Freesurfer February 2014

freesurfer@nmr.mgh.harvard.edu

128 participants
236 discussions

optseq2 tnullmax
by Wei-chun Wang 06 Feb '14

06 Feb '14

Hi, I am trying to set up a design using optseq2, but the tnullmax command doesn't seem to be functioning. the script runs and outputs files, but they exceed the tnullmax which i specify. is anyone familiar with this issue? this is what i am inputting: --tr 2 --psdwin 0 20 1 --ev easy 4 36 --ev hard 4 36 --nsearch 100000 --nkeep 1000 --ntp 234 --o output --tnullmax 6 --tnullmin 1 thanks. wei-chun

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possible to render hippocampal subfield segmentations as 3D structures?
by Salil Soman 06 Feb '14

06 Feb '14

Hi, I generated hippocampal subfield segmentations, can generate statistics, but was wondering if there was a way to visualized the subfield segmentations as a 3D structure? (e.g. like the figure in this paper: http://niacal.northwestern.edu/projects/17) Thank you for your consideration. Best wishes, -- Salil Soman, MD, MS Postdoctoral Research Fellow - Stanford Radiological Sciences Laboratory Fellow - Palo Alto War Related Illness and Injury Study Center WOC Neuroradiology Attending - Veterans Affairs Palo Alto Health Care System

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dicom loading difficulty
by Borzello, Mia 06 Feb '14

06 Feb '14

Hi Freesurfers, I'm trying to convert CT dicoms to the MGZ format, but am getting an error saying "the pixel data cannot be loaded as it is JPEG compressed." I originally got dicoms without the extension .dcm, but then resaved them with the extension. Using either version didn't work. If you can shed some light on this, that would be great! Thanks, m

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FSFAST surface-based analysis to w-file
by Caspar M. Schwiedrzik 06 Feb '14

06 Feb '14

Hi! I need to export results from a surface-based analysis in FSFAST (v5.1) to another program (Caret) that accepts .w files. I was wondering what the recommended way of doing this is. It seems that mri_surf2surf will do the trick? Do I set the source and the target to be the same? Thanks, Caspar

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Re: [Freesurfer] Fwd: trac-all -path error
by Anastasia Yendiki 06 Feb '14

06 Feb '14

Hi Jon - You need to look at the aparc+aseg after it has been mapped to diffusion space. It's possible that it looks fine in its original space but then maybe something goes wrong with the registration. So you should look at the aparc+aseg and aparc+aseg_mask files from the tracula dlabel/diff directory. These are in diffusion space and you can overlay them on the FA map to see if there's anything strange in the ILF area. Hope this helps, a.y On Tue, 14 Jan 2014, Jon Wieser wrote: > Hi anastasia > I looked at the brainmask and the aparc+aseg. I did see anything missing in the area of the left ILF. > I have attached the files. can you take a look at them? > Thanks > JOn > > ----- Original Message ----- > From: "Anastasia Yendiki" <ayendiki(a)nmr.mgh.harvard.edu> > To: "Jon Wieser" <wieser(a)uwm.edu> > Cc: "freesurfer" <freesurfer(a)nmr.mgh.harvard.edu> > Sent: Friday, January 10, 2014 6:15:23 PM > Subject: Re: [Freesurfer] Fwd: trac-all -path error > > > Hi Jon - Have you checked the brain mask and aparc+aseg for this subject? > Anything missing there that might affect the left ILF? > > a.y > > On Wed, 8 Jan 2014, Jon Wieser wrote: > >> >> Dear freesurfer experts >> I'm getting the following error when runing trac-all -c dmrirc_single_subject -path >> >> >> Loading initial proposal SD's from /BrainLabDocs/Studies/Nicotine_MJ_Ecstasy_Study/Data/MRI/N1084/data/freesurfer/dlabel/diff/lh.ilf_AS_avg23_mni_flt_cpts_5_std.txt >> Processing pathway 3 of 18... >> Initializing MCMC >> Segmentation fault >> Darwin cerebrum.uwm.edu 10.8.0 Darwin Kernel Version 10.8.0: Tue Jun 7 16:33:36 PDT 2011; root:xnu-1504.15.3~1/RELEASE_I386 i386 >> >> >> I have attached the trac-all.log and trac-all.error files >> >> I am running tracula 5.3 >> > > > 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. > >

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Actual Thickness Values
by Natasha Haris 06 Feb '14

06 Feb '14

Dear Freesurfers, My measure is thickness and I want to be able to get a list of all the maximum thickness values at the centers of each significant cluster - is there any simple way to do that on QDEC? Also, I would like to get an average of all of the thickness values at each voxel for each cluster - is there a way to do that as well? Many thanks, Natasha

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A question on fsaverage
by peng 06 Feb '14

06 Feb '14

Hi everyone, I am a new user of freesurfer. As a first step, I wrote a script (see below between ---) to run recon-all on the anatomical data. Since I found it very slow, and our server has multi-cores, I run this script manually several times, thus it appeared to be parallel.Then I have several questions: 1 From the screen output, I guess if a certain subject folder exists, freesurfer will refuse to work on this subject. Then I have assumption that if I run the same script multiple times would not overwrite results from previous session. Can I hold this believe? 2 After certain time, I found new folders with name such as [fsaverage], which I assumed as kind of average of subjects. Then I worry this was generated from one session (either the first one or the last one, depending on overwriting policy of this folder). For example, if session one worked on subject 1 4 7 ... and session two worked on subject 2 5 8... and session three worked on subject 3 6 9 ... ; is this [fsaverage] an average of (subject 1, 4, 7) or (subject 3, 6, 9)? Or I am so lucky that it is the average all processed subjects? 3 Is there a proper way to work in parallel than my stone-age way? 4 I searched the wiki and found some slides and pages which may help but not answering the above question. Would you please suggest an example "full" script of analysis? Thank you very much! ======= My environment: 64-bit Linux with OpenSUSE. 8-CPUs/32G mem Script: ------------- #!/bin/csh echo "beginning ..." #environment setup source ~/1tests/FreeSurferEnv.csh #Set environment and get the filelist set raw_dir = '~/2rawdata/' set fileNameList = `ls {$raw_dir}` #Try all the subjects in a loop foreach file ($fileNameList) echo "Now processing file ($file): ..." echo "" set inName = ($raw_dir$file) recon-all -i $inName -s $file -autorecon-all end echo "done!" ------------- =======

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Rotation involved in recon-all
by Ed Gronenschild 06 Feb '14

06 Feb '14

Hi, Using recon-all (freesurfer v5.1.0, MacOSX10.6) I noticed a rotation of the T1 data early in the pipeline, i.e., converting rawavg.mgz to orig.mgz., see excerpt of output of mri_info below rawavg.mgz: xform info: x_r = 0.0081, y_r = -0.0913, z_r = 0.9958, c_r = 0.0813 : x_a = -0.9999, y_a = -0.0066, z_a = 0.0076, c_a = 14.8386 : x_s = 0.0059, y_s = -0.9958, z_s = -0.0913, c_s = 13.1335 orig.mgz: xform info: x_r = -1.0000, y_r = -0.0000, z_r = 0.0000, c_r = 0.0813 : x_a = 0.0000, y_a = -0.0000, z_a = 1.0000, c_a = 14.8386 : x_s = 0.0000, y_s = -1.0000, z_s = 0.0000, c_s = 13.1335 Is that the default way of processing the data? Cheers, Ed

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dmri_motion Error bvals
by Liliana Maia 06 Feb '14

06 Feb '14

Hi, Within the new Tracula update and with outputs resulted from *trac-all -prep -noqa* I ran *: * *dmri_motion --out './test.txt' --dwi './dwi_orig.nii.gz' --bval './bvals' --mat './dwi.ecclog'* And an error message appears: *machine x86_64Output motion measure file: /home/lapsi/test/motion.txtInput transform file: /home/lapsi/test/dwi.ecclogInput DWI file: /home/lapsi/test/dwi_orig.nii.gzInput b-value table: /home/lapsi/test/bvalsLow-b image intensity threshold: 100Nominal diffusivity: 0.001Loading volume-to-baseline affine transformationsComputing between-volume head motion measuresINFO: Processed transforms for 33 volumesLoading DWI volume series from /home/lapsi/test/dwi_orig.nii.gzLoading b-value table from /home/lapsi/test/bvalsERROR: Could not open /home/lapsi/test/bvals for reading* I tried with the b-values one value for each line in file bvalsT (see attachments): *dmri_motion --out 'teste.txt' --dwi 'dwi_orig.nii.gz' --bval './bvalsT' --mat 'dwi.ecclog'*,but the same error occurred. What can I do to verify this head motion? Thank you Best, -- Liliana Maia MEng Biomedical Engineering

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Tracula only outputs merged flt file (and missing bbr)
by Salil Soman 06 Feb '14

06 Feb '14

Hi, Is there a specific issue to troubleshoot if Tracula only creates the merged ... flt file and not the merged ... bbr file in paths? All of my dmrirc files have both bbr and flt =1, and most of my outputs have both, but occasionally I only get 1. Thanks! -- Salil Soman, MD, MS Postdoctoral Research Fellow - Stanford Radiological Sciences Laboratory Fellow - Palo Alto War Related Illness and Injury Study Center WOC Neuroradiology Attending - Veterans Affairs Palo Alto Health Care System

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Freesurfer February 2014