Freesurfer

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30088 discussions

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

06 Feb '14

So there's your culprit. You need to fix the intra-subject (diffusion-to-T1) registration. Did you use flirt or bbregister for that? On Thu, 6 Feb 2014, Jon Wieser wrote: > Hi Anastasia, > I looked at the dlabel/diff/Aparc+aseg overlayed on the dmri/dtifit_FA.nii.gz > the alignemenst is way off (in freeview, in the coronal view, the aparc+seg is rotated 45 degrees anti-clockwise), and parts of the FA map in the L ILF area are missing. the original DTI is not missing data in these areas. I have attached screenshots > Jon > > > > ----- Original Message ----- > From: "Anastasia Yendiki" <ayendiki(a)nmr.mgh.harvard.edu> > To: "Jon Wieser" <wieser(a)uwm.edu> > Cc: freesurfer(a)nmr.mgh.harvard.edu > Sent: Wednesday, February 5, 2014 6:35:12 PM > Subject: Re: [Freesurfer] Fwd: trac-all -path error > > > 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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basic math operations for volume labels?
by Kami Koldewyn 06 Feb '14

06 Feb '14

Hi All, I was thinking that there was a freesurfer tool that performed simple math operations on volumetric labels (similar to those that mris_label_calc performs for surface labels) but I can't seem to find one. Is there such a tool that I am simply missing? I am hoping to easily create non-overlapping labels from a set of currently overlapping labels. Thanks, -kami Rhif Elusen Gofrestredig 1141565 - Registered Charity No. 1141565 Gall y neges e-bost hon, ac unrhyw atodiadau a anfonwyd gyda hi, gynnwys deunydd cyfrinachol ac wedi eu bwriadu i'w defnyddio'n unig gan y sawl y cawsant eu cyfeirio ato (atynt). Os ydych wedi derbyn y neges e-bost hon trwy gamgymeriad, rhowch wybod i'r anfonwr ar unwaith a dilewch y neges. Os na fwriadwyd anfon y neges atoch chi, rhaid i chi beidio a defnyddio, cadw neu ddatgelu unrhyw wybodaeth a gynhwysir ynddi. Mae unrhyw farn neu safbwynt yn eiddo i'r sawl a'i hanfonodd yn unig ac nid yw o anghenraid yn cynrychioli barn Prifysgol Bangor. Nid yw Prifysgol Bangor yn gwarantu bod y neges e-bost hon neu unrhyw atodiadau yn rhydd rhag firysau neu 100% yn ddiogel. Oni bai fod hyn wedi ei ddatgan yn uniongyrchol yn nhestun yr e-bost, nid bwriad y neges e-bost hon yw ffurfio contract rhwymol - mae rhestr o lofnodwyr awdurdodedig ar gael o Swyddfa Cyllid Prifysgol Bangor. This email and any attachments may contain confidential material and is solely for the use of the intended recipient(s). If you have received this email in error, please notify the sender immediately and delete this email. If you are not the intended recipient(s), you must not use, retain or disclose any information contained in this email. Any views or opinions are solely those of the sender and do not necessarily represent those of Bangor University. Bangor University does not guarantee that this email or any attachments are free from viruses or 100% secure. Unless expressly stated in the body of the text of the email, this email is not intended to form a binding contract - a list of authorised signatories is available from the Bangor University Finance Office.

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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. > >

2 1

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

2 1

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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