Freesurfer May 2017

freesurfer@nmr.mgh.harvard.edu

145 participants
219 discussions

FSFAST
by John Anderson 05 May '17

05 May '17

Dear Doug, I have Bold fMRI data (6 minutes of acquisition which is equal to 180 volume for every run). The total number for images is 140 (50 controls and 90 patients). I plan to use FSFAST (FS V6.0) to study: 1. The difference between the groups in global functional connectivity 2. Seed-based functional connectivity analysis depending on an ROI for a difference in a voxel-wise analysis between PET images for the same subjects. My questions are: 1. In this data set I have only one run for every subject. I am wondering if FSFAST can analyze fMRI data (one run per subject). 2. FSFAST depends on the recons, meaning it depends on the ROIs in wmparc, aseg and apare+aseg atlases. Can FSFAST accept an external ROI for seed based functional connectivity analysis? I highly appreciate your advice John

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Re: [Freesurfer] perform group analysis on user defined maps
by Ladan Shahshahani 05 May '17

05 May '17

It didn't crash. I got the following line in the terminal window: Invalid argument WARNING: 319 NaNs found in subjid.map.mgh When the NaNs were common in all the subjects, mri_glmfit did not end successfully. After I omitted the common NaN values, there were still a few subjects with NaN values, in this case, it printed the above lines in the terminal; but the mri_glmfit proceeded and sig.mgh was created alongside other outputs.

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Freeview libpng warning
by Kanoff, Kristen Elise 05 May '17

05 May '17

Hello FreeSurfer community, I am having an issue with the icon graphics displaying properly in freeview (Linux virtual machine - Ubuntu). I receive the following warning when opening the application: "libpng warning: Application built with libpng-1.2.7 but running with 1.6.25" The newer version of libpng was downloaded as part of the Miniconda 2 package (which I need to run the MNE-Python pipeline). I've been unable to find a way to revert back to the older version of libpng. If anyone else has dealt with this compatibility issue before, suggestions on how to proceed would be very much appreciated! Thank you in advance, Kristen

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Transform volume in Freeview cuts off MRI volumes
by Hamilton, Liberty 04 May '17

04 May '17

Dear Freesurfer list, We have been using Freeview's "transform volume" functionality to do AC-PC alignment on some of our T1 scans before processing with recon-all. We had previously been using SPM, but wanted to move to an entirely free method rather than relying on MATLAB. It turns out that, for some scans where a lot of translation is needed to move the subject into AC-PC alignment, the volume will get cut off after performing the transform. This is in Freeview v.1.0 running on Mac OS 10.10.5. When I tried running the same thing in the new version of Freeview (v.2.0), loading the T1 image crashes freeview, which I believe to be a separate issue. Is there any way to do the AC-PC alignment in freeview or freesurfer without having issues with the field of view being cut? Thanks, Liberty — Liberty Hamilton Postdoctoral Fellow, Laboratory of Dr. Edward Chang Center for Integrative Neuroscience, University of California San Francisco

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QDec not allowing keyboard input on Display or Subjects Page
by Funk, Quentin 04 May '17

04 May '17

Freesurfer experts, QDEC won't allow me to type any information in on the subjects of Display page--i.e. in the FDR rate box, or in either threshold box. I found some emails regarding this from 2013, but no information that helps vis a vis the newest version. Is there a reason this is happening that I just can't find? For reference, I'm using Centos 7. Thanks! Houston Methodist. Leading Medicine. U.S. News & World Report has recognized Houston Methodist as one of the nation’s top 20 hospitals, placing it for the second time on the magazine’s prestigious Honor Roll. It is also designated as a Magnet hospital for excellence in nursing. Visit us at houstonmethodist.org. Follow us at twitter.com/MethodistHosp and facebook.com/HoustonMethodist. ***CONFIDENTIALITY NOTICE*** This e-mail is the property of Houston Methodist and/or its relevant affiliates and may contain restricted and privileged material for the sole use of the intended recipient(s). Any review, use, distribution or disclosure by others is strictly prohibited. If you are not the intended recipient (or authorized to receive for the recipient), please contact the sender and delete all copies of the message. Thank you.

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error with mris_anatomical_stats OR mris_sample_parc
by Jared P Zimmerman 04 May '17

04 May '17

Hi FS Experts, I’m having trouble getting anatomical stats from a parcellation I made out of scanner-space volume ROIs. I have taken the following steps to do this. mri_vol2vol --mov myROI.nii.gz --targ orig.mgz --regheader --o myROI_orig.nii.gz --interp nearest mris_sample_parc Subj111 lh myROI_orig.nii.gz myROIs.annot -ct ROI_test_table.txt On this step I ALWAYS get an error “could not open translation file /share/apps/freesurfer/5.3.0/cma_parcellation_colors.txt” even though I specify a CT with -ct, or when I specify a table with -t, or with both This seems to work though and I can view this annot on the surface with tksurfer mris_anatomical_stats -a /path/to/myROIs.annot -b Subj111 lh When I run mris_anatomical_stats I get the following error: CTABfindAnnotation: ct was NULL Segmentation fault (core dumped) I’m guessing this is from the color-table not being embedded in the annot file, but I’ve tried to get that embedded in many ways. My questions are: What is causing the error with mris_anatomical_stats? What is the difference between the -t and -ct flags for mris_sample_parc and which should I use? Should I use a specific color-table for this? I made my own which was just a space delimited file with “index name r g b a” for all my ROIs, but should I be adding this data to some existing color-table to make this work? Thanks, Jared

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lme_mass_RgGrow problem
by David Pagliaccio 04 May '17

04 May '17

Hello, We have been trying to analyze some longitudinal structural data using the FreeSurfer Mixed Effects Model toolbox and have been running into some issues. We have 2-3 timepoints per individual imaged across adolescence and 3 groups of interest. We set up a design matrix to examine potential quadratic effects of age by group including factors for: 1. Intercept 2. time 3. time ^2 4. Group 1 vs. others 5. Group 1 x time 6. Group 1 x time ^2 7. Group 2 vs. others 8. Group 2 x time 9. Group 2 x time ^2 10. age at baseline 11. sex We started a model to examine thickness, testing out the first model below [lhTh0,lhRe] = lme_mass_fit_EMinit(X,[1 2 3],Y,ni,lhcortex); Then, we have been getting stuck at [lhRgs,lhRgMeans] = lme_mass_RgGrow(lhsphere,lhRe,lhTh0,lhcortex,2,95); This starts the segmentation into homogeneous region but seems to get stuck after displaying "Computing seeds..." Is there a way to diagnose or fix this problem? Any thoughts would be great, thanks!

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Question for stat experts
by Martin Juneja 03 May '17

03 May '17

Hi everyone, I have a question for stat experts. I calculated cortical thickness for a region X for a group of patients (Group A: At baseline and after treatment A). Then I calculated cortical thickness for same region X for a group of patients (Group B: At baseline and after treatment B). I have behavioral data: At baseline and after placebo treatment A and At baseline and after treatment B. I found that: *For Behavioral Data:* - Paired t-test between baseline and after treatment A is not significant (magnitude after treatment > baseline). - Paired t-test between baseline and after treatment B is significant (magnitude after treatment > baseline). - Using repeated measures ANOVA, I found that the interaction between Time (baseline/post-treatment) and Group (A/B) is not significant. *For Cortical Thickness:* - Paired t-test between baseline and after treatment A is not significant (magnitude after treatment < baseline). - Paired t-test between baseline and after treatment B is also not significant (but magnitude after treatment > baseline). - Using repeated measures ANOVA, I found that the interaction between Time (baseline/post-treatment) and Group (A/B) is significant. Lastly, correlation between changes in behavioral data and changes in cortical thickness is not significant for group A but is significant and positive for group B. I was wondering how can I interpret these results because in one case I am having significant interaction (for cortical thickness) between groups and in other case there is no significant interaction (for behavioral data) but paired t-test showed significant difference. In addition, there was a correlation between changes in behavioral data and changes in cortical thickness for group B. So I am not sure how can I proceed from here onwards and justify my findings that interaction is important for cortical thickness but not for behavioral data and paired t-test is important for behavioral data but not for cortical thickness. Any help would be really appreciated. Thanks.

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CentOS 7 and freeview
by Ly, Kien-Ninh Ina,M.D. 03 May '17

03 May '17

Hi Freesurfer experts, I installed CentOS 7 on my computer and tried running freeview in the terminal window after ssh’ing into a remote computer. The software opened up correctly and I was able to see the toolbars; however, the main screen where the images should be showed a distorted background. Has anyone encountered this problem before? Is there anything I need to install before running freeview? When I previously ssh’ed into the same remote computer using Mac OS Sierra, freeview worked perfectly fine. Many thanks for your help. Best, Ina

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Re: [Freesurfer] freesurfer 6 hippocampal longitudinal processing workflow question, more LH than RH files
by Salil Soman 03 May '17

03 May '17

Thank you for your email. Just to follow up, the rh and lh hippocampal hippoSfVolumes-T1.v10.txt files are present, but for a large number of cases, only the lh hippoSfVolumes-T1.long.v10.txt files are present. I reran the exact same recon-all -long command for all the cases, and I reran them after your suggestion, but there is no change in the number of missing rh.hippoSfVolumes-T1.long.v10.txt files. The log file for the longitudinal processing for recon-all says the process completed with no errors. Is there anything else I should check? Thanks! On Fri, Apr 14, 2017 at 3:54 AM Alan Francis <alandarkenergy(a)gmail.com> wrote: > Hi Salil: > > It could be that the HSF script may have `errored out' mid way through the > analysis. If you go through the recon processing steps which are one of the > output files, you will see exactly where the error occurred. Just reprocess > that brain and see if that happens again. > > Hope this helps, > > best, > > Alan > > > > On Thu, Apr 13, 2017 at 4:49 PM, Salil Soman <sal(a)jhu.edu> wrote: > >> Hi, >> >> I have run a number of cases through the FS6 hippocampal longitudinal >> processing steps listed at https://surfer.nmr.mgh.harvard.edu/fswiki/LongitudinalHippocampalSubfields >> and https://surfer.nmr.mgh.harvard.edu/fswiki/LongitudinalProcessing >> >> It seems that all steps completed, but when it came time to collect the >> results, I find I have many more lh.hippoSfVolumes-T1.long.v10.txt (67) >> than rh.hippoSfVolumes-T1.long.v10.txt files (25). Any suggestions on what >> I may be doing incorrectly? >> >> Thanks! >> >> Salil Soman >> >> _______________________________________________ >> 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. >> >> > > > -- > |~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~| > > *Alan N. Francis PhD* > Regional Sales Manager/ Application specialist > Nordic Neurolab > Boston. > alan(a)nordicneurolab.com > > > *Previously:* > Instructor - Imaging Neuroscience > Brain Imaging Center > McLean Hospital > Harvard Medical School > 115 Mill Street, Belmont, MA 02478 > alanf(a)bwh.harvard.edu <ezra_wegbreit(a)brown.edu> > afrancis(a)mclean.harvard.edu > > > |~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~| >

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Freesurfer May 2017