Freesurfer

freesurfer@nmr.mgh.harvard.edu

18 participants
30131 discussions

cropping of average T1
by Siddharth Srivastava 23 Jan '09

23 Jan '09

Hi everyone, I am attaching a tiff file showing the tkmedit view of the average T1 that freesurfer created during make_average_subject. I am a bit concerned about the cropping that is evident at the posterior aspect of the brain. The individual T1's are complete and ok, so i am guessing that something went wrong during the transform of the individual brain during the process. Can anyone help me find out the problem ? The average surfaces also look all right. thanks, sid.

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labels and transforming them
by Ian Malone 23 Jan '09

23 Jan '09

Hi, I'm trying to work out how to use a transformation matrix derived from FSL to transform labels from Freesurfer into a standard space (MNI152). If I use mri_label2vol to convert the label to a volume with the scan from subject/mri/orig/001.mgz as a template and then flirt to apply the FSL transformation I end up with something that corresponds correctly to the standard space (and the intermediate volume looks correct compared to the original scan). If on the other hand I multiply the positions in the label file by the transformation matrix from FSL (i.e. M*[x y z 1]') then the labelled region does not appear in the correct space. I have also tried adjusting the translation component of the FSL matrix by half the difference between the standard space and original image dimensions with no success. I've also tried to generate a .mat to pass to mri_label2vol using tkregister2, but despite trying different combinations of I and S in --targ-orientation and --mov-orientation I seem to always have one volume upside down (target if I don't specify the orientation, moveable if I do, the FSL matrix does not have this flip). Any suggestions for things that might be going wrong here or other strategies to try? Also, assuming I get the transformation right, will adjusting the label point volume to match the new voxel dimensions make any difference if the the threshold is set at zero? Thanks, Ian

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mri_convert
by Jared Price 23 Jan '09

23 Jan '09

Hi everyone, I have a quick question but an important one. We are working on a 5 year study involving well over 1000 scans. Processing of these patients is primarily done using a cluster machine loaded with freesurfer version x86_64-redhat-linux-gnu-dev4-20080904. However, sometimes it is useful to be able to do certain preliminary steps of the processing locally in our lab which is full of Macs running the 4.0.5 version of freesurfer. Also, because of the long nature of the study in the past these computers have been loaded with 4.0.0 4.0.1 4.0.2 etc. Anyway, my question is that although all of the recon-all processing has been done on the cluster machine some scans have undergone mri_convert locally in the lab to create a 001.mgz file which is then fed to the cluster for further processing. Would there be any concern in this? I know the version of mri_convert for freesurfer version 4.0.5 is mri_convert 1.146.2.3 and the one on our cluster machine is 1.146.2.1, but I am not sure what the versions of mri_convert were that were used in 4.0.0 4.0.1 etc. Anyway, any reason for concern in having some variability only in the version invoked to create the 001.mgz file using mri_convert?

2 1

mri_convert
by Jared Price 23 Jan '09

23 Jan '09

.... correction to the previous message (which is below). The Macs in the local lab are now running Darwin-leopard-i686-stable 4.1.0 and the version of mri_convert on that seems to be 1.146.2.3 Hi everyone, I have a quick question but an important one. We are working on a 5 year study involving well over 1000 scans. Processing of these patients is primarily done using a cluster machine loaded with freesurfer version x86_64-redhat-linux-gnu-dev4-20080904. However, sometimes it is useful to be able to do certain preliminary steps of the processing locally in our lab which is full of Macs running the 4.0.5 version of freesurfer. Also, because of the long nature of the study in the past these computers have been loaded with 4.0.0 4.0.1 4.0.2 etc. Anyway, my question is that although all of the recon-all processing has been done on the cluster machine some scans have undergone mri_convert locally in the lab to create a 001.mgz file which is then fed to the cluster for further processing. Would there be any concern in this? I know the version of mri_convert for freesurfer version 4.0.5 is mri_convert 1.146.2.3 and the one on our cluster machine is 1.146.2.1, but I am not sure what the versions of mri_convert were that were used in 4.0.0 4.0.1 etc. Anyway, any reason for concern in having some variability only in the version invoked to create the 001.mgz file using mri_convert? _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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Mri_convert issue
by Barnali Basu 22 Jan '09

22 Jan '09

HI I am trying to convert a .nii file to .mgz , however, it throws the following when i run it mri_convert -it nii -i NAG_S3_anatomical_CLEAN.nii.gz -ot mgz -o anat.mgz mri_convert -it nii -i NAG_S3_anatomical_CLEAN.nii.gz -ot mgz -o anat.mgz $Id: mri_convert.c,v 1.146.2.3 2008/08/11 22:18:58 nicks Exp $ reading from NAG_S3_anatomical_CLEAN.nii.gz... INFO: using NIfTI-1 qform 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 anat.mgz... sh: gzip: not found Broken pipe barnali-work:/usr/local/freesurfer/subjects/bert> could you throw some light on this? FYI, I have converted a .vmr (from Brainvoyager) to .nii and wanting to convert it to .mgz so that i can work with it on Freesurfer. Thanks Barnali Basu

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Problem with lgi
by Christian Scheel 22 Jan '09

22 Jan '09

Dear all, It looks like I have found a workaround for the problem that I encountered when calculating the local gyrification index. I am not sure how common my problem is, but as the solution might interest some other people aswell I decided to post it here. The problem was that in my case Matlab did not find the temporary directory 'tmp-mris_compute_lgi-?h.pial' and its file '?h.pial.filled.mgz' - both created by the mris_compute_lgi script (see terminal error message below). My solution was to edit mris_compute_lgi (which can be found in $FREESURFER_HOME/bin) in line 68 replacing set tmpdir = (tmp-mris_compute_lgi-${input}) with set tmpdir = ($PWD/tmp-mris_compute_lgi-${input}) $PWD is a unix environment variable for the path to the current directory (which in this case is $SUBJECTS_DIR/subjid/surf). I have started the computation now and so far everything seems to work fine. Best wishes, Christian Scheel --- ps: this is the terminal error message before editing mris_compute_lgi: [r...@localhost christian]$ recon-all -s bert -localGI Subject Stamp: freesurfer-Linux-centos4-stable-pub-v4.1.0 Current Stamp: freesurfer-Linux-centos4-stable-pub-v4.1.0 INFO: SUBJECTS_DIR is /home/freesurfer/christian Actual FREESURFER_HOME /usr/local/freesurfer_410 -rw-rw-r-- 1 freesurfer freesurfer 906671 Jan 20 14:30 /home/freesurfer/christian/bert/scripts/recon-all.log Linux localhost.localdomain 2.6.9-67.ELsmp #1 SMP Fri Nov 16 12:48:03 EST 2007 i686 i686 i386 GNU/Linux INFO: current FREESURFER_HOME does not match that of previous processing. Current: /usr/local/freesurfer_410 Previous: /space/freesurfer/build/pub-releases/freesurfer /home/freesurfer/christian/bert/surf #-------------------------------------------- #...@# Local Gyrification Index lh Tue Jan 20 14:43:39 CET 2009 mris_compute_lgi --i lh.pial ================= rm -Rf tmp-mris_compute_lgi-lh.pial ================= ================= mkdir -p tmp-mris_compute_lgi-lh.pial ================= ================= mris_fill -c -r 1 lh.pial tmp-mris_compute_lgi-lh.pial/lh.pial.filled.mgz ================= reading surface from lh.pial... writing filled volume to tmp-mris_compute_lgi-lh.pial/lh.pial.filled.mgz... conforming output volume setting resolution for intermediate calculations to 1.0000 ================= make_outer_surface('tmp-mris_compute_lgi-lh.pial/lh.pial.filled.mgz',15,'tmp-mris_compute_lgi-lh.pial/lh.pial-outer'); exit ================= ---------------------------------------------------------------------------- Warning: glibc 2.3.4 - Your version glibc 2.3.6 - MATLAB built using this version ---------------------------------------------------------------------------- Warning: Unable to open display 'iconic'. You will not be able to display graphics on the screen. < M A T L A B (R) > Copyright 1984-2008 The MathWorks, Inc. Version 7.7.0.471 (R2008b) September 17, 2008 To get started, type one of these: helpwin, helpdesk, or demo. For product information, visit www.mathworks.com. >> reading filled volume... zcat: tmp-mris_compute_lgi-lh.pial/lh.pial.filled.mgz.gz: No such file or directory ERROR: problem reading fname ??? SWITCH expression must be a scalar or string constant. Error in ==> load_mgh at 158 switch type Error in ==> MRIread at 88 [mri.vol, M, mr_parms, volsz] = load_mgh(fspec,[],[],headeronly); Error in ==> make_outer_surface at 24 vol=MRIread(filled_volume); >> ERROR: make_outer_surface did not create output file 'tmp-mris_compute_lgi-lh.pial/lh.pial-outer'! Linux localhost.localdomain 2.6.9-67.ELsmp #1 SMP Fri Nov 16 12:48:03 EST 2007 i686 i686 i386 GNU/Linux recon-all exited with ERRORS at Tue Jan 20 14:43:55 CET 2009 -- NUR NOCH BIS 31.01.! GMX FreeDSL - Telefonanschluss + DSL für nur 16,37 EURO/mtl.!* http://dsl.gmx.de/?ac=OM.AD.PD003K11308T4569a

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(no subject)
by Al-Radaideh Ali 22 Jan '09

22 Jan '09

Dear FreeSurfer experts, I did contact you before regarding the problem below ( Talairach Failure Detection ) and one suggestion was to use lower resolution MPRAGE rather than using .5mm one. ( Our MPRAGEs were acquired at 7T scanner with 0.5mm isotropic resolution). I acquired a new MPRAGE at 7T scanner with 0.8mm isotropic resolution but unfortunately it failed again. ( Note, regarding the inhomogeniety, I used SPM5 for normalization. Furthermore, I tried also using flag '-notal-check' once but did not work) Any other suggestions I can try, Please? Thu Jan 22 11:22:45 GMT 2009 talairach_avi done cp transforms/talairach.auto.xfm transforms/talairach.xfm #-------------------------------------------- #@# Talairach Failure Detection Thu Jan 22 11:22:46 GMT 2009 /data_local/ali/freesurfer/subjects/low2n/low2n/mri talairach_afd -T 0.005 -xfm transforms/talairach.xfm ERROR: talairach_afd: Talairach Transform: transforms/talairach.xfm ***FAILED*** (p=0.0000, pval=0.0000 < threshold=0.0050) Linux comp03 2.6.11.4-21.11-smp #1 SMP Thu Feb 2 20:54:26 GMT 2006 x86_64 x86_64 x86_64 GNU/Linux recon-all exited with ERRORS at Thu Jan 22 11:22:46 GMT 2009 Many thanks in advance Ali This message has been checked for viruses but the contents of an attachment may still contain software viruses, which could damage your computer system: you are advised to perform your own checks. Email communications with the University of Nottingham may be monitored as permitted by UK legislation.

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Freesurfer Tutorials
by jbrace＠ucla.edu 21 Jan '09

21 Jan '09

Hello - I am a new graduate student working with Dr. Russ Poldrack at UCLA and I am trying to learn how to use Freesurfer. I downloaded all of the sample data from the page FSTutorial/Data, but many of the tutorials seem to refer to data that is not included in the sample data. The first tutorial I tried was FSTutorial/MorphAndRecon. - Exercise B in this tutorial is the page FSTutorial/Talairach. This page refers to the files tal_before and tal_after which are not in the sample data. - Exercise C in this tutorial is the page FSTutorial/ControlPoints. This page refers to the file cp_before which is not in the sample data. - Exercise D in this tutorial is the page FSTutorial/SkullStripFix. This page refers to the files skullstrip1_before, skullstrip2_before, skullstrip2_after and skullstrip3_before which are not in the sample data - Exercise F in this tutorial is the page FSTutorial/WhiteMatterEdits. This page refers to the files wm1_edits_before, wm2_edits_before and wm3_edits_before whic are not in the sample data - Exercise G in this tutorial is the page FSTutorial/PialEdits. This page refers to the file pial_edits_before which is not in the sample data. The second tutorial I tried was FSFastTutorial. This tutorial seems to refer to data from the FsFastTutorialData page (from files fsfast-tutorial.tar.gz and fsfast-tutorial.subjects.tar.gz). However, I am unable to download these files from this page. Please either let me know where I can find these files so I can complete the tutorials, or if there are different tutorials that correspond with the data I downloaded from FSTutorial/Data. Thank you very much. Sincerely, Jennifer Brace

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failed Talairach quality check; alternatives?
by Jeff Phillips 21 Jan '09

21 Jan '09

Hi all, I have an MPRAGE which consistently fails the Talairach quality check (see attached error) in autorecon1. (A 32-channel coil was used in this scan, and I suspect that might be a cause of the failure.) Per the wiki's suggestion, I have tried to manually fix the transform in tkregister2 and rerun reconstruction, but despite multiple attempts, I haven't been able to get a transform which satisfies the quality check. From similar list posts, I thought it might be possible for me to Talairach in an external program (BET, AFNI, etc.) and create a transform file that FreeSurfer can read. If this is possible, could you give me an overview of the process, or point me to existing documentation? Thanks, Jeff Phillips

2 1

contrast + interpretation
by Siddharth Srivastava 21 Jan '09

21 Jan '09

Hi group, I have some questions about the interpretation of my results based on the contrasts that i have used in my analysis. It is, i am sure a very basic question, and i would like to check if my interpretation of the results is correct/valid. I have 2 groups, and 1 variable, and i am setting up a dods design, hence i have used 4 regressors. I query with a contrast vector of [0 0 1 -1], intending to discover regions where the measure x variable interaction between the groups is significant. Am i correct in the interpretation of the design and contrasts so far? In case yes, does the sign of the value in sig.mgh file indicate the direction of the interaction (i.e +ve values for positive correlation, and vice-versa) ? I realize that i am using "interaction" and "correlation" interchangeably: is this valid? How do i proceed from inferences about interactions to statements about correlation? thanks, sid.

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