Freesurfer November 2011

freesurfer@nmr.mgh.harvard.edu

110 participants
165 discussions

Problem with mri_glmfit-sim cache option in freesurfer 4.5.0
by ALEXA HUBER 30 Nov '11

30 Nov '11

Hi all, I am a new freesurfer user and am trying to use mri_glmfit-sim with --cache option from my freesurfer 4.5.0 installation. I followed the instructions on this page: http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg14415.html but as the files are not available for download any more from the link indicated on that page, I instead downloaded the newest freesurfer version (v5.1.0) and took the files from there. I copied the "mult-comp-cor" directory into $FREESURFER_HOME/average/. and replaced the "mri_glmfit-sim" file in $FREESURFER_HOME/bin/. as suggested. I then ran the simulation on a previously done glm analysis like this: mri_glmfit-sim --glmdir n49.lh.ZM11_2age_oldf2.thick.glmdir --cache 2 pos The programme stops with error and gives me feedback as shown below. Does anybody know what I did wrong? I prefer not to switch to the newest freesurfer version as I heard this is not a good idea during an analysis (is that right?). Many thanks for any help! Alexa Here is the feedback: cmdline mri_glmfit --y n49.lh.M11_2age_oldf2.thick.10.mgh --fsgd n49_ZM11_2grp_2age_oldf2.fsgd doss --C M11_C01_C-P_000_doss.mtx --C M11_C02_00aCaP0_doss.mtx --C M11_C03_00aP-aC0_doss.mtx --C M11_C04_0000oldf2_doss.mtx --surf fsaverage lh --cortex --glmdir n49.lh.ZM11_2age_oldf2.thick.glmdir WARNING: unrecognized mri_glmfit cmd option doss SURFACE: fsaverage lh log file is n49.lh.ZM11_2age_oldf2.thick.glmdir/cache.mri_glmfit-sim.log cd /STORAGES/storage2/dati/FREESURFER/glm /usr/local/freesurfer-4.5.0/bin/mri_glmfit-sim --glmdir n49.lh.ZM11_2age_oldf2.thick.glmdir --cache 2 pos $Id: mri_glmfit-sim,v 1.36.2.1 2011/03/28 15:46:10 greve Exp $ Wed Nov 23 18:37:40 CET 2011 Linux fisiologia24 2.6.37.6-0.5-default #1 SMP 2011-04-25 21:48:33 +0200 x86_64 x86_64 x86_64 GNU/Linux neuroscienze setenv SUBJECTS_DIR /STORAGES/img800/home/neuroscienze/subjects FREESURFER_HOME /usr/local/freesurfer-4.5.0 Original mri_glmfit command line: cmdline mri_glmfit --y n49.lh.M11_2age_oldf2.thick.10.mgh --fsgd n49_ZM11_2grp_2age_oldf2.fsgd doss --C M11_C01_C-P_000_doss.mtx --C M11_C02_00aCaP0_doss.mtx --C M11_C03_00aP-aC0_doss.mtx --C M11_C04_0000oldf2_doss.mtx --surf fsaverage lh --cortex --glmdir n49.lh.ZM11_2age_oldf2.thick.glmdir DoSim = 0 UseCache = 1 DoPoll = 0 DoPBSubmit = 0 DoBackground = 0 DiagCluster = 0 gd2mtx = doss fwhm = 14.676053 CSD /usr/local/freesurfer-4.5.0/average/mult-comp-cor/fsaverage/lh/cortex/fwhm15/pos/th20/mc-z.csd fname2ext: Command not found. mri_surfcluster --in n49.lh.ZM11_2age_oldf2.thick.glmdir/M11_C01_C-P_000_doss/sig.mgh --csd /usr/local/freesurfer-4.5.0/average/mult-comp-cor/fsaverage/lh/cortex/fwhm15/pos/th20/mc-z.csd --mask n49.lh.ZM11_2age_oldf2.thick.glmdir/mask.mgh --cwsig n49.lh.ZM11_2age_oldf2.thick.glmdir/M11_C01_C-P_000_doss/cache.th20.pos.sig.cluster. --vwsig n49.lh.ZM11_2age_oldf2.thick.glmdir/M11_C01_C-P_000_doss/cache.th20.pos.sig.voxel. --sum n49.lh.ZM11_2age_oldf2.thick.glmdir/M11_C01_C-P_000_doss/cache.th20.pos.sig.cluster.summary --ocn n49.lh.ZM11_2age_oldf2.thick.glmdir/M11_C01_C-P_000_doss/cache.th20.pos.sig.ocn. --oannot n49.lh.ZM11_2age_oldf2.thick.glmdir/M11_C01_C-P_000_doss/cache.th20.pos.sig.ocn.annot --annot aparc --csdpdf n49.lh.ZM11_2age_oldf2.thick.glmdir/M11_C01_C-P_000_doss/cache.th20.pos.pdf.dat --cwpvalthresh .05 --o n49.lh.ZM11_2age_oldf2.thick.glmdir/M11_C01_C-P_000_doss/cache.th20.pos.sig.masked. --no-fixmni --surf white ERROR: Option --no-fixmni unknown -- Dipartimento di Scienze Biomediche Università degli Studi di Modena e Reggio Emilia Via G. Campi, 287 41125 Modena, Italia Tel: +39-059 205 5684

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mri_glmfit-sim error with v5.0
by yukoyy 30 Nov '11

30 Nov '11

Hello I'm having a trouble with mri_glmfit-sim with v5.0, which is locally installed on Mac 10.6.8. Whan I ran: mri_glmfit-sim --glmdir MPglm.wls --cache 3.0 pos --cwpvalthresh .0166 I got: ERROR: cannot find /Applications/freesurfer/average/mult-comp-cor///cortex/fwhm15/pos/th30/mc-z.csd I have /Applications/freesurfer/average/mult-comp-cor/fsaverage/lh/cortex/fwhm15/pos/th30/mc-z.csd in my directory. It looks like I need to somehow tell freesurfer "/fsaverage/lh/", but how? Before mri_glmfit-sim, I did the followings: isxconcat-sess -df sessdirfile -sf sessidlist -analysis PreL -hemi lh -c 16vs4 -o MPgroup mri_glmfit --y ces.008.nii --wls cesvar.008.nii --osgm --surface fsaverage lh --glmdir MPglm.wls --nii.gz % ------------------------------------------------------------------------- Also, when I did: mri_glmfit-sim --glmdir MPglm.wls --sim mc-z 100 2 mc-z.abs.2 --sim-sign abs --overwrite I got several warnings and errors (full error message pasted at the end of this email): > cmdline mri_glmfit --y ces.008.nii --wls cesvar.008.nii --osgm --surface fsaverage lh --glmdir MPglm.wls --nii.gz > WARNING: unrecognized mri_glmfit cmd option --surface > WARNING: unrecognized mri_glmfit cmd option fsaverage > WARNING: unrecognized mri_glmfit cmd option lh > WARNING: unrecognized mri_glmfit cmd option --nii.gz .... > mri_glmfit --y /Users/kawabata/Documents/freesurfer/sessions/MP/MEAN/MPgroup/PreL/16vs4/ces.008.nii --C > MPglm.wls/tmp.mri_glmfit-sim-6456/osgm.mtx --mask MPglm.wls/mask.nii.gz --sim mc-z 100 2 MPglm.wls/csd > /mc-z.abs.2.j001 --sim-sign abs --fwhm 15.248189 --X MPglm.wls/Xg.dat --wls /Users/kawabata/Documents/freesurfer > /sessions/MP/MEAN/MPgroup/PreL/16vs4/cesvar.008.nii > Bus error I don't understand why mri_glmfit-sim calls mri_glmfit, and gives warnings? When I paste "mri_glmfit --y ces.008.nii --wls cesvar.008.nii --osgm --surface fsaverage lh --glmdir MPglm.wls --nii.gz" in the command line, it works without any error. Thanks in advance! Yuko Yotsumoto % full error message regarding the second question ------------------------------------------- cmdline mri_glmfit --y ces.008.nii --wls cesvar.008.nii --osgm --surface fsaverage lh --glmdir MPglm.wls --nii.gz WARNING: unrecognized mri_glmfit cmd option --surface WARNING: unrecognized mri_glmfit cmd option fsaverage WARNING: unrecognized mri_glmfit cmd option lh WARNING: unrecognized mri_glmfit cmd option --nii.gz log file is MPglm.wls/mc-z.abs.2.mri_glmfit-sim.log cd /Users/kawabata/Documents/freesurfer/sessions/MP/MEAN/MPgroup/PreL/16vs4 /Applications/freesurfer/bin/mri_glmfit-sim --glmdir MPglm.wls --sim mc-z 100 2 mc-z.abs.2 --sim-sign abs --overwrite $Id: mri_glmfit-sim,v 1.24.2.5 2010/07/27 22:49:00 greve Exp $ Wed Nov 23 13:55:01 JST 2011 Darwin Hideaki-Kawabata-no-MacBook-Pro.local 10.8.0 Darwin Kernel Version 10.8.0: Tue Jun 7 16:32:41 PDT 2011; root:xnu-1504.15.3~1/RELEASE_X86_64 x86_64 kawabata setenv SUBJECTS_DIR /Users/kawabata/Documents/freesurfer/subjects FREESURFER_HOME /Applications/freesurfer DoSim = 1 UseCache = 0 DoPoll = 0 DoPBSubmit = 0 DoBackground = 0 DiagCluster = 0 gd2mtx = dods fwhm = 15.248189 nSimPerJob = 100 1/1 Wed Nov 23 13:55:01 JST 2011 mri_glmfit --y /Users/kawabata/Documents/freesurfer/sessions/MP/MEAN/MPgroup/PreL/16vs4/ces.008.nii --C MPglm.wls/tmp.mri_glmfit-sim-6456/osgm.mtx --mask MPglm.wls/mask.nii.gz --sim mc-z 100 2 MPglm.wls/csd/mc-z.abs.2.j001 --sim-sign abs --fwhm 15.248189 --X MPglm.wls/Xg.dat --wls /Users/kawabata/Documents/freesurfer/sessions/MP/MEAN/MPgroup/PreL/16vs4/cesvar.008.nii Bus error

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Tkmedit Talairach coordinates
by Tanner,Jared J 30 Nov '11

30 Nov '11

Hi, I just wanted to verify what the Talaiarch coordinates reported in tkmedit actually are. Are they based on Matthew Brett's 10/8/98 non-linear transform from MNI305 space or are they actually MNI305 coordinates? See screenshot. I would like to get coordinates of voxels within subcortical structures for some fMRI work and need MNI coordinates rather than "true" Talaiarch. I'm trying to minimize the number of transformations. Thank you, Jared Tanner Doctoral Candidate Clinical and Health Psychology University of Florida

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extracting ROIs from the freesurfer atlases in Qdec
by Catherine Wan 30 Nov '11

30 Nov '11

Dear list, I would like to use specific regions from either the Destrieux Atlas (aparc.a2009s.annot), Desikan-Killiany Atlas (aparc.annot) for an ROI analysis. Is there a way to use these ROIs in Qdec (similar to WFUpicktlas)? If we need to trace them manually based on these atlases, what do we need to do within qdec to load the annot files? Many thanks, Catherine

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Students for position (fwd)
by Bruce Fischl 29 Nov '11

29 Nov '11

FYI ---------- Forwarded message ---------- Date: Tue, 29 Nov 2011 14:26:21 -0500 From: Thomas Talavage <tmt(a)purdue.edu> To: "Sutton, Brad" <bsutton(a)illinois.edu>, Bruce Fischl <fischl(a)nmr.mgh.harvard.edu>, Noam Harel <noam(a)cmrr.umn.edu>, dnoll(a)umich.edu, Peter A. Bandettini <bandettini(a)nih.gov>, xhu3(a)emory.edu, Steve Wright <smwright(a)tamu.edu> Subject: Students for position Hey folks --- If you could do one last ping of folks, anyone who wishes to apply for a position in BME here at Purdue should do so in the next few days (letters not needed immediately). We anticipate doing a first review of the imaging-related apps in the next week or so. https://engineering.purdue.edu/BME/AboutUs/FacultyPositions Thanks immensely! Tom

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TAL-to-avg35
by Antonella Kis 29 Nov '11

29 Nov '11

Dear experts, I would appreciate if you can provide me with the TAL-to-avg35 template. Thank you very much! ANtonella

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How to display the dtrecon results
by Antonella Kis 29 Nov '11

29 Nov '11

Dear Lilla, Sorry I am bother you one more time with a question: I was trying to display the dtrecon result smore exactly the GLM group analysis results. After I did the mri_concat */fa-tal.nii --o group-fa-tal.nii I created a mask: mri_concat */mask-tal.nii --o group-masksum-tal.nii --mean mri_binarize --i group-masksum-tal.nii --min .999 --o group-mask-tal.nii then I ran the GLM Fit: mri_glmfit --y group-fa-tal.nii --mask group-mask-tal.nii\ --fsgd your.fsgd --C contrast --glmdir group_analysis.glmdir My questions are: 1) How I can display the uncorrected significance map values for the group analysis? What files should I use? I checked the DTI basic tutorial and I was trying the following: freeview -v /media/1Tra/Antonella_2011/DTI_FS/dtrecon/group-masksum-tal.nii \ /media/1Tra/Antonella_2011/DTI_FS/dtrecon/group_analysis.glmdir/contrast/sig.mgh:colormap=heat Is this right? Or I should use the mask.mgh 2) If my contrast is C = +1.00000 -1.00000 (I am not accounting for age nor for gender) the what the colours represents and how I can get the p values for the forming clusters? THANK YOU VERY MUCH! Antonella

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Installation FS
by nooshin n.zade 28 Nov '11

28 Nov '11

Dear FreeSurfer Group I have some problem for installing the FS. Using following links, I downloaded and installed freesurfer-Darwin-leopard. For next step, in terminal when I write "source $FREESURFER_HOME/SetUpFreeSurfer.sh" or "source $FREESURFER_HOME/SetUpFreeSurfer.csh" it says that "No such file or directory" while I can see both in freesurfer folder. Can you please guide me what is the reason and how I can solve it. http://surfer.nmr.mgh.harvard.edu/fswiki/MacOsInstall http://surfer.nmr.mgh.harvard.edu/fswiki/SetupConfiguration -- Best Regards --------------------------------------------------- Nooshin N. Zadeh Graduate Assistant Departments of Electrical Engineering and Neurology University of Miami ** * * * *

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Scalp removal
by Antonella Kis 28 Nov '11

28 Nov '11

Dear Bruce: 1).I am planning to do a GLM group comparison of FA/DTI data, using dtrecon. I checked all the recon-all results and I found that there is a small amount of scalp left for one subject (it appears only on 3 slices). I wonder if this small amount will affect my subject registration and if I should remove it or if I can continue my data analysis with this small amount of scalp left only for this subject (it shows only on few slices). Please see the attached image. 2). Is there a way to download the cvs template? Why this is called cvs_avg35? Does this mean that the age avg is 35 or what exactly means 35? Many thanks, Antonella

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Re: [Freesurfer] trac-all "Error: bvecs and bvals don't have the same number of entries"
by Peter J. Molfese 28 Nov '11

28 Nov '11

Sorry for the delay in responding, I wanted to try every permutation that I could think of. I updated the tracula binaries for snow leopard (https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2011-August/019946.h…) and that gives me some of the same, and some different issues that may help. First, if the bvec file is in the correct format (3 columns), then it copies the file correctly and trac-all continues smoothly. If the file is in the 3 row format (needing to be transposed), then tracula will only copy the first 9 numbers out of it giving the error of not having the correct number of bvecs to bvals. So that seems fixable, I just need to reorient all of our bval and bvec files into the correct format. I'm still a bit unsure why tracula won't create the bvec and bval files during the mri_convert stage. I have been using dcm2nii to create these two files but then continue to give tracula the path to the dicom files. So the orientation of this file could be related to how dcm2nii writes the files. Any suggestions would be very welcome. As it stands, my current workflow is: 1. use dcm2nii to create bvec and bval files 2. reorient bvec and bval files to be 3 column and 1 column format respectively. 3. run trac-all -prep with a config file showing where the dicom images are and hand specifying the bvec and bval files Peter Peter J. Molfese, Ph.D. Postdoctoral Associate Haskins Laboratories 300 George Street, Suite 900 New Haven, CT 06511 peter.molfese(a)yale.edu CONFIDENTIALITY NOTICE: This e-mail message, including any attachments, is for the sole use of the intended recipient(s) and may contain confidential and privileged information. Any unauthorized review, use, disclosure or distribution is prohibited. If you are not the intende d recipient, please contact the sender immediately by reply e-mail and destroy all copies of the original message.

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Freesurfer November 2011