Freesurfer

freesurfer@nmr.mgh.harvard.edu

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30089 discussions

bbregister with PET data
by Marco Loggia, PhD 21 Aug '12

21 Aug '12

Hi Doug and Freesurfer team, I am trying to coregister some PET maps with their relative high resolution MEMPRAGE files. I was thinking that bbregister might be my best option but the results are still not satisfactory, likely due to the intrinsic features of my radioligand (the resulting maps are quite 'noisy' in terms of anatomical details). Do you have any suggestions on how to improve the results of bbregister (e.g., flags to use, or preprocessing steps prior to running bbregister)? - the PET map for one subject is here: /autofs/space/katahdin_005/users/marco/PBR28/data/PBR_CLBP001/PET/PBR_CLBP001_average8-28_BET_hdrOK.nii - my SUBJECTS_DIR is here /autofs/space/katahdin_005/users/marco/PBR28/data/ - The command I ran is: bbregister --init-fsl --mov PBR_CLBP001_average8-28_BET_hdrOK.nii --t2 --s PBR_CLBP001 --reg PET2brain.BB.reg --o PET2brain.BB.nii Thanks! Marco ______________________________ Marco L. Loggia, PhD Postdoctoral Fellow Massachusetts General Hospital Brigham and Women's Hospital Harvard Medical School 149 Thirteenth Street, Room 2301 Charlestown, MA 02129 Phone: (617) 643-7267 Fax: (617) 726-7422 marco(a)nmr.mgh.harvard.edu

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GCA file for non-human recon-all use
by Jeff Thompson 21 Aug '12

21 Aug '12

Hello, I have a few questions that I hope can be answered: Q1:How can '.label' files be turned into the necessary '.gca' file needed for the recon-all pipeline. Starting for the first step in auto-recon2.What else other than the '.label' files would be needed to create this '.gca' file? Q2: How to get the seg_edited.mgz file? I would want to use this file in the rebuild_gca_atas.csh script. Q3:Can the rebuild_gca_atlas.csh script be used to make a replacement for the RB_all_2008-03-26.gca file from the average folder? Q4:Is there a way to avoid needing the .gca file if cortical thickness measurements is the only goal?Or could there be a limited number of labels needed incorporated into the .gca file for this goal. Ex. Just Cerebral cortex ROI's. Thank you for any help, Jeff Thompson

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mri_segstats error
by Blazey, Tyler 21 Aug '12

21 Aug '12

Hi, I recently installed the updated mri_segstats (ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mri_segstats.…) This seems to work fine for recalculating the supratentorial volume. However, it is causing my new recons to fail (see example error below). Any suggestions? Thanks, -Tyler $Id: mri_segstats.c,v 1.86 2012/07/16 14:39:07 greve Exp $ cwd cmdline mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.24644/ones.mgz --i ./tmp.mri_nu_correct.mni.24644/nu2.mnc --sum ./tmp.mri_nu_correct.mni.24644/sum.junk --avgwf ./tmp.mri_nu_correct.mni.24644/output.mean.dat sysname Linux hostname login001 machine x86_64 user tblazey UseRobust 0 Loading ./tmp.mri_nu_correct.mni.24644/ones.mgz Loading ./tmp.mri_nu_correct.mni.24644/nu2.mnc Voxel Volume is 1 mm^3 Generating list of segmentation ids Found 1 segmentations Computing statistics for each segmentation 0 1 0 0 Reporting on 0 segmentations Computing spatial average of each frame Writing to ./tmp.mri_nu_correct.mni.24644/output.mean.dat (standard_in) 1: parse error ________________________________ The material in this message is private and may contain Protected Healthcare Information (PHI). If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail.

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Upload the data in virtuell box!
by Fouladi-Movahed, Sarah 21 Aug '12

21 Aug '12

Hello, I don't know how can I upload the DICOM Data in Virtuellbox.I installed the Virtuellbox in windows PC and would like to upload my Image but until now with out any sucsess. Should I install any extra programm to upload any files? Thanks for your Feedback. Best Regards Sarah

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freesurfer license on multi-user cluster
by John Donners 21 Aug '12

21 Aug '12

Dear developers, I just installed freesurfer 5.1.0 system-wide on one of our clusters. All of our users can now access the software, although there is only one license key in the installation directory. Maybe you prefer that every user on our system uses their own license key for your usage statistics? An environment variable FREESURFER_LICENSE could maybe be used for this purpose? Or an additional check for a local license file ~/.freesurfer_license? With regards, John -- John Donners Consultant OSD SARA Science Park 140 1098 XG Amsterdam T +31 (0)20 592 3055 F +31 (0)20 668 3167 M +31 (0)6 1903 9023 E John.Donners(a)sara.nl www.sara.nl

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QDEC's clusters and connectivity maps
by Antonella Kis 21 Aug '12

21 Aug '12

Dear FS team, I am trying to find what is the connection between white matter tracts with reduced FA and a number of cortical regions/clusters with significant reduction in cortical thickness from QDEC. Is there a way to overlap my cortical regions with reduced thickness more exactly the clusters from QDEC on the connectivity maps in FSL. How I create a mask of the QDEC clusters and used them in tractography? The tractography/ connectivity maps has been performed on the MNI standard space. Any suggestion will be greatly appreciated. Antonella

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mri_convert introduces flip
by Janosch Linkersdörfer 21 Aug '12

21 Aug '12

Hi experts, I´m trying to convert original images in native space from the LPBA40-Atlas (http://www.loni.ucla.edu/Atlases/LPBA40/) from img/hdr to nii/nii.gz. Conversion always results in a left/right flip. Also, mri_convert complains that no .mat file is available but there are no mat files provided... Here my command and output: mri_convert S01.native.mri.img S01.native.mri.nii.gz $Id: mri_convert.c,v 1.179.2.2 2011/05/16 20:53:47 greve Exp $ reading from S01.native.mri.img... ----------------------------------------------------------------- INFO: could not find /Users/Januz/Downloads/__Tests/__test/S01.native.mri.mat file for direction cosine info. INFO: use Analyze 7.5 hdr->hist.orient value: 0, transverse unflipped (default). INFO: if not valid, please provide the information in /Users/Januz/Downloads/__Tests/__test/S01.native.mri.mat file ----------------------------------------------------------------- TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, 0) j_ras = (0, 1, 0) k_ras = (0, 0, 1) writing to S01.native.mri.nii.gz... Thanks for your help, Janosch

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Re: [Freesurfer] empty CSD folder?
by lordowen 21 Aug '12

21 Aug '12

2012/8/20 lordowen <lordowentu(a)gmail.com>: > The enclosed file please find the edited log file and screen-shot > picture. We edit the log file because it is too big (about 20 MB). We > kept the command-line record and removed most poll record. Basically, > our Mac workstation polled once for every 10 seconds. > > 2012/8/20 Bruce Fischl <fischl(a)nmr.mgh.harvard.edu>: >> Can you send us your command line and screen out? Really, two months? >> Bruce >> >> >> >> On Aug 19, 2012, at 11:39 PM, lordowen <lordowentu(a)gmail.com> wrote: >> >>> Dear experts: >>> >>> We performed permutation analysis (with -sim perm) for our thickness >>> data. After 2 month calculation, the process completed but the CSD >>> folder only contained an empty folder named "poll". No CSD file in >>> them. So I wonder if the CSD file has been stored in another place or >>> something wrong with them? Please advise us. >>> >>> -- >>> Best regards >>> -- >>> 杜政昊 >>> >>> Cheng-Hao Tu, PhD >>> Post Doctoral Research Fellow >>> Integrated Brain Research Unit >>> Department of Medical Research and Education >>> Taipei Veterans General Hospital >>> No.201, Sect.2, Shih-Pai Rd. >>> Taipei >>> Taiwan >>> Email: lordowen(a)ms10.hinet.net or lordowentu(a)gmail.com >>> Tel: +886-2-28712121 ext 3474 >>> Fax: +886-2-28745182 >>> >>> _______________________________________________ >>> 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. > > > > -- > Best regards > -- > 杜政昊 > > Cheng-Hao Tu, PhD > Post Doctoral Research Fellow > Integrated Brain Research Unit > Department of Medical Research and Education > Taipei Veterans General Hospital > No.201, Sect.2, Shih-Pai Rd. > Taipei > Taiwan > Email: lordowen(a)ms10.hinet.net or lordowentu(a)gmail.com > Tel: +886-2-28712121 ext 3474 > Fax: +886-2-28745182 -- Best regards -- 杜政昊 Cheng-Hao Tu, PhD Post Doctoral Research Fellow Integrated Brain Research Unit Department of Medical Research and Education Taipei Veterans General Hospital No.201, Sect.2, Shih-Pai Rd. Taipei Taiwan Email: lordowen(a)ms10.hinet.net or lordowentu(a)gmail.com Tel: +886-2-28712121 ext 3474 Fax: +886-2-28745182

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Problems with ICV calculations in fs5.1.0?
by Cheryl McCreary 20 Aug '12

20 Aug '12

Dear fs Experts, In the most recent Freesurfer Digest (vol102, Issue13), a question regarding ICV calculations in version 5.1.0 was raised (message 4). Can you please expand on the problems with this? I am using version 5.1.0 and the estimate of ICV is of interest. Thanks, Cheryl McCreary

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More problems created when adding WMCP
by Mark Fletcher 20 Aug '12

20 Aug '12

Dear FreeSurfers, I have been working on cross-sectional MRI's of healthy older adults (55-88), and have been correcting the FreeSurfer 5.1 output using the instructions given here ( http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/TroubleshootingData) to correct the FreeSurfer errors that we have found. For the majority of the subjects, we have been able to fix the errors as described by your website. However, for about 7 of our subjects, whenever we attempt to add WMCP to non-traced white matter regions (especially noticed in the anterior region of the temporal lobe), the new "main surface" and "Pial" tracings end up much worse than they were originally (thus, new problems that never previously existed are created). At this point we have tried a variety of things. We have tried going back to the original FreeSurfer Output to add WMCP differently, yet a variety of new problems are consistently being created (on some of these subjects we have tried over 10+ different ways of adding WMCP in order to fix the brains). After this has occured, we simply tried fixing the "new problems" as well, but it has created a never ending loop of new problems (upon fixing the new problems, even newer problems were created). For some of our subjects (besides these 7), this eventually leads to a correct segmentation. However, for these 7, we have been unable to ever end up at an adequate tracing?? I would love you send you images and or the files themselves to figure out how to proceed (however, when I tried to send it as an attachment my message was rejected due to size issures). Is there a way I can directly send you the FS output (via a ftp site, or dropbox) so you can look at the problem directly? The IRB has approved our "sharing" of this data if it helps us in our processing. Also, do you have any suggestions on how we might proceed? Is there a way besides adding WMCP to assist our fixing of the anterior temporal regions? Thanks in advance. Sincerely, Mark Fletcher

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