Freesurfer

freesurfer@nmr.mgh.harvard.edu

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30132 discussions

Fw: manually specifying design matrix
by raka maitra 10 Feb '10

10 Feb '10

Hello Sorry for reposting again. Would really appreciate a feedback on the following mail. Thanks in advance for your time Raka ----- Forwarded Message ---- From: raka maitra <rakamaitra(a)yahoo.com> To: Douglas N Greve <greve(a)nmr.mgh.harvard.edu> Sent: Fri, January 15, 2010 9:34:02 PM Subject: Re: [Freesurfer] manually specifying design matrix Thank you Doug. I am trying to create a design matrix for repeated measures anova. Lets say subjects A and B have been measured at sitting and standing positions. As the same subjects have been measured at the same positions, hence both the factors i.e subjects and positions are fixed factors. Hence a design matrix exploring the within subject effects of positions would be 1 0 1 0 0 1 1 0 1 0 0 1 0 1 0 1 The first two columns are position and the last two are the subjects. But mri_glmfit does not accept this design and I get the following error message: 'Matrix condition is 1e+08 ERROR: matrix is ill-conditioned or badly scaled, condno = 1e+08 Possible problem with experimental design: Check for duplicate entries and/or lack of range of continuous variables within a class.' Looking forward to your suggestion Thanks in advance Raka ________________________________ From: Douglas N Greve <greve(a)nmr.mgh.harvard.edu> To: raka maitra <rakamaitra(a)yahoo.com> Cc: freesurfer(a)nmr.mgh.harvard.edu Sent: Thu, January 14, 2010 7:05:28 PM Subject: Re: [Freesurfer] manually specifying design matrix If you specify it manually, you don't specify groups, etc, or pass an fsgd file. You just create your design matrix pass it to mri_glmfit directly with the --X flag. doug raka maitra wrote: > > Hi all > > I want to specify a design matrix manually. > > In the usual pipeline for analysis in freesurfer, one specifies the > groups, regressors in the fsgd and then when mri_glmfit is run, it > creates the design matrix. > For eg if I have two classes with 3 subjects each, in my fsgd, > mri_glmfit would create the following design matrix > 1 0 > 1 0 > 1 0 > 0 1 > 0 1 > 0 1 > > If I want to specify the above design matrix manually, how and where > do I specify the groups, regressors ? > > > Thanks in advance > Raka > > ------------------------------------------------------------------------ > > _______________________________________________ > 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: www.nmr.mgh.harvard.edu/facility/filedrop/index.html _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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tksurfer error
by Daniel Ferreira Padilla 10 Feb '10

10 Feb '10

Dear Freesurfer users, I hope you could help me with that problem. I do the recon-all preprocessing step and then I try tksurfer. But the following error comes up. Moreover tksurfer window open up but it looks like 'empty'. Please find it attached. Thank you very much! Daniel Ferreira -------- freesurfer-Linux-centos4-stable-pub-v4.5.0 -------- Setting up environment for FreeSurfer/FS-FAST (and FSL) FREESURFER_HOME /home/Neuropsicologia/freesurfer FSFAST_HOME /home/Neuropsicologia/freesurfer/fsfast FSF_OUTPUT_FORMAT nii SUBJECTS_DIR /home/Neuropsicologia/DANI/subjects MNI_DIR /home/Neuropsicologia/freesurfer/mni FSL_DIR /home/Neuropsicologia/fsl Neuropsicologia@linux-tand:~> cd DANI/subjects Neuropsicologia@linux-tand:~/DANI/subjects> tksurfer GJ25_3D lh inflated -aparc -gray surfer: current subjects dir: /home/Neuropsicologia/DANI/subjects surfer: not in "scripts" dir ==> using cwd for session root surfer: session root data dir ($session) set to: surfer: /home/Neuropsicologia/DANI/subjects surfer: Reading header info from /home/Neuropsicologia/DANI/subjects/GJ25_3D/mri/T1.mgz surfer: vertices=123902, faces=247800 surfer: curvature read: min=-1.349975 max=2.259740 reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/amaebi_026/users/buckner_cortical_atlas/scripts/colortable_fin al.txt) Found embedded color table in annotation. surfer: single buffered window surfer: tkoInitWindow(GJ25_3D) surfer: using interface /home/Neuropsicologia/freesurfer/lib/tcl/tksurfer.tcl Reading /home/Neuropsicologia/freesurfer/lib/tcl/tkm_common.tcl Reading /home/Neuropsicologia/freesurfer/lib/tcl/tkm_wrappers.tcl Reading /home/Neuropsicologia/freesurfer/lib/tcl/fsgdfPlot.tcl Reading /home/Neuropsicologia/freesurfer/lib/tcl/tkUtils.tcl Successfully parsed tksurfer.tcl reading white matter vertex locations... %

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Re: [Freesurfer] Freesurfer Digest, Vol 72, Issue 25
by Sebastian Moeller 10 Feb '10

10 Feb '10

Hi Tamara, neuroecon is not ia64 but x86_64, that is you binaries will probanbly never run on this cluster no matter the permissions. You can just ask the neuroecon support people (help-hpc(a)caltech.edu) to install 4.5.0 under /share/apps. In addition to actually use freesurfer on this system (say with NX remote control) you will need some adjustement to the calls to tkregister2 and /or tksurfer/tkmedit. I can simp[ly copy you the version of FS 4.5.0 we got working on that machine... best Sebastian On Feb 10, 2010, at 6:30 AM, freesurfer-request(a)nmr.mgh.harvard.edu wrote: > Message: 3 > Date: Tue, 9 Feb 2010 20:41:13 -0500 (EST) > From: Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> > Subject: Re: [Freesurfer] Trouble installing freesurfer to a cluster > To: Tamara Knutsen <knutsen(a)gmail.com> > Cc: freesurfer(a)nmr.mgh.harvard.edu > Message-ID: > <Pine.LNX.4.62.1002092040520.20105(a)gate.nmr.mgh.harvard.edu> > Content-Type: TEXT/PLAIN; charset=US-ASCII; format=flowed > > hmmm, have you tried: > > chmod a+x /home/knutsen/freesurfer/bin/* > > not sure why they wouldn't be executable though. > Bruce > On Tue, 9 Feb 2010, Tamara > Knutsen > wrote:

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question abt mri_vol2surf - projfrac
by ridatta＠mail.med.upenn.edu 10 Feb '10

10 Feb '10

Hello, I also had a question abt projfrac I have 3 x 3 x 3 mm voxel functional data - BOLD and ASL that I am trying to resample to fsaverage. Is the projfrac label applicable here at all ? In the help page it specifies only for thickness. If it is applicable, what value ? Thanks Ri

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projection depth using tksurfer or mri_vol2surf
by Sepideh Sadaghiani 10 Feb '10

10 Feb '10

Hi, I am rendering an analyze format img onto the fsaverage surface. I was wondering whether it is possible to specify the MAXIMAL depth of activation that is supposed to be projected onto the surface. Hereby I mean an ADDITIVE depth: The option --projdist (and also --projfrac) are not doing what I want. They lead to a translation of the projection surface into depth, but I seem to loose the more superficial activations. I know that my goal could be achieved in the older versions of FreeSurfer using --dmax for the paint command. So I wonder how I can do the same thing in the current FreeSurfer. Thanks, Sepideh -- NEU: Mit GMX DSL über 1000,- ¿ sparen! http://portal.gmx.net/de/go/dsl02

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SPM vol .nii to w file surface overlay
by Nela Cicmil 10 Feb '10

10 Feb '10

Dear Freesurfer users, I have tried to convert a volumetric SPM activity image from the form of a .nii file (created against the subjects T1.nii image) into a w file (paint file) to be overlaid on the inflated surface of the same subject's brain anatomy (created with Freesurfer recon-all), using the command below: mri_vol2surf --mov ~/<name>.nii --out ~/<name>-rh.w --hemi rh --surf inflated --out_type paint --regheader $SUBJECT However, the pattern on the surface does not *quite* match what I see from the volumetric image, and one of the reasons for this could be that I am not converting from volume image to surface overlay correctly - I would be very grateful, if there is a better way to do this, if someone could let me know. Thanks and best wishes, Nela ---- Nela Cicmil D.Phil Candidate, Neurophysiology Dept. Physiology, Anatomy & Genetics University of Oxford

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recon-all analyze 7.5 format
by SG KIM 10 Feb '10

10 Feb '10

Hi all, I've got .IMG and .HDR files in analyze 7.5 format, and ran recon-all -s subject -i file.img it doesn't seem to refer the .hdr file. What else should I do to use analyze format in Freesurfer? SG

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Trouble installing freesurfer to a cluster
by Tamara Knutsen 09 Feb '10

09 Feb '10

Hi, I am trying to install the freesurfer-Linux-suse-ia64-stable-pub-v4.5.0.tar to my user home directory (/home/knutsen) on the following Caltech cluster: Neuroecon Cluster 12 Dell Poweredge 1950 nodes 16 GB RAM per node Gigabit ethernet interconnect Matlab Distributed compute engine Rocks 5.1 Provisioning Maui/Torque scheduling and resource management 60 TB Lustre File System DDN 9700 The files seem to have unpacked correctly. ls -a /home/knutsen/freesurfer . build-stamp.txt FreeSurferEnv.sh mni subjects .. DefectLUT.txt fsafd SegmentNoLUT.txt tkmeditParcColorsCMA ASegStatsLUT.txt diffusion fsfast sessions AUTHORS docs lib SetUpFreeSurfer.csh average FreeSurferColorLUT.txt .license SetUpFreeSurfer.sh bin FreeSurferEnv.csh matlab Simple_surface_labels2009.txt I ran the SetUpFreesurfer.sh and it properly recognizes $FREESURFER_HOME I then tried to import some Siemens dicom files to the subjects dir using the following command from /home/knutsen: recon-all -s ATM -i Subjects/100/Anatomy/2/1.3.12.2.1107.5.2.13.20524.30000010011116574178100000018.dcm -i Subjects/100/Anatomy/3/1.3.12.2.1107.5.2.13.20524.30000010011116574178100000196.dcm -i Subjects/100/Anatomy/4/1.3.12.2.1107.5.2.13.20524.30000010011116574178100000374.dcm -i Subjects/100/Anatomy/5/1.3.12.2.1107.5.2.13.20524.30000010011116574178100000552.dcm And get the following errors: Subject Stamp: freesurfer-ia64-suse-linux-stable4-20090905 Current Stamp: freesurfer-ia64-suse-linux-stable4-20090905 INFO: SUBJECTS_DIR is /home/knutsen/freesurfer/subjects Actual FREESURFER_HOME /home/knutsen/freesurfer Linux neuroecon.caltech.edu 2.6.18-128.1.14.el5 #1 SMP Mon Jun 1 15:52:58 EDT 2009 x86_64 x86_64 x86_64 GNU/Linux /home/knutsen/freesurfer/bin/mri_convert: Exec format error. Binary file not executable. /home/knutsen/freesurfer/bin/flirt: Exec format error. Binary file not executable. /home/knutsen/freesurfer/bin/mri_convert: Exec format error. Binary file not executable. /home/knutsen/freesurfer/bin/tkregister2_cmdl: Exec format error. Binary file not executable. /home/knutsen/freesurfer/bin/mri_normalize: Exec format error. Binary file not executable. /home/knutsen/freesurfer/bin/mri_watershed: Exec format error. Binary file not executable. /home/knutsen/freesurfer/bin/mri_segment: Exec format error. Binary file not executable. /home/knutsen/freesurfer/bin/mri_label2label: Exec format error. Binary file not executable. /home/knutsen/freesurfer/bin/mri_em_register: Exec format error. Binary file not executable. /home/knutsen/freesurfer/bin/mri_ca_normalize: Exec format error. Binary file not executable. /home/knutsen/freesurfer/bin/mri_ca_register: Exec format error. Binary file not executable. /home/knutsen/freesurfer/bin/mri_ca_label: Exec format error. Binary file not executable. /home/knutsen/freesurfer/bin/mri_pretess: Exec format error. Binary file not executable. /home/knutsen/freesurfer/bin/mri_fill: Exec format error. Binary file not executable. /home/knutsen/freesurfer/bin/mri_tessellate: Exec format error. Binary file not executable. /home/knutsen/freesurfer/bin/mri_concatenate_lta: Exec format error. Binary file not executable. /home/knutsen/freesurfer/bin/mri_normalize_tp2: Exec format error. Binary file not executable. /home/knutsen/freesurfer/bin/mris_smooth: Exec format error. Binary file not executable. /home/knutsen/freesurfer/bin/mris_inflate: Exec format error. Binary file not executable. /home/knutsen/freesurfer/bin/mris_curvature: Exec format error. Binary file not executable. /home/knutsen/freesurfer/bin/mris_sphere: Exec format error. Binary file not executable. /home/knutsen/freesurfer/bin/mris_fix_topology: Exec format error. Binary file not executable. /home/knutsen/freesurfer/bin/mris_topo_fixer: Exec format error. Binary file not executable. /home/knutsen/freesurfer/bin/mris_ca_label: Exec format error. Binary file not executable. /home/knutsen/freesurfer/bin/mris_euler_number: Exec format error. Binary file not executable. /home/knutsen/freesurfer/bin/mris_make_surfaces: Exec format error. Binary file not executable. /home/knutsen/freesurfer/bin/mris_register: Exec format error. Binary file not executable. /home/knutsen/freesurfer/bin/mris_anatomical_stats: Exec format error. Binary file not executable. /home/knutsen/freesurfer/bin/mrisp_paint: Exec format error. Binary file not executable. /home/knutsen/freesurfer/bin/mris_curvature_stats: Exec format error. Binary file not executable. /home/knutsen/freesurfer/bin/mri_robust_register: Exec format error. Binary file not executable. /home/knutsen/freesurfer/bin/mri_robust_template: Exec format error. Binary file not executable. /home/knutsen/freesurfer/bin/mri_and: Exec format error. Binary file not executable. /home/knutsen/freesurfer/bin/mri_or: Exec format error. Binary file not executable. /home/knutsen/freesurfer/bin/mri_fuse_segmentations: Exec format error. Binary file not executable. /home/knutsen/freesurfer/subjects/ATM mri_convert /home/knutsen/Subjects/100/Anatomy/2/1.3.12.2.1107.5.2.13.20524.30000010011116574178100000018.dcm /home/knutsen/freesurfer/subjects/ATM/mri/orig/001.mgz /home/knutsen/freesurfer/bin/mri_convert: Exec format error. Binary file not executable. Linux neuroecon.caltech.edu 2.6.18-128.1.14.el5 #1 SMP Mon Jun 1 15:52:58 EDT 2009 x86_64 x86_64 x86_64 GNU/Linux recon-all exited with ERRORS at Tue Feb 9 17:24:49 PST 2010 Wondering what I did wrong in the install that all the binaries are not executable. It's probably something obvious. Thanks for any help/advice, Tamara

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Pallidum Volume Assymetry in hemispheres and fs versions
by Jeff Sadino 09 Feb '10

09 Feb '10

Hello Everyone, I ran 106 subjects through fs 3.0.5 and also through fs 4.3.1 and then compared the volumes of the subcortical structures. Most of them correlated well between versions, but for the pallidum, there was a strong bias both hemispherically and between versions. In fs3, the left pallidum was 1995 and the right was 1756 for a difference of 239. In fs4, the left pallidum was 1882 and the right was 1593 for a difference of 289. Between fs versions, this gives a 6% difference [ (1995-1882) / ((1995+1882)/2) ] for the left pallidum and a 9.7% difference [ (1756-1593) / ((1756+1593)/2) ] for the right pallidum. Between hemispheres, the difference is 19% [ (289-239) / ((289+239)/2) ]. I was wondering particularly as to the 19% variability of the pallidum measurements between fs versions. Is this much of a difference common between these two freesurfer versions, or is it unique to our study? Also, is 6% and 9.7% difference for the pallidum between hemispheres typical in freesurfer? Attachment is plotting automated results between fs3 and fs4. Thank you very much for your feedback! Jeff Sadino

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diagnostic level
by Guang Zeng 09 Feb '10

09 Feb '10

Hi, there, Both mris_ca_label and mris_ca_train have a -v option which is called: diagnostic level. What is the meaning of this diagnostic level? Thanks! Guang _________________________________________________________________ Hotmail: Trusted email with powerful SPAM protection. http://clk.atdmt.com/GBL/go/201469227/direct/01/

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Freesurfer