Freesurfer May 2013

freesurfer@nmr.mgh.harvard.edu

174 participants
299 discussions

Fwd: Re: repeat: trouble loading nifti files
by Akshay 07 May '13

07 May '13

mri_convert path-to-nifti file mask.mgz --resample_type nearest -cs 256 On 5/7/13 2:55 PM, Bruce Fischl wrote: > can you send me the full mri_convert command line that is run? > On Tue, 7 May 2013, Akshay wrote: > >> Hi Bruce >> >> Please find the file attached >> >> Best, >> >> Akshay >> >> >> On 5/7/13 2:40 PM, Bruce Fischl wrote: >>> Hi Akshay >>> >>> is you send us that file we'll take a look. >>> >>> cheers >>> Bruce >>> On Tue, 7 May 2013, Akshay wrote: >>> >>>> Hi All, >>>> >>>> I am re-posting this question since there was no response to my >>>> previous >>>> attempt. >>>> >>>> I have a problem conforming certain nifti files, the following is the >>>> log when i try to convert them, >>>> >>>> reading from >>>> /home/akshay/ADNI/137_S_1041/MIDAS_Whole_Brain_Mask/2006-11-09_09_35_11.0/S22310/ADNI_137_S_1041_MR_MIDAS_Whole_Brain_Mask_Br_20120723235935683_S22310_I317755.nii... >>>> INFO: using NIfTI-1 qform >>>> TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 >>>> i_ras = (0, -4.99113e-10, -1) >>>> j_ras = (-4.99113e-10, -1, 4.99113e-10) >>>> k_ras = (-1, 4.99113e-10, 0) >>>> WARNING >>>> ==================++++++++++++++++++++++++======================================= >>>> The physical sizes are (281.25 mm, 280.14 mm, 216.72 mm), which cannot >>>> fit in 256^3 mm^3 volume. >>>> The resulting volume will have 282 slices. >>>> If you find problems, please let us know >>>> (freesurfer(a)nmr.mgh.harvard.edu) >>>> ==================================================++++++++++++++++++++++++=============== >>>> >>>> Original Data has (1.09862, 1.09429, 1.20399) mm size and (256, 256, >>>> 180) voxels. >>>> Data is conformed to 1 mm size and 282 voxels for all directions >>>> Reslicing using nearest >>>> >>>> >>>> This is understood, however I want them to be conformed to 256^3 >>>> mm. If >>>> I use -cs 256 flag, it does resample the image to 256^3mm but the >>>> image >>>> is blank. >>>> >>>> Is there something wrong I am doing? How do I conform these files >>>> to 256^3mm? >>>> >>>> Any help will be greatly appreciated. >>>> >>>> Best, >>>> >>>> Akshay >>>> >>>> >>>> _______________________________________________ >>>> 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. >>> >> >>

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TrackVis "either end" command
by Chu, Catherine,M.D. 07 May '13

07 May '13

Dear Freesurfer/TrackVis experts, I am using the following command in a batchfile to identify tracks counts between dozens of preset ROIs. track_vis DATAPATHtob0.trk -roi DATAPATHTOROI1.nii -roi2 DATAPATHTOROI2.nii -o PATHTOOUTPUT.trk > OUTPUT.txt -nr', i, j, i, j, i, j Is there a line command I can use so that the tracks identified follow the rule "either end" in the ROIs instead of the default "any part"? Thank you! Cat

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repeat: trouble loading nifti files
by Akshay 07 May '13

07 May '13

Hi All, I am re-posting this question since there was no response to my previous attempt. I have a problem conforming certain nifti files, the following is the log when i try to convert them, reading from /home/akshay/ADNI/137_S_1041/MIDAS_Whole_Brain_Mask/2006-11-09_09_35_11.0/S22310/ADNI_137_S_1041_MR_MIDAS_Whole_Brain_Mask_Br_20120723235935683_S22310_I317755.nii... INFO: using NIfTI-1 qform TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (0, -4.99113e-10, -1) j_ras = (-4.99113e-10, -1, 4.99113e-10) k_ras = (-1, 4.99113e-10, 0) WARNING ==================++++++++++++++++++++++++======================================= The physical sizes are (281.25 mm, 280.14 mm, 216.72 mm), which cannot fit in 256^3 mm^3 volume. The resulting volume will have 282 slices. If you find problems, please let us know (freesurfer(a)nmr.mgh.harvard.edu) ==================================================++++++++++++++++++++++++=============== Original Data has (1.09862, 1.09429, 1.20399) mm size and (256, 256, 180) voxels. Data is conformed to 1 mm size and 282 voxels for all directions Reslicing using nearest This is understood, however I want them to be conformed to 256^3 mm. If I use -cs 256 flag, it does resample the image to 256^3mm but the image is blank. Is there something wrong I am doing? How do I conform these files to 256^3mm? Any help will be greatly appreciated. Best, Akshay

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BBregister issue during autorecon3 with T2pial option (5.2.0 with updated beta binaries)
by Todd Thompson 06 May '13

06 May '13

Hi, all. I'm trying to refine my pial surfaces with a T2 (or, in this case, t2*) image and I'm running into an error inside bbregister/fslregister. I'm running the command: recon-all -s gf04 -3T -autorecon3 -T2pial -T2 /mindhive/gablab/fluid/Analysis/Nipype/flash/gf04/tissue_parameters/T2star.mgz and the recon process makes it to the point of #@# Refine Pial Surfs w/ T2/FLAIR when it runs: bbregister --s gf04 --mov /mindhive/gablab/fluid/Data/gf04/mri/orig/T2raw.mgz --lta /mindhive/gablab/fluid/Data/gf04/mri/transforms/T2raw.lta --init-fsl --T2 bbregister does some initial processing, then calls fslregister, like so: fslregister --s gf04 --mov /mindhive/gablab/fluid/Data/gf04/mri/transforms/tmp.bbregister.23921/template.nii --reg /mindhive/gablab/fluid/Data/gf04/mri/transforms/tmp.bbregister.23921/reg.init.dat --niters 1 --maxangle 90 --nobetmov --tmp /mindhive/gablab/fluid/Data/gf04/mri/transforms/tmp.bbregister.23921/fslregister --dof 6 --fsvol brainmask which immediately crashes with: /mindhive/gablab/fluid/Data/gf04 mri_convert ERROR: could not determine file for /mindhive/gablab/fluid/Data/gf04/mri/ERROR: /mindhive/gablab/fluid/Data/gf04/mri/transforms/tmp.bbregister.23921/fslregister/refvol.fslregister.nii And so on. running the fslregister command manually and changing "brainmask" to "brainmask.mgz" seems to fix the problem (after manually creating/filling the appropriate tmp directory, of course). Any thoughts? Thanks!

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Pial surface errors
by Contarino Valeria 06 May '13

06 May '13

Dear Freesurfers, I usually get very satisfying results but in my last analysis I noticed some errors in a few subjects' pial surface (see attached example image). I really don't get how it failed in that way. What I know I can surely do is to manually modify the WM and run again the autorecon command. Could someone kindly advice me on how to avoid/solve the problem in a less time-consuming way? Thank you. Regards, Valeria Elisa Contarino, MEng Neuroradiology Department IRCCS Foundation Neurological Institute "C.Besta" Via Celoria 11, 20133 Milano, Italy ph: +39 02 23942472

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Open Brain Mapping at the 1st HBM Hackathon
by Nolan Nichols 06 May '13

06 May '13

Sent on behalf of Thomas Grabowski, OHBM 2013, LOC Chair: Open Brain Mapping at the 1st HBM Hackathon: Open Brain Mapping in the Cloud ** OHBM 2013 is only six weeks away, bringing the brain mapping community to Seattle, a city at the forefront of open neuroscience and information technology. The Local Organizing Committee, the Allen Institute for Brain Science, and Amazon Web Services are excited for the opportunity to highlight these aspects of our field in the HBM Hackathon<http://humanbrainmapping.org/hackathon>, a meeting-long event integrated with and running parallel to the activity in the poster and exhibition space. Our goals are to accelerate the development of a critical mass of cloud-based data, analytic, and computational resources for human brain mapping, and to provide OHBM attendees with access to and knowledge about them. The event is being supported by a broad spectrum of partners from the open neuroimaging community, making it possible to allow an unprecedented degree of access to key resources in the field, including the Allen Human Brain Atlas, the first data release of the Human Connectome Project, the NITRC Computational Environment, and more. Experts from the Allen Institute, Amazon Web Services, Human Connectome Project, NITRC, INCF, LONI, NDAR, BIRN, and others will bring their expertise on-venue. Register for the HBM Hackathon <http://humanbrainmapping.org/hackathon> to participate in a contest organized around three challenges, to tinker less formally, or just to be open to open neuroscience. You’ll also receive $100 in free AWS credits to make use of cloud computing technologies. The contest is organized around three Challenges: ** Challenge 1. Best imaging and gene expression relationship discovered via integration of imaging data with the Allen Human Brain Atlas. ** Challenge 2. Best cortical neural systems relationship or visualization based on integration of resting state fMRI data with other HBM Hackathon accessible datasets. ** Challenge 3. To be announced the week of the meeting and pursued completely on site. *See the list of datasets <http://ohbm-seattle.github.io/datasets>* ** Winning entries in each category receive: * - An invitation to submit project to Frontiers in Brain Imaging Methods with Open Access Publication Fees waived (must undergo standard peer review) - Amazon Kindle Fire and/or Paperwhite (limit 3 per team) - AWS hosts AMI and/or data resulting from the hackathon free of charge - Free GitHub Membership with private repositories (Challenge 1: one year silver, Challenge 2: 1 year bronze, Challenge 3: six months bronze) * ** To learn more, visit the HBM Hackathon Blog <http://ohbm-seattle.github.io/>or join the discussion group <http://www.linkedin.com/groups/HBM-Hackathon-4957800>. And be sure to register at: humanbrainmapping.org/hackathon

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R: Re: version 5.3 coming out soon
by stdp82＠virgilio.it 06 May '13

06 May '13

Hi Bruce, thank for new 5.3. I'm finishing tracula analyis with 5.2 (I only have a subject that give me some problem). Do you advice me to cancel my analysis and re-run it by new version 5.3? Is the results obtained with version 5.2 reliable? Thank you very much, Stefano ----Messaggio originale---- Da: fischl(a)nmr.mgh.harvard.edu Data: 4-mag-2013 14.55 A: <Lukas.Scheef(a)ukb.uni-bonn.de> Cc: <freesurfer(a)nmr.mgh.harvard.edu> Ogg: Re: [Freesurfer] version 5.3 coming out soon Hi Luke Nick will post a command line you can run that should take about 2 hours/dataset. Rerunning shouldn't be necessary. Sorry for the trouble, I really, really wish we had more engineering resources. Bruce On Sat, 4 May 2013, Lukas.Scheef(a)ukb.uni-bonn.de wrote: > > Hi Bruce, > > Thanks a lot for the info. Would it mean we have to completely reprocess the > data processed with 5.2? Or at which point of the preprocessing pipeline we > should step in to fix the problems of 5.2...? I just have finished to > process about 200 data sets with 5.2... > > Best wishes, > > Luke > > Am 03.05.2013 um 02:58 schrieb "Bruce Fischl" <fischl(a)nmr.mgh.harvard.edu>: > > > Hi All, > > > > We have recently uncovered problems with version 5.2. Based on these > > problems, we are recommending that people stop using 5.2, mainly in > > regards to usage of the surface data. A new version, 5.3, will be > > released within two weeks, and a beta version for each platform will be > > available within a couple days. > > > > There were two main problems that were uncovered. First, a change was made > > that was only meant to affect the white surface placement in > > high-resolution data sets, but unfortunately is being applied to all data > > sets. This causes the white surface to contract a small amount. This > causes > > the surface area to be smaller and cortex to be measured as thicker > > relative to version 5.1. Visually, the surfaces do not necessarily look > > less accurate, but we feel that the systematic differences with previous > > versions are ill-advised without a clear reason for the change. > > > > Second, a change made to the placement of the pial surface in order to > > improve the positioning based on T2/FLAIR that caused it to extend too far > > in some data sets during the T1-based pial surface deformation. This > > unfortunately became the default behavior, which was not intended. None of > > the dozens of test data sets we ran displayed this problem. The behavior > > was reported by other users which led us to the bug. > > > > In general, we rigorously test each version. However, our systematic > > comparison of a new version with previous versions which would have caught > > these problems was conducted prior to these changes. We are now tightening > > and regimenting our testing procedures to ensure this doesnt happen again. > > Note that there are no problems with the volumetric segmentation (aseg) > > in version 5.2. > > > > We realize that this will cause a substantial inconvenience for users. We > > have isolated and fixed the problems and have run two rounds of alpha > > testing and have one more to go, after which we will release a beta > version > > in a couple of days to anyone that wants it. > > > > sorry for the problems. > > > > Bruce > > _______________________________________________ > > 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. > > > > >_______________________________________________ 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.

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Re: [Freesurfer] question about glm setup
by Subhabrata Chaudhury 06 May '13

06 May '13

Hello Dr. Greve, Thank you for your reply. I have set up the qdec. I have gender as the discrete factor and age and clinical score as continuous factors. In order to look at the relationship between clinical score and whole brain cortical thickness while accounting for age and gender effects, do I select score as the continuous factor and age as the nuisance factor or should it be the other way round ? Thanking you in anticipation, Subha ----- Original Message ----- From: Douglas Greve Sent: 05/05/13 11:53 PM To: freesurfer(a)nmr.mgh.harvard.edu Subject: Re: [Freesurfer] question about glm setup Hi Subha, yes, you can. You will need to create a table in the format with QDEC expects. Have you looked at the tutorial? http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/QdecGroupAnalysis doug On 5/4/13 11:31 AM, Subhabrata Chaudhury wrote: Hi, I am new to freesurfer. I have run reconall on 50 AD subjects. I have also run recon-all -qcache. So I have the following - 1) Whole brain thickness map for each AD subject 2) age of each subject 3) gender of each subject 4) clinical score of each subject I DO NOT have control subjects. I want to run a glm to investigate whether if there is a relation between the clinical score for each subject and their cortical thickness while accounting for age, gender and whole brain average thickness. Can I use qdec for this ? This is my first time doing this sort of analysis, so I will be grateful if I can get some step-by-step help. Thank you very much Subha _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

1 0

The Asymmetry of surface area or thickness
by xiangbo_2010 06 May '13

06 May '13

Dear experts I want to analysis the asymmetry of surface area or thickness, what I do next? thanks! Bo Xiang

2 1

tip and tricks with patient with one big ventricle...
by Gonzalo Rojas Costa 06 May '13

06 May '13

Hi: I has the MPRAGE of a patient with one big ventricle, and the other has normal shape and size... Any tip and tricks to process it ?... Because freesurfer fails from the beggining of the process (VERY BAD talairach registration)... I test -bigventricle option of recon-all, but I got the same problems... Sincerely, -- Gonzalo Rojas Costa Laboratory for Advanced Medical Image Processing Department of Radiology Clínica las Condes Lo Fontecilla 441, Las Condes, Santiago, Chile. Tel: 56-2-2105170 Cel: 56-9-97771785 www.clc.cl

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Freesurfer May 2013