Freesurfer July 2018

freesurfer@nmr.mgh.harvard.edu

112 participants
165 discussions

Hippocampal Subfields Logitudinal Processing Error
by Maksimovskiy, Arkadiy 06 Jul '18

06 Jul '18

Dear Experts, I am attempting to initiate a longitudinal portion of the hippocampal subfield module and am getting an error. I was wondering if someone might have a suggestion for troubleshooting. I am using the following version of freesurfer: freesurfer-Darwin-OSX-ElCapitan-dev-20180124-2459312abf I have the Matlab runtime installed using the following command: curl "https://surfer.nmr.mgh.harvard.edu/fswiki/MatlabRuntime?action=AttachFile&d…" -o "runtime.tar.gz" Here is the command I use to initiate the stream: segmentHA_T1_long.sh SILVA008_Template Here is the error message: [arkadiysnewimac:Freesurfer/Freesurfer_Files_with_Freesurfer_Masks/Post_Manual_Edits] arkadiy% segmentHA_T1_long.sh SILVA008_Template #-------------------------------------------- #@# Longitudinal Hippocampal Subfields processing (T1) left Fri Jul 6 12:43:59 EDT 2018 ------------------------------------------ Setting up environment variables --- DYLD_LIBRARY_PATH is .:/Applications/freesurfer_Dev_El_Capitan//MCRv84//runtime/maci64:/Applications/freesurfer_Dev_El_Capitan//MCRv84//bin/maci64:/Applications/freesurfer_Dev_El_Capitan//MCRv84//sys/os/maci64:/Applications/freesurfer_Dev_El_Capitan/lib/gcc/lib:/Applications/freesurfer_6.0/lib/gcc/lib:/opt/X11/lib/flat_namespace dyld: Library not loaded: @loader_path/libmwmclmcrrt.8.0.dylib Referenced from: /Applications/freesurfer_Dev_El_Capitan/bin/SegmentSubfieldsT1Longitudinal.app/Contents/MacOS/SegmentSubfieldsT1Longitudinal Reason: image not found /Applications/freesurfer_Dev_El_Capitan/bin/run_SegmentSubfieldsT1Longitudinal.sh: line 37: 58577 Abort trap: 6 "${exe_dir}"/SegmentSubfieldsT1Longitudinal.app/Contents/MacOS/SegmentSubfieldsT1Longitudinal $args Darwin arkadiysnewimac.mclean.harvard.edu 17.6.0 Darwin Kernel Version 17.6.0: Tue May 8 15:22:16 PDT 2018; root:xnu-4570.61.1~1/RELEASE_X86_64 x86_64 longitudinal subfields exited with ERRORS at Fri Jul 6 12:43:59 EDT 2018 For more details, see the log file /Volumes/silverilab/Arkadiy/Freesurfer/Freesurfer_Files_with_Freesurfer_Masks/Post_Manual_Edits/SILVA008_Template/scripts/long-hippocampal-subfields-T1.log I would love to hear if anyone has suggestions for fixing this. Thanks, arkadiy -- Arkadiy L. Maksimovskiy, Ph.D. Postdoctoral Research Fellow McLean Imaging Center, McLean Hospital Department of Psychiatry, Harvard Medical School

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POSTDOCTORAL FELLOWSHIP IN NEUROIMAGING (MRI and DTI)
by Meaghan Perdue 06 Jul '18

06 Jul '18

External Email - Use Caution *POSTDOCTORAL FELLOWSHIP IN NEUROIMAGING (MRI and DTI)* The LandiLab (PI: Nicole Landi, PhD *https://landi.lab.uconn.edu/ <https://urldefense.proofpoint.com/v2/url?u=https-3A__landi.lab.uconn.edu_&d…>*) at Haskins Laboratories *https://haskinslabs.org/ <https://haskinslabs.org/>* (which is closely affiliated with Yale and the University of Connecticut) is seeking to hire a postdoctoral research fellow. This postdoc will join a project investigating the neurobiological basis (brain structure, genetics) of reading. The successful applicant will be responsible for conducting and interpreting analyses of neuroimaging data (structural and diffusion imaging data). This position is part of a multi-site project (Haskins Laboratories, University of Houston, Baylor College of Medicine) that is aggregating and analyzing neuroimaging and genotyping data from multiple locations to explore gene-brain-behavior relationships. Applicants must have a background conducting research using MRI. The ideal candidate will also have experience with diffusion weighted imaging (DWI) and experience with advanced statistical analysis of imaging data (e.g. imaging-genetic analyses, Bayesian methods, machine learning). *For details regarding required qualifications and application procedure, please visit: https://haskinslabs.org/postdoctoral-fellowship-neuroimaging-mri-and-dti <https://haskinslabs.org/postdoctoral-fellowship-neuroimaging-mri-and-dti>*

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Polar retinotopy using FSFAST
by Paul Scotti 05 Jul '18

05 Jul '18

External Email - Use Caution Hello, I am trying to use FSFAST to map polar angle retinotopy and wanted to make sure I am following the right steps as well as understanding the final visualization. These are the current list of commands I am using, after already making a flattened occipital patch: preproc-sess -sf sessid -df SUBJ01 -surface self lhrh -fwhm 0 -fsd bold > -per-session > mkanalysis-sess -a rtopy.self.lh -surface self lh -TR 2 -retinotopy 24 > -paradigm rtopy.par -per-session -fsd bold -fwhm 0 -ngroups 3 > selxavg3-sess -a rtopy.self.lh -sf sessid > fieldsign-sess -a rtopy.self.lh -patch lh.occip.patch.flat -sf sessid > rtview --s s101 --hemi lh --polar --real polar/real.nii.gz --imag > polar/imag.nii.gz --fsig polar/fsig.nii.gz --flat 1. Am I correct in saying that to do retinotopy with only polar mapping runs, I have to make a fake folder with eccentricity data (otherwise selxavg3 will error)? 2. After rtview, I am using this color wheel <http://t.sidekickopen08.com/e1t/c/5/f18dQhb0S7lC8dDMPbW2n0x6l2B9nMJW7t5XX45…> after changing the color scheme from "color wheel" to "RYGB colors" in tksurfer. However, I am not even sure this is the right color wheel to be looking at. (If it is, do I need to flip it horizontally when looking at the left hemisphere -- the stripes seem to follow the same color pattern across l and r hemispheres for me?) 3. Is the color wheel represented in radians? If so, how can I figure out what radian a certain color is? 4. I specified -ngroups 3 because I used multiband with a factor of 3, but I also tried running this all without -ngroups specified and everything seemed to come out the same. Is ngroups necessary if we collected slices using multiband or no? Thanks very much for any assistance, Paul Scotti

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mri_vol2surf: dACC/Insula clusters on surface not found
by srishti goel 05 Jul '18

05 Jul '18

External Email - Use Caution Hello, I am using mri_vol2surf to project my volume maps on to the surface. There is a dACC/insula cluster visible in my volume maps that doesn't show up when I project it on the surface. Is that because dACC/insula is not included in surfaces on Freesurfer? Thanks! Best, Srishti Social/Clinical Research Specialist Child Imaging Research and Life Experiences Lab University of North Carolina at Chapel Hill email (W): srishtig(a)email.unc.edu skype: srishti.goel12

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Longitudinal processing in v6.0 using manual edits from v5.3.0 - recon-all.log
by KALEY E ELLIS 04 Jul '18

04 Jul '18

External Email - Use Caution Hello FreeSurfer experts, I previously emailed regarding processing longitudinal data in v6.0 using bases with manual edits that had been completed in v5.3. I went ahead and ran recon-all -all on the base of a subject (originally generated in v5.3) in v6.0, but it looks like the header of the recon-all.log still indicates v5.3. Looking at the /stats output, all files indicate v6.0. Below is the head of the log from running recon-all -all on this subject. Is this what you would expect if you ran recon-all -all on a subject_base in v6.0 that was generated in v5.3? If so, is this okay? Recon-all log: setenv SUBJECTS_DIR /study1/nccam3/data/mri/freesurfer_v6/subjects FREESURFER_HOME /apps/x86_64_sci7/freesurfer-latest Actual FREESURFER_HOME /apps/freesurfer-5.3.0/x86_64_sci6 build-stamp.txt: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 Linux c139.keck.waisman.wisc.edu 3.10.0-514.6.1.el7.x86_64 #1 SMP Tue Jan 17 11:12:41 CST 2017 x86_64 x86_64 x86_64 GNU/Linux Thank you! Kaley Ellis Associate Research Specialist Center for Healthy Minds Waisman Center for Brain Imaging and Behavior University of Wisconsin-Madison

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Longitudinal processing: cannot find input volume error
by Arsenije Subotic 04 Jul '18

04 Jul '18

External Email - Use Caution Dear Freesurfer experts, I’m having problems with one of my participants when I am trying to create the base template for my longitudinal analysis. I get an error saying that the input volume (norm.mgz) for my followup time-point cannot be opened, even though the volume is not missing and loads perfectly fine in Freeview. Is this a bug or is something wrong with my norm.mgz volume by any chance? Please let me know. Thank you, Arsenije

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Longitudinal analysis of multiple scanner acquisitions
by zalewk 04 Jul '18

04 Jul '18

External Email - Use Caution Good afternoon Freesurfer team, I want to run the longitudinal pipeline on multiple groups of subjects, the problem is we are at the mercy of the scanners available to us at the various time-points. We have two different Siemens 1.5 scanners (same type of scanner, there was an effort made to match them) at time point 1 and 2 with a Phillips 3T at time point 3. Is it worth the time to attempt a longitudinal analysis on this cohort? Best, Kody Zalewski

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Longitudinal errors, Voxel size differs
by Erik O'Hanlon 04 Jul '18

04 Jul '18

External Email - Use Caution Hi FS Experts, I'm trying to run a longitudinal analysis across three timepoints and have run the cross steps for the data. I then ran the base step but found that my voxel dimensions are slightly different across the timepoints and I got the following error ERROR: MultiRegistration::loadMovables: images have different voxel sizes. Currently not supported, maybe first make conform? Debug info: size(2) = 0.881117, 0.881117, 0.881117 size(0) = 0.884507, 0.884507, 0.884507 MultiRegistration::loadMovables: voxel size is different /projects/pi-vokeane/HPC_16_00925/MC_FS_testdata_EOH/freesurfer/subjects/abd025_tp3/mri/norm.mgz. I assume I need to resample the data to the voxel size of the first time point and then rerun. Can you advise on what command to use to resample the images from time 2 and time 3 to those of time 1 before rerunning from scratch. I assume I can't avoid rerunning the initial reconall step once I resample my data. Any guidance is much appreciated Best regards Erik Erik O'Hanlon Postdoctoral researcher [cid:rcsi-crest-signature_f581c185-1d03-45c8-a786-23d8ece3d391.png] RCSI Psychiatry Royal College of Surgeons in Ireland Beaumont Road, Beaumont D9 Ireland T: 8093740 E: erikohanlon(a)rcsi.ie W: www.rcsi.com<http://www.rcsi.com/> Transforming Healthcare Education, Research and Service: RCSI Strategic Plan 2018-2022<http://www.rcsi.ie/strategy2018> RCSI DEVELOPING HEALTHCARE LEADERS WHO MAKE A DIFFERENCE WORLDWIDE [cid:both3_b9da8717-e91f-4ea7-8729-dc2c4d0a7a5f.png]

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Longitudinal Process
by Samir Rekic 04 Jul '18

04 Jul '18

External Email - Use Caution Dear FreeSurfers, I am trying to run the longitudinal process including (recon-all -base and -long) for 5 different timepoints. But in my original data one the of five differs in the acquisition orientation and in the size of the field of view, so the results and especially the statistic is distorted. Four of my data sets have RPI as acquisition Parameter and a FOV of 230, the last data set has LPI and a FOV of 257. Does it even make sense to include this last dataset – is it even possible (due to different Parameters)? Do I have to pre-process this different data set? Thank you in advance! Sam

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"WARNING: Image geometries differ across time" upon running base step of longitudinal pipeline
by Tudor Popescu 04 Jul '18

04 Jul '18

External Email - Use Caution Dear all, I have pre and post-intervention data for a single group of subjects, and I'd like to extract the cortical thickness pre and post, for all standard regions in the atlas, and use those in subsequent analyses. Following the standard approach <https://surfer.nmr.mgh.harvard.edu/fswiki/LongitudinalProcessing#Longitudin…>for longitudinal studies, I used the following types of commands: 1. *recon-all -i 01_1.nii.gz -subjid 01_1 recon-all -i 01_2.nii.gz -subjid 01_2 recon-all -i 02_1.nii.gz -subjid 02_1 .. where e.g. 01 is the subj code, and _1 and _2 represent pre and post scans* 2. *recon-all -subjid 01_1 -all recon-all -subjid 01_2 -all ..* 3. *recon-all -base 01 -tp 01_1 -tp 01_2 -all .. * 4. *recon-all -long 01_1 01 -all recon-all -long 01_2 01 -all .. * However, the base step has led to warnings of the type: "WARNING: Image geometries differ across time, maybe due to aquisition changes? This can potentially bias a longitudinal study! ", and consequently to an empty /stats folder -- even though my pre and post images are aligned and have similar acquisition parameters. Have I done something wrong, and how can I fix this warning/error? Many thanks in advance for any help. Best wishes, Tudor

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Freesurfer July 2018