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label2MNI152 Transformation Help
by JacobML＠nmr.mgh.harvard.edu 14 Jul '14

14 Jul '14

Hello Freesurfer, I am attempting to take label files generated in fsaverage surface space and transform them into MNI152 volume space. Using the commands below, I am able to view the final output image with fslview in the the same space as the MNI brain. However, the registration is very off. Additionally, tkregister2 also displays the image in the same incorrect location. Any help identifying what may be going wrong with the registration/the transformation matrix would be greatly appreciated! Thank you for the help and or suggestions, Jacob 1. mri_label2vol --label M4_LH.label --subject fsaverage --temp /autofs/cluster/ablood/1/AdjustedParadigmFiles/Adjusted_recons/fsaverage/mri/orig.mgz --o M4_LH_orig.mgz --identity Terminal output: orig.mgz --identity INFO: subject not needed, igorning. Number of labels: 1 M4_LH.label Annot File: (null) Template Volume: /autofs/cluster/ablood/1/AdjustedParadigmFiles/Adjusted_recons/fsaverage/mri/orig.mgz Outut Volume: M4_LH_orig.mgz Registration File: (null) Fill Threshold: 0 Label Vox Vol: 1 ProjType: (null) ProjTypeId: 0 ProjStart: 0 ProjStop: 0 ProjDelta: 0.1 Subject: fsaverage Hemi: (null) UseNewASeg2Vol: 1 DoLabelStatVol 0 LabelCodeOffset 0 setenv SUBJECTS_DIR /cluster/ablood/1/AdjustedParadigmFiles/Adjusted_recons $Id: mri_label2vol.c,v 1.34.2.5 2012/06/08 17:31:03 greve Exp $ Template RAS-to-Vox: -------- -1.000 0.000 0.000 128.000; -0.000 -0.000 -1.000 128.000; -0.000 1.000 -0.000 128.000; 0.000 0.000 0.000 1.000; Template Voxel Volume: 1 nHits Thresh: 0 Using Identity Matrix RegMat: -------- 1.000 0.000 0.000 0.000; 0.000 1.000 0.000 0.000; 0.000 0.000 1.000 0.000; 0.000 0.000 0.000 1.000; Label RAS-to-Vox: -------- -1.000 0.000 0.000 128.000; 0.000 0.000 -1.000 128.000; 0.000 1.000 0.000 128.000; 0.000 0.000 0.000 1.000; nlabels = 1 Allocating Hit Volume (16777216) voxels Loading M4_LH.label PVF (null) Thesholding hit volume. mri_label2vol done 2. mri_vol2vol --mov M4_LH_orig.mgz --targ $FSLDIR/data/standard/MNI152_T1_2mm.nii.gz --o M4_LH_orig_MNI152.nii.gz --interp nearest --reg $FREESURFER_HOME/average/mni152.register.dat Terminal output: Matrix from regfile: 0.998 -0.007 0.018 0.957; -0.013 -0.009 0.997 -17.816; -0.015 -1.001 0.002 -18.550; 0.000 0.000 0.000 1.000; movvol M4_LH_orig.mgz targvol /usr/pubsw/packages/fsl/current/data/standard/MNI152_T1_2mm.nii.gz outvol M4_LH_orig_MNI152.nii.gz regfile /usr/local/freesurfer/stable5_3_0/average/mni152.register.dat invert 0 tal 0 talres 2 regheader 0 noresample 0 interp nearest (0) precision float (3) Gdiag_no -1 Synth 0 SynthSeed 1406309355 Final tkRAS-to-tkRAS Matrix is: 0.998 -0.007 0.018 0.957; -0.013 -0.009 0.997 -17.816; -0.015 -1.001 0.002 -18.550; 0.000 0.000 0.000 1.000; Vox2Vox Matrix is: 1.995 0.035 0.015 33.682; -0.029 0.005 2.002 56.525; 0.026 -1.994 -0.019 218.527; 0.000 0.000 0.000 1.000; Resampling Output registration matrix is identity INFO: writing registration to M4_LH_orig_MNI152.nii.gz.lta transformed matrix: 1.000 -0.000 -0.000 -1.000; -0.000 -0.000 -1.000 -17.000; -0.000 1.000 -0.000 19.000; 0.000 0.000 0.000 1.000; transformed matrix: 0.500 0.000 0.000 -18.500; 0.000 0.500 0.000 -9.500; 0.000 0.000 0.500 -18.500; 0.000 0.000 0.000 1.000; INFO: writing registration matrix to M4_LH_orig_MNI152.nii.gz.reg To check registration, run: tkregister2 --mov M4_LH_orig_MNI152.nii.gz --targ /usr/pubsw/packages/fsl/current/data/standard/MNI152_T1_2mm.nii.gz --reg M4_LH_orig_MNI152.nii.gz.reg mri_vol2vol done 3. tkregister2 --mov M4_LH_orig_MNI152.nii.gz --targ /usr/pubsw/packages/fsl/current/data/standard/MNI152_T1_2mm.nii.gz --reg M4_LH_orig_MNI152.nii.gz.reg Terminal output: tkregister_tcl /usr/local/freesurfer/stable5_3_0/tktools/tkregister2.tcl target volume /usr/pubsw/packages/fsl/current/data/standard/MNI152_T1_2mm.nii.gz movable volume M4_LH_orig_MNI152.nii.gz reg file M4_LH_orig_MNI152.nii.gz.reg LoadVol 1 ZeroCRAS 0 $Id: tkregister2.c,v 1.121.2.1 2011/03/28 20:25:16 greve Exp $ Diagnostic Level -1 ---- Input registration matrix -------- 1.000 0.000 0.000 0.000; 0.000 1.000 0.000 0.000; 0.000 0.000 1.000 0.000; 0.000 0.000 0.000 1.000; float2int = 0 --------------------------------------- INFO: loading target /usr/pubsw/packages/fsl/current/data/standard/MNI152_T1_2mm.nii.gz INFO: target does not conform to COR format, so I'm going to reslice to COR. This will not affect the final registration. Ttarg: -------------------- -1.000 0.000 0.000 128.000; 0.000 0.000 1.000 -128.000; 0.000 -1.000 0.000 128.000; 0.000 0.000 0.000 1.000; INFO: loading movable M4_LH_orig_MNI152.nii.gz Tmov: -------------------- -2.000 0.000 0.000 91.000; 0.000 0.000 2.000 -91.000; 0.000 -2.000 0.000 109.000; 0.000 0.000 0.000 1.000; mkheaderreg = 0, float2int = 0 ---- Input registration matrix -------- 1.000 0.000 0.000 0.000; 0.000 0.000 1.000 0.000; 0.000 -1.000 0.000 0.000; 0.000 0.000 0.000 1.000; Determinant 1 subject = fsaverage Zoom Factor = 2, SQR() = 4 FOV = 256 Opening window fsaverage Opening fsaverage, xnum = 256, xdim = 512 Setting scale tkregister2: interface: /usr/local/freesurfer/stable5_3_0/tktools/tkregister2.tcl tkregister.tcl: startup done tkregister.tcl: default macro interface (to change: macro,mini,micro) tkregister.tcl: or: setenv tkregisterinterface {macro,mini,micro}

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holes in inflated using mris_label2annot
by April Clausen 14 Jul '14

14 Jul '14

When viewed on the inflated surface in tksurfer, we are seeing “holes” in annot files we created defining our own ROIs. We first created 6 label files on fsaverage then mapped these 6 label files to 5 different subjects using mri_label2label. Once the 6 label files were mapped to each subject, we used mris_label2annot to create an annot from the 6 labels for each subject. This process all seemed to run without errors. We then used tksurfer to view the annot file on the inflated surface for each subject. “holes” appeared in 1-2 of the regions defined by the label files for each subject. We are concerned that these “holes” imply that not all the surface is being included in the region which will in turn result in not all surface being included in the stats files created with the kris_anatomical_stats program.

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recon-all for kids
by Alshikho, Mohamad J. 14 Jul '14

14 Jul '14

Hi Fs Expert, I have a group of kids subjects (4-15) year old. I want to do cortical reconstruction process using Freesurfer. My question is: is still correct to use the command line <recon-all -all -subjid> in this age group? Do I need to use the flag -noseg ? (i.e can I use aseg for this range of age) Thanks, Mohamad

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Re: [Freesurfer] Fw: Aw: Re: Problem with uploading Cluster Simulation data
by Douglas N Greve 14 Jul '14

14 Jul '14

what is your command line? Or otherwise, how are you visualizing it? On 07/14/2014 08:09 AM, carina(a)van-vlodrop.de wrote: > *Gesendet:* Sonntag, 06. Juli 2014 um 22:48 Uhr > *Von:* "carina(a)van-vlodrop.de" <carina(a)van-vlodrop.de> > *An:* "Freesurfer support list" <freesurfer(a)nmr.mgh.harvard.edu> > *Betreff:* Aw: Re: [Freesurfer] Fw: Problem with uploading Cluster > Simulation data > Hi Doug, > I have already uploaded a text file of my corrected results from the > Monte Carlo Cluster Simulation which reports 15 Clusters (attached > picture). > There is another file ending with .mgh and the tutorial identifies it > to be the overlay (clusterwise corrected map) which I can upload in > freeview. > In freeview there are the alternatives of uploading a surface or a > volume. If I upload the file ending with .mgh as a volume I just > recieve a black image with a few numbers on the coordinate plane > (attached picture). There is no brain visible. > Is it correct to upload the overlay (file ending with .mgh) as a > volume or how should I proceed? Do I have to upload a template first > and which is the right template? > Thank you so much. > Yours sincerely, > Carina > *Gesendet:* Montag, 16. Juni 2014 um 12:45 Uhr > *Von:* "Douglas Greve" <greve(a)nmr.mgh.harvard.edu> > *An:* "carina(a)van-vlodrop.de" <carina(a)van-vlodrop.de>, "free surfer" > <freesurfer(a)nmr.mgh.harvard.edu> > *Betreff:* Re: [Freesurfer] Fw: Problem with uploading Cluster > Simulation data > > You should be able to view the map results in freeview just as you > would any other map. > doug > > > > > > On 6/12/14 12:19 PM, carina(a)van-vlodrop.de wrote: > > *Gesendet:* Dienstag, 10. Juni 2014 um 11:18 Uhr > *Von:* "carina(a)van-vlodrop.de" <carina(a)van-vlodrop.de> > *An:* freesurfer(a)nmr.mgh.harvard.edu > *Betreff:* Problem with uploading Cluster Simulation data > Dear freesurfer experts, > we are conducting cortical-thickness analysis using > freesurfer-4.4.0 and the final analysis with qdec. I have a > question concerning the Clusterwise Correction for Multiple > Comparison. > Is it correct that I have to visualize the results of the Monte > Carlo Simulation in freeview? > Do I have to upload a special model in freeview before uploading > the Cluster Simulation data? > Yours sincerely, > Carina > > > _______________________________________________ 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/

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Question about LGI
by pfotiad＠nmr.mgh.harvard.edu 14 Jul '14

14 Jul '14

Hi FS Community, I was wondering whether LGI and Surface Area need to be corrected for total Intracranial Volume. Thanks in advance, Panos

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trac-all -prep error field map error
by Eileen Moore 14 Jul '14

14 Jul '14

Hi - I'm using freesurfer 5.3 on an Ubuntu operating system. I'm tyring to run tracula on some images acquired from a GE scanner. I am running into problems when I try to perform the registration-based B0-inhomogeneity compensation, getting an error in the terminal output: "ERROR: Unrecognized format of phase map". However, trac-all -prep runs fine when I skip the B0-inhomogeneity compensation step. Is there something else I need to do to use field map correction? I've attached the trac-all.log and a copy of the terminal output. Thanks, Eileen.

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LME Longitudinal QDEC Table
by Elijah Mak 14 Jul '14

14 Jul '14

Hello Freesurfer Experts, I am performing a mass-univariate analyses using the LME toolbox for longitudinal studies. After running both mris_preproc and mri_surf2surf , I load the lh.thickness_sm10.mgh file using *[Y,mri] = fs_read_Y('lh.thickness_sm10.mgh');* Next, I run the following command: *Qdec = fReadQdec('qdec.table.dat');* However, it seems that the output is entirely in string format "166 x 1 cell". The first row reads as "'fsid fsid-base years group gender age'" in a single column. Because of this, I am running into problems when I try to execute the following steps: *Qdec = rmQdecCol(Qdec,1);* (removes first column) *sID = Qdec(2:end,1); (grabs the subjects' IDs)* *Qdec = rmQdecCol(Qdec,1);* (removes the subjects'ID column) *M = Qdec2num(Qdec);* (converts to a numeric matrix) *[M,Y,ni] = sortData(M,1,Y,sID);* (sorts the data) Your help will be greatly appreciated! Many thanks. Best Regards, Elijah -- Elijah Mak, Gates Scholar PhD Candidate *|* Psychiatry University of Cambridge Trinity College, Cambridge, CB2 1TQ

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Re: [Freesurfer] Patch that adds parapool support to lme_mass_F, lme_mass_fit_EMinit, lme_mass_fit, lme_mass_fit_init. lme_mass_fit_Rgw
by jorge luis 14 Jul '14

14 Jul '14

Hi Knut Thank you very much for your contribution. I'll take a look at it and apply the patches as soon as I have time (probably next weekend) on github: https://github.com/NeuroStats Best -Jorge >________________________________ > De: Knut J Bjuland <knut.j.bjuland(a)ntnu.no> >Para: jorge luis <jbernal0019(a)yahoo.es> >Enviado: Jueves 26 de junio de 2014 5:16 >Asunto: Patch that adds parapool support to lme_mass_F,lme_mass_fit_EMinit, lme_mass_fit,lme_mass_fit_init. lme_mass_fit_Rgw > > >Dear Dr Rusiel > >Matlabpool is deprecated in Matlab 2014a. I have therefore written a >patch, which adds parapool support when Matlab 2013B and above is used >vertex wise linear mixed model is used. >Please review the patch? Is the patch sound? Please apply the patch. > >Your sincerly > >Knut J Bjuland > > > >

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Hippocampal Subsectioning
by Joshua S 13 Jul '14

13 Jul '14

Hi, I was doing a hippocampal subsectioning <https://surfer.nmr.mgh.harvard.edu/fswiki/HippocampalSubfieldSegmentation> on a data set. Previously recon-all -all was used, and then I did recon-all -hippo-subfields. I then used the script kvlQuantifyHippocampalSubfieldSegmentations.sh to find the volume of the hippocampus and its sub parts. I was confused as to the data I was getting out. The hippocampus seems to large. The voxel size is 0.5 mm * 0.5 mm * 0.5 mm so the hippocampal areas seem to large. Also the subunits of the hippocampus are larger than the actual hippocampus which again does not make sense. I attached one of the output files Thank you for any replies, From Joshua Segaran

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Understanding Hippocampal volume stats
by Zia, Mohammad 13 Jul '14

13 Jul '14

Hi, Freesurfer reported the following hippocampal volumes for a subject volumeInVoxels: right_CA1: 2652.3 right_CA2_3: 7245.11 right_CA4_DG: 3967.28 right_fimbria: 423.555 right_hippocampal_fissure: 191.897 right_presubiculum: 3598.99 right_subiculum: 4868.1 Right-Hippocampus: 3258.77 I have two questions about it 1. I don’t understand why the right_subiculum volume is more than the Right-Hippocampus volume. 2. Since the voxel size for the volumes is 0.5^mm, do we have to divide these volumes by 8 to convert them to voxel size 1^mm so that we can do direct comparison with other freesurfer stats volume (for example the volumes in rh.aparc.stats)? Thanks --Mohammad Zia 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 intended recipient, please contact the sender by e-mail and destroy all copies of the original.

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