Freesurfer

freesurfer@nmr.mgh.harvard.edu

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30088 discussions

Bedpost Not successfully completed
by ebelleau＠uwm.edu 20 Nov '13

20 Nov '13

Hello, I am finding that my bedposting is not completing successfully. I was able to get my first two subjects to run successfully, however, for the other two subjects that I have run I have gotten the following message: For some reason the bedpostX process DOES NOT appear to have successfully completed. Please examine your results carefully. /opt/psych_imaging/Freesurfer_5.3//bin/bedpostx_mgh: line 345: kill: (30896) - No such process Any ideas of what I should be looking for or troubleshooting to get this step to work? Thanks so much, Emily

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accessing old releases?
by Ruth Carper 20 Nov '13

20 Nov '13

Hi, I need to reinstall an older version of Freesurfer, but the only link I found: Old releases are here. seems to require a login and password. How can I access this?

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hippocampus region in an atlas?
by Gregg, Brian E. 20 Nov '13

20 Nov '13

Hello, I didn't see hippocampus listed in the Desikan-Killiany, Destrieux, or DKTatlas40 atlases. Is there an existing atlas that contains the hippocampal subfields? If not, what options exist for getting the hippocampus into an atlas? Thank you, Brian

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T2pial/FLAIRpial processing issues
by Martijn Steenwijk 20 Nov '13

20 Nov '13

Dear all, There seem to be some serious issues with the T2pial / FLAIRpial processing options provided in the latest versions of FreeSurfer. First of all, although not clearly documented, T2pial / FLAIRpial processing does require the FSLDIR to be set (in order to use bbregister with --init-fsl). If not set, recon-all will finish just without using the T2 or FLAIR information. Importantly, no clear warning about this is given although the user expects that T2/FLAIR has been used for pial surface refinement. I think this is a very easy source of errors, so it might be a good idea to just throw an error when FSLDIR is missing and T2pial/FLAIRpial processing is requested. Second, if FSLDIR has been set. T2pial/FLAIRpial uses bbregister with FLIRT initialisation to align the T2 or FLAIR image to orig.mgz. However, we have some high-res 3DFLAIR data in which this registration (more specifially, the FLIRT initialisation step of bbregister) seems to fail in more than half of the cases. Apparently, the FSL initialisation is not capable to change the orientation such that it fits to the coordinate system used for orig.mgz. Again, no warning or error is thrown, but the processing just continues with the wrong registration and without noticing the results will get worse compared to not using T2 or FLAIR. Although I know its essential to look at the output data; would it be possible to put some effort in letting the user know that things got wrong? As a sidenote; I tried to fix this registration issue, but it seems to be very complicated using bbregister (other than just inserting my own registration obtained by using FLIRT to register native FLAIR to native T1, and subsequently transform the result to Freesurfer space in order to obtain FLAIR.mgz). Best, Martijn

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(no subject)
by pietro de rossi 20 Nov '13

20 Nov '13

Good morning Dr Vinke, did you have the chance to take a look at the subject I uploaded a few days ago? thanks again. Kind regards, Pietro -- Pietro De Rossi, MD ------------------------------------- Sapienza Università di Roma, Facoltà di Medicina e Psicologia, Dipartimento NESMOS (Neuroscienze, Salute Mentale, Organi di Senso), Ospedale Sant'Andrea, Via di Grottarossa 1035-1039, 00189 Roma NESMOS Department (Neurosciences, Mental Health and Sensory Functions), School of Medicine and Psychology, Sapienza University, Sant’Andrea Hospital, Via di Grottarossa 1035-1039, 00189 Rome, Italy Laboratorio di Neuropsichiatria, Dipartimento di Neurologia Clinica e Comportamentale, IRCCS Fondazione Santa Lucia, via Ardeatina 306 - 00179 Roma Tel. +39 (0)6 51501358 Fax +39 (0)6 90280774 web: http://www.neuropsichiatrialab.com<http://www.neuropsichiatrialab.com/it/personale/sabrina-fagioli>

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how to obtain subjects cortical thickness and then analyze unpair t-test
by Rujing Zha 19 Nov '13

19 Nov '13

Dear all, Ater recon-all,which image can I select to group t-test? And do they need process in advance? Thanks very much. All the best. 2013-11-19 Rujing Zha

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Fwd: RLE Lossless dicom compression
by Nathaniel Reynolds 19 Nov '13

19 Nov '13

Hi, I'm working with some clinical DICOMs which appear to have their image data compressed with a RLE lossless algorithm. I need to decompress these images. When I run into jpeg compression, I can use the "dcmdjpeg" function. The "dcmdjpeg" function doesn't work on the RLE-compressed files, naturally. I can't find an equivalent function for RLE-lossless decompression. Does anybody know of one? Thanks, Nathaniel

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lobe mapping
by Mojdeh Zamyadi 19 Nov '13

19 Nov '13

Hi all, I'm interested in getting a lobar segmentation of the cortex and I've already ran recon-all on my subjects. I'm now confused by the outputs and was wondering if someone could tell me which output file contains segmentation that can be merged to get a 4 lobe parcellation similar to: http://freesurfer.net/fswiki/CorticalParcellation? Thanks a lot, -Mojdeh

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Recon-all problem
by Devin Sodums 19 Nov '13

19 Nov '13

Dear Freesurfer experts, I have recently installed Freesurfer onto a VirtualBox Linux environment, and had no problems running the supplied practice subject, 'Bert', all the way through reconstruction. However, when I started trying to analyze my own subject's, recon-all keeps exiting just after the "mri_nu_correct.mni" step, without any specific error message. I have copied and pasted the error message from the unsuccessful, and successful run below, as well as the output from the "bugr" command. I realize that tcsh is out of date, and I have tried updating it (which I am not sure if I was successful or not), but I got the same message with the successful run so I don't think that is the issue. Any suggestions would be greatly appreciated. Best, Devin General info: fsuser@xubuntu-VirtualBox:~/share/SMIP_MNI_structural_files/b_s_20131018_124417$ which freesurfer /usr/local/freesurfer/bin/freesurfer FREESURFER_HOME: /usr/local/freesurfer Build stamp: freesurfer-Linux-centos4-stable-pub-v5.3.0 Debian version: wheezy/sid Kernel info: Linux 3.2.0-56-generic i686 Unsuccessful Run: xubuntu-VirtualBox:~/share/SMIP_MNI_structural_files/boucher_suzanne_20131018_12 4417> recon-all -subjid b_s_20131018_fs -all WARNING: tcsh v6.17.06 has an exit code bug! Please update tcsh! Subject Stamp: freesurfer-Linux-centos4-stable-pub-v5.3.0 Current Stamp: freesurfer-Linux-centos4-stable-pub-v5.3.0 INFO: SUBJECTS_DIR is /home/fsuser/share/SMIP_MNI_structural_files/b_s_20131018_124417 Actual FREESURFER_HOME /usr/local/freesurfer Linux xubuntu-VirtualBox 3.2.0-56-generic #86-Ubuntu SMP Wed Oct 23 17:31:43 UTC 2013 i686 i686 i386 GNU/Linux #-------------------------------------------- #@# MotionCor Fri Nov 15 16:30:12 EST 2013 Found 1 runs /home/fsuser/share/SMIP_MNI_structural_files/b_s_20131018_124417/b_s_20131018_fs/mri/orig/001.mgz Checking for (invalid) multi-frame inputs... WARNING: only one run found. This is OK, but motion correction cannot be performed on one run, so I'll copy the run to rawavg and continue. cp /home/fsuser/share/SMIP_MNI_structural_files/b_s_20131018_124417/b_s_20131018_fs/mri/orig/001.mgz /home/fsuser/share/SMIP_MNI_structural_files/b_s_20131018_124417/b_s_20131018_fs/mri/rawavg.mgz /home/fsuser/share/SMIP_MNI_structural_files/b_s_20131018_124417/b_s_20131018_fs mri_convert /home/fsuser/share/SMIP_MNI_structural_files/b_s_20131018_124417/b_s_20131018_fs/mri/rawavg.mgz /home/fsuser/share/SMIP_MNI_structural_files/b_s_20131018_124417/b_s_20131018_fs/mri/orig.mgz --conform mri_convert /home/fsuser/share/SMIP_MNI_structural_files/b_s_20131018_124417/b_s_20131018_fs/mri/rawavg.mgz /home/fsuser/share/SMIP_MNI_structural_files/b_s_20131018_124417/b_s_20131018_fs/mri/orig.mgz --conform $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from /home/fsuser/share/SMIP_MNI_structural_files/b_s_20131018_124417/b_s_20131018_fs/mri/rawavg.mgz... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (0.0156845, -0.970744, 0.239606) j_ras = (0.0185749, 0.239877, 0.970626) k_ras = (0.999704, 0.0107731, -0.0217938) Original Data has (1, 1, 1) mm size and (256, 256, 176) voxels. Data is conformed to 1 mm size and 256 voxels for all directions changing data type from float to uchar (noscale = 0)... MRIchangeType: Building histogram Reslicing using trilinear interpolation writing to /home/fsuser/share/SMIP_MNI_structural_files/b_s_20131018_124417/b_s_20131018_fs/mri/orig.mgz... mri_add_xform_to_header -c /home/fsuser/share/SMIP_MNI_structural_files/b_s_20131018_124417/b_s_20131018_fs/mri/transforms/talairach.xfm /home/fsuser/share/SMIP_MNI_structural_files/b_s_20131018_124417/b_s_20131018_fs/mri/orig.mgz /home/fsuser/share/SMIP_MNI_structural_files/b_s_20131018_124417/b_s_20131018_fs/mri/orig.mgz INFO: extension is mgz #-------------------------------------------- #@# Talairach Fri Nov 15 16:30:45 EST 2013 /home/fsuser/share/SMIP_MNI_structural_files/b_s_20131018_124417/b_s_20131018_fs/mri mri_nu_correct.mni --n 1 --proto-iters 1000 --distance 50 --no-rescale --i orig.mgz --o orig_nu.mgz Linux xubuntu-VirtualBox 3.2.0-56-generic #86-Ubuntu SMP Wed Oct 23 17:31:43 UTC 2013 i686 i686 i386 GNU/Linux recon-all -s b_s_20131018_fs exited with ERRORS at Fri Nov 15 16:30:58 EST 2013 SUCCESSFUL RUN: INFO: extension is mgz #-------------------------------------------- #@# Talairach Fri Nov 15 15:53:35 EST 2013 /usr/local/freesurfer/subjects/bert/mri mri_nu_correct.mni --n 1 --proto-iters 1000 --distance 50 --no-rescale --i orig.mgz --o orig_nu.mgz talairach_avi --i orig_nu.mgz --xfm transforms/talairach.auto.xfm INFO: transforms/talairach.xfm already exists! The new transforms/talairach.auto.xfm will not be copied to transforms/talairach.xfm This is done to retain any edits made to transforms/talairach.xfm Add the -clean-tal flag to recon-all to overwrite transforms/talairach.xfm #-------------------------------------------- #@# Talairach Failure Detection Fri Nov 15 15:55:03 EST 2013 /usr/local/freesurfer/subjects/bert/mri talairach_afd -T 0.005 -xfm transforms/talairach.xfm talairach_afd: Talairach Transform: transforms/talairach.xfm OK (p=0.7614, pval=0.6675 >= threshold=0.0050) awk -f /usr/local/freesurfer/bin/extract_talairach_avi_QA.awk /usr/local/freesurfer/subjects/bert/mri/transforms/talairach_avi.log tal_QC_AZS /usr/local/freesurfer/subjects/bert/mri/transforms/talairach_avi.log TalAviQA: 0.97409 z-score: 0 #-------------------------------------------- #@# Nu Intensity Correction Fri Nov 15 15:55:03 EST 2013 mri_nu_correct.mni --i orig.mgz --o nu.mgz --uchar transforms/talairach.xfm --n 2 /usr/local/freesurfer/subjects/bert/mri /usr/local/freesurfer/bin/mri_nu_correct.mni --i orig.mgz --o nu.mgz --uchar transforms/talairach.xfm --n 2 nIters 2 $Id: mri_nu_correct.mni,v 1.18.2.1 2013/01/09 21:23:42 nicks Exp $ Linux xubuntu-VirtualBox 3.2.0-56-generic #86-Ubuntu SMP Wed Oct 23 17:31:43 UTC 2013 i686 i686 i386 GNU/Linux Fri Nov 15 15:55:03 EST 2013 Program nu_correct, built from: Package MNI N3, version 1.10, compiled by nicks@fishie (i686-pc-linux-gnu) on 2010-02-20 at 20:19:13 tmpdir is ./tmp.mri_nu_correct.mni.10351 /usr/local/freesurfer/subjects/bert/mri mri_convert orig.mgz ./tmp.mri_nu_correct.mni.10351/nu0.mnc -odt float mri_convert orig.mgz ./tmp.mri_nu_correct.mni.10351/nu0.mnc -odt float $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from orig.mgz... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, 0) j_ras = (0, 0, -1) k_ras = (0, 1, 0) changing data type from uchar to float (noscale = 0)... writing to ./tmp.mri_nu_correct.mni.10351/nu0.mnc...

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Re: [Freesurfer] Aseg2feat: Missing segmentations
by Douglas N Greve 19 Nov '13

19 Nov '13

Can you send the aseg2feat log file? Also, please remember to post to the list instead of to me personally. thanks! doug On 11/19/2013 03:17 PM, Sudhin A. Shah wrote: > yes, it looks fine.. > ________________________________________ > From: Douglas N Greve [greve(a)nmr.mgh.harvard.edu] > Sent: Tuesday, November 19, 2013 2:50 PM > To: Sudhin A. Shah; Freesurfer(a)nmr.mgh.harvard.edu > Subject: Re: [Freesurfer] Aseg2feat: Missing segmentations > > Those are some big segs. Have you checked the registration? > > > On 11/19/2013 02:41 PM, Sudhin A. Shah wrote: >> yes :) For example in this 1 subject segs ( >> 2005 2008 2010 2011 2013 2021 2023 2025 2029 1005 1008 1011 1013 1021) are all missing.. >> >> The missing segs are not consistent across subjs(i.e. other subjs have different segs missing). I chose a list of 86 segs to 'cover' the brain and not sure if I was over-reaching..Also some segs are reading with value 100 (i.e. all voxels have a value of 100)? >> >> >> >> ________________________________________ >> From: freesurfer-bounces(a)nmr.mgh.harvard.edu [freesurfer-bounces(a)nmr.mgh.harvard.edu] on behalf of Douglas N Greve [greve(a)nmr.mgh.harvard.edu] >> Sent: Tuesday, November 19, 2013 2:34 PM >> To: freesurfer(a)nmr.mgh.harvard.edu >> Subject: Re: [Freesurfer] Aseg2feat: Missing segmentations >> >> there were probably some small segmentations that were lost. Is this >> causing a problem? >> On 11/19/2013 02:22 PM, Sudhin A. Shah wrote: >>> Hello, >>> >>> This is regarding the registration of functional data to freesurfer >>> parcellations >>> (http://freesurfer.net/fswiki/FsTutorial/MapSegmentationsToFunctionalSpace) >>> >>> The rsfMRI is sampled at 2x2x2. >>> >>> After running reg-feat2anat and aseg2feat >>> >>>>> a = MRIread('aparc+aseg'); %Original aparc+aseg output from >>> freesurfer recon-all >>>>> size(unique(a.vol(:))) % 114 segs >>>>> a = MRIread('aparc+aseg'); % this is the output file after aseg2feat >>>>> size(unique(a.vol(:))) % 98 segs >>> Any advice? >>> >>> Thanks >>> >>> >>> >>> _______________________________________________ >>> Freesurfer mailing list >>> Freesurfer(a)nmr.mgh.harvard.edu >>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> -- >> Douglas N. Greve, Ph.D. >> MGH-NMR Center >> greve(a)nmr.mgh.harvard.edu >> Phone Number: 617-724-2358 >> Fax: 617-726-7422 >> >> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting >> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 >> www.nmr.mgh.harvard.edu/facility/filedrop/index.html >> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ >> >> _______________________________________________ >> 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. >> >> >> > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > greve(a)nmr.mgh.harvard.edu > Phone Number: 617-724-2358 > Fax: 617-726-7422 > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 > www.nmr.mgh.harvard.edu/facility/filedrop/index.html > Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ > > > -- Douglas N. Greve, Ph.D. MGH-NMR Center greve(a)nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/

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