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Re: [Freesurfer] ADNI protocol anisotropic resolution
by Antonio Algaze Beato 19 Nov '14

19 Nov '14

Thank you very much for your response. Out of curiosity, does someone know why the ADNI protocol has an anisotropic voxel resolution? I was wondering if it had to do with the increased SNR being more beneficial for accurate segmentation than the gain in resolution from a 1mm isotropic voxel... or, perhaps it is meant to speed things up and and cover the whole brain a bit quicker? Cheers, Antonio On Wednesday, November 19, 2014, Antonio Algaze Beato < antonio.algaze(a)upr.edu> wrote: > Dear group, > > I am new to FS and the ADNI protocol, thus my question: is it ok to have a > slice thickness of 1.2 mm and in-plane resolution of 1.05 mm for cortical > segmentation and brain volume analyses? This seems to be a sequence > suggested on the FreeSurferWiki (I am using a GE750 3T). > > Doesn't the anisotropic resolution introduce a bias? > > Thanks a lot! > > > > > -- > Antonio Algaze, PhD > University of Puerto Rico > Physics, UPR-Bayamón > Radiology, UPR-School of Medicine > >

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multiple comparisons compensation for first-level analysis
by Milde, Christopher 19 Nov '14

19 Nov '14

Dear Freesurfer experts, I'm not sure how to apply cluster-wise correction for multiple comparisons when one is not interested in doing group statistics. For group analysis you concatenate individuals into one file and use mri_glmfit and mri_glmfit-sim to run general linear model and simulations. I want to apply multiple comparisons only within the individual subjects (stay at first-level), so that I don't have glm directories created by mri_glmfit. I ran recon-all with -qcache, so I have pre-computed MC simulations. I used the -fwhm option during selxavg3-sess to estimate smoothness. è pre-cached simulation I have fMRI-data. Do you have any suggestions? Sincerely yours, Christopher

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ADNI protocol anisotropic resolution
by Antonio Algaze Beato 19 Nov '14

19 Nov '14

Dear group, I am new to FS and the ADNI protocol, thus my question: is it ok to have a slice thickness of 1.2 mm and in-plane resolution of 1.05 mm for cortical segmentation and brain volume analyses? This seems to be a sequence suggested on the FreeSurferWiki (I am using a GE750 3T). Doesn't the anisotropic resolution introduce a bias? Thanks a lot! -- Antonio Algaze, PhD University of Puerto Rico Physics, UPR-Bayamón Radiology, UPR-School of Medicine

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intersection pial & pial-outer-smoothed
by Octavian Lie 19 Nov '14

19 Nov '14

Dear All, The ?h.pial and its corresponding ?h.pial-outer-smoothed surface in a subject with a well reconstructed pia are intersecting, see attached (green- pial, gray- smoothed pia). 1. Is this expected? and 2. Can the ?h.pial-outer-smoothed constrained by a command flag to strictly encompass pia and not intersect it? Thank you, Octavian

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How does freesurfer smoothes the data?
by ye tian 18 Nov '14

18 Nov '14

Hello freesurfers, I would like to understand intuitively how data is smoothed by Freesurfer. Is it an analogue to kernel smoothing, with the different FWHM equivalent to different bandwidths? Thank you very much! Sincerely, Ye

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QAtools errors with aseg QA
by Morgan Hough 18 Nov '14

18 Nov '14

Hi there, Just trying out the QAtools and I notice that there are a number of "(standard_in) 1: syntax error" reports for each subcortical label: checking subcortical label: Endosteum, . +/- . (standard_in) 1: syntax error (standard_in) 1: syntax error (standard_in) 1: syntax error (standard_in) 1: syntax error (standard_in) 1: syntax error As best as I can tell its in some bc calculations that are being done and I assume these errors are why there are no aseg reports made. All the other calculations and snapshots seem to work just fine. I am running FreeSurfer 5.3 and QAtools 1.1 on Ubuntu 12.04. Thanks in advance. Cheers, -Morgan

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Re: [Freesurfer] registration problem
by Douglas N Greve 18 Nov '14

18 Nov '14

Hi Shahin, I finally tracked it down. The problem is that in the analysis you specified -native but after that you specified -per-run. These two are incompatible, so it uses whatever is specified last. This caused it to take the intersection of all the run masks. But the run masks are not registered to each other, so the intersection became much smaller than the original masks. Reanalyze without -per-run and see if that helps things. I've put an error trap in the new version of mkanalysis-sess to prevent this in the future. doug On 11/14/2014 03:05 PM, shahin(a)nmr.mgh.harvard.edu wrote: > Hi Doug, > > It is: /cluster/tootell/pitcairn/1/users/good_subjects_anat > > >> what is your SUBJECTS_DIR ? >> On 11/14/2014 11:22 AM, SHAHIN NASR wrote: >>> Hi, >>> For one of my subjects, I have noticed a misalignment between >>> sig.nii and orig.mgz when I try to show the sig map using either >>> tkmedit (as below): >>> >>> cd /autofs/cluster/tootell/pitcairn/1/shahin/V2_Ori/Analysis >>> tkmedit-sess -s ../Subjects/auil2 -a OriExp_TR3_1p5mm_PR -c ANG_90_45 >>> >>> or tkmedit-sess: >>> >>> cd /autofs/cluster/tootell/pitcairn/1/shahin/V2_Ori/Subjects >>> tkmedit auil_anat orig.mgz -overlay >>> auil2/bold/OriExp_TR3_1p5mm_PR/ANG_90_45/abs_sig.nii.gz -reg >>> auil2/bold/register.dof6.dat~ >>> >>> I checked the registration file for this subjects and I don't see this >>> problem there. >>> >>> tkregister2 --reg ../Subjects/auil2/bold/register.dof6.dat~ --mov >>> ../Subjects/auil2/bold/template.nii.gz --surf >>> >>> I also checked the brain.mask and it covers the whole brain and looks >>> fine to me. I also checked my other subjects and their results are fine. >>> >>> Do you have any idea why this is happening? >>> >>> P.S.: I process my data in in nmr-dev-env but I have also checked the >>> above lines in nmr-stable53-env and problem is still there. >>> >>> -- >>> Shahin Nasr >>> >>> PhD in Cognitive Neuroscience >>> Martinos Imaging Center, MGH >>> Harvard Medical School >>> >> -- >> Douglas N. Greve, Ph.D. >> MGH-NMR Center >> greve(a)nmr.mgh.harvard.edu >> Phone Number: 617-724-2358 >> Fax: 617-726-7422 >> >> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting >> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 >> www.nmr.mgh.harvard.edu/facility/filedrop/index.html >> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ >> >> >> > -- Douglas N. Greve, Ph.D. MGH-NMR Center greve(a)nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/

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outer pial error
by Octavian Lie 18 Nov '14

18 Nov '14

Dear All, I tried to get an outer pial surface on a previously processed pt subjid, and I got the following error. (recon-all was running another subject in a separate window, for what's worth) Please advise, Octavian recon-all -localGI -s subjid WARNING: tcsh v6.17.06 has an exit code bug! Please update tcsh! Subject Stamp: freesurfer-Linux-centos6_x86_64-dev-20131217 Current Stamp: freesurfer-Linux-centos6_x86_64-dev-20131217 INFO: SUBJECTS_DIR is /usr/local/fs5.3/freesurfer/subjects Actual FREESURFER_HOME /usr/local/fs5.3/freesurfer -rw-rw-r-- 1 ovl ovl 3224039 Nov 17 07:58 /usr/local/fs5.3/freesurfer/subjects/subjid/scripts/recon-all.log Linux ovl-Wild-Dog-Performance 3.2.0-56-generic #86-Ubuntu SMP Wed Oct 23 09:20:45 UTC 2013 x86_64 x86_64 x86_64 GNU/Linux /usr/local/fs5.3/freesurfer/subjects/subjid/surf #-------------------------------------------- #@# Local Gyrification Index lh Mon Nov 17 08:03:50 CST 2014 mris_compute_lgi --i lh.pial ================= rm -Rf /usr/local/fs5.3/freesurfer/subjects/subjid/surf/tmp-mris_compute_lgi-lh.pial ================= ================= mkdir -p /usr/local/fs5.3/freesurfer/subjects/subjid/surf/tmp-mris_compute_lgi-lh.pial ================= ================= mris_fill -c -r 1 lh.pial /usr/local/fs5.3/freesurfer/subjects/subjid/surf/tmp-mris_compute_lgi-lh.pial/lh.pial.filled.mgz ================= reading surface from lh.pial... writing filled volume to /usr/local/fs5.3/freesurfer/subjects/subjid/surf/tmp-mris_compute_lgi-lh.pial/lh.pial.filled.mgz... conforming output volume setting resolution for intermediate calculations to 1.0000 ================= *make_outer_surface('/usr/local/fs5.3/freesurfer/subjects/* *subjid/surf/tmp-mris_compute_lgi-lh.pial/lh.pial.filled.mgz',15,'/usr/local/fs5.3/freesurfer/subjects/**subjid/surf/tmp-mris_compute_lgi-lh.pial/lh.pial-outer'); exit* ================= ERROR:: Too many arguments. Linux ovl-Wild-Dog-Performance 3.2.0-56-generic #86-Ubuntu SMP Wed Oct 23 09:20:45 UTC 2013 x86_64 x86_64 x86_64 GNU/Linux recon-all -s subjid exited with ERRORS at Mon Nov 17 08:03:54 CST 2014

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Issue with smoothing in local gyrification process
by Claire Morley 18 Nov '14

18 Nov '14

Hello Freesurfer Gurus, I am trying to compute LGI analysis using Qdec and have successfully loaded my qdec.table.dat file as well as created .Qrecrc to include the new pial_lgi measure. However, when I try to analyze using this measure (or with any measure for that matter), an error pops up saying that it was not able to locate the fwhm10.fsaverage.mgh file. I am guessing that this is the smoothed file and therefore that I need to run recon-all -qcache -measure pial_lgi -average -s, but when I run this while in my subjects directory, it tells me the -average flag is unrecognized. (I also tried this with -fsaverage and got the same error). Can you please help troubleshoot what might be going on? The lh pial files have already been created. When those are created I am guessing the smoothed files aren't created automatically as well? I was getting these instructions from the Schaer article here: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3369773/#!po=31.2500 Thank you so much for your help! Claire -- *We shall not cease from exploration. And the end of all our exploring will be to arrive where we started and know the place for the first time- T.S. Eliot*

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Displaying the color-coded mean paths of TRACULA in Freeview: shell script?
by Emad Ahmadi 18 Nov '14

18 Nov '14

Hello FreeSurfers! I have generated TRACULA mean paths for a number of subjects and I want to show them in Freeview. I’m color coding each pathway with a text file. So I’m having 18 text files with the names fmajor.txt, fminor.txt, lh.atr.txt, etc each having the info on color coding of each pathway. Assuming that $anat is the address of the anatomical image and that I’m in the stats folder, I use the following command to load all mean paths into Freeview and to overlay them on the anatomical image: freeview -v $anat -w *.path.mean.txt and it loads all mean paths into TRACULA. So far so good! Now to color-code the pathways using my text files, I should click on each pathway and click on spline color, blah blah blah, and it takes so much time. I wonder if this step of color-coding the pathways with the text files can also be implemented into the the script for viewing the pathways. (That way I can write a shell function to do all of this stuff). If the Min, Mid and Max of the heatscale can also be set by the shell script, it would be awesome! I’ve attached an image that I’ve generated using the multiple-clicking process! Thank you so much, Emad Emad Ahmadi, MD ----------------------------------------------- Research Fellow Department of Radiology Massachusetts General Hospital Harvard Medical School 25 New Chardon Street, Suite 400 Boston, MA 02114 Tel: 617 726 5237 Email: emad(a)nmr.mgh.harvard.edu

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