Freesurfer

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19 participants
30088 discussions

PET input file for mri_gtmpvc
by Jane Tseng 17 Sep '19

17 Sep '19

External Email - Use Caution Dear Freesurfer experts, I was wondering if there is any recommendation on the PET input file for partial volume correction using mri_gtmpvc? Should I use a non-skullstripped SUV or a skullstripped SUV? If a skullstripped SUV can be used, would a tight (just aparc+aseg binarized) or a lenient (e.g. aparc+aseg binarized and dilated by 2mm) mask be better? I am interested in using the GTM regional values. Thank you for your help! Best wishes, Jane

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Extract ThickAvg ThickStd from rh/lh.aparc.stats of a specific structure for group of subjects
by vin rasa 16 Sep '19

16 Sep '19

External Email - Use Caution Dear Freesurfer experts, Is there a shortcut to extract mean thickness(ThickAvg) and std (ThickStd) from rh/lh.aparc.stats for let's say 4 structures only. I found aparcstats2table command, which seems to extract all the segmented regions. https://surfer.nmr.mgh.harvard.edu/fswiki/aparcstats2table Thanks in advance

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Questions about labels and tkmedit
by Zeng,Victor (BIDMC - Psychiatry) 16 Sep '19

16 Sep '19

Hi all, ? I know tkmedit has been deprecated, but we're thinking about using it just for quality check purposes since we found that it is less resource intensive. We're trying to load multiple labels, is there a way to do that so that each label is assigned a different color (we know that's possible for Freeview). best Victor Zeng Beth Israel Deaconess Medical Center Keshavan Lab ph: 617 754 1237 -- ________________________________ This message is intended for the use of the person(s) to whom it may be addressed. It may contain information that is privileged, confidential, or otherwise protected from disclosure under applicable law. If you are not the intended recipient, any dissemination, distribution, copying, or use of this information is prohibited. If you have received this message in error, please permanently delete it and immediately notify the sender. Thank you.

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001 vs brainmask views in freeview
by Alexopoulos, Dimitrios 16 Sep '19

16 Sep '19

External Email - Use Caution Hi all, I ran a 2yo subject through FS6.0 using 'recon-all -i /firstdicom.dcm -all' and the output segmentations and surfaces looks good. Can someone explain why I see different alignments when I view the 001.mgz and brainmask.mgz files in freeview, depending on the order files are opened. 001.mgz AND brainmask.mgz -- 001 opened first in freeview followed by brainmask.mgz. Alignemnts OK but brainmask looks grainy. [cid:image001.jpg@01D56C83.BD016B00] [cid:image002.jpg@01D56C83.BD016B00] Brainmask.mgz opened only in a new terminal. Rotated and looks smoother than brainmask above. [cid:image003.jpg@01D56C83.BD016B00] ________________________________ 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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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.

2 1

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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