Freesurfer January 2016

freesurfer@nmr.mgh.harvard.edu

130 participants
204 discussions

Cortical MS lesions - correcting pial surfaces
by Granberg, Erik Tobias 15 Jan '16

15 Jan '16

Dear FreeSurfer colleagues, We’re working with MS data and wanted your input on how we could best handle patients with extensive cortical pathology causing inaccurate reconstructions of the surfaces. In short the pial surfaces “dips” in too deep towards the WM surface due to the T1-hypointensity. A lot of the problems can be mediated by doing wm.mgz edits and actually including the lesioned tissues, which pushes out both surfaces to an accurate position. Sometimes though, the cortical lesion affects the whole depth of the surface and this trick does not help. Is there any way to directly push out or “anchor” the pial surface? Thank you for the help! Kind regards, Tobias Post-doctoral research fellow Multiple Sclerosis Imaging Group MGH/HMS/MIT Athinoula A. Martinos Center for Biomedical Imaging 149 13th St Charlestown, MA 02129

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some questions about optseq
by charujing123 15 Jan '16

15 Jan '16

Hi FS experts, I try to design the schedule by optseq2. However it is beyond my ability as our experiment has a little complicated. Here is our goal: two successive trials decide condition. For example, this is our sequence:2 2 1 1 2 2 2 1 1 2 2 1 2 1 1 2 1 2 2 1 1 1 1 2 2 2 2 1 1 1 2 1 2 1 1 1 1 1 1 2 1 2 1 2 1 2 1 2 2 1 1 2 2 2 2 2 2 1 1 1 2 2 2 1 2 2 2 2 1 2 2 1 1 2 1 1 2 1 1 1 2 .22 and 11 is the same condition(this condition has 40 repeats); 12 and 21 is the same condition(this condition also has 40 repeats). That is to say, there are two conditons in this run. 81 trials in this run, and each trial has 1.5s intervels. And mean intertrial intervals is 3.5s. Our TR is 2s. According the efficiency about these two conditions, how could I design the intertrial intervals to get a appropriate sequence? I tried this: optseq2 --ntp 203 --tr 2 --psdwin 0 20 --ev ev1 2 40 --ev ev2 2 40 --nkeep 2 --o ex2 --nsearch 1000 Although it echo a result, I know, it is not what I need, because of every condition having two trials. So how I complete that? Thanks. All the best. Rujing Zha 2014-06-20 charujing123

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15 Jan '16

Hi freesurfer list. I have a surface label for a region-of-interest in the right hemisphere, which I generated from a cortical thickness analysis. I am now doing an analysis on the white matter below this roi, by moving the label into volume space with mri_label2vol, and sampling below the surface with the --proj option. I want to repeat this white matter analysis in the homologous region-of-interest in the left hemisphere, as accurately as possible. I found the documentation for xhemi, and an earlier post about interhemispheric registration of rois ( https://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/2012-July/024821.html) but I'm not clear on what the xhemi option does, nor what the outputs are, nor what fsaverage_sym is, and so I haven't been able to figure out how to use it for my purpose. Is there more info available somewhere on interhemispheric registration with freesurfer tools, and/or does anyone have suggestions for how I should proceed? Thank you, Martha -- Martha M. Shiell, PhD

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Interpreting white matter regressor dat file
by Afzal, Afsana 15 Jan '16

15 Jan '16

Hi, I have generated white matter regressor files for resting state analysis using fcseed-config and fcseed-sess. The resulting files include: wm.dat, wm.dat.pca-stats.dat and wm.dat.log. How do I interpret the wm.dat.pca-stats.dat file? There are 388 numbered rows (I'm guessing one per acquisition since # of acquisitions is 388?) and five columns. What do the columns represent? Thanks for your help! - Afsana ______________________________ Afsana Afzal Clinical Research Coordinator Massachusetts General Hospital Division of Neurotherapeutics Department of Psychiatry: Neurosciences 149 13th St, Room 2612 Charlestown, MA 02129 Phone: 617-643-5129 Fax: 617-726-4078

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Issue after mri_convert update
by Hunter Johndro 15 Jan '16

15 Jan '16

Hi All, Currently running freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 We replaced our mri_convert function in freesurfer/bin/ with the new mri_convert function that was patched to appropriately handle 16bit SMS/Multiband sequences (the patch intended to fix errors related to the SMS-BOLD voxel intensity ranges). After swapping our mri_convert functions, unpacksdcmdir now freezes when executing mri_parse_sdcmdir (see output below). Unpacksdcmdir previously worked with this same dataset, so the mri_parse_sdcmdir error appears to be specific to the new patched mri_convert file. Any thoughts are greatly appreciated. Thanks very much! - Hunter Error output: Log File is unpack//unpack.log INFO: Logfile is unpack//unpack.log SkipMoCo 0 Scanning source directory ... INFO: summary file is unpack//dicomdir.sumfile INFO: status file is unpack//parse.status Scanning directory Wed Jan 13 14:20:01 EST 2016 mri_parse_sdcmdir --sortbyrun --d raw/ --o unpack//dicomdir.sumfile --status unpack//parse.status 0

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FW: problem with hard coded directory (/scratch)
by Fengji Geng 15 Jan '16

15 Jan '16

Hi Doug, After reading your most recent reply, I just found that many of previous freesurfer emails had gone to my junk box automatically, so I missed some of your replies. Sorry! Looking at the strace output I generated last time, here are the lines where the program tries to stat and mkdir something in /scratch. And, the prev execve() system call. So, I'm guessing that bin/segmentSubjectT1_autoEstimateAlveusML or something it in turn runs is leading to "/scratch" directory problem. ========================= 13174 execve("/cell_root/software/freesurfer/dev/sys/bin/segmentSubjectT1_autoEstimateAlveusML", ["/cell_root/software/freesurfer/d"..., "HMN042", "/export/extra/pkd-fstest/FG_Temp", "0.333333333333333333333333333333"..., "/cell_root/software/freesurfer/d"..., "/cell_root/software/freesurfer/d"..., "/cell_root/software/freesurfer/d"..., "0.05", "left", "ConjGrad", "v10", "/cell_root/software/freesurfer/d"..., "0"], [/* 86 vars */]) = 0 13182 stat("/scratch/", {st_mode=S_IFDIR|0555, st_size=512, ...}) = 0 13182 stat("/scratch/HMN042_hippoSF_T1_v10_left/", 0x7f4e226015b0) = -1 ENOENT (No such file or directory) 13182 stat("/scratch/HMN042_hippoSF_T1_v10_left/", 0x7f4e226015e0) = -1 ENOENT (No such file or directory) 13182 lstat("/scratch", {st_mode=S_IFDIR|0555, st_size=512, ...}) = 0 13182 lstat("/scratch/HMN042_hippoSF_T1_v10_left", 0x7f4e226004b0) = -1 ENOENT (No such file or directory) 13182 stat("/scratch", {st_mode=S_IFDIR|0555, st_size=512, ...}) = 0 13182 mkdir("/scratch/HMN042_hippoSF_T1_v10_left", 0775) = -1 EROFS (Read-only file system) ========================= I do see, however, MCRv80 references to before the mkdir("/scratch/HMN042_hippoSF_T1_v10_left" call. So, it could be something in the MCRv80 addition that's causing this issue. And, things like this: ========================= 13182 open("/mathworks/BLR/devel/bat/A3p1/build/3p/install/319992/glnxa64/ITK/share/gdcm/gdcm.dic", O_RDONLY) = -1 ENOENT (No such file or directory) 13182 open("/mathworks/BLR/devel/bat/A3p1/build/3p/install/319992/glnxa64/ITK/share/gdcm/dicomVR.dic", O_RDONLY) = -1 ENOENT (No such file or directory) 13182 open("/mathworks/BLR/devel/bat/A3p1/build/3p/install/319992/glnxa64/ITK/share/gdcm/dicomTS.dic", O_RDONLY) = -1 ENOENT (No such file or directory) 13182 open("/mathworks/BLR/devel/bat/A3p1/build/3p/install/319992/glnxa64/ITK/share/gdcm/DictGroupName.dic", O_RDONLY) = -1 ENOENT (No such file or directory) 13182 open("/mathworks/BLR/devel/bat/A3p1/build/3p/install/319992/glnxa64/ITK/share/gdcm/DicomDir.dic", O_RDONLY) = -1 ENOENT (No such file or directory) ========================= are probably more MCRv80 (matlab runtime) package related and referencing a /mathworks/BLR directory on the machine that it was built, but not on our systems. Please let me know if you need more information. I will keep my eyes wide open this time. Thanks!! --------------------------------------------------------------------------------------------------------------------------------------- Hi Fengji, you have sent several emails. I keep asking you to give us a specific binary that has the problem, but you seem to ignore my request, wait a couple of weeks, then post the question back to the list. I'm happy to take look, but please send me something more specific! thanks doug ----- Fengji ________________________________ From: Fengji Geng Sent: Thursday, January 14, 2016 1:46 PM To: freesurfer(a)nmr.mgh.harvard.edu Subject: FW: [Freesurfer] FW: problem with hard coded directory (/scratch) Hi FS's experts, I sent out a couple of emails to seek for help on an error from running recon-all using freesurfer 6.0 beta. Could anyone help with the question? Thank you! ----- Fengji ________________________________ From: Fengji Geng Sent: Thursday, January 07, 2016 8:15 AM To: freesurfer(a)nmr.mgh.harvard.edu Subject: Re: [Freesurfer] FW: problem with hard coded directory (/scratch) Hi Douglas, You asked us to give you an example of the problem program. I will try to do it here, but if it is not what you want, please let me know. we ran recon-all -all -s <subject_name> -hippocampal-subfields-T1T2 <file name of additional scan> <analysisID>. We saw the program tried to create /scratch/$subject_hippoSF_T1_v10_right directory and failing with (Read-only file system) because the user does not have permission to write to /scratch. I can also send you the strace output if needed. Thank you! --------------------------------------------------------------------------------- Message: 4 Date: Mon, 4 Jan 2016 13:37:48 -0500 From: Douglas N Greve <greve(a)nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] FW: problem with hard coded directory (/scratch) To: freesurfer(a)nmr.mgh.harvard.edu Message-ID: <568ABBFC.5000702(a)nmr.mgh.harvard.edu> Content-Type: text/plain; charset=windows-1252; format=flowed Can you give us specific examples of problem programs? On 01/04/2016 09:54 AM, Fengji Geng wrote: > Hello Bruce, > > Happy New Year! > > After we reported the error related to '/scratch' several weeks ago > (see the email attached below), we tested the newest version of > freesurfer 6.0 recently, it looks likes that a lot of "if (-e > /scratch)" have been changed to "if (-dw /scratch)". However, there > are still a lot of binaries in the bin directory that match the string > "scratch", which cause the same error that I encountered before. I am > wondering if it is possible for you to fix '/scratch' in the bin > directory. > > Thank you! ----- Fengji

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Use of PVC PET images (V6) : between versions compatibility and intensity normalisation
by Matthieu Vanhoutte 15 Jan '16

15 Jan '16

Dear FS experts, 1) First Is it possible to use the partial volume correction provided in the v6 beta version of FreeSurfer despite the fact that recon-all have been done for all subjects with the v5.3 ? 2) Does this method supply an intensity normalisation for PET images ? Best regards, Matthieu

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QA Tools, inespecific error: parse error (standard_in)
by Julio Alberto González Torre 15 Jan '16

15 Jan '16

Hi Freesurfer users, I am recently testing the QA Tools in order to identify errors, especially aseg outliers. I don''t know if this is the right place to make this question, but I followed the instructions for download, install and usage, explained on: https://surfer.nmr.mgh.harvard.edu/fswiki/QATools I installed QATools and its dependencies: ImageMagick and gwak When I run the QA Tools there is an unespected error when trying to get aseg values: Checking asegs for outliers... > Using asegLUT: aseg_output.txt > parsing arguments ... > checking parameters ... > checking logs ... > done checking logs ... > done checking parameters ... > moving previous log files to *.bak > done moving previous log files > Processing each subcortical label ... > (standard_in) 1: parse error > (standard_in) 1: parse error > (standard_in) 1: parse error > (standard_in) 1: parse error > (standard_in) 1: parse error > (standard_in) 1: parse error > (standard_in) 1: parse error > (standard_in) 1: parse error > (standard_in) 1: parse error > (standard_in) 1: parse error > ... (several times) I can't identify why this error happens, but the output text about aseg values file is empty. The snaps output is correct. Does anybody know why is this happening? Or is there any alternative to check outliers? Thanks.

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Re: [Freesurfer] recon-all issue
by Schell, Susanne 15 Jan '16

15 Jan '16

Dear Bruce, thanks for answering. What we did to transform the original dicom files in nii.gz files is the following freesurfer command: mri_convert the nii.gz files to standard oriented and cut files are the following commands in FSL: fsl swapdim <input> -z -x -y <output> robustfov -i input -r output -i -r Of course, the output files are different concerning some characteristics, but they should not differ in the segmentation produced, should they? In the files attached to my last mail, you can see just by looking at the pictures that there are some variations in the form of the brain, which souldnt be there, or am I mistaken? Thanks very much in advance Susanne Today's Topics: 1. Re: recon-all issue (Bruce Fischl) ---------------------------------------------------------------------- Message: 1 Date: Wed, 13 Jan 2016 10:59:04 -0500 (EST) From: Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] recon-all issue To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> Message-ID: <alpine.LRH.2.20.1601131057350.21689(a)gate.nmr.mgh.harvard.edu> Content-Type: text/plain; charset="utf-8" Hi Susanne can you include prior correspondance so we have some context for your emails. Certainly 2 vs. 1 and 3 will give different results since you have changed the input file. I would think think 1 and 3 would be the same, but we need to know how you did the conversion. Look at the 001.mgz in the subjects' mri/orig dir in the cases of 1 and 3 and see if they are the same (or use mri_diff) cheers Bruce On Wed, 13 Jan 2016, Schell, Susanne wrote: > > Dear Bruce, > > ? > > thanks for answering. The recon-all command lines we use is: > > ? > > recon-all ?s subjectID ?i /data/subjectID.nii.gz > > recon-all ?s subjectID -all > > ? > > The files we used are > > 1)????? DICOM files > > 2)????? nii.gz files, but standard oriented and cut > > 3)????? nii.gz files > > ? > > When we look at the output pictures, they look different (see attached > files) > > ? > > Greetings, > > Susanne > > ? > > ? > > ? > > ______________________________________ > > Susanne Schell, Dipl.-Psych. > > ? > > Sektion St?rungen der Pers?nlichkeitsentwicklung > > Klinik f?r Kinder- und Jugendpsychiatrie > > Universit?tsklinikum Heidelberg > > ? > > Tel: (+49) ? (0)6221-56 35135 > > e-mail: susanne.schell(a)med.uni-heidelberg.de > > ? > > > ------------------------------ _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer End of Freesurfer Digest, Vol 143, Issue 19 ******************************************* 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.

2 1

(no subject)
by Jasmin Alves 14 Jan '16

14 Jan '16

-- Jasmin Alves Predoctoral Student Medical Biology Graduate Program University of Southern California jalves(a)usc.edu

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Freesurfer January 2016