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30132 discussions

Issue with mri_convert on centOS 7
by Cooke,Danielle ( BIDMC - Neurology ) 31 Jan '18

31 Jan '18

Hello, I recently ran into issues using mri_convert on a CentOS 7 platform while having the same command work fine on CentOS 6. The error that results is: Segmentation fault (core dumped) I've tried on multiple machines with both operating systems to confirm the issue. I was wondering if you might have any insights or suggestions on how to fix this. Thank you! Danielle ________________________________ 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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Longitudinal TRACULA study
by Donatas Sederevicius 31 Jan '18

31 Jan '18

Hi, I want to clarify some aspects longitudinal TRACULA processing before processing my data. For example, I have 3 timepoints of data of the same participant: sub101_01 sub101_02 sub101_03 All of these have structural and diffusion data (same scanner, same acquisition parameters). I processed structural data using FS longitudinal pipeline and got the following: base_101 sub101_01.long.base_101 sub101_02.long.base_101 sub101_03.long.base_101 Now I want to run longitudinal TRACULA processing. If all data is OK after quality checking (struct and DWI) I could set the configuration file as follows: set subjlist = ( sub101_01 \ sub101_02 \ sub101_03 ) set baselist = ( base_101 \ base_101 \ base_101 ) It turns out that DWI data of sub101_01 is extremely distorted and cannot be used for processing. Should I re-process struct data based on the last two timepoints or is it perfectly fine to use the base and long derived from all timepoints although I’m running tracula for the last two timepoints of DWI? In addition to that, is it fine to run longitudinal TRACULA on a list of subjects where some of them have only one timepoint of data and structural processing underwent longitudinal pipeline for that one timepoint? Thank you for your answers. Best, Donatas

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annotation to volume with custom color scheme (Yeo parcellations)
by Dorit Kliemann 30 Jan '18

30 Jan '18

Hi, I’m trying to use the Yeo2011 annotations to create individual volume masks in subject space. I first use mri_surf2surf to map the annotations from fsaverage to individual subjects: mri_surf2surf --srcsubject fsaverage --trgsubject subject --hemi rh --sval-annot fsaverage/label/rh.Yeo2011_7Networks_N1000.annot --tval $SUBJECTS_DIR/subject/label/rh.Yeo2011_7Networks_N1000 Then I use mri_apar2aseg to map the annotation from the surface to the volume and thought he annot-table flag would use the labels provided in the custom color lut file. mri_aparc2aseg --s subject --o test.mgz --annot Yeo2011_7Networks_N1000 --annot-table path_to/Yeo2011_7Networks_ColorLUT.txt However the output is using different segmentation/color assignments. I can certainly find out which segmentation corresponds to which color and extract them separately (i.e. with fslmath or mri_binarize)..just wandering if I missed something or something changed since these posts? https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg35247.html Thanks Dorit

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Re: [Freesurfer] Strange Segmentation
by Antonin Skoch 30 Jan '18

30 Jan '18

Dear Arkadiy, I see sometimes these kind of errors. I think they are caused by local mis-segmentation due to WM hypointensities (enlarged perivascular spaces or other lesions, usually benign) located just under GM. Sometimes it is hard to discern where it is a hypointensity and where it is just a sulcus. I recommend to assess them using all 3 slice orientations. I correct them by editing wm.mgz (filling in voxels by value 255). Regards, Antonin Skoch Dear Experts, This brain looks a little bit strange to us, and I was wondering if someone might be able to chime in about whether this is worth editing, based on the screenshots of different slices from the sagittal view.. Thank you for your expertise. -Arkadiy

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A question about FS6 hippocampal subfield segmentation output file
by Darko Komnenić 30 Jan '18

30 Jan '18

Dear FreeSurfer experts, in the txt files [lr]h.hippoSfVolumes-T1.v10.txt we can see the volumes of individual hippocampal subfields - I was wondering what are the units in which volume is given? Millimeters cubic, voxels, or something else? Thanks in advance! Best, Darko

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Re: [Freesurfer] To Yendiki, Anastasia on TRACULA (Yendiki, Anastasia)
by Renew Andrade 30 Jan '18

30 Jan '18

What is the configuration file or where can I find it?

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Programmer/Research Tech position available at Washington University in St. Louis
by Westerhaus, Elizabeth 30 Jan '18

30 Jan '18

RESEARCH TECHNICIAN POSITION IN NEUROIMAGING POSITION SUMMARY: Applications are invited for a research technician at Washington University in St. Louis. This well-established laboratory studies the structural and functional organization of the human brain using multi-modal imaging: including magnetic resonance imaging (MRI) and positron emission tomography (PET). The primary focus of the lab is to understand how neurodegenerative diseases (especially Alzheimer’s disease) disrupt brain organization and mediates symptoms. Benefits of this position include: 1) Involvement in cutting edge research performed by a leading neuroimaging research laboratory 2) Potential to be involved as an author on manuscripts 3) Potential to present results at national and international conferences 4) Ability to attend talks and lectures in the field. Funding is guaranteed for up to 2 years. PRIMARY DUTIES AND RESPONSIBILITIES (Essential Functions): The primary responsibility of the research technician will be to archive/organize images (large multi-modal imaging datasets) and process neuroimaging data. The technician will study how disease affects the human brain by integrating large multi-modal imaging datasets and analyzing the relationship between brain imaging markers and clinical status. The technician will assist in various lab maintenance, transfer of files, database management, and organizational duties including tracking project progress, meet grant deadlines, and anticipate project needs. Qualifications: The qualified candidate should have at least a Bachelor's degree in human biology, neurosciences, psychology, bioengineering, computer sciences, or other related fields. The qualified candidate must have computer skills and knowledge of computer languages (e.g. Matlab, Python, shell scripting in CSH or BASH). The research technician must be dependable, have good attention to details, be well organized, be self-motivated, and be comfortable working as part of a team environment. Previous experience with neuroimaging data analysis programs is preferred but not required. Strong facility with statistical analyses is also desired. To apply, please send a letter of interest and CV to bances(a)wustl.edu<mailto:bances@wustl.edu>. Please arrange for three confidential letters of reference to be sent to the address below. Only applicants considered for employment will be contacted. Contact Information: Beau Ances MD, PhD Department of Neurology Washington University in Saint Louis Box 8111 660 South Euclid Ave Saint Louis, MO 63110 ****************************** Elizabeth Westerhaus MA  Clinical Research Specialist for Beau Ances MD, PhD Washington University School of Medicine Department of Neurology: Division of Infectious Disease 660 S. Euclid Ave.; Box 8111 St. Louis, MO 63110 Phone: 314-747-1125 Fax: 314-747-8427 <westerhause(a)neuro.wustl.edu<mailto:westerhause@neuro.wustl.edu>> Fed Ex or UPS Delivery: 620 S. Taylor Ave., Ste. 220 St. Louis, MO 63110 ________________________________ 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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Calculating cortex scalp distance of a region of interest
by Lucia B 30 Jan '18

30 Jan '18

Dear Freesurfer experts, I would like to calculate the mean distance from cortex to the scalp in a region of interest (the area under the stimulator), to investigate the influence of this distance on tDCS effects. A similar question was asked in the archives, and the use of mris_distance_transform was suggested. I am new to freesurfer, and I wasn't able to figure out if this approach is suitable for me and, if yes, what files I need to load in. I checked mris_distance_transform -help, yet I am still missing some parts. Could you point me to the right direction? As <label>, can I load in the ROI of the area under the scalp electrode? I tried to run the function with lh.pial and the lh.BA45.label just to see how it works, and I also have questions concenring the output: mris_distance_transform surf/lh.pial label/lh.BA45_exvivo.label unsigned lh.dist writing surface values to surf/lh.dist.w. avg = 101.288, stdev = 50.852, min = 0.206, max = 207.610 distance transform took 0.1 minutes How can I view the output file lh.dist.w.? And what do the values mean (is it by any chance already the mean distance from the surface to the label I am looking for, and if yes, what is the dimension)? Any suggestions would be highly appreciated! Many thanks! Lucia

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Re: [Freesurfer] TRACULA path segmentation fault error because of bedpostx?
by Yendiki, Anastasia 29 Jan '18

29 Jan '18

As a sanity check, you can downsample one of the data sets that fail to 2mm iso, and see if it runs that way. This would tell you if it's a data size issue. ________________________________ From: Carissa Nicole Weis <cnweis(a)uwm.edu> Sent: Monday, January 29, 2018 5:53:59 PM To: Yendiki, Anastasia Subject: RE: [Freesurfer] TRACULA path segmentation fault error because of bedpostx? I went back and checked and it was just a mistake in our paperwork. All of the subjects’ data were acquired at 1x1x2 resolution, but for some reason some of the subjects would run through bedp on the first pass while others required several passes. I’ve requested additional memory on our cluster to run the subjects who stalled, but that didn’t make a difference. If you don’t see any potential issues from your end, then I’m beginning to think it could be a technical issue with our cluster perhaps it’s timing out or freezing after running for too long. I’ll look into this more to see if I can find any issues there. Do you have any other recommendations for troubleshooting at this point? Thanks, Carissa From: Yendiki, Anastasia [mailto:AYENDIKI@mgh.harvard.edu] Sent: Monday, January 29, 2018 1:54 PM To: Carissa Nicole Weis <cnweis(a)uwm.edu> Subject: Re: [Freesurfer] TRACULA path segmentation fault error because of bedpostx? The subjects that run through with no problems have 2mm isotropic resolution and the subjects that give you the segmentation fault have higher resolution? Then it sounds like a problem of insufficient memory. ________________________________ From: Carissa Nicole Weis <cnweis(a)uwm.edu<mailto:cnweis@uwm.edu>> Sent: Sunday, January 28, 2018 9:44:08 PM To: Yendiki, Anastasia Subject: Re: [Freesurfer] TRACULA path segmentation fault error because of bedpostx? My mistake. It was acquired that way. Also, after running my subjects through the -bedp step several times I’ve now only got one subject who is lingering there, but some subjects had to run 7+ times through bedp before finishing properly. I do have another dataset to analyze that was acquired with the same parameters so it’s quite possible this issue may arise again. Thanks again for your help, Carissa The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.

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Re: [Freesurfer] aparc-aseg vs aseg label maps
by elisabetta_delre＠hms.harvard.edu 29 Jan '18

29 Jan '18

Hi FS team, running FS 5.3 and checking the labelmaps, there are some differences between the aseg and the aparc-aseg maps. The aparc-aseg are more inclusive. My understanding is that volumes for global measures are calculated from aseg. Could that cause problems in accuracy? Thank you so much, best, Elisabetta > > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > The information in this e-mail is intended only for the person to whom it > is > addressed. If you believe this e-mail was sent to you in error and the > e-mail > contains patient information, please contact the Partners Compliance > HelpLine at > http://www.partners.org/complianceline . If the e-mail was sent to you in > error > but does not contain patient information, please contact the sender and > properly > dispose of the e-mail. > >

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