notify us immediately. ________________________________ The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail.

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recon-al- -make all ERRORS
by Alexopoulos, Dimitrios 13 Sep '19

13 Sep '19

External Email - Use Caution Hi, We ran a 2yo subject successfully through FS6.0 with no errors using recon-all -all. We then made some edits to the brainmask.mgz and added controls points and reran the pipeline using: recon-all -make all -s subjectID The rerun failed with error. The log fie is attached. Can someone troubleshoot as to why it failed? Thank. Jim ________________________________ The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail.

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timewindow parameter in mkanalysis-sess
by Caspar M. Schwiedrzik 13 Sep '19

13 Sep '19

External Email - Use Caution Hi! I am having difficulties setting the timewindow parameter in mkanalysis-sess in Freesurfer v5.3. I am trying to use 80 (data acquired with MION), but the parameter does not seem to affect analysis.info, where it is always 40. Is it possible to force a different timewindow? Below is some info from analysis.info. Thanks, Caspar # FSBUILD freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 # MKAVERSION $Id: mkanalysis-sess,v 1.64.2.5 2013/01/22 21:52:07 greve Exp $ # MKACMD /neuro_tools/freesurfer/fsfast/bin/mkanalysis-sess -fsd bold -native -timeoffset -2/2 -event-related -paradigm xxxx.para -nconditions 4 -TR 2 -gammafit 0 8 -gammaexp 0.3 *-timewindow 80* -refeventdur 0.5 -polyfit 2 -hpf 0.0109 -analysis xxxx -funcstem xxxx -runlistfile xxxx.list -nuisreg motion.dat 6 -tpef tpef.dat -acfbins 14 -acffwhm 0 -mask xxxx -force analysis xxxx mcstem fmc funcstem xxxx fsd bold runlistfile xxxx.list TR 2 RegDOF 6 PerSession 1 RawSpace volume native mask xxxx RawFWHM 0 RawSTC none UseB0DC 0 ApplySubCortMask 1 inorm 100 acfbins 14 fixacf 1 acffwhm 0 acfsvd 0 designtype event-related tpexclude tpef.dat nskip 0 polyfit 2 HPFCutoffHz 0.0109 HeteroGCor 0 nconditions 4 parname xxxx.para RefEventDur 0.5 *timewindow 40.000000* prestim 0 TER 0.050000 gamma 0 8 0.3 0 stimulusdelay -2/2 Condition 1 Condition01 Condition 2 Condition02 Condition 3 Condition03 Condition 4 Condition04 nuisreg motion.dat 6

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multiple comparisons correction for brain-behaviour correlations
by Annelies Vant Westeinde 13 Sep '19

13 Sep '19

External Email - Use Caution Dear members, I have run several analyses in which we correlate cognitive performance with vertex-wise cortical surface area, thickness and volume. We ran monte carlo simulation for each correlation. However, we would like to correct the outcome for the number of associations we did, that is for the for 10 different cognitive scales that we tested. How can this be done? We would rather not use bonferroni correction, as it is so strict, but would prefer fdr. Do we need to somehow get the p-values of the cluster peaks that correlated with the cognitive scales and do FDR on those? Or should we adjust the monte carlo simulation threshold to account for the 10 different tests? Thank you in advance, Annelies Annelies van't Westeinde | PHD Candidate Department of Women's and Children's Health | Karolinska Institutet 171 77 Solna | Karolinskavägen 37A +46 760967499 annelies.vant.westeinde(a)ki.se | ki.se<http://ki.se/en/startpage> ______________________________________ Karolinska Institutet – a medical university När du skickar e-post till Karolinska Institutet (KI) innebär detta att KI kommer att behandla dina personuppgifter. Här finns information om hur KI behandlar personuppgifter<https://ki.se/medarbetare/integritetsskyddspolicy>. Sending email to Karolinska Institutet (KI) will result in KI processing your personal data. You can read more about KI’s processing of personal data here<https://ki.se/en/staff/data-protection-policy>.

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Freesurfer September 2019