Freesurfer April 2017

freesurfer@nmr.mgh.harvard.edu

123 participants
217 discussions

bbregister vs spmregister vs mri_coreg
by John Anderson 06 Jul '17

06 Jul '17

Dear Freesurfer experts, I see that the tool "mri_coreg" has been implemented recently in Free Surfer 6 and I really wanted to know what are the differences between the registration tools "bbregister", " spmregister" and "mri_coreg"! Kindly: 1. Are these tools similar? if not what are the differences ? 2. Is there any preference of using a tool over the others for specific type of data. For example: A. If I want to register FA map to T1 image which tool is more robust? B. if I want to register FA map to MNI space which tool is more robust? I highly appreciate your input on this! John

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Raw Cortical thickness values
by Muhammad Naveed Iqbal Qureshi 06 Jul '17

06 Jul '17

Dear Community, I need to know how can I read the numeric cortical thickness values from freesurfer processed files. (as there are too many in the surf folder) Thank you. Best Regards Naveed

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Average myelination within ROI
by SHAHIN NASR 06 Jul '17

06 Jul '17

Hi Surfers, I want to measure the average amount of myelinations within my ROI(s), I have already generated my myelination maps on surfaces (e.g. lh.myelin_ProjFrac0p5.nii ). Then I used mri_segstats as below: mri_segstats --i lh.myelin_ProjFrac0p5.nii --slabel SBJ_001 lh lh.V1 --sum V1_Stats.txt --accumulate but the numbers don't make any sense. For instance: # ColHeaders Index SegId NVertices Area_mm2 StructName Mean StdDev Min Max Range 1 0 125261 82573.4 Seg0000 110280.4453 0.2922 -5.5000 51.0000 56.5000 2 1 1138 764.8 Seg0001 941.0988 0.1572 0.2675 1.4203 1.1527 How can mean=941.0988 when the max=1.4203 ??? Regards -- Shahin Nasr PhD in Cognitive Neuroscience Martinos Imaging Center, MGH Harvard Medical School

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ERROR: nu_correct
by Das S. 20 May '17

20 May '17

Dear Freesurfer Developers, I was trying to use the recon-all -autorecon1 -subjid bert and got an error. When I checked I found the error was coming while executing the below command: nu_correct -clobber ./tmp.mri_nu_correct.mni.7555/nu0.mnc ./tmp.mri_nu_correct.mni.7555/nu1.mnc -tmpdir ./tmp.mri_nu_correct.mni.7555/0/ -iterations 1000 -distance 50 When I executed the command separately I got below error message: Can't use 'defined(@array)' (Maybe you should just omit the defined()?) at /usr/local/freesurfer/mni/bin/nu_estimate_np_and_em line 165. nu_correct: crashed while running nu_estimate_np_and_em (termination status=65280) ERROR: nu_correct Can you please suggest why the error is coming and how to remove it. Many thanks Sarbani

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Maps showing correlations between structural measures
by Martin Juneja 16 May '17

16 May '17

Hello FreeSurfer experts, I came across a paper: http://www.sciencedirect.com/science/article/pii/S0166432815001837 where correlation maps between volume and gyrification are reported. I am familiar with GLM in FreeSurfer i.e. correlating behavioral measures with volume and gyrification but I was wondering how to correlate structure measures with each other e.g. volume and gyrification. I would really appreciate any help. Thanks.

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Re: [Freesurfer] TRACULA tract reconstruction
by Antonin Skoch 12 May '17

12 May '17

Dear Joelle, regarding the conversion to .bvecs, could you please show the example of difference between bvecs converted by mri_convert of FreeSurfer and mrconvert of mrtrix3? Do you have most recent version of mrtrix3? There have been a quite extensive discussion on implementation of FSL .bvec convention in mrtrix3 in spring 2016: http://www.mrtrix.org/2016/04/15/bug-in-fsl-bvecs-handling/ However, there have been quite a big effort to settle this issue and I am pretty convinced that the recent versions should have this issue resolved. Maybe you can also post this to the mrtrix community forum, they are usually responding very quickly and each post gives detailed attention. Regards, Antonin Skoch ??Dear Tracula experts, I am applying Tracula on a longitudinal data set, and have some questions I am hoping you could help me with: Firstly, upon visual inspection, several tracts appear to be quite messy, or small (on the default freeview threshold) for most subjects. However, the -stat step from Tracula does not necessarily flag these tracts as outliers. What is then the best way to decide whether tracts are not correctly reconstructed and need to be rerun separately once more? Can I rely on the flagged outliers? Or should I rerun all the tracts that do not look ok after visual inspection? And in the last case, for tracts that look small, are they considered as correctly reconstructed if looking ok at lower thresholds than the default of freeview? Second, concerning the rerunning of poorly reconstructed tracts, I was wondering if there might be a more automated way to configure the dmrirc file in order to adapt it for each subject/each tract to rerun (and its corresponding control points). Third, I was wondering if there is a recommended software for obtaining bvecs and bvals. For the moment I used mrconvert (from MRtrix, using the -export_grad_fsl option) and the new mri_convert from freesurfer 6.0. As they give different outputs, I was wondering if this may impact the reconstruction. Lastly, would you recommend using freesurfer 5.3 or 6.0 for applying the longitudinal stream of Tracula? Related to this, is it recommended to use the same freesurfer version to obtain the long/base images, and to run Tracula? Thank you for your time, Best regards, Joëlle van der Molen

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Two stage model question
by Clara Kühn 09 May '17

09 May '17

Dear FreeSurfer experts, I have a longitudinal design with 3 groups and 3 time points. For one group the intervention did not work so for now I would like to look at 2 groups only. Can I do this with the Longitudinal Two Stage Model by looking at the spc from tp1 to tp2 and then looking at the spc from tp2 to tp3? Are there statistical reasons that forbid this procedure of comparing the change across time between groups? Thanks for your help! Clara -- Clara Kühn, Phd Student Max-Planck-Institute for Human Cognitive and Brain Science Department of Neuropsychology Stephanstrasse 1A 04103 Leipzig, Germany Phone: +49 341 - 9940 2271 Fax: +49 341 - 9940 2260 Web: www.cbs.mpg.de E-Mail: ckuehn(a)cbs.mpg.de

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Differences in aseg volumes between FreeSurfer 5.3.0 and FreeSurfer 6.0
by Knut J Bjuland 07 May '17

07 May '17

Dear FreeSurfer expert, I have compared the aseg volume between FreeSurfer 5.3 and FreeSurfer 6.0 with asegstatsdiff from FreeSurfer 6.0 for each subject in my data set. I have enclosed the range for some of the volume. I found the largest differences in subcortical structures, especially in Corpus callosum(CC). I found that FreeSurfer 6.0 CC posterior volume was 525.51 % larger than in FreeSurfer 5.3. Nevertheless, these differences were much smaller for lhCortex, but also here FreeSurfer 6.0 was on average larger than FreeSurfer 5.3. I ran the FreeSurfer 6.0 using the same option as FreeSurfer 5.30. Both versions of FreeSurfer were run on Centos. I am also enclosing a table with mean values along with min and max for differences between FreeSurfer 5.3 and FreeSurfer 6.0 aseg volumes. Best regards Knut Jørgen Bjuland PhD NTNU Left-Lateral-Ventricle 7.4 (-0.13,130.72) Left-Cerebellum-White-Matter 0.64 (-22.9,56.15) Left-Cerebellum-Cortex 7.56 (-10.3,19.17) Left-Thalamus-Proper 0.12 (-16.31,32.42) Left-Caudate -4.25 (-12,33.64) Left-Putamen -16.72 (-27.99,8.3) Left-Pallidum 16.23 (-22.94,84.75) Left-Hippocampus -1.74 (-13.53,15.93) Left-Amygdala 2.29 (-19.28,41.04) Right-Lateral-Ventricle 4.6 (-24.77,102.12) Right-Cerebellum-White-Matter -3.2 (-20.87,49.37) Right-Cerebellum-Cortex 4.88 (-12.99,14.36) Right-Thalamus-Proper 1.06 (-22.34,19.99) Right-Caudate -6.08 (-14.59,6.13) Right-Putamen -12.87 (-31.37,10.17) Right-Pallidum 14.01 (-27.79,89.19) Right-Hippocampus -1.71 (-9.29,12.02) Right-Amygdala 3.74 (-18.6,51.01) Right-Accumbens-area -9.14 (-37.89,61.02) CC_Posterior 22.07 (-47.04,525.51) CC_Mid_Posterior 53.59 (-11.3,537.3) CC_Central 36.77 (-21.36,317.24) CC_Mid_Anterior 24.09 (-18.86,128.31) CC_Anterior 10.64 (-33.71,152.33) lhCortexVol 3.13 (-1.31,12.37) rhCortexVol 3.16 (-0.36,14.2) CortexVol 3 (-4.47,13.26) EstimatedTotalIntraCranialVol 0.65 (-0.05,26.52)

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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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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 April 2017